A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.

Somatic mosaicism is an important cause of disease, but mosaic and somatic variants are often challenging to detect because they exist in only a fraction of cells. To address the need for benchmarking subclonal variants in normal cell populations, we developed a benchmark containing mosaic variants in the Genome in a Bottle Consortium (GIAB) HG002 reference material DNA from a large batch of a normal lymphoblastoid cell line. First, we used a somatic variant caller with high coverage (300x) Illumina whole genome sequencing data from the Ashkenazi Jewish trio to detect variants in HG002 not detected in at least 5% of cells from the combined parental data.

Proof-of-concept evaluation of next-generation sequencing-based liquid biopsy for non-invasive cancer detection in cats.

This proof-of-concept evaluation demonstrates that next-generation sequencing-based liquid biopsy can detect genomic alterations in the blood of cats with cancer and the absence of such alterations in the blood of presumably cancer-free cats. Two cats with cytologically confirmed lymphoma and nine presumably cancer-free cats were included in this analysis. Whole blood was collected from each subject and samples were subjected to DNA extraction, library preparation, and next-generation sequencing.

[RYR1 myopathies in childhood: phenotype-genotype correlation and incidence].

Introduction: Ryanodine receptor type 1-related myopathies (RYR1-RM) represent the most prevalent category of congenital myopathies. The introduction of genetic techniques has shifted the diagnostic paradigm, suggesting the prioritization of molecular studies over biopsies. This study aims to explore the clinical and epidemiological characteristics of patients with RYR1 gene variants in a tertiary pediatric hospital, intending to enhance the understanding of the genotype-phenotype correlation in RYR1-RM.

Clinical validation of a blood-based liquid biopsy test integrating cell-free DNA quantification and next-generation sequencing for cancer screening in dogs.

Objective: To validate the performance of a novel, integrated test for canine cancer screening that combines cell-free DNA quantification with next-generation sequencing (NGS) analysis.

Sample: Retrospective data from a total of 1,947 cancer-diagnosed and presumably cancer-free dogs were used to validate test performance for the detection of 7 predefined cancer types (lymphoma, hemangiosarcoma, osteosarcoma, leukemia, histiocytic sarcoma, primary lung tumors, and urothelial carcinoma), using independent training and testing sets.

Methods: Cell-free DNA quantification data from all samples were analyzed using a proprietary machine learning algorithm to determine a Cancer Probability Index (High, Moderate, or Low).

Next-generation sequencing-based liquid biopsy may be used for detection of residual disease and cancer recurrence monitoring in dogs.

Objective: The purpose of this study was to evaluate the performance of a next-generation sequencing-based liquid biopsy test for cancer monitoring in dogs.

Samples: Pre- and postoperative blood samples were collected from dogs with confirmed cancer diagnoses originally enrolled in the CANcer Detection in Dogs (CANDiD) study. A subset of dogs also had longitudinal blood samples collected for recurrence monitoring.

Detection of Age-Related Somatic Alterations in Canine Blood Using Next-Generation Sequencing-Based Liquid Biopsy: An Analysis of over 4800 Dogs.

Age-related somatic genomic alterations in hematopoietic cell lines have been well characterized in humans; however, this phenomenon has not been well studied in other species. Next-generation sequencing-based liquid biopsy testing for cancer detection was recently developed for dogs and has been used to study the genomic profiles of blood samples from thousands of canine patients since 2021. In this study, 4870 client-owned dogs with and without a diagnosis or suspicion of cancer underwent liquid biopsy testing by this method.

Clinical experience with next-generation sequencing-based liquid biopsy testing for cancer detection in dogs: a review of 1,500 consecutive clinical cases.

Objective: To review ordering patterns, positivity rates, and outcome data for a subset of consecutive samples submitted for a commercially available, blood-based multicancer early-detection liquid biopsy test for dogs using next-generation sequencing at 1 laboratory.

Sample: 1,500 consecutively submitted blood samples from client-owned dogs with and without clinical suspicion and/or history of cancer for prospective liquid biopsy testing between December 28, 2021, and June 28, 2022.

Procedures: We performed a retrospective observational study, reviewing data from 1,500 consecutive clinical samples submitted for liquid biopsy testing.

RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity.

Mapping of short metagenomic (or metatranscriptomic) read data to reference isolate or single-cell genomes or metagenome-assembled genomes (MAGs) to assess microbial population relative abundance and/or structure represents an essential task of many studies across environmental and clinical settings. The filtering for the quality of the read match and assessment of read mapping results are frequently performed without visual aids or with the assistance of visualizations produced through ad-hoc, in-house approaches. Here, we introduce RecruitPlotEasy, a fully automated, user-friendly pipeline for these purposes that integrates statistical approaches to quantify intra-population sequence and gene-content diversity and identify co-occurring relative populations in the sample.

