Search

ABSTRACTThe resolution of variation within species is critical for interpreting and acting on many microbial measurements. In the key foodborne pathogens Salmonella and Escherichia coli, the primary subspecies classification scheme used is serotyping: differentiating variants within these species by surface antigen profiles. Serotype prediction from whole-genome sequencing (WGS) of isolates is now seen as comparable or preferable to traditional laboratory methods where WGS is available. However, laboratory and WGS methods depend on an isolation step that is time-consuming and incompletely represents the sample when multiple strains are present. Community sequencing approaches that skip the isolation step are, therefore, of interest for pathogen surveillance. Here, we evaluated the viability of amplicon sequencing of the full-length 16S rRNA gene for serotyping Salmonella enterica and E. coli. We developed a novel algorithm for serotype prediction, implemented as an R package (Seroplacer), which takes as input full-length 16S rRNA gene sequences and outputs serovar predictions after phylogenetic placement into a reference phylogeny. We achieved over 89% accuracy in predicting Salmonella serotypes on in silico test data and identified key pathogenic serovars of Salmonella and E. coli in isolate and environmental test samples. Although serotype prediction from 16S rRNA gene sequences is not as accurate as serotype prediction from WGS of isolates, the potential to identify dangerous serovars directly from amplicon sequencing of environmental samples is intriguing for pathogen surveillance. The capabilities developed here are also broadly relevant to other applications where intraspecies variation and direct sequencing from environmental samples could be valuable.IMPORTANCEIn order to prevent and stop outbreaks of foodborne pathogens, it is important that we can detect when pathogenic bacteria are present in a food or food-associated site and identify connections between specific pathogenic bacteria present in different samples. In this work, we develop a new computational technology that allows the important foodborne pathogens Escherichia coli and Salmonella enterica to be serotyped (a subspecies level classification) from sequencing of a single-marker gene, and the 16S rRNA gene often used to surveil bacterial communities. Our results suggest current limitations to serotyping from 16S rRNA gene sequencing alone but set the stage for further progress that we consider likely given the rapid advance in the long-read sequencing technologies and genomic databases our work leverages. If this research direction succeeds, it could enable better detection of foodborne pathogens before they reach the public and speed the resolution of foodborne pathogen outbreaks.

Mass spectrometry-based thermal stability assays (MS-TSA) are a promising approach to characterize protein-ligand interaction, and several strategies have been recently developed to improve their performance. Here, the authors combine three recent strategies to qualitatively and quantitatively improve aspects of MS-TSA.

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics. Video abstract.

Abstract We introduce a variant of Quantum Amplitude Estimation (QAE), called Iterative QAE (IQAE), which does not rely on Quantum Phase Estimation (QPE) but is only based on Grover’s Algorithm, which reduces the required number of qubits and gates. We provide a rigorous analysis of IQAE and prove that it achieves a quadratic speedup up to a double-logarithmic factor compared to classical Monte Carlo simulation with provably small constant overhead. Furthermore, we show with an empirical study that our algorithm outperforms other known QAE variants without QPE, some even by orders of magnitude, i.e., our algorithm requires significantly fewer samples to achieve the same estimation accuracy and confidence level.

The following article addresses a complex combinatorial optimization and integer-programming problem, referred to as the vehicle routing problem, which is typically related to the field of transportation logistics. The aim of the research is to combine a set of objective functions, number of common generalizations and extensions of the problem, arising in distributed services or goods supply. For this purpose, literature on the subject has been analysed, leading to the mathematical modelling method being applied. At the current moment such complicated variants of the problem present high importance for research because of both practical applications and high complexity. The paper proposes a new generalized multi-objective vehicle routing problem with multiple depots and heterogeneous vehicles fleet with regard to various factors affecting costs. The problem statement is presented as a mixed integer linear program. Objectives scalarization approach is proposed in order to reduce decision-maker participation. Shortcomings of the single-criterion formulation and negative effects of replacing the criteria with constraints are shown. The results provide initial data for solving a large number of transportation problems that are reduced to the vehicle routing problem. In particular, the application of the ant colony optimization as a method for solving the problem is discussed.

Introduction: The oral route of L-arginine intake, despite its great comfort, is less effective in comparison with infusions. The development of new pharmaceutical forms for oral preparation is of undoubted interest. Objectives: To obtain a new dosage form of L-arginine by complexation with sodium salt of cellulose sulfate acetate (Na-CSA) followed by immobilization on activated carbon, and to evaluate its endothelial, cardioprotective and antihypertensive activity. Methods: UV-, visible spectroscopy, FTIR spectroscopy, viscometry, molecular mechanics, animal experiments with male Wistar albino rats in the modeling of L-NAME-induced endothelium dysfunction. Results: The physicochemical parameters of complexation, the adsorption activity of activated carbons of various origins with respect to individual L-arginine and its complex with Na-CSA were investigated. The greatest amount of adsorption and its smaller difference between L-arginine and the complex were taken into account when choosing activated carbon as a carrier (AUT-MI: GL-Arginine=320.2±0.1 mg/g, Gcomplex=340.2±0.1 mg/g; OU-A: GL-Arginine=210.1±0.1 mg/g, Gcomplex=235.1±0.1 mg/g; TH-90G: GL-Arginine=190.1±0.1 mg/g, Gcomplex=190.2±0.1 mg/g). Release of L-arginine as a result of its desorption into the model media of the human body was higher (96.3±0.5 wt.%) for the alkaline medium of intestines than for the acidic medium of stomach (10.0±0.1 wt.%). In animal experiments, it was shown that a combined preparation of L-arginine complex immobilized at doses of 30 mg/kg, 70 mg/kg and 200 mg/kg exhibits a pronounced antihypertensive, endothelioprotecive and cardioprotective activity at a dose of 200 mg/kg with L-NAME-induced nitric oxide deficiency (p

For the first time a complex of L-arginine sodium salt of sulfate of cellulose acetate on activated carbon. To investigate the processes of sorption-desorption of L-arginine in a model environment. In animal experiments it was shown that granulirovannye the form of a combined preparation in dosages of 30 mg/kg, 70 mg/kg and 200 mg/kg exhibits a pronounced anti-hypertensive, endothelioprotecive and cardioprotective activity in a dosage of 200 mg/kg.