PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization

PA-GOSUB (Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization) is a publicly available, web-based, searchable and downloadable database that contains the sequences, predicted GO molecular functions and predicted subcellular localizations of more than 107 000 proteins from 10 model organisms (and growing), covering the major kingdoms and phyla for which annotated proteomes exist (http://www.cs.ualberta.ca/~bioinfo/PA/GOSUB). The PA-GOSUB database effectively expands the coverage of subcellular localization and GO function annotations by a significant factor (already over five for subcellular localization, compared with Swiss-Prot v42.7), and more model organisms are being added to PA-GOSUB as their sequenced proteomes become available. PA-GOSUB can be used in three main ways. First, a researcher can browse the pre-computed PA-GOSUB annotations on a per-organism and per-protein basis using annotation-based and text-based filters. Second, a user can perform BLAST searches against the PA-GOSUB database and use the annotations from the homologs as simple predictors for the new sequences. Third, the whole of PA-GOSUB can be downloaded in either FASTA or comma-separated values (CSV) formats

BASys: a web server for automated bacterial genome annotation

BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data and an optional list of gene identification information and provides extensive textual annotation and hyperlinked image output. BASys uses >30 programs to determine ∼60 annotation subfields for each gene, including gene/protein name, GO function, COG function, possible paralogues and orthologues, molecular weight, isoelectric point, operon structure, subcellular localization, signal peptides, transmembrane regions, secondary structure, 3D structure, reactions and pathways. The depth and detail of a BASys annotation matches or exceeds that found in a standard SwissProt entry. BASys also generates colorful, clickable and fully zoomable maps of each query chromosome to permit rapid navigation and detailed visual analysis of all resulting gene annotations. The textual annotations and images that are provided by BASys can be generated in ∼24 h for an average bacterial chromosome (5 Mb). BASys annotations may be viewed and downloaded anonymously or through a password protected access system. The BASys server and databases can also be downloaded and run locally. BASys is accessible at

Early Antibiotic Exposure Is Not Detrimental to Therapeutic Effect from Immunotherapy in Hepatocellular Carcinoma

BACKGROUND AND RATIONALE: Immune checkpoint inhibitor (ICI) therapy is an expanding therapeutic option for hepatocellular carcinoma (HCC). Antibiotics (ATB) taken prior to or early during ICI therapy can impact immunotherapy efficacy across indications; however, the effect of ATB is undefined in HCC. METHODS: In a large international cohort of 450 ICI recipients from Europe, North America, and Asia, we categorized patients according to timing of ATB focusing on exposure within −30 to +30 days from ICI (early immunotherapy period [EIOP]). EIOP was evaluated in association with overall survival (OS), progression-free survival (PFS), and best radiologic response using RECIST 1.1 criteria. RESULTS: Our study comprised mostly cirrhotic (329, 73.3%) males (355, 79.1%) with a Child-Turcotte Pugh class of A (332, 73.9%), receiving ICI after 1 therapy line (251, 55.9%) for HCC of Barcelona clinic liver cancer stage C (325, 72.4%). EIOP (n = 170, 37.9%) was independent of baseline clinicopathologic features of HCC and correlated with longer PFS (6.1 vs. 3.7 months, log-rank p = 0.0135). EIOP+ patients had similar OS, overall response, and disease control rates (DCRs) compared to EIOP. The effect of EIOP persisted in landmark time analyses and in multivariable models, confirming the independent predictive role of EIOP in influencing PFS following adjustment for covariates reflective of tumor burden, liver function, and ICI regimen administered. In patients receiving programmed cell death-1 receptor/ligand inhibitors monotherapy, EIOP was also associated with higher DCRs (61.4% vs. 50.9%, p = 0.0494). CONCLUSIONS: Unlike other oncological indications, ATB in the 30 days before or after ICI initiation is associated with improved benefit from immunotherapy, independent of disease and treatment-related features. Evaluation of the immune microbiologic determinants of response to ICI in HCC warrants further investigation

Genetic Data from Nearly 63,000 Women of European Descent Predicts DNA Methylation Biomarkers and Epithelial Ovarian Cancer Risk

DNA methylation is instrumental for gene regulation. Global changes in the epigenetic landscape have been recognized as a hallmark of cancer. However, the role of DNA methylation in epithelial ovarian cancer (EOC) remains unclear. In this study, high-density genetic and DNA methylation data in white blood cells from the Framingham Heart Study (N = 1,595) were used to build genetic models to predict DNA methylation levels. These prediction models were then applied to the summary statistics of a genome-wide association study (GWAS) of ovarian cancer including 22,406 EOC cases and 40,941 controls to investigate genetically predicted DNA methylation levels in association with EOC risk. Among 62,938 CpG sites investigated, genetically predicted methylation levels at 89 CpG were significantly associated with EOC risk at a Bonferroni-corrected threshold of P <7.94 x 10(-7). Of them, 87 were located at GWAS-identified EOC susceptibility regions and two resided in a genomic region not previously reported to be associated with EOC risk. Integrative analyses of genetic, methylation, and gene expression data identified consistent directions of associations across 12 CpG, five genes, and EOC risk, suggesting that methylation at these 12 CpG may influence EOC risk by regulating expression of these five genes, namely MAPT, HOXB3, ABHD8, ARHGAP27, and SKAP1. We identified novel DNA methylation markers associated with EOC risk and propose that methylation at multiple CpG may affect EOC risk via regulation of gene expression. Significance: Identification of novel DNA methylation markers associated with EOC risk suggests that methylation at multiple CpG may affect EOC risk through regulation of gene expression.Peer reviewe

Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer.

To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3 and 9q31.1) and one for endometrioid EOC (5q12.3). We then performed meta-analysis on the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC. This identified three additional susceptibility loci at 2q13, 8q24.1 and 12q24.31. Integrated analyses of genes and regulatory biofeatures at each locus predicted candidate susceptibility genes, including OBFC1, a new candidate susceptibility gene for low-grade and borderline serous EOC

Porous media properties of reticulated shape memory polymer foams and mock embolic coils for aneurysm treatment

BACKGROUND: Shape memory polymer (SMP) foams are being investigated as an alternative aneurysm treatment method to embolic coils. The goal of both techniques is the reduction of blood flow into the aneurysm and the subsequent formation of a stable thrombus, which prevents future aneurysm rupture. The purpose of this study is to experimentally determine the parameters, permeability and form factor, which are related to the flow resistance imposed by both media when subjected to a pressure gradient. METHODS: The porous media properties—permeability and form factor—of SMP foams and mock embolic coils (MECs) were measured with a pressure gradient method by means of an in vitro closed flow loop. We implemented the Forchheimer-Hazen-Dupuit-Darcy equation to calculate these properties. Mechanically-reticulated SMP foams were fabricated with average cell sizes of 0.7E-3 and 1.1E-3 m, while the MECs were arranged with volumetric packing densities of 11-28%. RESULTS: The permeability of the SMP foams was an order of magnitude lower than that of the MECs. The form factor differed by up to two orders of magnitude and was higher for the SMP foams in all cases. The maximum flow rate of all samples tested was within the inertial laminar flow regime, with Reynolds numbers ranging between 1 and 35. CONCLUSIONS: The SMP foams impose a greater resistance to fluid flow compared to MECs, which is a result of increased viscous and inertial losses. These results suggest that aneurysms treated with SMP foam will have flow conditions more favorable for blood stasis than those treated with embolic coils having packing densities ≤ 28%