Targeted Sequencing for Studying Economically Useful Traits and Phylogenetic Diversity of Ancient Sheep

Russian Journal of Genetics - Sheep were one of the first animals to be domesticated. The history of sheep domestication and their widespread distribution dates to about ten thousand years ago,...     

Polymorphism in a histone H1 subtype with a short N-terminal domain in three legume species (Fabaceae, Fabaeae)

A number of alleles of an orthologous gene His6 encoding histone H1 subtype f (H1-6 in pea) accumulated in chromatin of old tissues were sequenced in three legume species: seven alleles in Pisum sativum, four in Vicia unijuga and eight in Lathyrus gmelinii. In the total of 19 alleles sequenced in the three species, 29 non-synonymous substitutions and six indels were found in the coding region; most of amino acid substitutions (26 of 29) and all indels occurred in the C-terminal hydrophilic domain of the encoded protein. All species were polymorphic for some non-synonymous substitutions, V. unijuga was also polymorphic for one and P. sativum for two indels. Three near-isogenic lines of P. sativum bearing different alleles showed differences in many quantitative traits; that in the growth dynamic could be tentatively attributed to the allelic substitution of subtype H1-6. The frequencies of four electromorphs in a sampled locality of V. unijuga were found to be close to those observed 25?years ago, although their rapid change in the past was supposed in the previous study.     

Determination of cell concentrations in stationary growing <Emphasis Type="Italic">Lactobacillus salivarius</Emphasis> cultures in relation to formation of biofilms and cell aggregates

Lactobacillus salivarius belongs to the microbiota of human oral cavity and gastrointestinal tract, as well as of bird and pig intestines. Probiotic activity of various L. salivarius strains has been recently extensively investigated. Production of exopolysaccharides and formation of biofilms as a mechanism providing for resistance to unfavorable factors are also of interest. The goal of this work was to assess the efficiency of microbiological methods for analysis of bacterial concentrations in the cultures of L. salivarius strain NBR2. Samples of lactobacteria grown in liquid medium were collected at equal intervals. The parameters determined were the number of colony-forming units (CFU/mL), share of dead cells by the membrane permeabilization test (LIVE/DEAD) using flow cytometry and fluorescence microscopy, optical density at 595 nm, and pH. After 10 h of cultivation, formation of aggregates commenced, which consisted mainly of living cells and were detected throughout the experiment (30 h). This resulted in underestimation of bacterial abundance determined by plating (CFU/mL). Optical density of the culture and the share of dead cells determined by the LIVE/DEAD method are more reliable criteria of growth of the statically developing L. salivarius culture, which is prone to formation of biofilms and cell aggregates.     

NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions

Multiplex polymerase chain reaction (PCR) has multiple applications in molecular biology, including developing new targeted next-generation sequencing (NGS) panels. We present NGS-PrimerPlex, an efficient and versatile command-line application that designs primers for different refined types of amplicon-based genome target enrichment. It supports nested and anchored multiplex PCR, redistribution among multiplex reactions of primers constructed earlier, and extension of existing NGS-panels. The primer design process takes into consideration the formation of secondary structures, non-target amplicons between all primers of a pool, primers and high-frequent genome single-nucleotide polymorphisms (SNPs) overlapping. Moreover, users of NGS-PrimerPlex are free from manually defining input genome regions, because it can be done automatically from a list of genes or their parts like exon or codon numbers. Using the program, the NGS-panel for sequencing the LRRK2 gene coding regions was created, and 354 DNA samples were studied successfully with a median coverage of 97.4% of target regions by at least 30 reads. To show that NGS-PrimerPlex can also be applied for bacterial genomes, we designed primers to detect foodborne pathogens Salmonella enterica, Escherichia coli O157:H7, Listeria monocytogenes, and Staphylococcus aureus considering variable positions of the genomes.