Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider

Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.

AXEAP: a software package for X-ray emission data analysis using unsupervised machine learning

The Argonne X-ray Emission Analysis Package (AXEAP) has been developed to calibrate and process X-ray emission spectroscopy (XES) data collected with a two-dimensional (2D) position-sensitive detector. AXEAP is designed to convert a 2D XES image into an XES spectrum in real time using both calculations and unsupervised machine learning. AXEAP is capable of making this transformation at a rate similar to data collection, allowing real-time comparisons during data collection, reducing the amount of data stored from gigabyte-sized image files to kilobyte-sized text files. With a user-friendly interface, AXEAP includes data processing for non-resonant and resonant XES images from multiple edges and elements. AXEAP is written in MATLAB and can run on common operating systems, including Linux, Windows, and MacOS.

High resolution x-ray emission spectrometer for multiple hard x-ray emission lines: Demonstration for Cu Kα and Kβ emissions

We present a compact 3D printed x-ray emission spectrometer based on the von Hamos geometry that represents a significant upgrade to the existing von Hamos geometry-based miniature x-ray emission spectrometer (miniXES) [Mattern et al., Rev. Sci. Instrum. 83(2), 023901 (2012)]. The upgrades include the incorporation of a higher pixel density 500K detector for improved energy resolution and an enlarged sample area to accommodate a wider range of sample formats. The versatile spectrometer houses removable crystal holders that can be easily exchanged, as well as movable alignment eyelets that give flexibility in Bragg angle selection. Designed for ease of manufacture, all the components, except for the apertures, can be 3D printed and readily assembled. We describe its implementation in measurements of resonant and non-resonant Cu Kα and Kβ x-ray emission and report the theoretical and measured energy resolution and collected solid angle of the emission.

The Study of the Solid Polymer Electrolyte Oxygen Concentrator with Nanostructural Catalysts Based on Hydrophobized Support

The efficient production of gaseous oxygen used in many branches of industry to provide human life in anaerobic environments and in medicine (e.g., in the case of acute respiratory failure as one of COVID-19 complications) is challenging nowadays. The electrochemical oxygen pump (concentrator) with a solid polymer electrolyte representing an electrolyzer with air cathode depolarization is a very promising device, which provides the portable, safe, and efficient in situ production of highly pure oxygen at a twice lower energy consumption as compared to the water electrolyzer with a solid polymer electrolyte. The effect produced by the hydrophobization of a nanostructured oxygen reduction catalyst on the oxygen pump characteristics and the endurance of a cathode catalytic layer to flooding has been considered. The modification of a carbon support with polytetrafluoroethylene particles improves the removal of excessive water from the catalytic layer and increases the limiting current characterizing the appearance of transport limitations. The operational parameters (air temperature, flow rate, and pressure) also have an essential effect on the oxygen pump performance and must be optimized to improve water transport in catalytic layers, increase the operating current densities, and reduce the energy consumption in oxygen production.

[Determination of cytokines and adhesion molecules in elderly and senile patients with aortic valve calcification.]

A laboratory study of the cytokine profile and the content of the intercellular adhesion molecules was performed in 38 patients with initial signs of aortic hemilunus calcification. It has been determined that the content of IL-6 and IL-8 had significantly higher values compared with the control group, which indicates the direct role of nonspecific chronic inflammation in the development of calcifying aortic valve damage. A significantly lower content of sE-selectin was also identified, which may indicate the absence of activation of adhesion molecules at the initial stage of aortic valve calcification. Further study of the dynamics of sE- and sP-selectins content in the process of development of acceleration of blood flow in the aortic valve and the formation of stenosis is needed.

[Indicators of lipid exchange as early markers of development calcific aortic valve disease.]

A comprehensive study of lipidograms of 36 patients with initial signs of calcification of aortic semilunium was performed. It was determined that the content of apolipoprotein A-1 was significantly lower in comparison with the control groups, which requires further studies of the evaluation of the effect on the process of early development of calcification of drugs capable to increasing its content. If the concentration of apolipoprotein A-1 is less than 1,1 mg/dl and/or the apoB/apoA ratio is increased by more than 1, it is advisable to recommend dispensary follow-up with regular (no less than 1 time in 5 years) echocardiographic study with a detailed study of the functional state of the aortic valve.

[Actuality of pathomorphogenesis investment in calcific aortic valve stenosis.]

The increasing of lifetime industrial countries population leads to widespreading diseases of age. Dramatic growth of sclerodegenerative heart valve diseases in last decades is one of the best examples. We observed 814 patients of different gender and age with acquired heart valve diseases using echocardiography. We found out that the most common heart valve disease is degenerative aortic stenosis. Unfortunately, nowadays in Russia no more than 20% of the necessary operations on aortic valve are performed, the main reason of it is, more likely, insufficient and untimely diagnosis of the defect. However, the surgery of vice serves only as a mechanical elimination of the problem, without affecting the causes which led to its development. So we need modern data about sclerodegenerative heart valve diseases epidemiology and discloses actuality of the problem.