ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome

The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.

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.

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.

Imaging and Interventions for Lymphatic and Lymphatic-related Disorders

The lymphatic system is critical in fluid balance homeostasis. Yet, until recently, lymphatic imaging has been outside of mainstream medicine due to a lack of robust imaging and interventional options. However, during the last 20 years, both clinical lymphatic imaging and interventions have shown dramatic advancement. The key to imaging advancement has been the interstitial delivery of contrast agents through lymphatic-rich tissues. These techniques include intranodal lymphangiography and dynamic contrast-enhanced MR lymphangiography. These methods provide the ability to image and recognize lymphatic anatomy and pathologic conditions. Percutaneous thoracic duct catheterization and embolization became the first widely accepted interventional technique for the management of chyle leaks. Advances in interstitial lymphatic embolization, as well as liver and mesenteric lymphatic interventions, have broadened the scope of possible lymphatic interventions. Also, recent techniques of lymphatic decompression allow for the treatment of a variety of lymphatic disorders. Finally, immunologic studies of central lymphatic fluid reveal the potential of lymphatic interventions on immunity. These advances herald an exciting new chapter for lymphatic imaging and interventions in the coming years.

NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

Microbial specialized metabolites are an important source of and inspiration for many pharmaceuticals, biotechnological products and play key roles in ecological processes. Untargeted metabolomics using liquid chromatography coupled with tandem mass spectrometry is an efficient technique to access metabolites from fractions and even environmental crude extracts. Nevertheless, metabolomics is limited in predicting structures or bioactivities for cryptic metabolites. Efficiently linking the biosynthetic potential inferred from (meta)genomics to the specialized metabolome would accelerate drug discovery programs by allowing metabolomics to make use of genetic predictions. Here, we present a k-nearest neighbor classifier to systematically connect mass spectrometry fragmentation spectra to their corresponding biosynthetic gene clusters (independent of their chemical class). Our new pattern-based genome mining pipeline links biosynthetic genes to metabolites that they encode for, as detected via mass spectrometry from bacterial cultures or environmental microbiomes. Using paired datasets that include validated genes-mass spectral links from the Paired Omics Data Platform, we demonstrate this approach by automatically linking 18 previously known mass spectra (17 for which the biosynthesis gene clusters can be found at the MIBiG database plus palmyramide A) to their corresponding previously experimentally validated biosynthetic genes (e.g., via nuclear magnetic resonance or genetic engineering). We illustrated a computational example of how to use our Natural Products Mixed Omics (NPOmix) tool for siderophore mining that can be reproduced by the users. We conclude that NPOmix minimizes the need for culturing (it worked well on microbiomes) and facilitates specialized metabolite prioritization based on integrative omics mining.

Direct current magnetic Hall probe technique for measurement of field penetration in thin film superconductors for superconducting radio frequency resonators

Superconducting Radio Frequency (SRF) cavities used in particle accelerators are typically formed from or coated with superconducting materials. Currently, high purity niobium is the material of choice for SRF cavities that have been optimized to operate near their theoretical field limits. This brings about the need for significant R & D efforts to develop next generation superconducting materials that could outperform Nb and keep up with the demands of new accelerator facilities. To achieve high quality factors and accelerating gradients, the cavity material should be able to remain in the superconducting Meissner state under a high RF magnetic field without penetration of quantized magnetic vortices through the cavity wall. Therefore, the magnetic field at which vortices penetrate a superconductor is one of the key parameters of merit of SRF cavities. Techniques to measure the onset of magnetic field penetration on thin film samples need to be developed to mitigate the issues with the conventional magnetometry measurements that are strongly influenced by the film orientation and shape and edge effects. In this work, we report the development of an experimental setup to measure the field of full flux penetration through films and multi-layered superconductors. Our system combines a small superconducting solenoid that can generate a magnetic field of up to 500 mT at the sample surface and three Hall probes to detect the full flux penetration through the superconductor. This setup can be used to study alternative materials that could potentially outperform niobium, as well as superconductor-insulator-superconductor (SIS) multilayer coatings on niobium.

Critical Assessment of Metagenome Interpretation: the second round of challenges

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.

This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis.

