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Summary Whole genome assembly (WGA) of bacterial genomes with short reads is a quite common task as DNA sequencing has become cheaper with the advances of its technology. The process of assembling a genome has no absolute golden standard and it requires to perform a sequence of steps each of which can involve combinations of many different tools. However, the quality of the final assembly is always strongly related to the quality of the input data. With this in mind we built WGA-LP, a package that connects state-of-the-art programs for microbial analysis and novel scripts to check and improve the quality of both samples and resulting assemblies. WGA-LP, with its conservative decontamination approach, has shown to be capable of creating high quality assemblies even in the case of contaminated reads. Availability and implementation WGA-LP is available on GitHub (https://github.com/redsnic/WGA-LP) and Docker Hub (https://hub.docker.com/r/redsnic/wgalp). The web app for node visualization is hosted by shinyapps.io (https://redsnic.shinyapps.io/ContigCoverageVisualizer/). Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Aims: This work aimed to evaluate the antimicrobial activity of pure (ZnO) and doped (ZnMgO) zinc oxide (ZnO) nanoparticles on bacterial pathogens and Saccharomyces cerevisiae to confirm their applicability as an alternative to antibiotics and to estimate their biocompatibility. Methods and Results: Microbial growth inhibition on agar plates, microbial viability and adaptation tests in broth with ZnO nanoparticles, spore germination, random amplified polymorphic DNA and SDS‐PAGE analysis were conducted to evaluate the effects of ZnO nanoparticles on cell morphology, viability, DNA damage and protein production. For this purpose, Escherichia coli, Salmonella, Listeria monocytogenes, Staphylococcus aureus, Bacillus subtilis and S. cerevisiae were studied after the addition of ZnO nanoparticles to the growth media. The contact with ZnO nanoparticles produced changes in morphology, shape, viability, DNA arrangement (DNA fingerprints) and protein content (SDS‐PAGE) in treated cells. Conclusions: As reported in this study, ZnO nanoparticles have an antimicrobial effect on both prokaryotic and eukaryotic cells. Before using ZnO nanoparticles as antimicrobial agents, it is important to evaluate the target because their effect depends on their composition, size and dose. Significance and Impact of the Study: We believe that the results obtained can help to optimize manufactured metal oxide nanoparticles in terms of their composition, size and working concentration. The parameters obtained directly define the applicability and biocompatibility of ZnO nanoparticles and thus are essential for any utilization in food, medicine and industry where pathogen control is crucial. [ABSTRACT FROM AUTHOR]

In the defense against downy mildew, copper is still widely used, particularly in organic management. At any rate, specific investigations are needed to significantly reduce the use of copper and minimize its environmental impact. This study, conducted in several farms in Friuli-Venezia Giulia (Northeast Italy), aimed to evaluate the concentration of copper on leaves in various climatic conditions, in order to create an important database for the development of a rapid control system through image analysis. The tests involved sampling leaves and grapes from bud break until the last treatment with copper-based products. After copper recovery using a nitric acid solution, the copper values were analyzed via ICP-AES analysis. Cuprotesmo imprints were also made on the same leaves to develop an application (APP) capable of quickly and non-destructively detecting copper on the leaf surface through image analysis. The analytical data revealed significant correlations between image analysis and copper values only in certain situations involving adult leaves. However, due to the variability in treatment situations, the use of the APP with image analysis for all copper defense scenarios is not yet feasible. Nevertheless, the results are encouraging and will serve for further extensive investigations to develop an image analysis system capable of detecting truly active copper and optimizing pesticide treatments for a precision defense strategy. This strategy aims to ensure low environmental impact, production sustainability, and grape quality.