Damming the genomic data flood using a comprehensive analysis and storage data structure

Data generation, driven by rapid advances in genomic technologies, is fast outpacing our analysis capabilities. Faced with this flood of data, more hardware and software resources are added to accommodate data sets whose structure has not specifically been designed for analysis. This leads to unnecessarily lengthy processing times and excessive data handling and storage costs. Current efforts to address this have centered on developing new indexing schemas and analysis algorithms, whereas the root of the problem lies in the format of the data itself. We have developed a new data structure for storing and analyzing genotype and phenotype data. By leveraging data normalization techniques, database management system capabilities and the use of a novel multi-table, multidimensional database structure we have eliminated the following: (i) unnecessarily large data set size due to high levels of redundancy, (ii) sequential access to these data sets and (iii) common bottlenecks in analysis times. The resulting novel data structure horizontally divides the data to circumvent traditional problems associated with the use of databases for very large genomic data sets. The resulting data set required 86% less disk space and performed analytical calculations 6248 times faster compared to a standard approach without any loss of information

Volatile organic compounds associated with neonectria ditissima infection in apples (Malus pumila cv Gala)

Postharvest diseases in apples during long term storage result in loss and waste. This is mainly caused by fungal pathogens. Fungal contamination and rot can change some of the volatile organic compounds (VOC) emitted by apple fruits. In this study, disease free Gala apples were inoculated with Neonectria ditissima. The aim was to identify VOCs associated with N. ditissima infection in gala apples. The inoculated apples were placed in 5L glass flask, sealed, and incubated at 20oC for one hour after which a charcoal filtered airflow of 1 L/min was maintained for one hour through the Volatile Capture Trap (VCT) with volatile emissions captured on a porapak-Q absorbent filter. Captured volatiles were eluted using 1 mL of dichloromethane (DCM) into a standard Agilent 1.5 mL HPLC vial. Eluted volatiles were analysed using Gas Chromatography coupled with Mass Spectrometry (GC/MS). Volatiles were capture in three replicates for both inoculated and healthy control groups at 2 days, 8 days, 14 days, 21 days, 28 days, 35 days, and 42 days post-inoculation. The N. ditissima discriminatory volatile were identified/discriminated qualitatively based on the unique volatile compounds detected and quantitatively based on variation in peak area of certain combinations of volatile compounds. Some of the discriminatory volatiles such as dodecyl hexanoate, 9-decen-1-yl hexanoate, hexyl butanoate and pentyl acetate were detected in the early stages of the infection. Styrene, terpinene-4-ol, ethyl hexanoate, ethyl butanoate, ethyl pentanoate and 2-methylpentyl formate constituted the main VOCs emitted during apple fruit decay. Other compounds such as alpha Farnesene and hexyl acetate were common to both healthy and inoculated apples but the peak areas in the healthy apples were well above the peak areas in the inoculated apples. However, these compounds expressed a decline in peak area over time. Apples are stored commercially in sealed stores for months making visual observation for early detection of disease almost impossible. Disease of stored apples are most times only detected at advanced stages when it has become nearly impossible to prevent losses. These discriminatory volatile metabolites detected at early stages of infection are important for early non-visual detection of N. ditissima in stored apples. Further research is recommended to the use of these compounds in early detection of the disease caused by N. ditissima