Clinical validation of a next-generation sequencing-based multi-cancer early detection "liquid biopsy" blood test in over 1,000 dogs using an independent testing set: The CANcer Detection in Dogs (CANDiD) study.

Cancer is the leading cause of death in dogs, yet there are no established screening paradigms for early detection. Liquid biopsy methods that interrogate cancer-derived genomic alterations in cell-free DNA in blood are being adopted for multi-cancer early detection in human medicine and are now available for veterinary use. The CANcer Detection in Dogs (CANDiD) study is an international, multi-center clinical study designed to validate the performance of a novel multi-cancer early detection "liquid biopsy" test developed for noninvasive detection and characterization of cancer in dogs using next-generation sequencing (NGS) of blood-derived DNA; study results are reported here.

Transcriptomic and rRNA:rDNA Signatures of Environmental versus Enteric Enterococcus faecalis Isolates under Oligotrophic Freshwater Conditions.

The use of enterococci as a fecal indicator bacterial group for public health risk assessment has been brought into question by recent studies showing that "naturalized" populations of Enterococcus faecalis exist in the extraenteric environment. The extent to which these naturalized E. faecalis organisms can confound water quality monitoring is unclear.

Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones.

The diverse and ubiquitous members of the SAR11 lineage (Alphaproteobacteria) represent up to 30-40% of the surface and mesopelagic oceanic microbial communities. However, the molecular and ecological mechanisms that differentiate closely related, yet distinct, SAR11 members that often co-occur under similar environmental conditions remain speculative. Recently, two mesopelagic and oxygen minimum zone (OMZ)-associated subclades of SAR11 (Ic and IIa.

MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes.

Background: High-throughput sequencing has increased the number of available microbial genomes recovered from isolates, single cells, and metagenomes. Accordingly, fast and comprehensive functional gene annotation pipelines are needed to analyze and compare these genomes. Although several approaches exist for genome annotation, these are typically not designed for easy incorporation into analysis pipelines, do not combine results from different annotation databases or offer easy-to-use summaries of metabolic reconstructions, and typically require large amounts of computing power for high-throughput analysis not available to the average user.

Electroswitching of the single-molecule magnet behaviour in an octahedral spin crossover cobalt(ii) complex with a redox-active pyridinediimine ligand.

Thermal-assisted spin crossover and field-induced slow magnetic relaxation coexist in the solid state for the mononuclear cobalt(ii) complex with the non-innocent 2,6-bis(N-4-methoxyphenylformimidoyl)pyridine ligand. One-electron oxidation of the paramagnetic low-spin Co ion (S = 1/2) to the diamagnetic low-spin Co ion (S = 0) leads to the electroswitching of the slow magnetic relaxation in acetonitrile solution.

Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems.

Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via the formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia hartwegiana plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of Deinococcus swuensis showed a high survival rate of up to 60% after UVR treatment at 800J/m2 and was used for differential expression analysis using RNA-seq after exposing cells to 400J/m2 of UVR (with >95% survival rate).

Metal organic framework composite, nano-FeO@Fe-(benzene-1,3,5-tricarboxylic acid), for solid phase extraction of blood lipid regulators from water.

The magnetic metal-organic framework FeO@(Fe-(benzene-1,3,5-tricarboxylic acid) (MMOF) was prepared, characterized and studied as a magnetic sorbent for the dispersive solid-phase extraction (DSPE) of several widely used blood lipid regulators (i.e., bezafibrate, clofibric acid, clofibrate, gemfibrozil and fenofibrate) from water samples.

Prevalence of viral photosynthesis genes along a freshwater to saltwater transect in Southeast USA.

Bacteriophages encode host-acquired functional genes known as auxiliary metabolic genes (AMGs). Photosynthesis AMGs are commonly found in marine cyanobacteria-infecting Myoviridae and Podoviridae cyanophages, but their ecology remains understudied in freshwater environments. To advance knowledge of this issue, we analysed viral metagenomes collected in the summertime for four years from five lakes and two estuarine locations interconnected by the Chattahoochee River, Southeast USA.

Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus "Candidatus Fonsibacter" and proposal of Ca. Fonsibacter lacus sp. nov.