Transarterial Embolization Modulates the Immune Response within Target and Nontarget Hepatocellular Carcinomas in a Rat Model

Background Transarterial embolization (TAE) is the most common treatment for hepatocellular carcinoma (HCC); however, there remain limited data describing the influence of TAE on the tumor immune microenvironment. Purpose To characterize TAE-induced modulation of the tumor immune microenvironment in a rat model of HCC and identify factors that modulate this response. Materials and Methods TAE was performed on autochthonous HCCs induced in rats with use of diethylnitrosamine. CD3, CD4, CD8, and FOXP3 lymphocytes, as well as programmed cell death protein ligand-1 (PD-L1) expression, were examined in three cohorts: tumors from rats that did not undergo embolization (control), embolized tumors (target), and nonembolized tumors from rats that had a different target tumor embolized (nontarget). Differences in immune cell recruitment associated with embolic agent type (tris-acryl gelatin microspheres [TAGM] vs hydrogel embolics) and vascular location were examined in rat and human tissues. A generalized estimating equation model and t, Mann-Whitney U, and χ2 tests were used to compare groups. Results Cirrhosis-induced alterations in CD8, CD4, and CD25/CD4 lymphocytes were partially normalized following TAE (CD8: 38.4%, CD4: 57.6%, and CD25/CD4: 21.1% in embolized liver vs 47.7% [P = .02], 47.0% [P = .01], and 34.9% [P = .03], respectively, in cirrhotic liver [36.1%, 59.6%, and 4.6% in normal liver]). Embolized tumors had a greater number of CD3, CD4, and CD8 tumor-infiltrating lymphocytes relative to controls (191.4 cells/mm2 vs 106.7 cells/mm2 [P = .03]; 127.8 cells/mm2 vs 53.8 cells/mm2 [P < .001]; and 131.4 cells/mm2 vs 78.3 cells/mm2 [P = .01]) as well as a higher PD-L1 expression score (4.1 au vs 1.9 au [P < .001]). A greater number of CD3, CD4, and CD8 lymphocytes were found near TAGM versus hydrogel embolics (4.1 vs 2.0 [P = .003]; 3.7 vs 2.0 [P = .01]; and 2.2 vs 1.1 [P = .03], respectively). The number of lymphocytes adjacent to embolics differed based on vascular location (17.9 extravascular CD68+ peri-TAGM cells vs 7.0 intravascular [P < .001]; 6.4 extravascular CD68+ peri-hydrogel embolic cells vs 3.4 intravascular [P < .001]). Conclusion Transarterial embolization-induced dynamic alterations of the tumor immune microenvironment are influenced by underlying liver disease, embolic agent type, and vascular location. © RSNA, 2022 Online supplemental material is available for this article. See also the editorials by Kennedy et al and by White in this issue.

Aortic diameter, pulse wave velocity, central aortic pulse pressure, left ventricular parameters, and diastolic dysfunction in patients with aortic aneurysm

Background

The enlargement of aortic aneurysm can alters pulse wave propagation and reflection, which may influence to left ventricular (LV) afterload changes. The relevance of pulse wave velocity (PWV) and central blood pressure depending on the locus of the aneurysm for LV structure and diastolic function (DF) are not clearly unknown.

Purpose

Assess the relationship between central pulse pressure (CPP), PWV and LV structure and DF in patients with ascending aortic aneurysm (AA) and abdominal aortic aneurysm (AAA).

Methods

121 patients (95 male, 63±12 years) with aortic aneurysms and preserved LV systolic function were enrolled before aortic repair. 51 patients (37 male, 54±13 years) had AA and 70 patients (58 male, 69±7 years) had AAA. CPP and PWV were measured using applanation tonometry. A echocardiographic exam was performed with a Vivid 7 GE (USA). LV mass index (LVMI) and relative wall thickness (RWT) were calculated according to standard formulas. LV filling pressure (E/Em) was estimated by Doppler-derived ratio of mitral inflow velocity (E) to septal (Em) by tissue Doppler. Transmitral flow patterns (E/A ratio of E to late (A) ventricular filling velocities) were measured with the pulsed doppler method.