Poultry viruses: from threat to therapy

Infectious diseases are one of the major causes of economic losses in poultry industries. In many instances, there are no specific signs that are associated with a particular disease. Besides clinical signs and findings from post mortem examinations, diagnostic tools based on serological and molecular detections are used to confirm the causative agents. However, the identification of causative agents and the detection of specific antibody responses in relation to a clinical problem are complicated due to the concurrent infections and improper use of vaccines. Currently, the poultry industry is threatened by more virulent viruses of endemic diseases or by exotic and emerging diseases that can cause major economic losses to this sector. The emergence and re-emergence of avian influenza virus (AIV), particularly the highly pathogenic avian influenza (HPAI) H5N1, the presence of endemic low pathogenic avian influenza (LPAI) H9N2 in poultry flock and recently the detection of the novel H7H9 and H10N8 in certain regions in China posed threats to the poultry industry and public health sector. Infection with HPAI such as H5N1 is easy to diagnose. However, the real challenge is to confront H7N9, H9N2, H10N8 and other LPAI which act in concert with other factors such as management, environment, nutrition and concurrent infections which possess a continuous threat to the entire poultry production system. The repeated outbreaks of diseases caused by variant strains of infectious bronchitis virus (IBV), velogenic Newcastle disease viruses (NDV) and more virulent viruses of infectious bursal disease virus (IBDV), infectious laryngotracheitis virus (ILTV) and Marek’s disease virus (MDV) in well managed poultry flocks have prompted the need to evaluate the underlying factors contributing to the failure of vaccinations to provide protection against clinical infections and transmission of disease. In the field, vaccination failure is a complex event involving various factors associated with vaccine strains and vaccination program, the virulence of field pathogens and the host immune competence. In many situations, immunosuppressive agents, primarily the MDV, IBDV and chicken anemia virus play an important role in increasing the susceptibility of chickens to opportunistic infections and/or suppressing effective vaccine induced responses. Vaccination is the most cost-effective method available in preventing economic losses and increasing the lifespan of animals. Undoubtedly, diagnostic tools, vaccines and vaccination equipment have improved over the years through the use of innovative technology. However, vaccine is not evolution-proof and it may enhance virus evolution especially in the absence of sterilizing immunity allowing wild type viruses to be transmitted through vaccinated chickens.Despite advancements in genetic engineered tools, conventional laboratory diagnosis using serological tests and conventional vaccines are used extensively in health and disease management of poultry. Nearly all poultry vaccines are conventional vaccines which consist of live-attenuated and killed vaccines that have generally worked well. However, avian pathogens continue to change and develop ways to evade the immunity induced by the current vaccines. In addition, as the poultry industry become more intensive, accurate, economical and practical laboratory diagnostic tools are important for the effective control of disease outbreaks. The advancements in the use of molecular detection method using real-time PCR approach, highly automated instruments for antibody detection and development of rapid on site assays for virus antigen detection may have significant impact in the field of disease prevention and control. In the area of vaccinology, most of the advances in the development of recombinant vaccines against poultry diseases are based on the development of recombinant viral vectored, DNA plasmid and reverse genetic vaccines. However, it is anticipated that more recombinant based vaccines will be used in the field in the near future. In addition, the advancement on “omic” technology are paving novel approaches for the development of new generation adjuvants and vaccines as well as breeding for disease resistance based on our improving knowledge of the chicken immunogenomic response to disease. However, the development and delivery of new or improved poultry diagnostics, vaccines and pharmaceutical which fulfill the industry, regulatory and public acceptance is a challenging process. Although the majority of poultry viruses are pathogenic to chickens, some of them especially NDV has the potential to act as a live saver in humans due to its unique properties as viral vectored vaccine against other infectious diseases and selective oncolytic properties on human cancer cells. The continuous encouraging results of NDV oncolytic virotherapy in human clinical trials will facilitate the approval of NDV as ancillary therapy of human cancer in the near future. Innovative research on the use of NDV as human vaccines and therapeutics should be explored via multi-disciplinary approach by various expert groups. In conclusion, as the poultry industry is expanding and the globalization of poultry and poultry by products, much is needed to improve the control and prevention of diseases. The emerging and emerging of diseases especially transboundary diseases can impact socioeconomic of a country and global food security. The strengthening our scientific and technical capacity, especially through innovative technology and strategy, will help to meet the current challenges and ever changing needs of the nation and the world

Tuberculosis: new era for diagnosis and surveillance using whole-genome sequencing-based approaches

Tuberculosis (TB) has been declared as a global public health emergency by the WHO since 1993. It still accounts for almost 2 million deaths each year, making it the ninth leading cause of death worldwide. The major obstacle for an effective TB control is antimicrobial resistance, thus, to be successful, new strategies must be addressed, for instance, the implementation of new rapid TB diagnostic technologies that could translate into early treatment initiation and blocking of transmission chains. Considering the major constraints regarding the isolation and time of growth of M. tuberculosis strains, the main goal of this PhD dissertation was to acknowledge the potential of the use of WGS-based methodologies for routine diagnostic and epidemiological surveillance. We evaluated several software for in silico prediction of antibiotic resistance and developed bioinformatics pipelines for surveillance purposes, in particular for the identification of transmission chains. As they revealed high sensitivity, these approaches are already implemented in the routine of the Portuguese National Reference Laboratory (NRL). We also recognised the possibility to use these same approaches directly to samples collected from TB patients, lowering the time-to-results, for a complete drug resistance pattern and phylogeny analysis, for five to eight days. The validation of this methodology is ongoing and will be implemented in a near future. Additionally, and according to the new recommendations for TB treatment, we have initiated studies to identify new mutations associated with resistance to the recently adopted drugs, in order to enrich the available databases and improve the performance of the genotypic diagnostics pipelines. This PhD dissertation highlights WGS-based methodologies as powerful tools to surpass the difficulties of phenotypic TB diagnosis and surveillance and to provide a much more rapid information regarding resistance prediction and eventual transmission chains. It also supported the technological transition performed at the NRL for TB surveillance

