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)

Owing to the fast development of wireless information technologies at the high-frequency range, the electromagnetic interference problem has been of increasing significance and attracting global attention. One key solution for this problem is to develop materials that are able to attenuate the unwanted electromagnetic waves. The desired properties of these materials include low reflection loss value, wide attenuation band, light weight, and low cost. This review gives a brief introduction to graphene-based composites and their electromagnetic absorption properties. The ultimate goal of these graphene absorbers is to achieve a broader effective absorption frequency bandwidth (fE) at a thin coating thickness (d). Representative and popular composite designs, synthesis methods, and electromagnetic energy attenuation mechanisms are summarized in detail. The two key factors, impedance matching behavior and attenuation ability, that determine the electromagnetic behavior of graphene-based materials are given particular attention in this article.

A brief introduction to the fabrication and synthesis of graphene based composites for the realization of electromagnetic absorbing materials

An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis, was constructed by using a twin-pronged approach. Pulsed-field gel electro- phoretic analysis enabled cleavage sites for Asn I and Dra I to be positioned on the 4.4-Mb circular chromosome, while, in parallel, clones from two cosmid libraries were ordered into contigs by means of fingerprinting and hybridization map- ping. The resultant contig map was readily correlated with the physical map of the genome via the landmarked restriction sites. Over 165 genes and markers were localized on the integrated map, thus enabling comparisons with the leprosy bacillus, Mycobacterium leprae, to be undertaken. Mycobacte- rial genomes appear to have evolved as mosaic structures since extended segments with conserved gene order and organization are interspersed with different flanking regions.

An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis H37Rv, and comparison with Mycobacterium leprae (genome mapping/contig mapping/ordered libraries/bacterial genomics/tuberculosis)

Organophosphates are one of the major constituent of herbicides, pesticides, insecticides and nerve gas. Azinophos-methyl, chlorpyrifos, diazinon, fonofos and disulfoton are well-known organophosph...

Toxicity, monitoring and biodegradation of organophosphate pesticides: A review

In this work, n–p heterostructure SnO2/BiOI photocatalyst was successfully fabricated through a facile chemical bath method. The photocatalysts was applied to minimize antibiotic oxytetracycline hydrochloride (OTTCH) and methyl orange (MO) under visible light irradiation. SnO2/BiOI composite exhibited excellent photocatalytic performance for the refractory pollutant OTTCH and MO decomposition. The sample of 30 wt % SnO2/BiOI possessed the best photocatalytic performance in all the obtained catalysts. Several reaction parameters affecting OTTCH degradation such as initial concentration, ion species, and concentration were investigated systematically. The optical and electrical properties of materials demonstrate that the transfer rate of electron–hole pairs dramatically improve though forming an n–p junction in SnO2/BiOI hybrid. Moreover, the energy band alignments of SnO2/BiOI junction were confirmed via combining DRS and XPS analysis, which provided strong support for the proposed mechanism. This work co...

Fabrication of SnO2 Nanopaticles/BiOI n–p Heterostructure for Wider Spectrum Visible-Light Photocatalytic Degradation of Antibiotic Oxytetracycline Hydrochloride

We report the enhanced photocatalytic activity of TiO2 by the surface decoration of CoO nanoparticles to degrade paraoxon. The CoO nanoparticles are precipitated in situ during heat treatments of Co doped amorphous TiO2 and enhance the degradation by 11–24 times that of pure TiO2 or Rh2O3–TiO2 or the oxide nanoparticles under white light (natural sunlight and fluorescence light). The enhanced activity is a combined result of visible light absorption by CoO and effective electron-hole separation at the CoO–TiO2 interfaces.

/pdf/environmentally-effective-photocatalyst-coo-tio2-synthesized-1o5glvujbd.pdf

Environmentally effective photocatalyst CoO-TiO2 synthesized by thermal precipitation of Co in amorphous TiO2

Developments in alternative treatments for organophosphate poisoning.

Organophosphates (OPs) form the bulk of pesticides that are currently in use around the world accounting for more than 30% of the world market. They also form the core for many nerve-based warfare agents including sarin and soman. The widespread use and the resultant build-up of OP pesticides and chemical nerve agents has led to the development of major health problems due to their extremely toxic interaction with any biological system that encounters them. Growing concern over the accumulation of OP compounds in our food products, in the soils from which they are harvested and in wastewater run-off has fuelled a growing interest in microbial biotechnology that provides cheap, efficient OP detoxification to supplement expensive chemical methods. In this article, we review the current state of knowledge of OP pesticide and chemical agent degradation and attempt to clarify confusion over identification and nomenclature of two major families of OP-degrading enzymes through a comparison of their structure and function. The isolation, characterization, utilization and manipulation of the major detoxifying enzymes and the molecular basis of degradation of OP pesticides and chemical nerve agents are discussed as well as the achievements and technological advancements made towards the bioremediation of such compounds.

A comparison of organophosphate degradation genes and bioremediation applications

Protein engineering of representative hydrolytic enzymes for remediation of organophosphates

A bacterial strain designated in this study as
POXN01 was found to be capable of degrading the synthetic organophosphorus
pesticides paraoxon and methyl parathion. The strain was initially isolated
through enrichment technique from rice field soil near Harlingen, Texas.
Phylogenetic analysis based on 16S rRNA, gyrB and rpoD gene
alignments identified the POXN01 isolate as a new strain of Pseudomonas putida,
which is closely related to the
recently discovered nicotine-degrading strain Pseudomonas putida S16.
While being unable to metabolize nicotine, the POXN01 isolate was observed to
actively proliferate using monocyclic aromatic hydrocarbons, in particular
toluene, as nutrients. Search for the genetic determinants of paraoxon
catabolism revealed the presence of organophosphorus-degrading gene, opd,
identical to the one from Sphingobium fuliginis (former Flavobacterium sp. ATCC 27551). Assimilation of aromatic compounds likely
relies on phc ARKLMNOPQ gene cluster for phenol, benzene and toluene
catabolism, and on benRABCDKGEF cluster for benzoate catabolism. The
observed versatility of POXN01 strain in degradation of xenobiotics makes it
useful for the multi-purpose bioremediation of contaminated sites in both
agricultural and industrial environmental settings.

/pdf/isolation-and-molecular-characterization-of-a-novel-4v4xsymq3n.pdf

Rupa Iyer

Papers

Environmentally effective photocatalyst CoO-TiO2 synthesized by thermal precipitation of Co in amorphous TiO2

Developments in alternative treatments for organophosphate poisoning.

A comparison of organophosphate degradation genes and bioremediation applications

Protein engineering of representative hydrolytic enzymes for remediation of organophosphates

Isolation and molecular characterization of a novel pseudomonas putida strain capable of degrading organophosphate and aromatic compounds