bluuebunny/crossref_metadata_2025 huggingface dataset:
Formation of Secondary Minerals and Uptake of Various Anions Under Naturally-Occurring Hyperalkaline Conditions in Oman
Authors: Anraku Sohtaro , Morimoto Kazuya , Sato Tsutomu , Yoneda Tetsuro
Published: December 2010

In Japanese transuranic (TRU) waste disposal facilities, 129I is the most important key nuclide for the long-term safety assessment. Thus, the Kd values of I to natural minerals are important factor in the safety assessment. However, the degradation of cement materials in the repositories can produce high pH pore fluid which can affect the anion transport behavior. Therefore, it is necessary to understand the behavior of anions such as I− under the hyperalkaline conditions. The natural hyperalkaline spring water (pH>11) in the Oman ophiolite is known to be generated from the partly serpentinized peridotites. The spring water is characteristically hyperalkaline, reducing, low-Mg, Si and HCO3−, and high-Ca, while the river water is moderately alkaline, oxidizing, high-Mg and HCO3−. The mixing of these spring and river water resulted in the formation of secondary minerals. In the present study, the naturally occurring hyperalkaline conditions near the springs in Oman were used as natural analogue for the interaction between cement pore fluid and natural Mg-HCO3− groundwater. The present aim of this paper is to examine the conditions of secondary mineral formation and the anion uptake capacity of these mineral in this system. Water and precipitate samples were collected from the different locations around the spring vent to identify the effect of mixing ratios between spring and river water on mineral composition and water-mineral distribution coefficient of various anions. On-site synthesis was also carried out to support these data quantitatively. Aragonite was observed in all precipitates, while calcite, brucite and Mg-Al hydrotalcite-like compounds (HTlc) were also determined in some samples. Calcite was observed only closed to the springs. At locations far from the springs, calcite formation was inhibited due to high-Mg fluid from river water. Brucite was observed from the springs with relatively low-Al concentration and HTlc was the opposite. During the formation of the minerals at the mixing points, HCO3- in the river water was fixed as carbonate minerals such as in aragonite and calcite while H3SiO4− in the river water was dominantly fixed into interlayers and surfaces of HTlc. Iodine in spring and river water was mainly fixed in aragonite. Therefore, the uptake I− by secondary minerals can be expected at hyperalkaline conditions as observed at Oman hyperalkaline springs.
Numerical Assessment of the Long-Term Safety of the Morsleben Repository for Low- and Intermediate-Level Radioactive Waste
Authors: Wollrath Ju¨rgen , Preuss Ju¨rgen , Becker Dirk-A. , Mo¨nig Jo¨rg
Published: December 2010

The Morsleben repository has been in operation since 1971 as a repository for low- and intermediate-level radioactive waste. Until the end of the disposal phase in 1998 a waste volume of about 37,000 m3 with a total activity of 4.5·1014 Bq was disposed of. Currently, the German Federal Office for Radiation Protection (BfS) is applying for the licence to finally close the repository. Concerning the possible release of radionuclides to the biosphere, the repository is subject to German radiation protection regulations. Their fulfilment has to be proven by means of numerical calculations as a part of the safety case. A simplified repository model has been developed by GRS and used for calculating the consequences of different scenarios and variants, as well as for a probabilistic uncertainty and sensitivity analysis. The application for licensing is, among others, based on these results. In this paper the main features of the model and the underlying assumptions, as well as the most important calculation results are presented and explained.
Practical Application of the KMS: 1) Total System Performance Assessment
Authors: Makino Hitoshi , Hioki Kazumasa , Umeki Hiroyuki , Yang Hongzhi , Takase Hiroyasu , McKinley Ian
Published: December 2010

Comprehensive total system performance assessment (PA) is a key component of the safety case. Within this PA there are a number of tasks that reuse specific models and datasets, together with associated knowledge base for the disposal system considered. These are tasks where recent developments in the Knowledge Management System by Japan Atomic Energy Agency (JAEA KMS) can lead to optimisation of procedures. This paper will outline the reformulation of PA as a Knowledge Management (KM) task, discuss application of KM technologies to PA tasks, and illustrate how these can be handled electronically in a “Performance assessment All-In-one Report System (PAIRS)” utilising hyperlinks and embedded tools to minimise duplication of material, ease Quality Assurance (QA) and facilitate the regular updating required in the Japanese programme.
Challenges for the JAEA KMS: Fostering Inventive Design and Problem Solving
Authors: Makino Hitoshi , Hioki Kazumasa , Umeki Hiroyuki , Tachibana Shoko , Takase Hiroyasu , McKinley Ian
Published: December 2010