Results

Concentric LV hypertrophy (LVH) was observed in 51 (42%), eccentric LVH – in 35 (29%) patients. CPP was positively related with LVMI (r=0.362, P=0.001), but PWV was inversely associated with LVMI (r=−0.244, P=0.029). CPP was not associated with RWT (P≥0.5), whereas PWV was positively related (r=0.223, P=0.004). PWV decreased with increasing aortic diameter in AA and AAA (r=−0.360, P=0.029 and r=−0.315, P=0.019, respectively). 12 (23%) patients with AA and 36 (56%) patients with AAA had grade I diastolic dysfunction, 20 (40%) patients with AA and 12 (18%) patients with AAA had grade II diastolic dysfunction (P&lt;0.001). Consequently, the E/A ratio was higher in patients with AA than in patients with AAA (1.21±0.39 vs 0.83±0.33; P=0.007). CPP and PWV was inversely associated with LV DF (E/A: r=−0.352 and −0.238; E/Em: r=−0.292 and −0.279, respectively; both P&lt;0.05). E/A and E/Em increased with the expansion of the maximum aortic diameter at the level of the AA and AAA (E/A: r=0.612 and 0.416; E/Em: r=0.719 and 0.339, respectively; both P&lt;0.005). RWT and LVMI were correlated with the aortic diameter at the level of the AA (r=−0.439, P=0.008 and r=0.286, P=0.05, respectively), but bore no relation with the aortic diameter at the level of the AAA.

Conclusions

In patients with aortic aneurysm CPP and PWV were conjointly but differently related to LV structure. Eccentric LV hypertrophy was accompanied by a significant decrease of PWV. Reduced PWV and decreased CPP exhibited association with more severe LV diastolic dysfunction, possibly due to the apparent effect of increased aortic aneurysm diameter. LV DF was severely reduced in the patients with AA compared by patients with AAA.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): Almazov National Medical Research Centre

MolDiscovery: learning mass spectrometry fragmentation of small molecules

Identification of small molecules is a critical task in various areas of life science. Recent advances in mass spectrometry have enabled the collection of tandem mass spectra of small molecules from hundreds of thousands of environments. To identify which molecules are present in a sample, one can search mass spectra collected from the sample against millions of molecular structures in small molecule databases. The existing approaches are based on chemistry domain knowledge, and they fail to explain many of the peaks in mass spectra of small molecules. Here, we present molDiscovery, a mass spectral database search method that improves both efficiency and accuracy of small molecule identification by learning a probabilistic model to match small molecules with their mass spectra. A search of over 8 million spectra from the Global Natural Product Social molecular networking infrastructure shows that molDiscovery correctly identify six times more unique small molecules than previous methods.

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.

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit

Computational methods are key in microbiome research, and obtaining a quantitative and unbiased performance estimate is important for method developers and applied researchers. For meaningful comparisons between methods, to identify best practices and common use cases, and to reduce overhead in benchmarking, it is necessary to have standardized datasets, procedures and metrics for evaluation. In this tutorial, we describe emerging standards in computational meta-omics benchmarking derived and agreed upon by a larger community of researchers. Specifically, we outline recent efforts by the Critical Assessment of Metagenome Interpretation (CAMI) initiative, which supplies method developers and applied researchers with exhaustive quantitative data about software performance in realistic scenarios and organizes community-driven benchmarking challenges. We explain the most relevant evaluation metrics for assessing metagenome assembly, binning and profiling results, and provide step-by-step instructions on how to generate them. The instructions use simulated mouse gut metagenome data released in preparation for the second round of CAMI challenges and showcase the use of a repository of tool results for CAMI datasets. This tutorial will serve as a reference for the community and facilitate informative and reproducible benchmarking in microbiome research.

Lymphatic Interventional Treatment for Chyluria via Retrograde Thoracic Duct Access

Chyluria is the leakage of intestinal lymph (chyle) into the urine. Novel lymphatic intervention techniques, such as interstitial lymphatic embolization, proved to be a useful treatment option for chyluria. However, one of the challenges of this approach is the difficulty in identifying connections between the lymphatic system and kidney collecting system. Here, embolization of the abnormal lymphatic connection through retrograde thoracic duct access in 3 chyluria patients is introduced.

metaFlye: scalable long-read metagenome assembly using repeat graphs

Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.

