Systems biology researchers need feasible solutions for editing and visualisation of large biological diagrams. Here, we present the ySBGN bidirectional converter that translates metabolic pathways, ...developed in the general-purpose yEd Graph Editor (using the GraphML format) into the Systems Biology Graphical Notation Markup Language (SBGN-ML) standard format and vice versa. We illustrate the functionality of this converter by applying it to the translation of the ReconMap resource (available in the SBGN-ML format) to the yEd-specific GraphML and back. The ySBGN tool makes possible to draw extensive metabolic diagrams in a powerful general-purpose graph editor while providing results in the standard SBGN format.
Abstract
Motivation
Visualization of cellular processes and pathways is a key recurring requirement for effective biological data analysis. There is a considerable need for sophisticated web-based ...pathway viewers and editors operating with widely accepted standard formats, using the latest visualization techniques and libraries.
Results
We developed a web-based tool named Newt for viewing, constructing and analyzing biological maps in standard formats such as SBGN, SBML and SIF.
Availability and implementation
Newt’s source code is publicly available on GitHub and freely distributed under the GNU LGPL. Ample documentation on Newt can be found on http://newteditor.org and on YouTube.
H2A.Z is an essential histone variant implicated in the regulation of key nuclear events. However, the metazoan chaperones responsible for H2A.Z deposition and its removal from chromatin remain ...unknown. Here we report the identification and characterization of the human protein ANP32E as a specific H2A.Z chaperone. We show that ANP32E is a member of the presumed H2A.Z histone-exchange complex p400/TIP60. ANP32E interacts with a short region of the docking domain of H2A.Z through a new motif termed H2A.Z interacting domain (ZID). The 1.48 Å resolution crystal structure of the complex formed between the ANP32E-ZID and the H2A.Z/H2B dimer and biochemical data support an underlying molecular mechanism for H2A.Z/H2B eviction from the nucleosome and its stabilization by ANP32E through a specific extension of the H2A.Z carboxy-terminal α-helix. Finally, analysis of H2A.Z localization in ANP32E(-/-) cells by chromatin immunoprecipitation followed by sequencing shows genome-wide enrichment, redistribution and accumulation of H2A.Z at specific chromatin control regions, in particular at enhancers and insulators.
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DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
Motivation
CellDesigner is a well-established biological map editor used in many large-scale scientific efforts. However, the interoperability between the Systems Biology Graphical Notation ...(SBGN) Markup Language (SBGN-ML) and the CellDesigner’s proprietary Systems Biology Markup Language (SBML) extension formats remains a challenge due to the proprietary extensions used in CellDesigner files.
Results
We introduce a library named cd2sbgnml and an associated web service for bidirectional conversion between CellDesigner’s proprietary SBML extension and SBGN-ML formats. We discuss the functionality of the cd2sbgnml converter, which was successfully used for the translation of comprehensive large-scale diagrams such as the RECON Human Metabolic network and the complete Atlas of Cancer Signalling Network, from the CellDesigner file format into SBGN-ML.
Availability and implementation
The cd2sbgnml conversion library and the web service were developed in Java, and distributed under the GNU Lesser General Public License v3.0. The sources along with a set of examples are available on GitHub (https://github.com/sbgn/cd2sbgnml and https://github.com/sbgn/cd2sbgnml-webservice, respectively).
Supplementary information
Supplementary data are available at Bioinformatics online.
Non-invasive scores have been proposed to identify patients with fibrotic, metabolic dysfunction-associated steatohepatitis (MASH), who are at the highest risk of progression to complications of ...cirrhosis and may benefit from pharmacologic treatments. However, data in patients with type 2 diabetes (T2DM) are lacking. The aim of this multicenter prospective study was to perform a head-to-head comparison of FAST (FibroScan-aspartate aminotransferase AST), MAST (MRI-AST), MEFIB (magnetic resonance elastography MRE plus FIB-4), and FNI (fibrotic NASH index) for detecting fibrotic MASH in patients with T2DM.
A total of 330 outpatients with T2DM and biopsy-proven metabolic dysfunction-associated steatotic liver disease (MASLD) from the QUID-NASH study (NCT03634098), who underwent FibroScan, MRI-proton density fat fraction and MRE at the time of liver biopsy were studied. The main outcome was fibrotic MASH, defined as NAS ≥4 (with at least one point for each parameter) and fibrosis stage ≥2 (centrally reviewed).
