An improved molecular inversion probe based targeted sequencing approach for low variant allele frequency

Deep targeted sequencing technologies are still not widely used in clinical practice due to the complexity of the methods and their cost. The Molecular Inversion Probes (MIP) technology is cost effective and scalable in the number of targets, however, suffers from low overall performance especially in GC rich regions. In order to improve the MIP performance, we sequenced a large cohort of healthy individuals (n = 4417), with a panel of 616 MIPs, at high depth in duplicates. To improve the previous state-of-the-art statistical model for low variant allele frequency, we selected 4635 potentially positive variants and validated them using amplicon sequencing. Using machine learning prediction tools, we significantly improved precision of 10–56.25% (P < 0.0004) to detect variants with VAF > 0.005. We further developed biochemically modified MIP protocol and improved its turn-around-time to ∼4 h. Our new biochemistry significantly improved uniformity, GC-Rich regions coverage, and enabled 95% on target reads in a large MIP panel of 8349 genomic targets. Overall, we demonstrate an enhancement of the MIP targeted sequencing approach in both detection of low frequency variants and in other key parameters, paving its way to become an ultrafast cost-effective research and clinical diagnostic tool.

Loss of the Periplasmic Chaperone Skp and Mutations in the Efflux Pump AcrAB-TolC Play a Role in Acquired Resistance to Antimicrobial Peptides in Salmonella typhimurium

Bacterial resistance to antibiotics is a major concern worldwide, leading to an extensive search for alternative drugs. Promising candidates are antimicrobial peptides (AMPs), innate immunity molecules, shown to be highly efficient against multidrug resistant bacteria. Therefore, it is essential to study bacterial resistance mechanisms against them. For that purpose, we used experimental evolution, and isolated a Salmonella enterica serovar typhimurium-resistant line to the AMP 4DK5L7. This AMP displayed promising features including widespread activity against Gram-negative bacteria and protection from proteolytic degradation. However, the resistance that evolved in the isolated strain was particularly high. Whole genome sequencing revealed that five spontaneous mutations had evolved. Of these, three are novel in the context of acquired AMP resistance. Two mutations are related to the AcrAB-TolC multidrug efflux pump. One occurred in AcrB, the substrate-binding domain of the system, and the second in RamR, a transcriptional regulator of the system. Together, the mutations increased the minimal inhibitory concentration (MIC) by twofold toward this AMP. Moreover, the mutation in AcrB induced hypersusceptibility toward ampicillin and colistin. The last mutation occurred in Skp, a periplasmic chaperone that participates in the biogenesis of outer membrane proteins (OMPs). This mutation increased the MIC by twofold to 4DK5L7 and by fourfold to another AMP, seg5D. Proteomic analysis revealed that the mutation abolished Skp expression, reduced OMP abundance, and increased DegP levels. DegP, a protease that was reported to have an additional chaperone activity, escorts OMPs through the periplasm along with Skp, but is also associated with AMP resistance. In conclusion, our data demonstrate that both loss of Skp and manipulation of the AcrAB-TolC system are alternative strategies of AMP acquired resistance in Salmonella typhimurium and might represent a common mechanism in other Gram-negative bacteria.

Characterization of manganese-oxidizing (MnII→MnIV) bacteria from Negev Desert rock varnish: implications in desert varnish formation

A collection of 79 bacterial isolates was obtained by plating scrapings and swabs from five rock varnish samples of the Negev Desert, Israel. Of the bacterial isolates which were obtained, 74 were able to oxidize manganese (MnII→MnIV) under laboratory conditions. The manganese-oxidizing bacteria were characterized and identified, when possible, to genus. The predominant genera were Bacillus, Geodermatophilus, Arthrobacter, and Micrococcus. Examples of all of these genera were found from more than one rock. These same genera have been reported from manganese-rich rock varnish samples from the Sonoran and Mojave Deserts of North America; however, many of the strains (species?) from the Negev appear to be different from those of the American Southwest. A single manganese-oxidizing actinomycete was also isolated. The high percentage of manganese-oxidizing bacteria to total cultivable bacteria (83 to 100% depending upon sample) from the Negev suggests that they are involved in desert varnish formation.

Geographical and environmental distribution of C3 and C4 grasses in the Sinai, Negev, and Judean deserts

The relation between photosynthetic pathway and habitat of the grass species recorded in the desert regions of Sinai, Negev, and Judea was investigated. The climatic conditions and micro-environments in the study area vary considerably, and the distribution of the various species is found to conform to specific patterns which reveal the adaptive advantages of the different photosynthetic pathways. There is also a distinct correlation between the phytogeographic origin of the grass species and the photosynthetic pathways that they utilize.The survey shows that the majority of the grass species in the region are of the C₃ type and all except one of these species belong to the Holarctic domain. This is in accordance with the fact that the region forms part of the Mediterranean winter rainfall regime and that C₃ species have an adaptive advantage where minimum temperatures are low during the winter growing season.The occurence of C₄ species increases with decreasing rainfall and they dominate in those districts where temperatures are high throughout the year. These C₄ grasses are of both Holarctic and Palaeotropic origin according to the classification adopted here, but they are essentially all elements of the Saharo-Arabian, Irano-Turanian, Sudanian, or Tropical phytogeographic regions and are not typical of the Mediterranean or Euro-Siberian floras. The plants with multi-regional distributions that occur in Mediterranean communities may well be intrusive.Analysis of the three subtypes of the C₄ species suggests that the malate-forming NADP-me grasses grow where water stress is not a dominating factor, while the aspartateforming NAD-me grasses are more successful under xeric conditions. The PEP-ck species are not abundant and form an intermediate group between the NADP-me and NAD-me subtypes.