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)

Assay for lipid peroxides in animal tissues by thiobarbituric acid reaction

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Methods Of Enzymatic Analysis

All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

Salinity is a major abiotic stress limiting growth and productivity of plants in many areas of the world due to increasing use of poor quality of water for irrigation and soil salinization. Plant adaptation or tolerance to salinity stress involves complex physiological traits, metabolic pathways, and molecular or gene networks. A comprehensive understanding on how plants respond to salinity stress at different levels and an integrated approach of combining molecular tools with physiological and biochemical techniques are imperative for the development of salt-tolerant varieties of plants in salt-affected areas. Recent research has identified various adaptive responses to salinity stress at molecular, cellular, metabolic, and physiological levels, although mechanisms underlying salinity tolerance are far from being completely understood. This paper provides a comprehensive review of major research advances on biochemical, physiological, and molecular mechanisms regulating plant adaptation and tolerance to salinity stress.

/pdf/mechanism-of-salinity-tolerance-in-plants-physiological-3ixvqhezre.pdf

Mechanism of Salinity Tolerance in Plants: Physiological, Biochemical, and Molecular Characterization

Silicon (Si) has been considered a beneficial element for plant growth. We have assessed the effects of Si application on rice (Oryza sativa L.) growth and its grain yield at field level. For this, we performed two experiments. In experiment 1, we applied Si of three different concentrations (liquid Si-10, 25 and 36%) to the seedbed of rice before transplantation into paddy field. The results of this experiment showed that Si application to rice seedbeds did not affected the rice plant height and shoot fresh weight but its application significantly increased the pushing resistance of rice plants from 12.2~16.7% as compared with water applied control plants. The lodging index of Si treated rice plants significantly decreased (13.7% on LS-25) as compared with control. Similarly, Si treated plants had significantly higher yield. Upon Si treatment (LS-36), the grain yield per 10 acre and panicles per plant were 15.1% and 6.3% higher than the water treated control plants respectively. The best concentration (LS-36%) revealed in the first experiment was foliar applied at 10 days before heading stage, initial tilling stage and panicle initiation stage to the rice leaves and we observed that shoot biomass was not significantly different between control and Si treated plants. However, significantly higher pushing resistance (10.5%~13.8%) and plant height (12.2%~16.7%) were observed while lower lodging index (7.6~7.8%) was recorded for Si treated plants as compared to control plants. Similarly, Si application increased the number of panicles per plant as well as the grain yield per 10 acre as compared to control. In conclusion, the Si application can significantly regulate plant growth and yield if applied at proper time with feasible concentration.

SILICON TREATMENT TO RICE (ORYZA SATIVA L. cv 'GOPUMBYEO') PLANTS DURING DIFFERENT GROWTH PERIODS AND ITS EFFECTS ON GROWTH AND GRAIN YIELD

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SILICON TREATMENT TO RICE (ORYZA SATIVA L. cv 'GOPUMBYEO') PLANTS DURING DIFFERENT GROWTH PERIODS AND ITS EFFECTS ON GROWTH AND GRAIN YIELD