The Knowledge Management System by Japan Atomic Energy Agency (JAEA KMS) is being developed to be flexible and able to respond to potential changes of boundary conditions. On a shorter timescale, the KMS must encourage flexibility in the methodology used for carrying out and presenting performance assessments. This is closely linked to development of advanced repository concepts; considering the requirements for a safe and practical repository tailored to specific site conditions, which reflects evolving technology. These coupled development tasks were, in the past, carried out by expert teams in a rather informal manner. As the technical challenges increase — and the need for transparency is accepted — a more formal method of developing innovative design solutions is needed. A knowledge engineering approach that is used in other financial and industrial applications has thus been tested for its usefulness for such tasks.
Overview of the JAEA Knowledge Management System Supporting Implementation and Regulation of Geological Disposal in Japan
Authors: Umeki Hiroyuki , Hioki Kazumasa , Takase Hiroyasu , McKinley Ian
Published: December 2010

The exponential growth in the knowledge base for radioactive waste management is a cause for concern in many national programmes. In Japan, this problem is exacerbated by a volunteering approach to siting of a deep geological repository, which requires particular flexibility in the tailoring of site characterisation plans, repository concepts and associated performance assessments. Recognition of this situation led, in 2005, to initiation by Japan Atomic Energy Agency (JAEA) of an ambitious project to develop an advanced Knowledge Management System (KMS) aimed to facilitate its role as the supplier of background R&D support to both regulators and implementers of geological disposal. This overview outlines the boundary conditions and milestones for the Japanese radioactive waste management programmes, the roles of key organisations and the particular responsibilities of JAEA that led to definition of the goals of the KMS.
Nuclear Power Plant Decommissioning in Germany: Projects, Regulation and Experience
Authors: Weil Leopold , Rehs Bernd
Published: December 2010

In Germany, altogether 19 nuclear power plants (NPPs) and prototype reactors have been permanently shut down. For 15 NPPs the dismantling is in progress with “green-field conditions” as planning target. Two units were completely dismantled and two are in safe enclosure. The main legal provision for all aspects of the peaceful use of nuclear energy in Germany is the Atomic Energy Act (AtG), which also contains the basic legal conditions for the decommissioning of nuclear facilities. It stipulates that decommissioning is subject to a licence by the regulatory body of the respective Federal State (Land). An emerging decommissioning practice in Germany is the removal of complete undismantled large components and their transport to interim storage facilities. During the period of storage, the radionuclide inventory of the components will decrease due to radioactive decay and the subsequent segmentation of the components can be done with less radiation protection effort. The commissioning of the Konrad repository in the near future might have consequences on planning of decommissioning, regarding the selection of a decommissioning strategy and the waste management.
Towards an “Implementing Geological Disposal Technology Platform” in Europe
Authors: Palmu P. Marjatta , Eng Torsten L.
Published: December 2010

Several European waste management organizations have started the work on creating a technology platform to accelerate the implementation of deep geological disposal of radioactive waste in Europe. There is an increasing consensus in the international community [1] about geological disposal as the preferred option for solving the long-term management of spent fuel, high-level waste, and other long-lived radioactive wastes. At the same time, the European citizens [2] have a widespread wish for a solution for high-level radioactive waste disposal. A majority of the European countries with nuclear power have active waste management programmes, but the current status and the main challenges of those programmes vary. The most advanced waste management programmes in Europe (i.e. Sweden, Finland and France) are prepared to start the licensing process of deep geological disposal facilities within the next decade. Despite the differences between the timing and the challenges of the different programmes, there is a joint awareness that cooperation on the scientific, technical, and social challenges related to geological disposal is needed, and the cooperation will be beneficial for the timely and safe implementation of the first geological disposal facilities. Such a demonstration of a viable solution for the management of high-level radioactive waste will enhance stakeholder confidence in Europe. Several decades of research, development and demonstration (RD&D) have been carried out in the field of geological disposal. International opportunities of cooperation and establishing a technology platform were explored in the European Commission co-funded projects like Net.Excel [3] and CARD [4]. According to the CARD project, the majority of the funding for RD&D in waste management comes from the implementing organizations. It is envisaged that a technology platform would enhance European cooperation in this area. The platform intends to constitute a tool for reducing overlapping work, to produce savings in total costs of research and implementation, and to make better use of existing competence and research infrastructures. After the final workshop of the CARD project in 2008, SKB (Sweden) and Posiva (Finland) were committed to lead the preparation work to set-up the Implementing Geological Disposal of Radioactive Waste Technology Platform (IGD-TP). Other implementers from France, Germany, Switzerland, Great Britain, Spain, and Belgium joined en suite. A Vision Document for the IGD-TP is about to be finalized after a wider consultation was carried out in July 2009. The final Vision Document and the platform are launched during November 2009. Simultaneously, the preparation of the Strategic Research Agenda for the technology platform’s joint work starts.
The KNOO Research Consortium: Work Package 3—An Integrated Approach to Waste Immobilisation and Management
Authors: Biggs Simon , Fairweather Michael , Young James , Grimes Robin W. , Milestone Neil , Livens Francis
Published: December 2010

