Abstract
The Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org) is designed to provide researchers with the tools and services that they need to perform genomic and other ‘omic’ ...data analyses. In response to mounting concern over antimicrobial resistance (AMR), the PATRIC team has been developing new tools that help researchers understand AMR and its genetic determinants. To support comparative analyses, we have added AMR phenotype data to over 15 000 genomes in the PATRIC database, often assembling genomes from reads in public archives and collecting their associated AMR panel data from the literature to augment the collection. We have also been using this collection of AMR metadata to build machine learning-based classifiers that can predict the AMR phenotypes and the genomic regions associated with resistance for genomes being submitted to the annotation service. Likewise, we have undertaken a large AMR protein annotation effort by manually curating data from the literature and public repositories. This collection of 7370 AMR reference proteins, which contains many protein annotations (functional roles) that are unique to PATRIC and RAST, has been manually curated so that it projects stably across genomes. The collection currently projects to 1 610 744 proteins in the PATRIC database. Finally, the PATRIC Web site has been expanded to enable AMR-based custom page views so that researchers can easily explore AMR data and design experiments based on whole genomes or individual genes.
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and ...some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by 'virtual integration' to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.
Repetitive elements within genomic DNA are both functionally and evolutionarily informative. Discovering these sequences ab initio is computationally challenging, compounded by the fact that ...selection on these repeats is often relaxed; thus sequence identity between repetitive elements can vary significantly. Here we present a new application, the Monomer Identification and Isolation Program (MiIP), which provides functionality to both search for a particular repeat as well as discover repetitive elements within a larger genomic sequence. To compare MiIP's performance with other repeat detection tools, analysis was conducted for synthetic sequences as well as several a21-II clones and HC21 BAC sequences. The primary benefit of MiIP is the fact that it is a single tool capable of searching for both known monomeric sequences as well as discovering the occurrence of repeats ab initio, per the user's required sensitivity of the search. Furthermore, the report functionality helps easily facilitate subsequent phylogenetic analysis.
Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate ...centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the AS arrays, and compared them to AS arrays found on other chromosomes. We find that the majority of the HC21 AS sequences are present on the p-arm of the chromosome and are organized into at least five distinct isolated clusters which are distributed over a larger distance from the functional centromere than that typically seen for AS on other chromosomes. Using both phylogenetic and L1 element age estimations, we found that all of the HC21 AS clusters outside the functional centromere are of a similar relatively recent evolutionary origin. HC21 contains none of the ancient AS layers associated with early primate evolution which is present on other chromosomes, possibly due to the fact that the p-arm of HC21 and the other acrocentric chromosomes underwent substantial reorganization about 20 million years ago.
High-throughput genetic sequencing technologies have driven the proliferation of new genomic data. From the advent of long-read Sanger sequencing to the now low-cost, short-read generation and ...upcoming era of single-molecule techniques, methods to address the complex genome assembly problem have evolved alongside and are introduced at an expeditious pace. These algorithms attempt to produce an accurate representation of a target genome from datasets filled with errors and ambiguities. Many of the challenges introduced, unfortunately, must be addressed through an algorithm's ad-hoc criteria and heuristics, and as a result, can output assembly hypotheses that contain significant errors. Without an inexpensive or computational approach to assess the quality of a given assembly hypothesis, researchers must make due with draft-level genome projects for downstream analysis. Solving three fundamental challenges will alleviate this issue: (i) automation and incorporation of algorithms from the dynamic landscape of genome assembly tools, (ii) developing optimal assembly algorithms best suited for various types, or mixtures, of sequencing data, and (iii) developing an approach to assess de novo genome assembly quality independence of a reference genome. We provide several contributions towards this effort: We first introduce AssemblyRAST, a general compute orchestration framework and accompanying domain-specific language that facilitates rapid workflow design for rapid genome assembly, analysis, and method discovery. Next, we demonstrate the improvement of genome assemblies through novel integrative algorithm techniques. Finally, we devise a method for reference-independent assembly evaluation and error identification through supervised learning, along with several applications to further improve existing techniques.
