Development and characterization of molecular tools for microbial forensics

Scope and Method of Study:The anthrax attacks of 2001 prompted the rapid establishment and growth of the fields of microbial and plant pathogen forensics. A complete forensic capability includes the ability to discriminate between a natural and an intentional disease outbreak, collection of forensic evidence, generation of genetic profiles for use during attribution and storage of samples. This document describes (i) the molecular characterization of plant virus populations derived from plants that were naturally and mechanically-inoculated with a model plant virus, (ii) the application of microarray-based technologies to genetically fingerprint plant viruses, (iii) the characterization of a previously-designed microarray platform for the identification and diagnosis of known and novel plant viruses, and (iv) the use of FAME profiles to aid in the discrimination of media components used to prepare Bacillus cereus T-strain spores. Though all of these projects are not directly related, they all fall within the scope of microbial forensics.Findings and Conclusions:The molecular characterization of plant virus populations derived from a natural inoculation event and those from mechanically-inoculated plants displayed minor differences in haplotype and pair-wise nucleotide diversities. Additionally, the number of recombination events was found to be lower in the mechanically-inoculated plants than those collected from the natural disease outbreak. These results indicate that differences between the two types of inoculation events exist and may be a direct function of the infection time, source(s) of inoculum(a) or environmental effects.The solution-based minisequencing and capture array technique demonstrated reproducibility at the same concentration of targets, but was less accurate using variable amounts of synthetic targets. The use of solution-based minisequencing followed by tag-array capture appears to be a promising approach to genotyping plant viruses.A significant amount of cross-hybridization was observed using the universal plant virus microarray (Virochip). The microarray platform failed to strongly hybridize to most of the known plant viruses that were applied to the array. Hybridization with Wheat streak mosaic virus-infected material indicated that the system strongly hybridized with the negative-sense strand, but not the corresponding positive-sense strands.Discrimination of individual media components was achieved by analyzing fatty acids derived from Bacillus cereus T-strain spores prepared in different media. One FAME biomarker, oleic acid, was found to be exclusively associated with media supplemented with blood

Genetic Characterization of Rvi12 Based Scab Resistance From Malus baccata 'HANSEN'S BACCATA # 2'

Apple scab caused by Venturia inaequalis is one of the most prevalent and devastating diseases of apple (Malus × domestica) worldwide. Breeding programs are attempting to introgress scab resistance genes from wild apples into commercial cultivars for sustainable disease control. Most of the commercially available scab-resistant varieties rely on the Rvi6 resistance gene from Malus floribunda 821. The evolution of new pathotypes of V. inaequalis, which have caused the breakdown of Rvi6-based resistance, highlights the need for the characterization and pyramiding of different scab resistance genes for durable scab resistance. This study was performed to characterize another scab resistance locus Rvi12 from Malus baccata ‘Hansen’s baccata #2’ (HB2). The Rvi12 locus was fine-mapped to a physical interval of approximately 882 kb by the use of ‘Golden Delicious’ reference genome guided marker development and a large mapping population. Through a BAC-library-based chromosome walking, additional markers were developed and a single BAC clone spanning the Rvi12 interval was identified. Following PacBio RS II sequencing and the use of the hierarchical genome assembly process, the BAC clone sequence was assembled. The Rvi12 resistance locus was further narrowed to a 62.3 kb genomic region of the HB2 genome. Gene prediction and in-silico characterization identified five putative candidate genes showing homology to known disease resistance genes or genes involved in disease resistance signaling. Protein domain analysis and quantitative real-time PCR (qRT-PCR) of the five putative candidate genes indicated a LRR receptor-like serine/threonine kinase as the most likely candidate gene for Rvi12 resistance. Overall, the novel markers developed from this study will be useful for the marker-assisted selection of apple genotypes carrying the Rvi12 resistance. Further the identification of candidate gene for Rvi12 based scab resistance will provide the initial resources required for developing scab resistant transgenic or cisgenic apple lines with the Rvi12 resistance

Tropical fruit tree diversity: good practices for in situ and on-farm conservation

Farmers have developed a range of agricultural practices to sustainably use and maintain a wide diversity of crop species in many parts of the world. This book documents good practices innovated by farmers and collects key reviews on good practices from global experts, not only from the case study countries but also from Brazil, China and other parts of Asia and Latin America

Assessment of plant genetic resources for water-use efficiency (WUE): managing water scarcity: Proceedings of the Bioversity International/INRA/IDRC/AARINENA Workshop for North Africa and West Asia, Marrakech, Morocco, 10-12 October 2005