Determinants of central aortic pressure and pulse pressure amplification changes in patients with aortic aneurysm: the role of aortic diameter and aortic aneurysm location level

Background

The presence of aortic aneurysm can alters pulse wave propagation and reflection, causing changes in central aortic pressure and pulse pressure amplification (PPA) between the aorta and the brachial artery that might be associated with unfavorable hemodynamic effects for the central arteries and the heart. However, the impact of the location of the aneurysm and increase of the aortic diameter on central blood pressure (CBP) is not fully understood.

Objective

To investigate central aortic pressure and PPA regarding to association with arterial stiffness and aortic diameter in patients with ascending aortic aneurysm (AA), descending thoracic and abdominal aortic aneurysm (TAA and AAA).

Methods

122 patients (96 males, 65±11 years) with aortic aneurysm were enrolled before aortic repair. The parameters of the aorta were evaluated by MSCT angiography: 44 patients (30 males, 55±13 years) had AA (the maximum diameter: 59.9±14.2 mm), 13 patients (11 males, 62±11 years) had TAA (the maximum diameter: 62.8±8.0 mm) and 65 patients (54 males, 69±8 years) had AAA (the maximum diameter: 52.3±17.2 mm). Brachial blood pressure (BBP) was measured by OMRON. CBP, augmentation index (AIx), carotid-femoral pulse wave velocity (PWV) were assessed by SphygmoCor. PPA was calculated as a difference between the values of central and brachial pulse pressure (CPP and BPP).

Results

Patients of the three groups did not differ in BPP (AA: 59.2±17.6; TAA 56.8±12.8; AAA: 59.3±11.4 mm Hg; P=0.5). Intergroup comparison revealed a difference in CPP between the three patients groups: CPP was higher in patients with AA and AAA, lower in patients with TAA (AA: 50.3±16.2; TAA 43.8±10.8; AAA: 50.0±11.2 mm Hg; P=0.05). PPA was lower in patients with AA and AAA than in patients with TAA (9.6±6.7 and 9.3±4.2 vs. 13.0±6.5 mm Hg; P=0.05 and P=0.04, respectively). IAx was higher in patients with AA and AAA than in patients with TAA (25.2±8.1 and 27.6±8.2 vs. 17.2±8.2 mm Hg; P=0.008 and P=0.001, respectively). A decrease of PPA across all patients correlated with an increase of IAx (r = - 0.268; P=0.003). CPP decreased with an increase of the aortic diameter for each level of the aneurysm (AA: r = - 0.460, P=0.016; TAA: r = - 0.833, P=0.003; AAA: r = - 0.275, P=0.05). PWV decreased with the expansion of the maximum aortic diameter at the level of the AA, TAA and AAA: (r = - 0.389, P=0.03; r = - 0.827, P=0.02 and r = - 0.350, P=0.01, respectively).

Conclusion

In patients with aortic aneurysm measurements of lower central pulse pressure and reduced PWV indicate an association with increased diameter of the aneurysm. An increase in augmentation index, early return of reflected waves, thus smaller PP amplification and higher CPP were identified in patients with ascending and abdominal aortic aneurysm compared by patients with descending thoracic aortic aneurysm.

Funding Acknowledgement

Type of funding source: None

TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats

MOTIVATION

Extra-long tandem repeats (ETRs) are widespread in eukaryotic genomes and play an important role in fundamental cellular processes, such as chromosome segregation. Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there are no tools for their quality assessment. Moreover, since the mapping of error-prone reads to ETRs remains an open problem, it is not clear how to polish draft ETR assemblies.

RESULTS

To address these problems, we developed the TandemTools software that includes the TandemMapper tool for mapping reads to ETRs and the TandemQUAST tool for polishing ETR assemblies and their quality assessment. We demonstrate that TandemTools not only reveals errors in ETR assemblies but also improves the recently generated assemblies of human centromeres.

AVAILABILITY AND IMPLEMENTATION

https://github.com/ablab/TandemTools.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

NPS: scoring and evaluating the statistical significance of peptidic natural product-spectrum matches

MOTIVATION

Peptidic natural products (PNPs) are considered a promising compound class that has many applications in medicine. Recently developed mass spectrometry-based pipelines are transforming PNP discovery into a high-throughput technology. However, the current computational methods for PNP identification via database search of mass spectra are still in their infancy and could be substantially improved.