Repetitive elements within genomic DNA are both functionally and evolutionarily informative. Discovering these sequences ab initio is computationally challenging, compounded by the fact that ...selection on these repeats is often relaxed; thus sequence identity between repetitive elements can vary significantly. Here we present a new application, the Monomer Identification and Isolation Program (MilP), which provides functionality to both search for a particular repeat as well as discover repetitive elements within a larger genomic sequence. To compare MilP's performance with other repeat detection tools, analysis was conducted for synthetic sequences as well as several α21-II clones and HC21 BAC sequences. The primary benefit of MilP is the fact that it is a single tool capable of searching for both known monomelic sequences as well as discovering the occurrence of repeats ab initio, per the user's required sensitivity of the search. Furthermore, the report functionality helps easily facilitate subsequent phylogenetic analysis.
In a recent computational study, we found that hydrogen bonding/partial deprotonation facilitates subsequent electron transfer from amides to HO•. We have now analyzed these and related reactions ...with a glycine derivative as a model peptide, investigating not only reaction energies but also barriers for the individual steps. We find that partial deprotonation not only assists subsequent electron transfer (a sequential proton-loss electron-transfer (SPLET)-type reaction pathway) but also promotes sequential hydrogen-atom transfer (HAT, in a sequential proton-loss hydrogen-atom-transfer (SPLHAT)-type process), both being potential alternatives to direct HAT as routes for peptide oxidation. Each of these alternative pathways is calculated to have energy requirements that make them accessible and competitive. These oxidative processes may produce α-carbon-centered peptide radicals that, through deprotonation, are readily oxidized to the corresponding imines. We have also examined the possibility of competing reactions of amino acid side chains by comparing reactions of the glycine model with those of an analogous valine derivative. We find that, while the side chains of amino acids are more reactive toward direct HAT, a preceding partial deprotonation instead continues to favor the SPLET- and SPLHAT-type reactions, leading to the production of α-carbon-centered peptide radicals. Taken together, these processes have broad implications that impact many aspects of the science and utility of peptides.
The optimal method of gallbladder drainage (GBD) for acute cholecystitis in nonsurgical candidates is uncertain. The aim of the current study was to conduct a network meta-analysis comparing the 3 ...methods of GBD (percutaneous PT, endoscopic transpapillary ETP, and EUS-guided).
A comprehensive literature search for all comparative studies assessing the efficacy of either 2 or all modalities used for treatment of acute cholecystitis in patients at high risk for cholecystectomy was performed. Primary outcomes of technical and clinical success and postprocedure adverse events were assessed. Secondary outcomes were reintervention, unplanned readmissions, recurrent cholecystitis, and mortality.
Ten studies were identified, comprising 1267 patients (472 EUS-GBD, 493 PT-GBD, and 302 ETP-GBD). In the network ranking estimate, PT-GBD and EUS-GBD had the highest likelihood of technical success (EUS-GBD vs PT-GBD vs ETP-GBD: 2.00 vs 1.02 vs 2.98) and clinical success (EUS-GBD vs PT-GBD vs ETP-GBD: 1.48 vs 1.55 vs 2.98). EUS-GBD had the lowest risk of recurrent cholecystitis (EUS-GBD vs PT-GBD vs ETP-GBD: 1.089 vs 2.02 vs 2.891). PT-GBD had the highest risk of reintervention (EUS-GBD vs PT-GBD vs ETP-GBD: 1.81 vs 2.99 vs 1.199) and unplanned readmissions (EUS-GBD vs PT-GBD vs ETP-GBD: 1.582 vs 2.944 vs 1.474), whereas ETP-GBD was associated with the lowest rates of mortality (EUS-GBD vs PT-GBD vs ETP-GBD: 2.62 vs 2.09 vs 1.29).
The 3 modalities of GBD have their respective advantages and disadvantages. Selection of technique will depend on available expertise. In centers with expertise in endoscopic GBD, the techniques are preferred over PT-GBD with improved outcomes. (Clinical trial registration number: CRD42020181972.)
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