An inbred line of the diploid strawberry Fragaria vesca f. semperflorens for genomic and molecular genetic studies in the Rosaceae

<p>Abstract</p> <p>Background</p> <p>The diploid woodland strawberry (<it>Fragaria vesca</it>) is an attractive system for functional genomics studies. Its small stature, fast regeneration time, efficient transformability and small genome size, together with substantial EST and genomic sequence resources make it an ideal reference plant for <it>Fragaria </it>and other herbaceous perennials. Most importantly, this species shares gene sequence similarity and genomic microcolinearity with other members of the Rosaceae family, including large-statured tree crops (such as apple, peach and cherry), and brambles and roses as well as with the cultivated octoploid strawberry, <it>F</it>. ×<it>ananassa</it>. <it>F. vesca </it>may be used to quickly address questions of gene function relevant to these valuable crop species. Although some <it>F. vesca </it>lines have been shown to be substantially homozygous, in our hands plants in purportedly homozygous populations exhibited a range of morphological and physiological variation, confounding phenotypic analyses. We also found the genotype of a named variety, thought to be well-characterized and even sold commercially, to be in question. An easy to grow, standardized, inbred diploid <it>Fragaria </it>line with documented genotype that is available to all members of the research community will facilitate comparison of results among laboratories and provide the research community with a necessary tool for functionally testing the large amount of sequence data that will soon be available for peach, apple, and strawberry.</p> <p>Results</p> <p>A highly inbred line, YW5AF7, of a diploid strawberry <it>Fragaria vesca </it>f. <it>semperflorens </it>line called "Yellow Wonder" (Y2) was developed and examined. Botanical descriptors were assessed for morphological characterization of this genotype. The plant line was found to be rapidly transformable using established techniques and media formulations.</p> <p>Conclusion</p> <p>The development of the documented YW5AF7 line provides an important tool for Rosaceae functional genomic analyses. These day-neutral plants have a small genome, a seed to seed cycle of 3.0 - 3.5 months, and produce fruit in 7.5 cm pots in a growth chamber. YW5AF7 is runnerless and therefore easy to maintain in the greenhouse, forms abundant branch crowns for vegetative propagation, and produces highly aromatic yellow fruit throughout the year in the greenhouse. <it>F. vesca </it>can be transformed with <it>Agrobacterium tumefaciens</it>, making these plants suitable for insertional mutagenesis, RNAi and overexpression studies that can be compared against a stable baseline of phenotypic descriptors and can be readily genetically substantiated.</p

Using Focus Groups to Develop a Bone Health Curriculum for After-school Programs

INTRODUCTION: Childhood behaviors influence peak bone mass and osteoporosis risk in later life. The after-school environment provides an opportunity to enrich a child’s learning and experience. Our objective was to gain a better understanding of the knowledge of, attitudes and beliefs about, and barriers to achieving bone health among children, parents, and after-school program leaders from low-income, ethnically diverse communities. Findings led to the development, implementation, and evaluation of a bone health curriculum in the after-school setting. METHODS: Eight focus groups were conducted in three representative communities. Focus group participants included children aged six to eight years, parents of children aged six to eight, and after-school program staff. Transcripts and written notes from each session were reviewed and common themes were identified within each group. RESULTS: Most adults had some understanding of osteoporosis, but did not recognize that childhood behaviors had a role in developing the disease. Program leaders raised concerns about their ability to implement a health program and recommended a flexible format. Parents and program leaders recognized the importance of maintaining a fun atmosphere. CONCLUSION: It is feasible to create a curriculum for a bone health program that meets the unique needs and interests of children and program leaders in the after-school setting. Addressing the needs, interests, and common barriers of the target population is an essential first step in curriculum development

Analyzing Dynamics of Cooperating Spacecraft

A software library has been developed to enable high-fidelity computational simulation of the dynamics of multiple spacecraft distributed over a region of outer space and acting with a common purpose. All of the modeling capabilities afforded by this software are available independently in other, separate software systems, but have not previously been brought together in a single system. A user can choose among several dynamical models, many high-fidelity environment models, and several numerical-integration schemes. The user can select whether to use models that assume weak coupling between spacecraft, or strong coupling in the case of feedback control or tethering of spacecraft to each other. For weak coupling, spacecraft orbits are propagated independently, and are synchronized in time by controlling the step size of the integration. For strong coupling, the orbits are integrated simultaneously. Among the integration schemes that the user can choose are Runge-Kutta Verner, Prince-Dormand, Adams-Bashforth-Moulton, and Bulirsh- Stoer. Comparisons of performance are included for both the weak- and strongcoupling dynamical models for all of the numerical integrators

