The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Nanomaterials (NMs) have gained prominence in technological advancements due to their tunable physical, chemical and biological properties with enhanced performance over their bulk counterparts. NMs are categorized depending on their size, composition, shape, and origin. The ability to predict the unique properties of NMs increases the value of each classification. Due to increased growth of production of NMs and their industrial applications, issues relating to toxicity are inevitable. The aim of this review is to compare synthetic (engineered) and naturally occurring nanoparticles (NPs) and nanostructured materials (NSMs) to identify their nanoscale properties and to define the specific knowledge gaps related to the risk assessment of NPs and NSMs in the environment. The review presents an overview of the history and classifications of NMs and gives an overview of the various sources of NPs and NSMs, from natural to synthetic, and their toxic effects towards mammalian cells and tissue. Additionally, the types of toxic reactions associated with NPs and NSMs and the regulations implemented by different countries to reduce the associated risks are also discussed.

/pdf/review-on-nanoparticles-and-nanostructured-materials-history-ukc67h8z6q.pdf

Review on nanoparticles and nanostructured materials: history, sources, toxicity and regulations.

VERY few veterinary surgeons have thought fit to write a book on diseases of poultry. Mr. Ernest Gray has done justice to the subject and is to be congratulated on his effort. A book of this size, written by one with specialized knowledge, will add to the value of any library or private bookshelf. Diseases of Poultry Their Aetiology, Diagnosis, Treatment and Control; with a Section on the Normal Anatomy and Physiology of the Fowl. By Ernest Gray. (Lockwood's Agricultural and Horticultural Handbooks.) Pp. x + 198 + 16 plates. (London: Crosby Lockwood and Son, Ltd., 1940.) 9s. 6d. net.

Diseases of Poultry

Pandemic influenza virus has its origins in avian influenza viruses. The highly pathogenic avian influenza virus subtype H5N1 is already panzootic in poultry, with attendant economic consequences. It continues to cross species barriers to infect humans and other mammals, often with fatal outcomes. Therefore, H5N1 virus has rightly received attention as a potential pandemic threat. However, it is noted that the pandemics of 1957 and 1968 did not arise from highly pathogenic influenza viruses, and the next pandemic may well arise from a low-pathogenicity virus. The rationale for particular concern about an H5N1 pandemic is not its inevitability but its potential severity. An H5N1 pandemic is an event of low probability but one of high human health impact and poses a predicament for public health. Here, we review the ecology and evolution of highly pathogenic avian influenza H5N1 viruses, assess the pandemic risk, and address aspects of human H5N1 disease in relation to its epidemiology, clinical presentation, pathogenesis, diagnosis, and management.

http://www.hkupasteur.hku.hk/publications/pdf/Peiris_et_al_2007.pdf

Avian Influenza Virus (H5N1): a Threat to Human Health

An overview of the epidemiology of avian influenza.

This review is focused on the acute form of infectious bursal disease (IBD) caused by very virulent IBD virus (vvIBDV). First described in Europe about 10 years ago, this new form of the disease has rapidly spread all over the world, causing dramatic losses; after a decade, it still represents a considerable threat to the poultry industry. Emergence of the acute forms of the disease has drastically changed the epidemiology of IBD. Although their origin is still under investigation, vvIBDVs have spread all over the world in a very explosive but conserved manner. This raises the question of the origin of vvIBDVs, of the possible existence of reservoirs and of the possible emergence of new, distinct lineages in the future. While it has become clear that amino acids within the variable region of virus protein VP2 account for the molecular basis of antigenic variation, no definite hot spot that determines pathogenicity has been identified. Fingerprints of VP2 on vvIBDVs have to be considered more as common evo...

https://www.tandfonline.com/doi/pdf/10.1080/03079450050045431

Acute infectious bursal disease in poultry: A review

We report the isolation and characterization of a highly pathogenic avian influenza A/H5N1 virus from Crested Hawk-Eagles smuggled into Europe by air travel. A screening performed in human and avian contacts indicated no dissemination occurred. Illegal movements of birds are a major threat for the introduction of highly pathogenic avian influenza.

