WebQUAST: online evaluation of genome assemblies

Selecting proper genome assembly is key for downstream analysis in genomics studies. However, the availability of many genome assembly tools and the huge variety of their running parameters challenge this task. The existing online evaluation tools are limited to specific taxa or provide just a one-sided view on the assembly quality. We present WebQUAST, a web server for multifaceted quality assessment and comparison of genome assemblies based on the state-of-the-art QUAST tool. The server is freely available at https://www.ccb.uni-saarland.de/quast/. WebQUAST can handle an unlimited number of genome assemblies and evaluate them against a user-provided or pre-loaded reference genome or in a completely reference-free fashion. We demonstrate key WebQUAST features in three common evaluation scenarios: assembly of an unknown species, a model organism, and a close variant of it

Epoxy Compositions with Reduced Flammability Based on DER-354 Resin and a Curing Agent Containing Aminophosphazenes Synthesized in Bulk Isophoronediamine

A method for the synthesis of an amine-containing epoxy resin curing agent by dissolving hexakis-[(4-formyl)phenoxy]cyclotriphosphazene in an excess of isophoronediamine was developed. The curing agent was characterized via NMR and IR spectroscopy and MALDI-TOF mass spectrometry, and its rheological characteristics were studied. Compositions based on DER-354 epoxy resin and the synthesized curing agent with different amounts of phosphazene content were obtained. The rheological characteristics of these compositions were studied, followed by their curing. An improvement in several thermal (DSC), mechanical (compression, tension, and adhesion), and physicochemical (water absorption and water solubility) characteristics, as well as the fire resistance of the obtained materials modified with phosphazene, was observed, compared with unmodified samples. In particular, there was an improvement in adhesive characteristics and fire resistance. Thus, compositions based on a curing agent containing a 30% modifier were shown to fulfill the V-1 fire resistance category. The developed compositions can be processed by contact molding, winding, and resin transfer molding (RTM), and the resulting material is suitable for use in aircraft, automotive products, design applications, and home repairs

Singularities of bi-Hamiltonian systems

We study the relationship between singularities of bi-Hamiltonian systems and algebraic properties of compatible Poisson brackets. As the main tool, we introduce the notion of linearization of a Poisson pencil. From the algebraic viewpoint, a linearized Poisson pencil can be understood as a Lie algebra with a fixed 2-cocycle. In terms of such linearizations, we give a criterion for non-degeneracy of singular points of bi-Hamiltonian systems and describe their types

Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery.

Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs

HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search

Recent analyses of public microbial genomes have found over a million biosynthetic gene clusters, the natural products of the majority of which remain unknown. Additionally, GNPS harbors billions of mass spectra of natural products without known structures and biosynthetic genes. We bridge the gap between large-scale genome mining and mass spectral datasets for natural product discovery by developing HypoRiPPAtlas, an Atlas of hypothetical natural product structures, which is ready-to-use for in silico database search of tandem mass spectra. HypoRiPPAtlas is constructed by mining genomes using seq2ripp, a machine-learning tool for the prediction of ribosomally synthesized and post-translationally modified peptides (RiPPs). In HypoRiPPAtlas, we identify RiPPs in microbes and plants. HypoRiPPAtlas could be extended to other natural product classes in the future by implementing corresponding biosynthetic logic. This study paves the way for large-scale explorations of biosynthetic pathways and chemical structures of microbial and plant RiPP classes

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Insulinoma in childhood: a retrospective review of 22 patients from one referral centre

BackgroundInsulinomas are very rare in childhood with sparse knowledge on the clinical aspects and the presence of Multiple Endocrine Neoplasia type 1 (MEN1).MethodsWe conducted a retrospective review of patients diagnosed with insulinoma between 1995 and 2021, presenting to one referral centre in Russia. Clinical, biochemical, genetic, imaging and histological data were collected. In addition, follow-up and family data were obtained.ResultsA total of twenty-two children aged 5 to 16 years were identified. The median (range) gap between the first hypoglycaemia symptoms and diagnosis was 10 (1–46) months. Twelve children (55%) were misdiagnosed to have epilepsy and were treated with anticonvulsants before hypoglycemia was revealed. Contrast enhanced MRI and/or CT were accurate to localize the lesion in 82% (n=18). Five patients (23%) had multiple pancreatic lesions. All children underwent surgical treatment. The median (range) diameter of removed tumors was 1.5 (0.3-6) cm. Histopathological studies confirmed the presence of insulinoma in all cases. Immunohistochemical studies revealed G2 differentiation grade in 10 out of 17 cases. Two patients were diagnosed with metastatic insulinoma. One of them had metastases at the time of insulinoma diagnosis, while the other was diagnosed with liver metastases eight years after the surgery. Eight children (36%) were found to carry MEN1 mutations, inherited n=5, de novo n=1, no data, n=2. Children with MEN1 had significantly higher number of pancreatic tumors compared to sporadic cases. All of them developed additional MEN1 symptoms during the following 2-13 years. In the five patients with inherited MEN1, seven family members had hitherto undiscovered MEN1 manifestations.ConclusionsIn this large cohort of children with rare pediatric insulinomas, MEN1 syndrome and G2 tumors were frequent, as well as hitherto undiscovered MEN1 manifestations in family members. Our data emphasize the need of genetic testing in all children with insulinoma and their relatives, even in the absence of any other features, as well as the importance of a prolonged follow-up observation

Critical Assessment of Metagenome Interpretation:A benchmark of metagenomics software

International audienceIn metagenome analysis, computational methods for assembly, taxonomic profilingand binning are key components facilitating downstream biological datainterpretation. However, a lack of consensus about benchmarking datasets andevaluation metrics complicates proper performance assessment. The CriticalAssessment of Metagenome Interpretation (CAMI) challenge has engaged the globaldeveloper community to benchmark their programs on datasets of unprecedentedcomplexity and realism. Benchmark metagenomes were generated from newlysequenced ~700 microorganisms and ~600 novel viruses and plasmids, includinggenomes with varying degrees of relatedness to each other and to publicly availableones and representing common experimental setups. Across all datasets, assemblyand genome binning programs performed well for species represented by individualgenomes, while performance was substantially affected by the presence of relatedstrains. Taxonomic profiling and binning programs were proficient at high taxonomicranks, with a notable performance decrease below the family level. Parametersettings substantially impacted performances, underscoring the importance ofprogram reproducibility. While highlighting current challenges in computationalmetagenomics, the CAMI results provide a roadmap for software selection to answerspecific research questions

NPvis: An Interactive Visualizer of Peptidic Natural Product–MS/MS Matches

Peptidic natural products (PNPs) represent a medically important class of secondary metabolites that includes antibiotics, anti-inflammatory and antitumor agents. Advances in tandem mass spectra (MS/MS) acquisition and in silico database search methods have enabled high-throughput PNP discovery. However, the resulting spectra annotations are often error-prone and their validation remains a bottleneck. Here, we present NPvis, a visualizer suitable for the evaluation of PNP–MS/MS matches. The tool interactively maps annotated spectrum peaks to the corresponding PNP fragments and allows researchers to assess the match correctness. NPvis accounts for the wide chemical diversity of PNPs that prevents the use of the existing proteomics visualizers. Moreover, NPvis works even if the exact chemical structure of the matching PNP is unknown. The tool is available online and as a standalone application. We hope that it will benefit the community by streamlining PNP data analysis and validation