RESULTS

Here we present NPS, a statistical learning-based approach for scoring PNP-spectrum matches. We incorporated NPS into two leading PNP discovery tools and benchmarked them on millions of natural product mass spectra. The results demonstrate more than 45% increase in the number of identified spectra and 20% more found PNPs at a false discovery rate of 1%.

AVAILABILITY AND IMPLEMENTATION

NPS is available as a command line tool and as a web application at http://cab.spbu.ru/software/NPS.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.

Dereplication of microbial metabolites through database search of mass spectra

Natural products have traditionally been rich sources for drug discovery. In order to clear the road toward the discovery of unknown natural products, biologists need dereplication strategies that identify known ones. Here we report DEREPLICATOR+, an algorithm that improves on the previous approaches for identifying peptidic natural products, and extends them for identification of polyketides, terpenes, benzenoids, alkaloids, flavonoids, and other classes of natural products. We show that DEREPLICATOR+ can search all spectra in the recently launched Global Natural Products Social molecular network and identify an order of magnitude more natural products than previous dereplication efforts. We further demonstrate that DEREPLICATOR+ enables cross-validation of genome-mining and peptidogenomics/glycogenomics results.

Novel Lymphatic Imaging and Percutaneous Treatment of Chyluria

Chyluria is characterized by the presence of chyle in the urine and often presents clinically as urinary obstruction. Traditional treatments include dietary modifications, surgery and sclerotherapy. The recently developed intranodal lymphangiography and dynamic contrast-enhanced MR lymphangiography (DCMRL) provide better imaging of the lymphatic system. Interstitial lymphatic embolization is a new interventional technique that allows delivery of n-butyl cyanoacrylate glue into the network of the lymphatic vessels. This report describes the demonstration of lympho-urinary tract communications using DCMRL and intranodal lymphangiography in three patients who presented with chyluria, and successful treatment of chyluria in two patients using interstitial lymphatic embolization.

Versatile genome assembly evaluation with QUAST-LG

Motivation

The emergence of high-throughput sequencing technologies revolutionized genomics in early 2000s. The next revolution came with the era of long-read sequencing. These technological advances along with novel computational approaches became the next step towards the automatic pipelines capable to assemble nearly complete mammalian-size genomes.

Results

In this manuscript, we demonstrate performance of the state-of-the-art genome assembly software on six eukaryotic datasets sequenced using different technologies. To evaluate the results, we developed QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for a given genome and set of reads, and compute theoretical limits on assembly correctness and completeness. Using QUAST-LG, we show how close the assemblies are to the theoretical optimum, and how far this optimum is from the finished reference.

Availability and implementation

http://cab.spbu.ru/software/quast-lg.

Supplementary information

Supplementary data are available at Bioinformatics online.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.

Icarus: visualizer for de novo assembly evaluation

: Data visualization plays an increasingly important role in NGS data analysis. With advances in both sequencing and computational technologies, it has become a new bottleneck in genomics studies. Indeed, evaluation of de novo genome assemblies is one of the areas that can benefit from the visualization. However, even though multiple quality assessment methods are now available, existing visualization tools are hardly suitable for this purpose. Here, we present Icarus-a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. The tool is available online and as a standalone application.

AVAILABILITY AND IMPLEMENTATION

http://cab.spbu.ru/software/icarus CONTACT: aleksey.gurevich@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online.

MetaQUAST: evaluation of metagenome assemblies

During the past years we have witnessed the rapid development of new metagenome assembly methods. Although there are many benchmark utilities designed for single-genome assemblies, there is no well-recognized evaluation and comparison tool for metagenomic-specific analogues. In this article, we present MetaQUAST, a modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference. MetaQUAST addresses such metagenome datasets features as (i) unknown species content by detecting and downloading reference sequences, (ii) huge diversity by giving comprehensive reports for multiple genomes and (iii) presence of highly relative species by detecting chimeric contigs. We demonstrate MetaQUAST performance by comparing several leading assemblers on one simulated and two real datasets.