The ubiquitous alpha-proteobacteria of the order "Candidatus Pelagibacterales" (SAR11) are highly abundant in aquatic environments, and among them, members of the monophyletic lineage LD12 (also known as SAR11 clade IIIb) are specifically found in lacustrine ecosystems. Clade IIIb bacteria are some of the most prominent members of freshwater environments, but little is known about their biology due to the lack of genome representatives. Only recently, the first non-marine isolate was cultured and described as "Candidatus Fonsibacter ubiquis".

Application of a Pillared-Layer Zn-Triazolate Metal-Organic Framework in the Dispersive Miniaturized Solid-Phase Extraction of Personal Care Products from Wastewater Samples.

The pillared-layer Zn-triazolate metal-organic framework (CIM-81) was synthesized, characterized, and used for the first time as a sorbent in a dispersive micro-solid phase extraction method. The method involves the determination of a variety of personal care products in wastewaters, including four preservatives, four UV-filters, and one disinfectant, in combination with ultra-high performance liquid chromatography and UV detection. The CIM-81 MOF, constructed with an interesting mixed-ligand synthetic strategy, demonstrated a better extraction performance than other widely used MOFs in D-µSPE such as UiO-66, HKUST-1, and MIL-53(Al).

Influence of Ligand Functionalization of UiO-66-Based Metal-Organic Frameworks When Used as Sorbents in Dispersive Solid-Phase Analytical Microextraction for Different Aqueous Organic Pollutants.

Four metal-organic frameworks (MOFs), specifically UiO-66, UiO-66-NH₂, UiO-66-NO₂, and MIL-53(Al), were synthesized, characterized, and used as sorbents in a dispersive micro-solid phase extraction (D-µSPE) method for the determination of nine pollutants of different nature, including drugs, phenols, polycyclic aromatic hydrocarbons, and personal care products in environmental waters. The D-µSPE method, using these MOFs as sorbents and in combination with high-performance liquid chromatography (HPLC) and diode-array detection (DAD), was optimized. The optimization study pointed out to UiO-66-NO₂ as the best MOF to use in the multi-component determination.

A green metal-organic framework to monitor water contaminants.

The CIM-80 material (aluminum(iii)-mesaconate) has been synthetized in high yield through a novel green procedure involving water and urea as co-reactants. The CIM-80 material exhibits good thermal stability with a working range from RT to 350 °C with a small contraction upon desolvation. Moreover, this material is stable in water at different pH values (1-10) for at least one week, and shows a LC value higher than 2 mg mL.

Insights in the analytical performance of neat metal-organic frameworks in the determination of pollutants of different nature from waters using dispersive miniaturized solid-phase extraction and liquid chromatography.

Five metal-organic frameworks (MOFs), specifically HKUST-1, MOF-5(Zn), MIL-53(Al), UiO-64 and MOF-74(Zn) are synthesized, characterized, and utilized in a miniaturized solid-phase extraction method under dispersive mode (D-µSPE) for the determination of six pollutants of different nature, including one polycyclic aromatic hydrocarbon, two hormones, two drugs, and one disinfectant, from environmental waters (tap water and wastewater). A discussion of possible interactions justifying the partitioning of target analytes to the MOFs is included, considering not only the analytes' physicochemical characteristics but also those of MOFs: metal nature, structural environment of MOF pores, pore size and pore aperture widths, among others. MIL-53(Al) is selected for its versatility and high extraction efficiency for the target compounds.

Reversible solvatomagnetic switching in a single-ion magnet from an entatic state.

A vast impact on molecular nanoscience can be achieved using simple transition metal complexes as dynamic chemical systems to perform specific and selective tasks under the control of an external stimulus that switches "ON" and "OFF" their electronic properties. While the interest in single-ion magnets (SIMs) lies in their potential applications in information storage and quantum computing, the switching of their slow magnetic relaxation associated with host-guest processes is insufficiently explored. Herein, we report a unique example of a mononuclear cobalt(ii) complex in which geometrical constraints are the cause of easy and reversible water coordination and its release.

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.

A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called "rare biosphere." How often, and via what mechanisms, e.

Endophytic Microbial Community DNA Extraction from the Plant Phyllosphere.

The plant phyllosphere, which represents all plant parts that are above the ground, is considered one of the most extensive ecosystems to be colonized by microorganisms, both at the surface as epiphytes or as endophytes within the plant. These plant-associated microbial communities are reservoirs of microbial diversity and they can be important for plant health. The characterization of microbial communities in diverse plants, such as plants that are endemic to the Paramo ecosystem in the Andes Mountains, can shed light regarding possible interactions among microorganisms and microbial functional properties.