Jasmine: Population-scale structural variant comparison and analysis

The increasing availability of long-reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare. Addressing this, we present Jasmine (https://github.com/mkirsche/Jasmine ), a fast and accurate method for SV refinement, comparison, and population analysis. Using an SV proximity graph, Jasmine outperforms five widely-used comparison methods, including reducing the rate of Mendelian discordance in trio datasets by more than five-fold, and reveals a set of high confidence de novo SVs confirmed by multiple long-read technologies. We also present a harmonized callset of 205,192 SVs from 31 samples of diverse ancestry sequenced with long reads. We genotype these SVs in 444 short read samples from the 1000 Genomes Project with both DNA and RNA sequencing data and assess their widespread impact on gene expression, including within several medically relevant genes

Validation of Human Telomere Length Multi-Ancestry Meta-Analysis Association Signals Identifies POP5 and KBTBD6 as Human Telomere Length Regulation Genes

Genome-wide association studies (GWAS) have become well-powered to detect loci associated with telomere length. However, no prior work has validated genes nominated by GWAS to examine their role in telomere length regulation. We conducted a multi-ancestry meta-analysis of 211,369 individuals and identified five novel association signals. Enrichment analyses of chromatin state and cell-type heritability suggested that blood/immune cells are the most relevant cell type to examine telomere length association signals. We validated specific GWAS associations by overexpressing KBTBD6 or POP5 and demonstrated that both lengthened telomeres. CRISPR/Cas9 deletion of the predicted causal regions in K562 blood cells reduced expression of these genes, demonstrating that these loci are related to transcriptional regulation of KBTBD6 and POP5. Our results demonstrate the utility of telomere length GWAS in the identification of telomere length regulation mechanisms and validate KBTBD6 and POP5 as genes affecting telomere length regulation

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.

Conventional targeted sequencing methods eliminate many of the benefits of nanopore sequencing, such as the ability to accurately detect structural variants or epigenetic modifications. The ReadUntil method allows nanopore devices to selectively eject reads from pores in real time, which could enable purely computational targeted sequencing. However, this requires rapid identification of on-target reads while most mapping methods require computationally intensive basecalling. We present UNCALLED ( https://github.com/skovaka/UNCALLED ), an open source mapper that rapidly matches streaming of nanopore current signals to a reference sequence. UNCALLED probabilistically considers k-mers that could be represented by the signal and then prunes the candidates based on the reference encoded within a Ferragina-Manzini index. We used UNCALLED to deplete sequencing of known bacterial genomes within a metagenomics community, enriching the remaining species 4.46-fold. UNCALLED also enriched 148 human genes associated with hereditary cancers to 29.6× coverage using one MinION flowcell, enabling accurate detection of single-nucleotide polymorphisms, insertions and deletions, structural variants and methylation in these genes

Isolation and characterisation of phages against Pseudomonas syringae pv. actinidiae

Purpose: Pseudomonas syringae pv. actinidiae causes bacterial canker of kiwifruit and is responsible for severe economic losses and emergence of drug-resistant bacteria. Bacteriophages are viruses that infect target bacterial hosts and may be the best strategy to prevent and control kiwifruit canker disease. The objective of this experiment was to monitor the prevalence of Pseudomonas syringae pv. actinidiae and provide insight for the use of phages in biological control. Materials and methods: In this study, 52 strains of Pseudomonas syringae pv. actinidiae were isolated from 68 stem samples of kiwi plant (cv. Hongyang & Jinkui). Following polymerase chain reaction (PCR) analysis, 15 isolates belonging to biovar 3 were identified, one of which was named XWY0007 and used as the target strain to isolate the phages. Thirty-six phages were isolated and purified from a total of 51 surface water samples collected in Shanghai. All phages were identified by transmission electron microscopy (TEM) and their host ranges were evaluated. Three phages, designated φXWY0013, φXWY0014 and φXWY0026 were selected and further characterised using one-step growth curve and stability at different temperatures and pH. Results and conclusions: The isolated phages are promising for use as antimicrobials against bacterial canker in kiwi. This report is regarding Pseudomonas syringae pv. actinidiae and its phages from major areas of kiwifruit cultivation

