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)

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

New insights into pectin methylesterase structure and function.

Viral vectors for the expression of proteins in plants.

Pectin methylesterase and its proteinaceous inhibitor: a review.

https://istina.msu.ru/media/publications/articles/290/c40/386540/Dorokhov_07.pdf

Superexpression of tuberculosis antigens in plant leaves

We reported recently that RNA-free spherical particles (SPs) generated by thermal remodelling of tobacco mosaic virus (TMV) are capable of binding GFP to their surface. Here, we show that SPs represent a universal particle platform that can form compositions by binding a diversity of various foreign proteins/epitopes of viral and non-viral origin to their surface. Numerous molecules of a foreign protein linked to the SP surface were revealed by immunogold electron microscopy. Several SP-based compositions were obtained containing one of the following foreign antigens: antigenic determinant A of rubella virus E1 glycoprotein; a recombinant protein containing the M2e epitope of influenza virus A protein M2; a recombinant antigen consisting of three epitopes of influenza virus A haemagglutinin; potato virus X (PVX) coat protein (CP); BSA; and PVX CP fused with the epitope of plum pox virus CP. The ‘mixed’ compositions could be also assembled by binding two different foreign antigens to each of the SPs. Immunogenicity of foreign antigens adsorbed or linked covalently to SPs in the SP-based compositions was examined. The antigenic specificity of foreign antigens was retained, whereas their immunogenicity increased significantly. It was inferred that SPs exhibit immunopotentiating activity, in particular in the form of compositions comprising SP and foreign antigen linked covalently to their surface by formaldehyde.

Immunogenic compositions assembled from tobacco mosaic virus-generated spherical particle platforms and foreign antigens.

Plum pox virus (PPV) exists as a complex of nine strains adapted to different Prunus hosts. Unusual PPV isolates that do not belong to the known cherry-adapted strains were discovered on sour cherry in Russia. Here, two complete genomes of isolates Tat-2 and Tat-4 were determined by sequencing on the Illumina HiSeq 2500 platform. Both were composed of 9,792 nucleotides, excluding the poly(A) tail, with the organization typical of PPV and had 99.4% and 99.7% identity between each other at the nucleotide and amino acid levels. The sequence identities between the Tat-2/Tat-4 and known PPV strains ranged from 77.6 to 83.3% for genomic RNA and from 80.0 to 93.8% for polyprotein. Phylogenetic analysis placed Tat-2 and Tat-4 in a separate clade, distinct from the C and CR strains. Three more Tat-2/Tat-4-like isolates were detected in local cherry plantings using the newly developed, specific RT-PCR assay. Based on the phylogenetic analysis, sequence identities and environmental distribution, the Tat-2, Tat-4 and...

https://apsjournals.apsnet.org/doi/pdf/10.1094/PDIS-07-17-1104-RE

Analysis of Genetic Diversity of Russian Sour Cherry Plum pox virus Isolates Provides Evidence of a New Strain.

Plum pox virus (PPV) is genetically diverse with nine different strains identified. Mutations, indel events, and interstrain recombination events are known to contribute to the genetic diversity of PPV. This is the first report of intrastrain recombination events that contribute to PPV's genetic diversity. Fourteen isolates of the PPV strain Winona (W) were analyzed including nine new strain W isolates sequenced completely in this study. Isolates of other strains of PPV with more than one isolate with the complete genome sequence available in GenBank were included also in this study for comparison and analysis. Five intrastrain recombination events were detected among the PPV W isolates, one among PPV C strain isolates, and one among PPV M strain isolates. Four (29%) of the PPV W isolates analyzed are recombinants; one of which (P2-1) is a mosaic, with three recombination events identified. A new interstrain recombinant event was identified between a strain M isolate and a strain Rec isolate, a known recombinant. In silico recombination studies and pairwise distance analyses of PPV strain D isolates indicate that a threshold of genetic diversity exists for the detectability of recombination events, in the range of approximately 0.78×10(-2) to 1.33×10(-2) mean pairwise distance. RDP4 analyses indicate that in the case of PPV Rec isolates there may be a recombinant breakpoint distinct from the obvious transition point of strain sequences. Evidence was obtained that indicates that the frequency of PPV recombination is underestimated, which may be true for other RNA viruses where low genetic diversity exists.

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-09-15-0211-R

Genome Sequence Analysis of New Isolates of the Winona Strain of Plum pox virus and the First Definitive Evidence of Intrastrain Recombination Events.

In studying the distribution and genetic diversity of Plum pox virus (PPV) in Russia, over a dozen new PPV isolates belonging to the strain Winona (PPV-W) were identified by immunocapture ...

https://apsjournals.apsnet.org/doi/pdf/10.1094/PDIS-12-11-1045-RE

Occurrence and Genetic Diversity of Winona-Like Plum pox virus Isolates in Russia

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