AVAILABILITY AND IMPLEMENTATION

http://bioinf.spbau.ru/metaquast

CONTACT

aleksey.gurevich@spbu.ru

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Assembly of Slx4 signaling complexes behind DNA replication forks

Obstructions to replication fork progression, referred to collectively as DNA replication stress, challenge genome stability. In Saccharomyces cerevisiae, cells lacking RTT107 or SLX4 show genome instability and sensitivity to DNA replication stress and are defective in the completion of DNA replication during recovery from replication stress. We demonstrate that Slx4 is recruited to chromatin behind stressed replication forks, in a region that is spatially distinct from that occupied by the replication machinery. Slx4 complex formation is nucleated by Mec1 phosphorylation of histone H2A, which is recognized by the constitutive Slx4 binding partner Rtt107. Slx4 is essential for recruiting the Mec1 activator Dpb11 behind stressed replication forks, and Slx4 complexes are important for full activity of Mec1. We propose that Slx4 complexes promote robust checkpoint signaling by Mec1 by stably recruiting Dpb11 within a discrete domain behind the replication fork, during DNA replication stress.

Assembling short reads from jumping libraries with large insert sizes

MOTIVATION

Advances in Next-Generation Sequencing technologies and sample preparation recently enabled generation of high-quality jumping libraries that have a potential to significantly improve short read assemblies. However, assembly algorithms have to catch up with experimental innovations to benefit from them and to produce high-quality assemblies.

RESULTS

We present a new algorithm that extends recently described exSPAnder universal repeat resolution approach to enable its applications to several challenging data types, including jumping libraries generated by the recently developed Illumina Nextera Mate Pair protocol. We demonstrate that, with these improvements, bacterial genomes often can be assembled in a few contigs using only a single Nextera Mate Pair library of short reads.

AVAILABILITY AND IMPLEMENTATION

Described algorithms are implemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/en/spades.

CONTACT

ap@bioinf.spbau.ru

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Probing dynamics and pinning of single vortices in superconductors at nanometer scales

The dynamics of quantized magnetic vortices and their pinning by materials defects determine electromagnetic properties of superconductors, particularly their ability to carry non-dissipative currents. Despite recent advances in the understanding of the complex physics of vortex matter, the behavior of vortices driven by current through a multi-scale potential of the actual materials defects is still not well understood, mostly due to the scarcity of appropriate experimental tools capable of tracing vortex trajectories on nanometer scales. Using a novel scanning superconducting quantum interference microscope we report here an investigation of controlled dynamics of vortices in lead films with sub-Angstrom spatial resolution and unprecedented sensitivity. We measured, for the first time, the fundamental dependence of the elementary pinning force of multiple defects on the vortex displacement, revealing a far more complex behavior than has previously been recognized, including striking spring softening and broken-spring depinning, as well as spontaneous hysteretic switching between cellular vortex trajectories. Our results indicate the importance of thermal fluctuations even at 4.2 K and of the vital role of ripples in the pinning potential, giving new insights into the mechanisms of magnetic relaxation and electromagnetic response of superconductors.

ExSPAnder: a universal repeat resolver for DNA fragment assembly

Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequencing projects. While various NGS assemblers can use information from several libraries of read-pairs, most of them were originally developed for a single library and do not fully benefit from multiple libraries. Moreover, most assemblers assume uniform read coverage, condition that does not hold for single-cell projects where utilization of read-pairs is even more challenging. We have developed an exSPAnder algorithm that accurately resolves repeats in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects.

AVAILABILITY AND IMPLEMENTATION

http://bioinf.spbau.ru/en/spades

Reduction of dissipative nonlinear conductivity of superconductors by static and microwave magnetic fields

A theory of dissipative nonlinear conductivity, σ(1)(ω,H), of s-wave superconductors under strong electromagnetic fields at low temperatures is proposed. Closed-form expressions for σ(1)(H) and the surface resistance R(s)(ω,H) are obtained in the nonequilibrium dirty limit for which σ(1)(H) has a significant minimum as a function of a low-frequency (ħω ≪ k(B)T) magnetic field H. The calculated microwave suppression of R(s)(H) is in good agreement with recent experiments on alloyed Nb resonator cavities. It is shown that superimposed dc and ac fields, H = H(0) + H(a)cosωt, can be used to reduce ac dissipation in thin film nanostructures by tuning σ(1)(H(0)) with the dc field.