The Keeping the Nuclear Option Open (KNOO) research consortium is a four-year research council funded initiative addressing the challenges related to increasing the safety, reliability and sustainability of nuclear power in the UK. Through collaboration between key industrial and governmental stakeholders, and with international partners, KNOO was established to maintain and develop skills relevant to nuclear power generation. Funded by a research grant of £6.1M from the “Towards a Sustainable Energy Economy Programme” of the UK Research Councils, it represents the single largest university-based nuclear research programme in the UK for more than 30 years. The programme is led by Imperial College London, in collaboration with the universities of Manchester, Sheffield, Leeds, Bristol, Cardiff and the Open University. These universities are working with the UK nuclear industry, who contributed a further £0.4M in funding. The industry/government stakeholders include AWE, British Energy, the Department for Environment, Food and Rural Affairs, the Environment Agency, the Health and Safety Executive, Doosan Babcock, the Ministry of Defence, Nirex, AMEC NNC, Rolls-Royce PLC and the UK Atomic Energy Authority. Work Package 3 of this consortium, led by the University of Leeds, concerns “An Integrated Approach to Waste Immobilisation and Management”, and involves Imperial College London, and the Universities of Manchester and Sheffield. The aims of this work package are: to study the re-mobilisation, transport, solid-liquid separation and immobilisation of particulate wastes; to develop predictive models for particle behaviour based on atomic scale, thermodynamic and process scale simulations; to develop a fundamental understanding of selective adsorption of nuclides onto filter systems and their immobilisation; and to consider mechanisms of nuclide leaving and transport. The paper describes highlights from this work in the key areas of multi-scale modeling (using atomic scale, thermodynamic and process scale models), the engineering properties of waste (linking microscopic and macroscopic behaviour, and transport and rheology), and waste reactivity (considering waste hosts and wasteforms, generation IV wastes, and waste interactions).
Hydraulic Behaviour of Nuclear Waste Flows
Authors: Biggs S. R. , Fairweather M. , Harbottle D. , Lin B. , Peakall J.
Published: December 2010

A great deal of existing nuclear waste is stored as a solid-liquid slurry, and the effective transportation of such systems is an essential element in the successful implementation of almost all waste treatment strategies involving particulate wastes within the nuclear industry. A detailed knowledge of turbulent, particle-laden liquid flow behaviour is therefore obviously important. However, systematic and detailed studies of solid-liquid flows by experimental investigation are still limited for pipe flows, contrary to the significant amount of work available for channel flows. Research is therefore required to understand the effects of physical parameters, such as particle shape, size and size distribution, and solids concentration, on the properties of solid-liquid systems, particularly in horizontal pipe flows where particles may settle out of the flow and form solid beds which can potentially lead to pipe blockages. The presence of particles in a turbulent pipe flow also modifies the characteristics of the flow, thereby changing its ability to maintain particles in suspension. The work described concerns pipe flows over a Reynolds number range of 1,000–10,000, with varying levels of solids concentration within the flow. Measurements of the flow and particle characteristics have been gathered using particle image velocimetry (PIV) and, for high solids concentrations, ultrasound Doppler velocity profiling (UDVP) techniques. This work has demonstrated that the intensity of turbulence within such flows can be significantly affected by the presence of solid particles, with small particles generally attenuating turbulence levels, while large particles often augment turbulence levels from the pipe centre-line to the near-wall region. In addition, the coagulation of particles into larger agglomerates is also of importance, with data demonstrating that whilst turbulence levels are influenced and augmented by such agglomerates at low Reynolds numbers, high turbulence levels at high Reynolds numbers can destroy the agglomerates and reduce their effect on the carrier fluid. Work has also been undertaken to examine the effect of particle size and Reynolds number on particle deposition within the flows, and also to establish the minimum transport velocity required to re-suspend particles from solid beds. All these findings are of importance in enhancing our understanding of flows of particles in pipes which in turn is of value in enabling the design of cost effective and efficient waste treatment processes.
A Summary of Radiological Waste Disposal Practices in the United States and the United Kingdom
Authors: Maranville Victoria M. , McGrath Richard
Published: December 2010

A systematic review of near-surface repositories for radioactive waste in the United States (US) was conducted. The main focus of the review consisted of a literature search of available documents and other published sources on low level radioactive waste (LLRW) disposal practices, remediation of LLRW sites in the US, and public participation for remediation efforts of near-surface radiological waste disposal sites in the US. This review was undertaken to provide background information in support of work by the United Kingdom’s (UK) Low Level Waste Repository (LLWR) and to aid in optimizing the future management of this site. The review contained a summary of the US and UK radiological waste classification requirements including a discussion of the waste types, disposal requirements, and the differences between US and UK disposal practices. A regulatory overview and evolution of regulatory requirements in the US is presented. The UK regulatory environment is also discussed and contrasted to the US process. The public participation, as part of the US regulatory process, is provided and the mechanism for stakeholder identification and involvement is detailed. To demonstrate how remediation of radiologically impacted sites is implemented in the US, existing US case studies, in which remediation activities were carried out, were reviewed. The following information was compiled: type of wastes disposed of to US shallow ground facilities [with comparison with UK classifications], facility designs (with special emphasis on those directly comparable to the subsurface conditions in the UK), and deficiencies identified in operation or in demonstrating safe post closure; and processes and difficulties in remedial actions encountered at the selected sites. Stakeholder involvement is discussed within the case studies. Publicly available information related to radiological waste management and disposal practices were reviewed. Two sites are presented in this publication for discussion. These US sites were selected based on the site similarities to conditions in the UK.
Decommissioning and Dismantling Solution Development for Volodarsky Civil Nuclear Fleet Support Ship
Authors: Koulikov Konstantin N. , Nizamutdinov Rinat A. , Abramov Andrey N. , Tsubanikov Anatoly I.
Published: December 2010