Wheat Improvement

This open-access textbook provides a comprehensive, up-to-date guide for students and practitioners wishing to access in a single volume the key disciplines and principles of wheat breeding. Wheat is a cornerstone of food security: it is the most widely grown of any crop and provides 20% of all human calories and protein. The authorship of this book includes world class researchers and breeders whose expertise spans cutting-edge academic science all the way to impacts in farmers’ fields. The book’s themes and authors were selected to provide a didactic work that considers the background to wheat improvement, current mainstream breeding approaches, and translational research and avant garde technologies that enable new breakthroughs in science to impact productivity. While the volume provides an overview for professionals interested in wheat, many of the ideas and methods presented are equally relevant to small grain cereals and crop improvement in general. The book is affordable, and because it is open access, can be readily shared and translated -- in whole or in part -- to university classes, members of breeding teams (from directors to technicians), conference participants, extension agents and farmers. Given the challenges currently faced by academia, industry and national wheat programs to produce higher crop yields --- often with less inputs and under increasingly harsher climates -- this volume is a timely addition to their toolkit

Biotic and Abiotic Constraints in Mungbean Production—Progress in Genetic Improvement

Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] is an important food and cash legume crop in Asia. Development of short duration varieties has paved the way for the expansion of mungbean into other regions such as Sub-Saharan Africa and South America. Mungbean productivity is constrained by biotic and abiotic factors. Bruchids, whitefly, thrips, stem fly, aphids, and pod borers are the major insect-pests. The major diseases of mungbean are yellow mosaic, anthracnose, powdery mildew, Cercospora leaf spot, halo blight, bacterial leaf spot, and tan spot. Key abiotic stresses affecting mungbean production are drought, waterlogging, salinity, and heat stress. Mungbean breeding has been critical in developing varieties with resistance to biotic and abiotic factors, but there are many constraints still to address that include the precise and accurate identification of resistance source(s) for some of the traits and the traits conferred by multi genes. Latest technologies in phenotyping, genomics, proteomics, and metabolomics could be of great help to understand insect/pathogen-plant, plant-environment interactions and the key components responsible for resistance to biotic and abiotic stresses. This review discusses current biotic and abiotic constraints in mungbean production and the challenges in genetic improvement

The European Hematology Association Roadmap for European Hematology Research: a consensus document

The European Hematology Association (EHA) Roadmap for European Hematology Research highlights major achievements in diagnosis and treatment of blood disorders and identifies the greatest unmet clinical and scientific needs in those areas to enable better funded, more focused European hematology research. Initiated by the EHA, around 300 experts contributed to the consensus document, which will help European policy makers, research funders, research organizations, researchers, and patient groups make better informed decisions on hematology research. It also aims to raise public awareness of the burden of blood disorders on European society, which purely in economic terms is estimated at €23 billion per year, a level of cost that is not matched in current European hematology research funding. In recent decades, hematology research has improved our fundamental understanding of the biology of blood disorders, and has improved diagnostics and treatments, sometimes in revolutionary ways. This progress highlights the potential of focused basic research programs such as this EHA Roadmap. The EHA Roadmap identifies nine ‘sections’ in hematology: normal hematopoiesis, malignant lymphoid and myeloid diseases, anemias and related diseases, platelet disorders, blood coagulation and hemostatic disorders, transfusion medicine, infections in hematology, and hematopoietic stem cell transplantation. These sections span 60 smaller groups of diseases or disorders. The EHA Roadmap identifies priorities and needs across the field of hematology, including those to develop targeted therapies based on genomic profiling and chemical biology, to eradicate minimal residual malignant disease, and to develop cellular immunotherapies, combination treatments, gene therapies, hematopoietic stem cell treatments, and treatments that are better tolerated by elderly patients

The European Hematology Association Roadmap for European Hematology Research. A Consensus Document

Abstract The European Hematology Association (EHA) Roadmap for European Hematology Research highlights major achievements in diagnosis and treatment of blood disorders and identifies the greatest unmet clinical and scientific needs in those areas to enable better funded, more focused European hematology research. Initiated by the EHA, around 300 experts contributed to the consensus document, which will help European policy makers, research funders, research organizations, researchers, and patient groups make better informed decisions on hematology research. It also aims to raise public awareness of the burden of blood disorders on European society, which purely in economic terms is estimated at Euro 23 billion per year, a level of cost that is not matched in current European hematology research funding. In recent decades, hematology research has improved our fundamental understanding of the biology of blood disorders, and has improved diagnostics and treatments, sometimes in revolutionary ways. This progress highlights the potential of focused basic research programs such as this EHA Roadmap. The EHA Roadmap identifies nine sections in hematology: normal hematopoiesis, malignant lymphoid and myeloid diseases, anemias and related diseases, platelet disorders, blood coagulation and hemostatic disorders, transfusion medicine, infections in hematology, and hematopoietic stem cell transplantation. These sections span 60 smaller groups of diseases or disorders. The EHA Roadmap identifies priorities and needs across the field of hematology, including those to develop targeted therapies based on genomic profiling and chemical biology, to eradicate minimal residual malignant disease, and to develop cellular immunotherapies, combination treatments, gene therapies, hematopoietic stem cell treatments, and treatments that are better tolerated by elderly patients. Received December 15, 2015. Accepted January 27, 2016. Copyright © 2016, Ferrata Storti Foundatio