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)

Short protocols in molecular biology

The Veterinary Clinics of North America

Section I: The Normal Bird: Systematics. Reproductive Physiology. Nutrition. Laws and Regulations Affecting Aviculture and the Pet Bird Industry. Embryology. Pediatricsand Hand Raising. Behavior. Avicultural Medicine and Flock Health Management. Nonsurgical Methods of Avian Sex Identification. Section II: Diagnostics, Hospital Techniques, And Supportive Care: Physical Examination. Avian Clinical Pathology: Hematologyand Chemistry. Diagnostic Necropsy and Pathology. Radiology. Ultrasonography. Cytology. Differential Diagnostics. Hospital Techniques and Supportive Care. Section III: Infectious Diseases: Bacteriology. Virology. Mycotic Diseases. Parasitology. Zoonotic Diseases. Chlamydia. Mycoplasmal Infections. Section IV: Noninfectious Diseases: Respiratory Disorders. Gastrointestinal Tract. Avian Nervous System. The Endocrine System. Avian Cardiac Disease. Nutritional Disorders. Disorders of the Musculoskeletal System. Avian Dermatology. Disorders of the Special Senses. Neoplasia. Toxicities. Urogenital Disorders. Diseases of the Avian Immune System. Behavioral Problems. Section V: Pharmacology and Therapeutics: Metabolism, Pharmacology, And Therapy. Formulary.

鳥類の内科学と外科学 : Avian medicine and surgery

Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses.

In the Neotropical region, the white-winged vampire bat (Diaemus youngi) is the rarest of the three species of vampire bats. This bat species feeds preferentially on bird blood, and there is limited information on the viruses infecting D. youngi. Hence, this study aimed to expand the knowledge about the viral diversity associated with D. youngi by sampling and pooling the lungs, liver, kidneys, heart, and intestines of all animals using high-throughput sequencing (HTS) on the Illumina MiSeq platform. A total of three complete and 10 nearly complete circular virus genomes were closely related to gemykrogvirus (Genomoviridae family), smacovirus (Smacoviridae family), and torque teno viruses (TTVs) (Anelloviridae family). In addition, three sequences of bat paramyxovirus were detected and found to be closely related to viruses reported in Pomona roundleaf bats and rodents. The present study provides a snapshot of the viral diversity associated with white-winged vampire bats and provides a baseline for comparison to viruses detected in future outbreaks. 

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The virome of the white-winged vampire bat Diaemus youngi is rich in circular DNA viruses

C.W., Ferreira D.J., Macagnan M., Fallavena L.C.B., Moraes H.L.S. & Wald V.B. 2004. Prevalence of antibodies against chicken anaemia virus (CAV) in broiler breeders Prevalence of antibodies against chicken anaemia virus (CAV) in broiler breeders Prevalence of antibodies against chicken anaemia virus (CAV) in broiler breeders Prevalence of antibodies against chicken anaemia virus (CAV) in broiler breeders Prevalence of antibodies against chicken anaemia virus (CAV) in broiler breeders in Southern Brazil. in Southern Brazil. in Southern Brazil. in Southern Brazil. in Southern Brazil. Pesquisa Veterinaria Brasileira 24(2):89-92. Centro de Diagnostico e Pesquisa em Patologia Aviaria (CDPA), Faculdade de Veterinaria da Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil. E-mail: claudio.canal@ufrgs.br Chicks infected during the first two weeks of life with chicken anaemia virus (CAV) manifest clinical disease that can be avoided if the breeder hens transfer enough antibodies to their progeny. The objective of the present work was to establish the prevalence and titer of anti-CAV antibodies in some Brazilian broiler hen breeder flocks and verify in which phase of life the birds were infected. A total of 1,709 serum samples from 12 broiler hen flocks vaccinated against CAV and 64 unvaccinated flocks were analyzed for CAV antibodies with an enzyme-linked immunosorbent assay (ELISA). All non-vaccinated breeder flocks were found to be infected with CAV, with 89% of the hens tested presenting antibodies, 52% of these with titers considered high enough to protect their progeny against CAV infection. Likewise, all vaccinated hens had antibody titer to CAV capable of conferring protection to their progeny. Thus, vaccination of hens seems capable of conferring protection to chicks against clinically apparent CAV-associated disease.

V) in broiler breeders in Southern Brazil 1

N., Furian T.Q., Leao J.A., Pereira R.A., Moraes L.B. & Canal C.W. 2004. (Detection of infectious laryngotracheitis virus in chickens in Brazil. of infectious laryngotracheitis virus in chickens in Brazil. of infectious laryngotracheitis virus in chickens in Brazil. of infectious laryngotracheitis virus in chickens in Brazil. of infectious laryngotracheitis virus in chickens in Brazil.) Deteccao do virus da laringotraqueite das galinhas no Brasil. Pesquisa Veterinaria Brasileira 24(2):85-88. Centro de Diagnostico e Pesquisa em Patologia Aviaria (CDPA), Faculdade de Veterinaria, UFRGS, Porto Alegre, RS 91540-000, Brazil. E-mail: nilzaneb@hotmail.com A study was carried out in search for evidences of infectious laryngotracheitis virus (ILTV) infections in some Brazilian chicken flocks. Tracheal tissues and swabs were collected from 10 different flocks of layers and broilers displaying respiratory signs of disease. Samples were processes for virus isolation in embryonated eggs and the membranes examined by histopathology. In addition, specimens were examined by polymerase chain reaction (PCR). Three flocks had ILTV positive chickens by virus isolation and PCR. These results confirm the occurrence of ILTV in chickens in

Detecção do vírus da laringotraqueíte das galinhas Detecção do vírus da laringotraqueíte das galinhas Detecção do vírus da laringotraqueíte das galinhas Detecção do vírus da laringotraqueíte das galinhas Detecção do vírus da laringotraqueíte das galinhas

Evaluate bovine viral diarrhea virus (BVDV) antigenicity by using virus neutralization titers (VNT) analyzed using the principal component analysis (PCA) from antisera generated against US-based vaccine strains against both US-origin field isolates and non-US-origin field isolates.Data from both independent analyses demonstrated that several US-origin and non-US-origin BVDV field isolates appear to be antigenically divergent from the US-based vaccine strains. Results from the combined analysis provided greater insight into the antigenic diversity observed among BVDV isolates. Data from this study further support genetic assignment into BVDV subgenotypes, as well as strains within subgenotypes is not representative of antigenic relatedness. PCA highlights isolates that are antigenically divergent from members of the same species and subgenotype and conversely isolates that belong to different subgenotypes have similar antigenic characteristics when using antisera from US-based vaccine isolates. 

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Multivariate analysis reveals that BVDV field isolates do not show a close VN-based antigenic relationship to US vaccine strains

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Cláudio Wageck Canal

Papers

The virome of the white-winged vampire bat Diaemus youngi is rich in circular DNA viruses

V) in broiler breeders in Southern Brazil 1

Detecção do vírus da laringotraqueíte das galinhas Detecção do vírus da laringotraqueíte das galinhas Detecção do vírus da laringotraqueíte das galinhas Detecção do vírus da laringotraqueíte das galinhas Detecção do vírus da laringotraqueíte das galinhas

Multivariate analysis reveals that BVDV field isolates do not show a close VN-based antigenic relationship to US vaccine strains

Pesquisa do vírus da diarreia viral bovina em touros mantidos a campo no estado do Rio Grande do Sul