Characterization of Pathogenicity, Virulence and Host-Pathogen Interractions

The threats of bio-terrorism and newly emerging infectious diseases pose serious challenges to the national security infrastructure. Rapid detection and diagnosis of infectious disease in human populations, as well as characterizing pathogen biology, are critical for reducing the morbidity and mortality associated with such threats. One of the key challenges in managing an infectious disease outbreak, whether through natural causes or acts of overt terrorism, is detection early enough to initiate effective countermeasures. Much recent attention has been directed towards the utility of biomarkers or molecular signatures that result from the interaction of the pathogen with the host for improving our ability to diagnose and mitigate the impact of a developing infection during the time window when effective countermeasures can be instituted. Host responses may provide early signals in blood even from localized infections. Multiple innate and adaptive immune molecules, in combination with other biochemical markers, may provide disease-specific information and new targets for countermeasures. The presence of pathogen specific markers and an understanding of the molecular capabilities and adaptations of the pathogen when it interacts with its host may likewise assist in early detection and provide opportunities for targeting countermeasures. An important question that needs to be addressed is whether these molecular-based approaches will prove useful for early diagnosis, complement current methods of direct agent detection, and aid development and use of countermeasures. Lawrence Livermore National Laboratory (LLNL) will host a workshop to explore the utility of host- and pathogen-based molecular diagnostics, prioritize key research issues, and determine the critical steps needed to transition host-pathogen research to tools that can be applied towards a more effective national bio-defense strategy. The workshop will bring together leading researchers/scientists in the area of host-pathogen interactions as well as policy makers from federal agencies. The main objectives of the workshop are: (1) to assess the current national needs, capabilities, near-term technologies, and future challenges in applying various diagnostics tools to public health and bio-defense; (2) to evaluate the utility and feasibility of host-response and pathogen biomarker profiling in the diagnosis and management of infectious diseases; and (3) to create a comprehensive developmental strategy from proof-of-concept, through validation, to deployment of appropriate advanced technology for the clinical/public health and bio-defense environments

Obtaining coincident image observations for Mission to Planet Earth science data return

One objective of the Mission to Planet Earth (MTPE) program involves comparing data from various instruments on multiple spacecraft to obtain a total picture of the Earth's systems. To correlate image data from instruments on different spacecraft, these spacecraft must be able to image the same location on the Earth at approximately the same time. Depending on the orbits of the spacecraft involved, complicated operational details must be considered to obtain such observations. If the spacecraft are in similar orbits, close formation flying or synchronization techniques may be used to assure coincident observations. If the orbits are dissimilar, the launch time of the second satellite may need to be restricted in order to align its orbit with that of the first satellite launched. This paper examines strategies for obtaining coincident observations for spacecraft in both similar and dissimilar orbits. Although these calculations may be performed easily for coplanar spacecraft, the non-coplanar case involves additional considerations which are incorporated into the algorithms presented herein

MODIS information, data and control system (MIDACS) operations concepts

The MODIS Information, Data, and Control System (MIDACS) Operations Concepts Document provides a basis for the mutual understanding between the users and the designers of the MIDACS, including the requirements, operating environment, external interfaces, and development plan. In defining the concepts and scope of the system, how the MIDACS will operate as an element of the Earth Observing System (EOS) within the EosDIS environment is described. This version follows an earlier release of a preliminary draft version. The individual operations concepts for planning and scheduling, control and monitoring, data acquisition and processing, calibration and validation, data archive and distribution, and user access do not yet fully represent the requirements of the data system needed to achieve the scientific objectives of the MODIS instruments and science teams. The teams are not yet formed; however, it is possible to develop the operations concepts based on the present concept of EosDIS, the level 1 and level 2 Functional Requirements Documents, and through interviews and meetings with key members of the scientific community. The operations concepts were exercised through the application of representative scenarios