Having about 200 tons of solid radioactive waste aboard, the Volodarskiy Floating Technical Base (FTB) is a potential radiation pollution source for the Murmansk region and Kola Bay, as her long-term berthing negatively affects the hull structures. Thereby, Atomflot collaborated with ANO Aspect-Konversia and JSC NIPTB Onega within the frameworks of Federal Special-purpose Program “Assurance of Nuclear and Radiation Safety for 2008 and for the period up to 2015” and developed the Volodarskiy FTB dismantling concept. In 2008 in the course of development of the Volodarskiy FTB dismantling concept the following works were carried out: 1) vessel condition survey, including SRW radiological analysis; 2) feasibility study of the Volodarskiy FTB dismantling alternatives. In this regard the following alternatives were analyzed: – formation of the package assembly in the form of vessel’s undivided hull for durable storage in the Saida long-term storage facility (LTSF); - formation of individual SRW package assemblies for durable storage in the Saida LTSF; - comprehensive recycling of all solid radioactive waste by disposal in protective containers. 3) selection and approval of the dismantling alternative. The alternative of formation of individual SRW package assemblies for durable storage in the Saida LTSF was selected by the Rosatom State Corporation. In this case the works will be performed on a step-by-step basis at the Atomflot enterprise and SRE Nerpa. The conceptual dismantling technology was developed for the selected Volodarskiy FTB dismantling option. The proceedings contain description of options, analysis procedure and proposal for further study of mentioned challenge.
NDA Generic Research Programme for Higher Activity Waste Management Issues
Authors: McKinney James , Brownridge Melanie
Published: December 2010

NDA has a responsibility to ensure decommissioning activities are sufficiently technically underpinned and appropriate Research and Development (R&D) is carried out. The NDA funds research and development (R&D) indirectly via the Site Licence Companies (SLCs) or directly. The main component of directly funded R&D is the NDA Direct Research Portfolio (DRP). The DRP is split into four framework areas: • University Interactions; • Waste Processing; • Material Characterisation; • Actinide and Strategic Nuclear Materials. These four framework areas were competed through an Official Journal of European Union (OJEU) process in 2008. Although all four areas involve waste management, Waste Processing and Material Characterisation specifically deal with Higher Activity Waste (HAW) waste management issues. The Waste Processing area was awarded to three groups: (i) National Nuclear Laboratory (NNL), (ii) Consortium led by Hyder Consulting Ltd, and (iii) Consortium led by UKAEA Ltd. The Material Characterisation area was awarded to three groups: (i) NNL, (ii) Serco, and (iii) Consortium led by UKAEA Ltd. The initial work in Waste Processing and Material Characterisation was centred on establishing a forward research programme to address the generic needs of the UK civil nuclear industry and the NDA strategic drivers for waste management and land quality. This has been achieved by the four main framework contractors from the Waste Processing and Materials Characterisation areas working together with the NDA to identify the key research themes and begin the development of the NDA’s HAW Management Research Programme. The process also involves active engagement with both industry and regulators via the Nuclear Waste Research Forum (NWRF). The NDA’s HAW Management Research Programme includes a number of themes: • Optimisation of Interim Store Operation & Design; • Alternative Waste Encapsulants; • Waste Package Integrity; • Alternative Waste treatment methods; • Alternative storage and disposal options; • Integrated waste management solutions; • Materials characterisation. The NDA, with additional support from its framework contractors and the Nuclear Waste Research Forum, is now developing a more detailed scope for each research theme and prioritising the research projects to ensure alignment with its strategic development programme.
The Nuclear Engineering Doctorate and NTEC CPD and Masters Programmes: Education, Training and Research for the Decommissioning Skillsbase
Authors: Roberts John W.
Published: December 2010

Since its establishment in 2005 the Nuclear Decommissioning Authority (NDA) has a remit to maintain the skillsbase for safe, secure and cost effective decommissioning of the existing UK civil nuclear power plants and associated facilities. With an aging workforce and a competitive tender process for each project a number of new companies are realising the potential of the UK decommissioning market. The Nuclear Engineering Doctorate and NTEC Masters Programmes have been designed to provide the nuclear workforce of the future. The doctorate is a partnership between industry, a university partner and the research engineer with the benefit to industry that the research engineer is based with the industrial partner. Technical and management modules are studied at the university whilst the research project is carried out in the industrial environment. The Masters programme draws on the expertise of 11 Higher Education Institutes and offers over 20 modules that are delivered in a short-fat format either as stand alone CPD courses or, by taking further modules, a certificate, diploma or on completion of a research project an M.Sc. Modules are available that cover the technical aspects of decommissioning as well as management of the decommissioning process. The availability of modules in a Distance Learning format now enables students based around the world to benefit from this programme. This paper will describe the two programmes in detail and provide examples of current projects that are delivering the research and workforce required for a successful decommissioning programme.
Collaborative ReTek Exchange: An Innovative Solution to the Skills and Resource Shortage in the Nuclear Industry
Authors: Parr Corhyn
Published: December 2010

