Impact of Postsynthetic Modification on the Electrical and Magnetic Properties of Materials

Postsynthetic modification is a promising tool for introducing multifunctional properties in metal–organic frameworks (MOFs). The effects of postsynthetic metal addition/exchange in a barium-based MOF have been well examined toward their magnetic and electrical properties. The rattling motion of the extraframework organic cation is responsible for the ferroelectric behavior. The strong magnetic frustration in <b>Tb@1</b> is found to arise from the nearly triangular arrangement of Tb³⁺ ions in its secondary building unit along the chain direction

Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology

<div><p>A wide variety of genome sequencing platforms have emerged in the recent past. High-throughput platforms like Illumina and 454 are essentially adaptations of the shotgun approach generating millions of fragmented single or paired sequencing reads. To reconstruct whole genomes, the reads have to be assembled into contigs, which often require further downstream processing. The contigs can be directly ordered according to a reference, scaffolded based on paired read information, or assembled using a combination of the two approaches. While the reference-based approach appears to mask strain-specific information, scaffolding based on paired-end information suffers when repetitive elements longer than the size of the sequencing reads are present in the genome. Sequencing technologies that produce long reads can solve the problems associated with repetitive elements but are not necessarily easily available to researchers. The most common high-throughput technology currently used is the Illumina short read platform. To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds.</p></div

Primers used for the analysis of single nucleotide polymorphisms in 65 <i>M. tuberculosis</i> isolates from New Delhi, India.

<p>Primers used for the analysis of single nucleotide polymorphisms in 65 <i>M. tuberculosis</i> isolates from New Delhi, India.</p

Shared-type and lineage/sub-lineage distribution of 65 <i>M. tuberculosis</i> isolates from New Delhi, India.

<p>Shared-type and lineage/sub-lineage distribution of 65 <i>M. tuberculosis</i> isolates from New Delhi, India.</p

Comparative statistics of CLA and Scaffolding tools generated using real dataset.

<p>Comparative statistics of CLA and Scaffolding tools generated using real dataset.</p

Schematic overview of CLA pipeline.

<p>The schema of CLA pipeline is divided into three stages. In the first stage, a reference based order is derived followed by the second stage where connections between the individual contigs are extracted based on alignment information. The final stage makes use of the information from the first two stages to decide the final order followed by scaffolding and gap filling.</p

Diversity of 65 <i>M. tuberculosis</i> isolates from New Delhi, India deduced from MIRU-VNTR, spoligotyping and single nucleotide polymorphism analyses.

<p>MIRU-VNTR clusters that could be discriminated by spoligotyping are highlighted in blue and clusters that could be discriminated based on mutations in the <i>katG</i>, <i>rpoB</i> and/or <i>embB</i> genes are highlighted in yellow. Clusters that could not be discriminated using a combination of all markers are highlighted in green. The dendrogram was produced following Pearson correlation and unweighted pair group method with arithmetic average analysis.</p

Number of single nucleotide polymorphisms observed for the 6 regions of interest in 65 <i>M. tuberculosis</i> isolates from New Delhi, India.

<p>Number of single nucleotide polymorphisms observed for the 6 regions of interest in 65 <i>M. tuberculosis</i> isolates from New Delhi, India.</p

Defining the start and end of a contig based on the insert size.

<p>Connectivity between two consecutive contigs is decided by the paired reads from a single insert. To find such connections between contigs, each contig is theoretically divided into start, mid and end regions based on the insert size.</p

Prevalence of Abs against homologous MAP3865c and ZnT8 epitopes in T2D patients.

<p>Prevalence of Abs against MAP3865c_125–133 (A) and its homologous ZnT8_178–186 (B); and against MAP3865c_133–141 (C) and its homologous ZnT8_186–194 (D) in T2D and healthy subjects. Data representation is the same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026931#pone-0026931-g001" target="_blank">Fig. 1</a>.</p