Combined Application of Bacteriophages and Carvacrol in the Control of Pseudomonas syringae pv. actinidiae Planktonic and Biofilm Forms

Pseudomonas syringae pv. actinidiae (Psa) is the causative agent of the bacterial canker of kiwifruit (Actinidia spp.). Phage therapy has been suggested as a viable alternative approach to controlling this disease, but its efficacy is limited by the emergence of phage-resistant mutants. Carvacrol is an essential oil that may be useful for the control of Psa. Combination therapies can be used to overcome resistance development. Here, the combination of phages (single phage suspensions of phages PN05 and PN09, and a cocktail of both phages) and carvacrol was investigated in controlling Psa planktonic and biofilm forms in vitro. The phage therapy alone (with phages PN05 and PN09), and the carvacrol alone (minimum inhibitory concentration 2.0 mg/mL), inhibited Psa growth, but the combined effect of both therapies was more effective. The phages alone effectively inhibited Psa growth for 24 h, but Psa regrowth was observed after this time. The carvacrol (2.0 mg/mL) alone prevented the biofilm formation for 48 h, but did not destroy the pre-formed biofilms. The combined treatment, phages and carvacrol (2.0 mg/mL), showed a higher efficacy, preventing Psa regrowth for more than 40 h. In conclusion, the combined treatment with phages and carvacrol may be a promising, environment-friendly and cost-effective approach to controlling Psa in the kiwifruit industry

Preparation of a Novel Formaldehyde-Free Impregnated Decorative Paper Containing MnO₂ Nanoparticles for Highly Efficient Formaldehyde Removal

The loading of catalytic manganese dioxide (MnO2) nanoparticles onto an impregnated decorative paper has been an effective method for the removal of indoor formaldehyde (HCHO) pollutants. However, its preparation can present numerous challenges, including instability in dipping emulsions and leaching. In this investigation, a novel and stable formaldehyde-free polyacrylate dipping emulsion containing MnO2 particles was prepared and then back-coated on a decorative paper. To improve the dispersion and fixation, the MnO2 was modified with silane. HCHO can undergo physical adsorption on the cellulosic fibers present in the paper, while it can also undergo chemical degradation into CO2 within the MnO2 groups. The silane not only enhanced the interfacial adhesion to a polyacrylate resin but also increased the interlayer distance, thereby creating a larger space for HCHO absorption. The impregnated decorative paper back-coated with 10 wt % of silane-modified MnO2 exhibited a removal efficiency of approximately 90% for HCHO at 20 °C. The removal rate further improved to approximately 100% when the temperature was increased to 60 °C. Moreover, it is worth noting that the release of volatile organic compounds was exceptionally minimal. Additionally, the particleboard bonded with this impregnated decorative paper exhibited an extremely low emission of HCHO, with a value that approached 0 mg·L–1. Furthermore, the bonding strength of the surface remained unaffected. Therefore, this study provides a simple and eco-friendly method for effectively removing HCHO, which can enhance indoor air quality

Formation of Amorphous Iron-Calcium Phosphate with High Stability

Amorphous iron-calcium phosphate (Fe-ACP) plays a vital role in the mechanical properties of teeth of some rodents, which are very hard, but its formation process and synthetic route remain unknown. Here, the synthesis and characterization of an iron-bearing amorphous calcium phosphate in the presence of ammonium iron citrate (AIC) are reported. The iron is distributed homogeneously on the nanometer scale in the resulting particles. The prepared Fe-ACP particles can be highly stable in aqueous media, including water, simulated body fluid, and acetate buffer solution (pH 4). In vitro study demonstrates that these particles have good biocompatibility and osteogenic properties. Subsequently, Spark Plasma Sintering (SPS) is utilized to consolidate the initial Fe-ACP powders. The results show that the hardness of the ceramics increases with the increase of iron content, but an excess of iron leads to a rapid decline in hardness. Calcium iron phosphate ceramics with a hardness of 4 GPa can be achieved, which is higher than that of human enamel. Furthermore, the ceramics composed of iron-calcium phosphates show enhanced acid resistance. This study provides a novel route to prepare Fe-ACP, and presents the potential role of Fe-ACP in biomineralization and as starting material to fabricate acid-resistant high-performance bioceramics