A Different Approach to the Skills and Resource Shortage The Nuclear Industry has for many years been concerned about a skills and resource shortage. This has been due to a poor perception of the industry by those on the outside, highly competitive industries vying for the same resource pool, a steep retirement curve for highly qualified staff and a lack of graduates entering industry. Here in the UK the creation of the National Skill Academy for Nuclear (NSAN) has put in place a framework to record skills and look to accredit the training providers in the nuclear industry to ensure that the correct skills for the future are available. This has gone some way to solving the skills problem and developing a well recognised accredited system but what about resource — where are the additional qualified resources going to be found? Part of the Solution – A Resource Exchange. How do we solve the skills shortage? We come together as an industry and share the available resource through a collaborative resource exchange. It has been done before in the IT industry when rates for specialists hit £1500 per day and recruitment agencies were charging extortionate fees for providing temporary resource. ReTek Consulting have developed the ReTek Resource Exchange to provide a neutral collaborative platform across the supply chain; from large scale infrastructure companies and joint venture platforms through to small companies and independent consultants. Using the ReTek Exchange permanent staff are made available to work for others during periods of underutilisation. Links with similar highly regulated industries enable further management of peaks and troughs and a growth in experienced nuclear professionals through focused training and development. The Benefits of the ReTek Exchange are: • Increased utilisation of your current workforce. • Shared cost of permanent staff. • Speedy access to staff available in your region. • Reduced need for contract or agency staff. • Access to wider skills & experience. • Retention of key staff through personal development. • Knowledge and experience transfer. Now is the time in the industry to make the most of the available resource and work together to ensure the required growth through training and development of all workers. The infrastructure required to make this resource exchange possible is available and proven many times. This paper will talk through the story of the development of the ReTek Exchange in the UK and how the same system can be used elsewhere in the world.
UK Nuclear Decommissioning Authority: Value Framework, Its Development and Role in Decision Making
Authors: Wareing Mark
Published: December 2010

As part of its day to day business NDA must be able to demonstrate that it is delivering value for money across its entire estate, as this is essential to securing funding from government and demonstrating to stakeholders that NDA is delivering on its mission. Value comes in many forms such as an improved environment, hazard reduction, changes in sky line, social amenities, money, employment etc. Depending on the perspective of the receiver, and their closeness to the effected area, the relative weighting they place on the different aspects of value will vary. Therefore the challenge to NDA has been how to get a consistent approach to measuring value that is broadly acceptable to stakeholders and allows the different aspects of value to be compared and decisions made on a national basis. This paper describes the work undertaken by NDA to develop a Value Framework to support decision making at both the strategic and tactical level and addresses the following topics: • The relationship between the value framework and UK government guidance on business case development and options appraisal; • The development of the value framework tool kit including previous work on the NDA prioritisation process and the derivation of Safety and Environmental Detriment scores; • How NDA uses the value framework in its decision making processes.
A Successful Remediation Project
Authors: Scott L. Max
Published: December 2010

As part of a program to visit formerly licensed sites to determine if they meet current uncontrolled release conditions, a United States Nuclear Regulatory Commission (USNRC) inspection was conducted in the fall of 1993 at a site that had possessed a radioactive material license from about 1955 to 1970. While the license was in force, the plant processed magnesium scrap containing up to 4 percent thorium. The source of the scrap is believed to be the aircraft manufacturing industry. The scrap was placed in furnaces and heated to the melting point of magnesium, and the molten magnesium was drawn off, leaving the thorium with the residue (dross). Under the regulation in existence at that time, the thorium dross was buried on site in an approximate 14 acre field. In 1993 the inspector found readings up to 900uR/h. Early in 1994 an informal grid survey of most of the 14 acre site was conducted. Based on that survey, it was concluded that the thorium was widespread and extended beyond the property lines. The preliminary findings were reported to the USNRC, and in 1994 the site was designated as a Site Decommissioning Management Plan (SMPD) site. A remediation team was formed which included the following disciplines: remediation health physics, geology, hydrology, engineering, law, public relations, and project management. This remediation team planned, participated in selecting vendors, and provided project over site for all activities from site characterization through the final status survey. In 2006 the site was released for uncontrolled access. A chronology of activities with lessons learned will be presented.
Solidification of Radioactive Liquid Wastes: Treatment Options for Spent Resins and Concentrates
Authors: Roth Andreas
Published: December 2010

Ion exchange is one of the most common and effective treatment methods for liquid radioactive waste. However, spent ion exchange resins are considered to be problematic waste that in many cases require special approaches and pre-conditioning during its immobilization to meet the acceptance criteria for disposal. Because of the function that they fulfill, spent ion exchange resins often contain high concentrations of radioactivity and pose special handling and treatment problems.
Mimicry in Akt-ion
Authors: VanHook Annalisa M.
Published: December 2010

A viral kinase mimics the activity of Akt despite their lack of sequence similarity.
GlcNAc in Place of Glucose
Authors: Gough Nancy R.
Published: December 2010

Addition of N-acetylglucosamine to the medium can substitute for glucose in maintaining cell growth, but not proliferation.
Mechanosomes Carry a Loaded Message
Authors: Bidwell Joseph P. , Pavalko Fredrick M.
Published: December 2010

Mechanical cues at the bone cell membrane can alter gene transcription through various signaling pathways.
Site-Specific Mutation of
Staphylococcus aureus
VraS Reveals a Crucial Role for the VraR-VraS Sensor in the Emergence of Glycopeptide Resistance
Authors: Galbusera Elena , Renzoni Adriana , Andrey Diego O. , Monod Antoinette , Barras Christine , Tortora Paolo , Polissi Alessandra , Kelley William L.
Published: December 2010

An initial response of
Staphylococcus aureus
to encounter with cell wall-active antibiotics occurs by transmembrane signaling systems that orchestrate changes in gene expression to promote survival. Histidine kinase two-component sensor-response regulators such as VraRS contribute to this response. In this study, we examined VraS membrane sensor phosphotransfer signal transduction and explored the genetic consequences of disrupting signaling by engineering a site-specific
vraS
chromosomal mutation. We have used
in vitro
autophosphorylation assay with purified VraS[64-347] lacking its transmembrane anchor region and tested site-specific kinase domain histidine mutants. We identified VraS H156 as the probable site of autophosphorylation and show phosphotransfer
in vitro
using purified VraR. Genetic studies show that the
vraS
(
H156A
) mutation in three strain backgrounds (ISP794, Newman, and COL) fails to generate detectable first-step reduced susceptibility teicoplanin mutants and severely reduces first-step vancomycin mutants. The emergence of low-level glycopeptide resistance in strain ISP794, derived from strain 8325 (Δ
rsbU
), did not require a functional σ
B
, but
rsbU
restoration could enhance the emergence frequency supporting a role for this alternative sigma factor in promoting glycopeptide resistance. Transcriptional analysis of
vraS
(
H156A
) strains revealed a pronounced reduction but not complete abrogation of the
vraRS
operon after exposure to cell wall-active antibiotics, suggesting that additional factors independent of VraS-driven phosphotransfer, or σ
B
, exist for this promoter. Collectively, our results reveal important details of the VraRS signaling system and predict that pharmacologic blockade of the VraS sensor kinase will have profound effects on blocking emergence of cell wall-active antibiotic resistance in
S. aureus
.
In Vitro
Effect of
qnrA1
,
qnrB1
, and
qnrS1
Genes on Fluoroquinolone Activity against Isogenic
Escherichia coli
Isolates with Mutations in
gyrA
and
parC
Authors: Briales A. , Rodríguez-Martínez J. M. , Velasco C. , Díaz de Alba P. , Domínguez-Herrera J. , Pachón J. , Pascual A.
Published: December 2010

This article provides an analysis of the
in vitro
effect of
qnrA1
,
qnrB1
, and
qnrS1
genes, combined with quinolone-resistant Ser83Leu substitutions in GyrA and/or Ser80Arg in ParC, on fluoroquinolone (FQ) resistance in isogenic
Escherichia coli
strains. The association of Ser83Leu substitution in GyrA, Ser80Arg substitution in ParC, and
qnr
gene expression increased the MIC of ciprofloxacin to 2 μg/ml.
qnr
genes present in
E. coli
that harbored a Ser83Leu substitution in GyrA increased mutant prevention concentration (MPC) values to 8 to 32 μg/ml.
qnr
gene expression in
E. coli
may play an important role in selecting for one-step FQ-resistant mutants.
Complete Nucleotide Sequence of Plasmid pTN48, Encoding the CTX-M-14 Extended-Spectrum β-Lactamase from anEscherichia coliO102-ST405 Strain
Authors: Billard-Pomares Typhaine , Tenaillon Olivier , Le Nagard Hervé , Rouy Zoé , Cruveiller Stéphane , Médigue Claudine , Arlet Guillaume , Denamur Erick , Branger Catherine
Published: December 2010

The sequence of pTN48, a plasmid of the FII-FIB replicon type that encodes a CTX-M-14 enzyme in anEscherichia colistrain of the phylogenetic group D2O102-ST405 clone, was determined. pTN48 is, for the most part, a mosaic of virulence, antibiotic resistance, and addiction system modules found in various other plasmids. The presence of multiple addiction systems indicates that the plasmid should be stably maintained in theE. coliclone, favoring dissemination of the CTX-M-14 enzyme.
Inhibitors of Endoplasmic Reticulum α-Glucosidases Potently Suppress Hepatitis C Virus Virion Assembly and Release
Authors: Qu Xiaowang , Pan Xiaoben , Weidner Jessica , Yu Wenquan , Alonzi Dominic , Xu Xiaodong , Butters Terry , Block Timothy , Guo Ju-Tao , Chang Jinhong
Published: December 2010

