4.8 Article

A genome-scale metabolic model of parasitic whipworm

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Immunology

High-fat diet-induced resistance to helminth infection via alternative induction of type 2 immunity

Evelyn Funjika et al.

Summary: Gastrointestinal nematode infections cause significant harm and economic losses in impoverished communities. The rise of obesity has led to the coexistence of obesity with endemic gastrointestinal nematode regions, resulting in a new comorbidity. However, the impact of a high-fat diet on the immune response against gastrointestinal infections is not well understood. A mouse model of nematode infection was used to study the effect of a high-fat diet on the immune response. Surprisingly, the high-fat diet led to parasite expulsion. Mechanistically, the high-fat diet increased the expression of the ST2 receptor on CD4+ T cells, promoting an enhanced type 2 immune response. This study provides insights into the emerging comorbidities of obesity and nematode infection.

MUCOSAL IMMUNOLOGY (2023)

Article Biochemistry & Molecular Biology

Rhea, the reaction knowledgebase in 2022

Parit Bansal et al.

Summary: Rhea is an expert-curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI, with recent developments including increased reaction coverage, adoption as the reference vocabulary for enzyme annotation in UniProtKB, and the development of a new Rhea website. These developments aim to enhance the utility of Rhea as a reference resource for studying enzymes and metabolic systems.

NUCLEIC ACIDS RESEARCH (2022)

Article Cell Biology

Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species

Shushan Sargsian et al.

Summary: Helminth colonization is associated with gut microbiota composition, and Peptostreptococcaceae isolated from the Orang Asli population in Malaysia display superior capacity to promote the life cycle of whipworm species.

CELL REPORTS (2022)

Article Biochemistry & Molecular Biology

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines

Sanathoi Gurumayum et al.

Summary: OGEE is an online database focusing on gene essentiality, providing data for 91 species and expanding collection of human essential genes for cancer research. It includes experimentally tested gene essentiality data and associated gene properties, allowing researchers to study the complex interplays between gene functions and environmental/experimental perturbations.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase in 2021

Alex Bateman et al.

Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.

NUCLEIC ACIDS RESEARCH (2021)

Review Microbiology

Understanding the host-microbe interactions using metabolic modeling

Jack Jansma et al.

Summary: Through in silico simulation methods based on flux balance analysis, interactions within the complex microbiota community in the human gut can be better investigated, aiding in understanding the intricate relationship between microbiota and the host. This approach can help researchers study the effects of various perturbations on different bacterial species in a shared metabolic environment, ultimately leading to improvements in human health.

MICROBIOME (2021)

Review Parasitology

The interplay between Trichuris and the microbiota

Melissa A. E. Lawson et al.

Summary: The relationship between gut bacteria and worm infections is complex, with bacteria influencing parasite survival through metabolite communication. This emerging field sheds new light on whipworm parasitology, highlighting the intricate interactions between hosts, gut microbiota, and parasites.

PARASITOLOGY (2021)

Review Parasitology

Trichuris muris and comorbidities - within a mouse model context

Kelly S. