Recombination analysis of Soybean mosaic virus sequences reveals evidence of RNA recombination between distinct pathotypes

RNA recombination is one of the two major factors that create RNA genome variability. Assessing its incidence in plant RNA viruses helps understand the formation of new isolates and evaluate the effectiveness of crop protection strategies. To search for recombination in Soybean mosaic virus (SMV), the causal agent of a worldwide seed-borne, aphid-transmitted viral soybean disease, we obtained all full-length genome sequences of SMV as well as partial sequences encoding the N-terminal most (P1 protease) and the C-terminal most (capsid protein; CP) viral protein. The sequences were analyzed for possible recombination events using a variety of automatic and manual recombination detection and verification approaches. Automatic scanning identified 3, 10, and 17 recombination sites in the P1, CP, and full-length sequences, respectively. Manual analyses confirmed 10 recombination sites in three full-length SMV sequences. To our knowledge, this is the first report of recombination between distinct SMV pathotypes. These data imply that different SMV pathotypes can simultaneously infect a host cell and exchange genetic materials through recombination. The high incidence of SMV recombination suggests that recombination plays an important role in SMV evolution. Obtaining additional full-length sequences will help elucidate this role

Novel Interactome of \u3cem\u3eSaccharomyces cerevisiae\u3c/em\u3e Myosin Type II Identified by a Modified Integrated Membrane Yeast Two-Hybrid (iMYTH) Screen

Nonmuscle myosin type II (Myo1p) is required for cytokinesis in the budding yeast Saccharomyces cerevisiae. Loss of Myo1p activity has been associated with growth abnormalities and enhanced sensitivity to osmotic stress, making it an appealing antifungal therapeutic target. The Myo1p tail-only domain was previously reported to have functional activity equivalent to the full-length Myo1p whereas the head-only domain did not. Since Myo1p tail-only constructs are biologically active, the tail domain must have additional functions beyond its previously described role in myosin dimerization or trimerization. The identification of new Myo1p-interacting proteins may shed light on the other functions of the Myo1p tail domain. To identify novel Myo1p-interacting proteins, and determine if Myo1p can serve as a scaffold to recruit proteins to the bud neck during cytokinesis, we used the integrated split-ubiquitin membrane yeast two-hybrid (iMYTH) system. Myo1p was iMYTH-tagged at its C-terminus, and screened against both cDNA and genomic prey libraries to identify interacting proteins. Control experiments showed that the Myo1p-bait construct was appropriately expressed, and that the protein colocalized to the yeast bud neck. Thirty novel Myo1p-interacting proteins were identified by iMYTH. Eight proteins were confirmed by coprecipitation (Ape2, Bzz1, Fba1, Pdi1, Rpl5, Tah11, and Trx2) or mass spectrometry (AP-MS) (Abp1). The novel Myo1p-interacting proteins identified come from a range of different processes, including cellular organization and protein synthesis. Actin assembly/disassembly factors such as the SH3 domain protein Bzz1 and the actin-binding protein Abp1 represent likely Myo1p interactions during cytokinesis

Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery

Bacterial protein synthesis is an essential, conserved, and environmentally responsive process. Yet, many of its components and dependencies remain unidentified. To address this gap, we used quantitative synthetic genetic arrays to map functional relationships among >48,000 gene pairs in Escherichia coli under four culture conditions differing in temperature and nutrient availability. The resulting data provide global functional insights into the roles and associations of genes, pathways, and processes important for efficient translation, growth, and environmental adaptation. We predict and independently verify the requirement of unannotated genes for normal translation, including a previously unappreciated role of YhbY in 30S biogenesis. Dynamic changes in the patterns of genetic dependencies across the four growth conditions and data projections onto other species reveal overarching functional and evolutionary pressures impacting the translation system and bacterial fitness, underscoring the utility of systematic screens for investigating protein synthesis, adaptation, and evolution

Ribosome-Dependent ATPase Interacts with Conserved Membrane Protein in Escherichia coli to Modulate Protein Synthesis and Oxidative Phosphorylation

Elongation factor RbbA is required for ATP-dependent deacyl-tRNA release presumably after each peptide bond formation; however, there is no information about the cellular role. Proteomic analysis in Escherichia coli revealed that RbbA reciprocally co-purified with a conserved inner membrane protein of unknown function, YhjD. Both proteins are also physically associated with the 30S ribosome and with members of the lipopolysaccharide transport machinery. Genome-wide genetic screens of rbbA and yhjD deletion mutants revealed aggravating genetic interactions with mutants deficient in the electron transport chain. Cells lacking both rbbA and yhjD exhibited reduced cell division, respiration and global protein synthesis as well as increased sensitivity to antibiotics targeting the ETC and the accuracy of protein synthesis. Our results suggest that RbbA appears to function together with YhjD as part of a regulatory network that impacts bacterial oxidative phosphorylation and translation efficiency

Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target

Simultaneous Mutations in Multi-Viral Proteins Are Required for Soybean mosaic virus to Gain Virulence on Soybean Genotypes Carrying Different R Genes

BACKGROUND: Genetic resistance is the most effective and sustainable approach to the control of plant pathogens that are a major constraint to agriculture worldwide. In soybean, three dominant R genes, i.e., Rsv1, Rsv3 and Rsv4, have been identified and deployed against Soybean mosaic virus (SMV) with strain-specificities. Molecular identification of virulent determinants of SMV on these resistance genes will provide essential information for the proper utilization of these resistance genes to protect soybean against SMV, and advance knowledge of virus-host interactions in general. METHODOLOGY/PRINCIPAL FINDINGS: To study the gain and loss of SMV virulence on all the three resistance loci, SMV strains G7 and two G2 isolates L and LRB were used as parental viruses. SMV chimeras and mutants were created by partial genome swapping and point mutagenesis and then assessed for virulence on soybean cultivars PI96983 (Rsv1), L-29 (Rsv3), V94-5152 (Rsv4) and Williams 82 (rsv). It was found that P3 played an essential role in virulence determination on all three resistance loci and CI was required for virulence on Rsv1- and Rsv3-genotype soybeans. In addition, essential mutations in HC-Pro were also required for the gain of virulence on Rsv1-genotype soybean. To our best knowledge, this is the first report that CI and P3 are involved in virulence on Rsv1- and Rsv3-mediated resistance, respectively. CONCLUSIONS/SIGNIFICANCE: Multiple viral proteins, i.e., HC-Pro, P3 and CI, are involved in virulence on the three resistance loci and simultaneous mutations at essential positions of different viral proteins are required for an avirulent SMV strain to gain virulence on all three resistance loci. The likelihood of such mutations occurring naturally and concurrently on multiple viral proteins is low. Thus, incorporation of all three resistance genes in a soybean cultivar through gene pyramiding may provide durable resistance to SMV

The concept of corporate social responsibility in terms of manufacturing companies of Chelyabinsk region, Russian Federation

Cílem této bakalářské práce je analyzovat vývoj a trendy sociální odpovědnosti firem, zejména v odvětví výrobních podniků Čeljabinské oblasti Ruské federace. Práce se skládá ze tří částí. První část je teoretická a zaměřena na vymezení pojmu společenská odpovědnost, vysvětlení konceptu a historického vývoje společenské odpovědnosti firem. Druhá část je také teoretická, ale se zaměřením na aktuální stav společenské odpovědnosti na uzemí Ruské federace. Praktická část představuje analýzu skutečné situace uplatňování zásad společenské odpovědnosti ve výrobních podnicích jednoho regionu Ruské federace a následnou komparaci tohoto stavu se stavem v České republice a Evropě.The aim of this work is to analyze the evolution and trends of corporate social responsibility, particularly in the manufacturing enterprises of Chelyabinsk region, Russian Federation. The work consists of three parts. The first part is theoretical and focuses on the definition of the concept of social responsibility, explanation the concept and historical development of corporate social responsibility. The second part is also theoretical, but focusing on the current state of corporate social responsibility in Russian Federation. The practical part presents an analysis of the actual situation of the application of principles of social responsibility in manufacturing enterprises in one region of Russian Federation and a comparison of this situation with the situation in the Czech Republic and Europe

Using Quantitative Synthetic Genetic Interaction Profiling in Escherichia coli to Investigate Bacterial Protein Synthesis

Bacterial protein synthesis depends on the coordination of a complex, multi-component machinery that processes ribosomal RNA, assembles ribosomes, and translates diverse messenger RNA transcripts to meet changing physiological and environmental demands. Despite decades of detailed investigations, which enabled basic mechanistic understanding of the core translation processes, the global functional connectivity and component memberships of this central system and its relationship to other biological pathways had remained unclear. Physical interaction data can suggest the biological roles and associations of gene products, but only genetic interaction (GI) screens can truly reveal pathway-level functional dependencies. For my Thesis, I performed quantitativePh.D.2016-11-30 00:00:0

Around Baikal: on the causes of ecological problems

This paper is devoted to the unique water body, Lake Baikal, the largest freshwater reservoir by volume in the world that was included on the list of UNESCO World Heritage Sites and is regulated by the federal law of its protection. The global role of Baikal as a strategic reserve of water resources of the highest class is increasing in importance. Furthermore, Lake Baikal and its surroundings are invariably the focus of ecological problems. The most challenging issues are the lake’s water pollution leading to changes in hydrobiocenoses, soil and vegetation digression in areas of increased recreational load, forest fires causing a decrease of the number of rare species of flora and fauna, etc. Imperfection of the legal framework, the lack of a unified managerial center and the attempts to deal with the problems solely at the federal level involve a number of incompetent decisions on the lake level regulation and on the setting of its water-protection zone. The conflicts of the interests of the subjects of the federal and regional levels in issues related to use and the protection of natural resources present serious obstacles to the development of a unified, ecologically oriented strategy of economic development of the territory. For a successful solution of the current challenges it is necessary to recognize the ecological problems of Lake Baikal as the priority concerns throughout the country, optimize management of the socio-economic development of the Baikal natural territory on the basis of nature-conservation principles by ensuring appropriate funding, develop a unified scheme of comprehensive monitoring of the ecological and sanitary-hygienic status of Lake Baikal and its protection zone, improve the system of scientific research on the Baikal natural territory, introduction ubiquitous ecological training and education of the population, organize the waste and effluent treatment system in accordance with the latest international technologies, etc