Muhammad Zubair Shabbir

Bio: Muhammad Zubair Shabbir is an academic researcher from University of Veterinary and Animal Sciences. The author has contributed to research in topics: Population & Newcastle disease. The author has an hindex of 23, co-authored 156 publications receiving 1900 citations. Previous affiliations of Muhammad Zubair Shabbir include DSO National Laboratories & Government College University, Faisalabad.

2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Abstract: In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Listeriosis in animals, its public health significance (food-borne zoonosis) and advances in diagnosis and control: a comprehensive review

Abstract: Listeriosis is an infectious and fatal disease of animals, birds, fish, crustaceans and humans. It is an important food-borne zoonosis caused by Listeria monocytogenes, an intracellular pathogen with unique potential to spread from cell to cell, thereby crossing blood-brain, intestinal and placental barriers. The organism possesses a pile of virulence factors that help to infect the host and evade from host immune machinery. Though disease occurrence is sporadic throughout the world, it can result in severe damage during an outbreak. Listeriosis is characterized by septicaemia, encephalitis, meningitis, meningoencephalitis, abortion, stillbirth, perinatal infections and gastroenteritis with the incubation period varying with the form of infection. L. monocytogenes has been isolated worldwide from humans, animals, poultry, environmental sources like soil, river, decaying plants, and food sources like milk, meat and their products, seafood and vegetables. Since appropriate vaccines are not available and infection is mainly transmitted through foods in humans and animals, hygienic practices can prevent its spread. The present review describes etiology, epidemiology, transmission, clinical signs, post-mortem lesions, pathogenesis, public health significance, and advances in diagnosis, vaccines and treatment of this disease. Special attention has been given to novel as well as prospective emerging therapies that include bacteriophage and cytokine therapy, avian egg yolk antibodies and herbal therapy. Various vaccines, including advances in recombinant and DNA vaccines and their modes of eliciting immune response, are also discussed. Due focus has also been given regarding appropriate prevention and control strategies to be adapted for better management of this zoonotic disease.

Infectivity and transmissibility of H9N2 avian influenza virus in chickens and wild terrestrial birds.

Abstract: Genetic changes in avian influenza viruses influence their infectivity, virulence and transmission. Recently we identified a novel genotype of H9N2 viruses in widespread circulation in poultry in Pakistan that contained polymerases (PB2, PB1 and PA) and non-structural (NS) gene segments identical to highly pathogenic H7N3 viruses. Here, we investigated the potential of these viruses to cause disease and assessed the transmission capability of the virus within and between poultry and wild terrestrial avian species. Groups of broilers, layers, jungle fowl, quail, sparrows or crows were infected with a representative strain (A/chicken/UDL-01/08) of this H9N2 virus and then mixed with naive birds of the same breed or species, or different species to examine transmission. With the exception of crows, all directly inoculated and contact birds showed clinical signs, varying in severity with quail showing the most pronounced clinical signs. Virus shedding was detected in all infected birds, with quail showing the greatest levels of virus secretion, but only very low levels of virus were found in directly infected crow samples. Efficient virus intra-species transmission was observed within each group with the exception of crows in which no evidence of transmission was seen. Interspecies transmission was examined between chickens and sparrows and vice versa and efficient transmission was seen in either direction. These results highlight the ease of spread of this group of H9N2 viruses between domesticated poultry and sparrows and show that sparrows need to be considered as a high risk species for transmitting H9N2 viruses between premises.

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

Abstract: 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.

Research Design: Qualitative, Quantitative, and Mixed Method Approaches

Abstract: หนงสอเรอง การออกแบบการวจย: วธการวจยเชงคณภาพ วธการวจยเชงปรมาณ และวธการวจยแบบผสม (Research Design: Qualitative, Quantitative, and Mixed Method Approaches) เปนหนงสอทเรยบเรยงเพออธบายเกยวกบความแตกตางของกระบวนทศนการวจยทง 2 แบบ ไดแก การวจย เชงปรมาณ และการวจยเชงคณภาพ และความจำเปนของประเดนปญหาการวจยทตองนำกระบวนทศนทง 2 มารวมกนหาขอคนพบเพอนำไปสผลการวจยทสามารถนำผลการวจยไปใชประโยชนไดอยางจรงมากยงขน เรยกวา “การวจยแบบผสมผสาน” ซงเปนหนงสอทอธบายวธการวจยทง 2 ประเภทไดอยางชดเจน และการรวมกนของกระบวนทศนการวจยทง 2 แบบอยางลงตว

Economy and Society

Abstract: The four Visegrad states — Poland, the Czech Republic, Slovakia (until 1993 Czechoslovakia) and Hungary — form a compact area between Germany and Austria in the west and the states of the former USSR in the east. They are bounded by the Baltic in the north and the Danube river in the south. They are cut by the Sudeten and Carpathian mountain ranges, which divide Poland off from the other states. Poland is an extension of the North European plain and like the latter is drained by rivers that flow from south to north west — the Oder, the Vlatava and the Elbe, the Vistula and the Bug. The Danube is the great exception, flowing from its source eastward, turning through two 90-degree turns to end up in the Black Sea, forming the barrier and often the political frontier between central Europe and the Balkans. Hungary to the east of the Danube is also an open plain. The region is historically and culturally part of western Europe, but its eastern Marches now represents a vital strategic zone between Germany and the core of the European Union to the west and the Russian zone to the east.

Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics

Abstract: With the continued interest in the role of the gut microbiota in health, attention has now turned to how to harness the microbiota for the benefit of the host. This Consensus Statement outlines the definition and scope of the term 'prebiotic' as determined by an expert panel convened by the International Scientific Association for Probiotics and Prebiotics in December 2016. In December 2016, a panel of experts in microbiology, nutrition and clinical research was convened by the International Scientific Association for Probiotics and Prebiotics to review the definition and scope of prebiotics. Consistent with the original embodiment of prebiotics, but aware of the latest scientific and clinical developments, the panel updated the definition of a prebiotic: a substrate that is selectively utilized by host microorganisms conferring a health benefit. This definition expands the concept of prebiotics to possibly include non-carbohydrate substances, applications to body sites other than the gastrointestinal tract, and diverse categories other than food. The requirement for selective microbiota-mediated mechanisms was retained. Beneficial health effects must be documented for a substance to be considered a prebiotic. The consensus definition applies also to prebiotics for use by animals, in which microbiota-focused strategies to maintain health and prevent disease is as relevant as for humans. Ultimately, the goal of this Consensus Statement is to engender appropriate use of the term 'prebiotic' by relevant stakeholders so that consistency and clarity can be achieved in research reports, product marketing and regulatory oversight of the category. To this end, we have reviewed several aspects of prebiotic science including its development, health benefits and legislation.