Although water is a renewable resource, its supply is not inexhaustible. It is unlikely that sufficient new water resources will be found to meet the projected increase in demand for water for food production, as existing water resources are already under pressure. It is vital, therefore, that existing resources be managed efficiently. This is particularly true with regard to agriculture, which utilizes more than two-thirds of the global water used by humans. Continued successful management of the limited amount of water available for agriculture is dependent upon better agronomic practices and an enhanced understanding of genetic variation for water-use efficiency (WUE) among crop genotypes, especially in areas prone to water scarcity. This document presents the proceedings of an inter-agency workshop dedicated to tackling the issue of water-use efficiency and water scarcity. Issues discussed relate to methods of managing water in agriculture, exploring opportunities for saving water and improving productivity by utilizing genetic resources, as well as other agronomic measures. The document is divided into three sections: the first section addresses themes related to water availability, current and future water needs, and water scarcity. The second section focuses on research strategies for a more efficient use of water resources - particularly in olive orchards - while the third section details the potential of genetic resources to manage water scarcity. It also addresses innovative approaches towards exploring the valuable genetic variation within crops, especially olives and almonds. The aim of the undertaking is to facilitate assessment of genetic variation for WUE and measurement of water requirements at the genotypic level, rather than simply at the crop level. Assessing plant genetic resources for complex traits such as those concerning water-use efficiency requires large numbers of samples to be taken. Lack of development of rapid, costeffective methods has hindered the use of WUE in practice and breeding. The effectiveness of characterization is also hindered by the lack of novel 'smart and rapid screens' needed to identify desirable traits in a cost-effective manner. The overview of concepts such as quantitative methods to model traits associated with water-use efficiency can also help in narrowing the phenotype gap. The overall aim of this text is to enhance the use of diversity through characterization, using novel approaches in order to improve productivity, and to ensure that knowledge about ongoing research on efficient water-use of plant genetic resources is readily available to all stakeholders

Program and abstracts book

"Organized by the Centers for Disease Control and Prevention (CDC), the Council of State and Territorial Epidemiologists CSTE), the CDC Foundation (CDCF), the Association of Public Health Laboratories (APHL), and the World Health Organization (WHO), the American Society for Microbiology (ASM)."Includes index

PHENOTYPIC CHARACTERIZATION OF THE INTERACTION BETWEEN PLASMOPARA VITICOLA AND VITIS VINIFERA.

Plasmopara viticola (Berk. et Curt.) Berl. and De Toni is an obligate biotrophic oomycete which causes grapevine downy mildew, one of the most important grapevine disease, affecting particularly the European grapevine Vitis vinifera L. The main objective of the study is to find possible sources of resistance to P. viticola in the less common V. vinifera germplasm (Caucasian origin) through the screening of an ample collection of cultivated and wild Caucasian accessions, grown in greenhouse and in open field. This could really simplify the genetic improvement programs. The level of susceptibility towards P. viticola has been assessed by experimental inoculations on 148 cultivated Caucasian (mainly Georgian) and Iranian accessions (V. vinifera var. vinifera) and 35 wild Georgian accessions (V. vinifera var. sylvestris) grown in pots in greenhouse. Moreover, natural downy mildew occurrence has been evaluated on 94 Georgian accessions cultivated in vineyard. These activities have been carried out for three consecutive years. Several accessions were characterized by an interesting resistance level, and in particular, the Georgian cv Mgaloblishvili N. was characterized by the most stable behavior. For this reason, further investigations, aiming at more deeply investigating the plant-pathogen interaction at the genetic and histological levels, were carried out on this cultivar. In order to get insights on the resistance mechanism at the genetic level, 272 Mgaloblishvili progenies were obtained by self pollination, open pollination and pollinated with \u2018Pinot noir\u2019 N and experimental inoculations have been carried out over a three-year period. The characterization of the interaction between P. viticola and Mgaloblishvili by histological analysis at different time points was assessed, in order to evaluate the type and the timing of the plant response and the development of the pathogen. To thoroughly analyze the effective level of resistance in Mgaloblishvili, experimental inoculation with different P. viticola strains characterized by different aggressiveness levels were carried out. Finally, the genetic variability of P. viticola in Italy was investigated to get insights on the possible durability of resistance in open field. The genetic diversity of P. viticola populations, collected from 13 different geographic Italian regions, has been investigated during one-month period at INRA, Institute de la vigne et du vin, Villeneuve d\u2019Ornon (Bordeaux) in France to evaluate if the genetic differences could modulate the aggressiveness level of the pathogen

Environmental Sciences Division: Summaries of research in FY 1996

This document describes the Fiscal Year 1996 activities and products of the Environmental Sciences Division, Office of Biological and Environmental Research, Office of Energy Research. The report is organized into four main sections. The introduction identifies the basic program structure, describes the programs of the Environmental Sciences Division, and provides the level of effort for each program area. The research areas and project descriptions section gives program contact information, and provides descriptions of individual research projects including: three-year funding history, research objective and approach used in each project, and results to date. Appendixes provide postal and e-mail addresses for principal investigators and define acronyms used in the text. The indexes provide indexes of principal investigators, research institutions, and keywords for easy reference. Research projects are related to climatic change and remedial action

Mutation breeding, genetic diversity and crop adaptation to climate change

This book presents reviews on the application of the technology for crop improvement towards food and nutrition security, and research status on mutation breeding and associated biotechnologies in both seed crops and vegetatively propagated crops. It also presents perspectives on the significance of next-generation sequencing and bioinformatics in determining the molecular variants underlying mutations and on emerging biotechnologies such as gene editing. Reviews and articles are organized into five sections in the publication: (1) Contribution of Crop Mutant Varieties to Food Security; (2) Mutation Breeding in Crop Improvement and Climate-Change Adaptation; (3) Mutation Induction Techniques for Enhanced Genetic Variation; (4) Mutation Breeding in Vegetatively Propagated and Ornamental Crops; and (5) Induced Genetic Variation for Crop Improvement in the Genomic Era. The contents of this volume present excellent reference material for researchers, students and policy makers involved in the application of induced genetic variation in plants for the maintenance of biodiversity and the acceleration of crop adaptation to climate change to feed a growing global population in the coming years and decades.illustrato