/pdf/highly-pathogenic-h5n1-influenza-virus-in-smuggled-thai-xfoh5loonc.pdf

Highly pathogenic H5N1 influenza virus in smuggled Thai eagles, Belgium.

Infectious Bursal Disease (IBD) is caused by a small, non-enveloped virus, highly resistant in the outside environment. Infectious Bursal Disease Virus (IBDV) targets the chicken's immune system in a very comprehensive and complex manner by destroying B lymphocytes, attracting T cells and activating macrophages. As an RNA virus, IBDV has a high mutation rate and may thus give rise to viruses with a modified antigenicity or increased virulence, as emphasized during the last decades. The molecular basis of pathogenicity and the exact cause of clinical disease and death are still poorly understood, as it is not clearly related to the severity of the lesions and the extent of the bursal damage. Recent works however, pointed out the role of an exacerbated innate immune response during the early stage of the infection with upregulated production of promediators that will induce a cytokine storm. In the case of IBDV, immunosuppression is both a direct consequence of the infection of specific target immune cells and an indirect consequence of the interactions occurring in the immune network of the host. Recovery from disease or subclinical infection will be followed by immunosuppression with more serious consequences if the strain is very virulent and infection occurs early in life. Although the immunosuppression caused by IBDV is principally directed towards B-lymphocytes, an effect on cell-mediated immunity (CMI) has also been demonstrated therefore increasing the impact of IBDV on the immunocompetence of the chicken. In addition to its zootechnical impact and its role in the development of secondary infections, it may affect the immune response of the chicken to subsequent vaccinations, essential in all types of intensive farming. Recent progress in the field of avian immunology has allowed a better knowledge of the immunological mechanisms involved in the disease but also should give improved tools for the measurement of immunosuppression in the field situation. Although satisfactory protection may be provided by the induction of high neutralizing antibody titres, interference from parental antibodies with vaccination has become the most important obstacle in the establishment of control programs. In this context, recombinant HVT and immune complex vaccines show promising results.

Infectious Bursal Disease: a complex host-pathogen interaction.

Although it is well accepted that the present Asian H5N1 panzootic is predominantly an animal health problem, the human health implications and the risk of human pandemic have highlighted the need for more information and collaboration in the field of veterinary and human health H5 and H7 avian influenza (AI) viruses have the unique property of becoming highly pathogenic (HPAI) during circulation in poultry Therefore, the final objective of poultry vaccination against AI must be eradication of the virus and the disease Actually, important differences exist in the control of avian and human influenza viruses Firstly, unlike human vaccines that must be adapted to the circulating strain to provide adequate protection, avian influenza vaccination provides broader protection against HPAI viruses Secondly, although clinical protection is the primary goal of human vaccines, poultry vaccination must also stop transmission to achieve efficient control of the disease This paper addresses these differences by reviewing the current and future influenza vaccines and vaccination strategies in birds

Influenza vaccines and vaccination strategies in birds.

The sequences of the L1 loop of the hexon protein from representative fowl adenovirus (FAdV) strains of the different European and American collections were determined and compared. This study highlighted the lack of consensus in the numbering of the individual serotypes between the American and the European classifications. An identification system is proposed based on restriction fragment length polymorphism of the hexonA/hexonB polymerase chain reaction product. In addition, new insights into the relationships among FAdV strains are presented and discussed on the basis of phylogenetic analysis of the L1 loops sequences. Six clusters of strains that are supported by high bootstrap values were identified. Three of them are clearly independent, forming groups A, B and C, whereas the three others are clustered in a single ‘supergroup’, denominated D. Interestingly, the Japanese strain TR22 that is presently classified as European type 5 (species B) could not be assigned to any of the aforementioned cluster...

https://www.tandfonline.com/doi/pdf/10.1080/03079450310001652086

Thierry van den Berg

Papers

Acute infectious bursal disease in poultry: A review

Highly pathogenic H5N1 influenza virus in smuggled Thai eagles, Belgium.

Infectious Bursal Disease: a complex host-pathogen interaction.

Influenza vaccines and vaccination strategies in birds.

Phylogenetic analysis of fowl adenoviruses.