α-Glucosidases I and II are endoplasmic reticulum-resident enzymes that are essential for N-linked glycan processing and subsequent proper folding of glycoproteins. In this report, we first demonstrate that downregulation of the expression of α-glucosidase I, II, or both in Huh7.5 cells by small hairpin RNA technology inhibited the production of hepatitis C virus (HCV). In agreement with the essential role of α-glucosidases in HCV envelope glycoprotein processing and folding, treatment of HCV-infected cells with a panel of imino sugar derivatives, which are competitive inhibitors of α-glucosidases, did not affect intracellular HCV RNA replication and nonstructural protein expression but resulted in the inhibition of glycan processing and subsequent degradation of HCV E2 glycoprotein. As a consequence, HCV virion assembly and secretion were inhibited. In searching for imino sugars with better antiviral activity, we found that a novel imino sugar, PBDNJ0804, had a superior ability to inhibit HCV virion assembly and secretion. In summary, we demonstrated that glucosidases are important host factor-based antiviral targets for HCV infection. The low likelihood of drug-resistant virus emergence and potent antiviral efficacy of the novel glucosidase inhibitor hold promise for its development as a therapeutic agent for the treatment of chronic hepatitis C.
Analysis of Low-Frequency Mutations Associated with Drug Resistance to Raltegravir before Antiretroviral Treatment
Authors: Liu Jia , Miller Michael D. , Danovich Robert M. , Vandergrift Nathan , Cai Fangping , Hicks Charles B. , Hazuda Daria J. , Gao Feng
Published: December 2010

Raltegravir is highly efficacious in the treatment of HIV-1 infection. The prevalence and impact on virologic outcome of low-frequency resistant mutations among HIV-1-infected patients not previously treated with raltegravir have not been fully established. Samples from HIV treatment-experienced patients entering a clinical trial of raltegravir treatment were analyzed using a parallel allele-specific sequencing (PASS) assay that assessed six primary and six secondary integrase mutations. Patients who achieved and sustained virologic suppression (success patients,n= 36) and those who experienced virologic rebound (failure patients,n= 35) were compared. Patients who experienced treatment failure had twice as many raltegravir-associated resistance mutations prior to initiating treatment as those who achieved sustained virologic success, but the difference was not statistically significant. The frequency of nearly all detected resistance mutations was less than 1% of viral population, and the frequencies of mutations between the success and failure groups were similar. Expansion of pre-existing mutations (one primary and five secondary) was observed in 16 treatment failure patients in whom minority resistant mutations were detected at baseline, suggesting that they might play a role in the development of drug resistance. Two or more mutations were found in 13 patients (18.3%), but multiple mutations were not present in any single viral genome by linkage analysis. Our study demonstrates that low-frequency primary RAL-resistant mutations were uncommon, while minority secondary RAL-resistant mutations were more frequently detected in patients naïve to raltegravir. Additional studies in larger populations are warranted to fully understand the clinical implications of these mutations.
BB0844, an RpoS-Regulated Protein, Is Dispensable for
Borrelia burgdorferi
Infectivity and Maintenance in the Mouse-Tick Infectious Cycle
Authors: Banik Sukalyani , Terekhova Darya , Iyer Radha , Pappas Christopher J. , Caimano Melissa J. , Radolf Justin D. , Schwartz Ira
Published: December 2010

The genome of
Borrelia burgdorferi
, the causative agent of Lyme disease, is comprised of a large linear chromosome and numerous smaller linear and circular plasmids.
B. burgdorferi
exhibits substantial genomic variation, and previous studies revealed genotype-specific variation at the right chromosomal telomere. A correlation has also been established between genotype and invasiveness. The correlation between chromosome length and genotype and between genotype and invasiveness suggested that a gene(s) at the right chromosome telomere may be required for virulence. Of particular interest was
bb0844
, an RpoS-regulated gene at the right telomere, the expression of which is induced when the spirochete undergoes adaptation to the mammalian host. The structure of the right chromosomal telomere was examined in 53
B. burgdorferi
clinical isolates of various genotypes. Four distinct patterns were observed for
bb0844
: (i) chromosomal localization, (ii) plasmid localization, (iii) presence on both chromosome and plasmid, and (iv) complete absence. These patterns correlated with the
B. burgdorferi
genotype. On the basis of available sequence data, we propose a mechanism for the genomic rearrangements that accounts for the variability in
bb0844
genomic localization. To further explore the role of BB0844 in the spirochete life cycle, a
bb0844
deletion mutant was constructed by allelic exchange, and the viability of wild-type and
bb0844
deletion mutants was examined in an experimental mouse-tick infection model. The
bb0844
mutant was fully infectious in C3H/HeJ mice by either needle inoculation or tick transmission with
B. burgdorferi
-infected
Ixodes scapularis
larvae. Naïve larval ticks acquired both wild-type and mutant spirochetes with equal efficiency from
B. burgdorferi
-infected mice. The results demonstrate that BB0844 is not required for spirochete viability, pathogenicity, or maintenance in the tick vector or the mammalian host. At present, a defined role for BB0844 in
B. burgdorferi
cannot be ascertained.
Invasion of Eukaryotic Cells byBorrelia burgdorferiRequires β1Integrins and Src Kinase Activity
Authors: Wu Jing , Weening Eric H. , Faske Jennifer B. , Höök Magnus , Skare Jon T.
Published: December 2010

