Biology subjects

Ustinova, V.

Publications and source records attributed to Ustinova, V..

2 recordsLinked to original sources

bioRxiv2020

An ERF transcription factor from Brassica oleracea: a new member of the emerging pathogenicity hub in plant-Xanthomonas interactions

- TAL effectors (TALEs), which induce the expression of specific plant genes to promote infection, are the main pathogenic determinants of different Xanthomonas bacteria. However, investigation of TALEs from Xanthomonas campestris pv. campestris, which causes black rot disease of crucifers, is in its infancy. - In this study, we used PCR-based amplification in conjunction with SMRT amplicon sequencing to identify TALE genes in several Xanthomonas campestris pv. campestris strains and performed computational prediction in conjunction with RT-PCR-based analysis to identify their target genes in Brassica oleracea. - Transcription factor from the AP2/ERF family was predicted to be putative target gene for the conserved TALEs present in multiple Xanthomonas campestris pv. campestris strains. Its expression dramatically increased upon leaf inoculation with strains harbouring such TALEs. - Several members of the AP2/ERF factor family from different plant species were identified as targets of TALEs from various Xanthomonas species, which suggests that they constitute a new pathogenicity hub in plant-Xanthomonas interactions.

plant biology↗

bioRxiv2017

Improved DOP-PCR (iDOP-PCR): a robust and simple WGA method for efficient amplification of low copy number genomic DNA

Whole-genome amplification (WGA) techniques are used for non-specific amplification of low-copy number DNA, and especially for single-cell genome and transcriptome amplification. There are a number of WGA methods that have been developed over the years. One example is degenerate oligonucleotide-primed PCR (DOP-PCR), which is a very simple, fast and inexpensive WGA technique. Although DOP-PCR has been regarded as one of the pioneering methods for WGA, it only provides low genome coverage and a high allele dropout rate when compared to more modern techniques. Here we describe an improved DOP-PCR (iDOP-PCR). We have modified the classic DOP-PCR by using a new thermostable DNA polymerase (SD polymerase) with a strong strand-displacement activity and by adjustments in primers design. We compared iDOP-PCR, classic DOP-PCR and the well-established PicoPlex technique for whole genome amplification of both high- and low-copy number human genomic DNA. The amplified DNA libraries were evaluated by analysis of short tandem repeat genotypes and NGS data. In summary, iDOP-PCR provided a better quality of the amplified DNA libraries compared to the other WGA methods tested, especially when low amounts of genomic DNA were used as an input material.

molecular biology↗