All data for score comparisons were available for 245 patients (median age 59 years, 65% male, median BMI 31 kg/m2; fibrotic MASH in 39%). FAST and MAST had similar accuracy (AUROCs 0.81 vs. 0.79, p = 0.41) but outperformed FNI (0.74; p = 0.01) and MEFIB (0.68; p <0.0001). When using original cut-offs, MAST outperformed FAST, MEFIB and FNI when comparing the percentage of correctly classified patients, in whom liver biopsy would be avoided (69% vs. 48%, 46%, 39%, respectively; p <0.001). When using cut-offs specific to our population, FAST outperformed FNI and MAST (56% vs. 40%, and 38%, respectively; p <0.001).
Our findings show that FAST, MAST, MEFIB and FNI are accurate non-invasive tools to identify patients with T2DM and fibrotic MASH in secondary/tertiary diabetes clinics. Cut-offs adapted to the T2DM population should be considered.
Among patients with type 2 diabetes (T2DM), identifying those with metabolic dysfunction-associated steatohepatitis and significant fibrosis, who are the most at risk of developing clinical liver-related outcomes and who may benefit from pharmacologic treatments, is an unmet need. In this prospective multicenter study, we compared four non-invasive scores, three based on imaging (MRI or ultrasound technologies) and one on laboratory blood tests, for this purpose, using original and study-specific cut-offs. Our findings show that FAST, MAST, MEFIB and FNI are accurate non-invasive tools to identify patients with T2DM and fibrotic MASH in secondary/tertiary diabetes clinics. Cut-offs adapted to the T2DM population should be considered.
NCT03634098.
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•Patients with type 2 diabetes and fibrotic MASH (NAS ≥4, and F≥2) are the most at risk of developing liver-related outcomes.•They may also benefit from pharmacologic treatments when they are available.•We performed a head-to-head comparison of FAST, MAST, MEFIB and FNI scores for identifying fibrotic MASH.•FAST and MAST scores outperformed MEFIB and FNI in patients with type 2 diabetes and MASLD.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
This work aims to compare two deposition methods to highlight the strong influence of the induced morphology on the sensitive film conductivity. Lanthanum oxycarbonate films have been deposited by ...drop coating and screen printing for carbon dioxide detection. The measurements are based on a change in resistance and provide sensitive responses to carbon dioxide concentrations in a humid environment maintained at 50%. Electrical measurements were made under 5 000 ppm of carbon dioxide in synthetic air. Our results highlighted the close link between the morphology of the sensitive layers and the electrical responses of the sensors, and therefore the need to master the deposition technique.
The goal of this work is the integration of the existing knowledge from molecular biology, cell biology, and medicine on asthma into a molecular and cellular interaction map of the disease to make ...possible advanced data interpretation, hypothesis generation, and validation for many related projects. Since the AsthmaMap project was first announced in a brief editorial,1 it has evolved into a browsable online resource accessible via https://asthma-map.org in which map modules are composed into a single hierarchically organized system. Recent advances in systems biology have enabled the creation of representations of mechanisms for multiple diseases2 including recently published examples for rheumatoid arthritis,3 atherosclerosis,4 and regulated cell death in cancer.5 These maps are used for modeling, hypothesis generation, and validation in a relevant clinical context as reviewed in the Disease Maps community article2 and described in a recent publication about the Atlas of Cancer Signalling Network applied in preclinical studies.6 Such resources are referred to as “disease maps” and are defined as conceptual models of the corresponding diseases, collections of interconnected signaling, and metabolic and gene regulatory processes2,7 (https://disease-maps.org). Cellular Interactions—an overview diagram of the involved cell types and corresponding pathways represented by cytokines and receptors; Molecular Relations—a collection of diagrams split according to cell types that can be seen as a single virtual map with an intermediate level of detail; and Biochemical Mechanisms—the most detailed layer where information is shown at the level of molecular processes.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Remarquable par son réseau de canaux radiaux, l’étang de Montady, drainé à la fin du xiii e siècle, est situé entre Béziers et Narbonne, au pied de l’oppidum d’Ensérune. Il a fait l’objet d’un ...programme pluridisciplinaire associant archéologues, géoarchéologues, historiens et géographes. Nous présentons ici les premiers résultats concernant l’histoire lacustre de l’ancien étang, la dynamique du peuplement à ses abords du haut Moyen Âge jusqu’à son assèchement. Les modalités en sont resituées dans le contexte social et politique de l’époque. La confrontation des données textuelles avec les archives du sol a permis de préciser les conditions édaphiques lors de la réalisation du réseau fossoyé, la fréquence et les formes de son entretien. Le système de culture associant céréales, herbages et plus tardivement la vigne est décrit à la lumière des contrats d’arrentement. L’architecture hydraulique savante de l’étang de Montady nécessite une gestion sociale et collective de ses composantes. Elle est nécessaire à la résilience du dispositif en raison de ses dysfonctionnements temporaires.
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