Lyme disease, caused by the bacteriumBorrelia burgdorferi, is the most widespread tick-borne infection in the northern hemisphere that results in a multistage disorder with concomitant pathology, including arthritis. During late-stage experimental infection in mice,B. burgdorferievades the adaptive immune response despite the presence of borrelia-specific bactericidal antibodies. In this study we asked whetherB. burgdorfericould invade fibroblasts or endothelial cells as a mechanism to model the avoidance from humorally based clearance. A variation of the gentamicin protection assay, coupled with the detection of borrelial transcripts following gentamicin treatment, indicated that a portion ofB. burgdorfericells were protected in the short term from antibiotic killing due to their ability to invade cultured mammalian cells. Long-term coculture ofB. burgdorferiwith primary human fibroblasts provided additional support for intracellular protection. Furthermore, decreased invasion ofB. burgdorferiin murine fibroblasts that do not synthesize the β1integrin subunit was observed, indicating that β1-containing integrins are required for optimal borrelial invasion. However, β1-dependent invasion did not require either the α5β1integrin or the borrelial fibronectin-binding protein BBK32. The internalization ofB. burgdorferiwas inhibited by cytochalasin D and PP2, suggesting thatB. burgdorferiinvasion required the reorganization of actin filaments and Src family kinases (SFK), respectively. Taken together, these results suggest thatB. burgdorferican invade and retain viability in nonphagocytic cells in a process that may, in part, help to explain the phenotype observed in untreated experimental infection.
MicroTracker: a Data Management Tool for Facilitating the Education of Undergraduate Students in Laboratory Research Environments
Authors: Ammons David , Rampersad Joanne
Published: December 2010

Many undergraduate laboratories are, too often, little more than an exercise in “cooking” where students are instructed step-by-step what to add, mix, and, most unfortunately, expect as an outcome. Although the shortcomings of “cookbook” laboratories are well known, they are considerably easier to manage than the more desirable inquiry-based laboratories. Thus the ability to quickly access, share, sort, and analyze research data would make a significant contribution towards the feasibility of teaching/mentoring large numbers of inexperienced students in an inquiry-based research environment, as well as facilitating research collaborations among students. Herein we report on a software tool (MicroTracker) designed to address the educational problems that we experienced with inquiry-based research education due to constraints on data management and accessibility.
A Small Group Activity About Bacterial Regulation And Complementation
Authors: Merkel Susan , Hanson Buck , Parks Adam
Published: December 2010

As teachers, we well understand the need for activities that help develop critical-thinking skills in microbiology. In our experience, one concept that students have difficulty understanding is transcriptional regulation of bacterial genes. To help with this, we developed and evaluated a paper-based activity to help students understand and apply the concepts of bacterial transcriptional regulation. While we don’t identify it as such, we use a complementation experiment to assess student understanding of how regulation changes when new DNA is introduced. In Part 1 of this activity, students complete an open-book, take-home assignment that asks them to define common terminology related to regulation, and draw the regulatory components of different scenarios involving positive and negative regulation. In Part 2, students work in small groups of 3–4 to depict the regulatory components for a different scenario. They are asked to explain the results of a complementation experiment based on this scenario. They then predict the results of a slightly different experiment. Students who completed the Regulation Activity did significantly better on post-test questions related to regulation, compared to pre-test questions.
Create a Bacterium: an Engaging Semester-Long Assignment
Authors: Liao Min-Ken
Published: December 2010

Like many other educators, I have adapted the “Adopt a Bacterium” exercise developed by Dr. Amy Cheng Vollmer for use in my microbiology course. Building upon the success of the “Adopt a Bacterium,” I developed the “Create a Bacterium” exercise aiming to challenge even more my upper-level undergraduate science majors. To create a bacterium, students not only had to search for and organize information, but also to analyze and evaluate information (higher-order learning skills). Most importantly, students were challenged to engage in the highest level of the cognitive domain of Bloom’s revised taxonomy, synthesis or creation.
Review of Three DNA Analysis Applications for Use in the Microbiology or Genetics Classroom
Authors: Treves David S.
Published: December 2010

Review of:
three widely used DNA analysis programs. Two of these (Chromas and Finch TV) are simple viewing and editing applications. The third (MEGA) also allows for viewing and editing but “ups the ante” considerably in terms of power in DNA data analysis. In evaluating these applications, special consideration was given to how easily an imported DNA sequence could be viewed, edited and submitted to GenBank using BLAST.