MODIS information, data and control system (MIDACS) level 2 functional requirements

The MODIS Information, Data and Control System (MIDACS) Level 2 Functional Requirements Document establishes the functional requirements for MIDACS and provides a basis for the mutual understanding between the users and the designers of the EosDIS, including the requirements, operating environment, external interfaces, and development plan. In defining the requirements and scope of the system, this document describes how MIDACS will operate as an element of the EOS within the EosDIS environment. This version of the Level 2 Requirements Document follows an earlier release of a preliminary draft version. The sections on functional and performance requirements do not yet fully represent the requirements of the data system needed to achieve the scientific objectives of the MODIS instruments and science teams. Indeed, the team members have not yet been selected and the team has not yet been formed; however, it has been possible to identify many relevant requirements based on the present concept of EosDIS and through interviews and meetings with key members of the scientific community. These requirements have been grouped by functional component of the data system, and by function within each component. These requirements have been merged with the complete set of Level 1 and Level 2 context diagrams, data flow diagrams, and data dictionary

MODIS Information, Data, and Control System (MIDACS) system specifications and conceptual design

The MODIS Information, Data, and Control System (MIDACS) Specifications and Conceptual Design Document discusses system level requirements, the overall operating environment in which requirements must be met, and a breakdown of MIDACS into component subsystems, which include the Instrument Support Terminal, the Instrument Control Center, the Team Member Computing Facility, the Central Data Handling Facility, and the Data Archive and Distribution System. The specifications include sizing estimates for the processing and storage capacities of each data system element, as well as traffic analyses of data flows between the elements internally, and also externally across the data system interfaces. The specifications for the data system, as well as for the individual planning and scheduling, control and monitoring, data acquisition and processing, calibration and validation, and data archive and distribution components, do not yet fully specify the data system in the complete manner needed to achieve the scientific objectives of the MODIS instruments and science teams. The teams have not yet been formed; however, it was possible to develop the specifications and conceptual design based on the present concept of EosDIS, the Level-1 and Level-2 Functional Requirements Documents, the Operations Concept, and through interviews and meetings with key members of the scientific community

Transition-ready technologies and expertise from the Chemical and Biological National Security Program at LLNL

HSARPA has initiated a new Bioinformatics and Assay Development solicitation, BIAD2 (BAA 06-01), to address a number of technology gaps and requirements for biodetection (www.hsarpabaa.com). This solicitation will leverage the vast research and development capabilities of the private sector and academia in order to meet the needs of HSARPA and Homeland Security. In order to meet these requirements, this solicitation will: (1) Develop and validate actionable assays for the public and private sector; (2) Develop and validate new assays and novel assay methodologies to enhance existing detection systems and enable future detection platforms; (3) Develop next generation assays which are robust against novel, emerging and engineered threats; (4) Develop novel assays that detect low levels of ribonucleic acid (RNA)-based viral threats in complex backgrounds; (5) Develop novel assays to characterize the viability, degree of virulence or toxicity, and countermeasure resistance of a biological agent; and (6) Develop new bioinformatics tools to support assay development and assay validation The Lawrence Livermore National Laboratory (LLNL) Bioassays and Signature Program (BSP) develops nationally-validated detection and identification assays to cover the full range of biological threat agents, starting from human, animal, and plant pathogens on the Select Agent list. The assays that have been co-developed by the CDC and the BSP are used internationally and represent the gold standard for molecular detection of select agent pathogens for the public health community. They are also used in the DHS environmental monitoring operations such as BioWatch and DHS National Security Special Events support. These reagents have been used to process and analyze more than 5 million samples and have delivered exceptional performance for the end users, with zero false positives since their deployment. Currently, highly-multiplexed nucleic acid assays that represent the ''next-generation'' in BioWatch assays have been developed at LLNL and are in final evaluation at CDC. LLNL is a full partner to the LRN network, as well as a formal LRN member, sanctioned to perform these diagnostics on field samples. The Program has assay extensive experience developing, testing, validating, deploying, and commercializing biodetection assays and instrumentation. The following pages contain additional descriptions of our Program's capabilities. We have a demonstrated track record of established collaborations and look forward to partnering with offerers to the HSARPA BAA to continue to meet the national needs and requirements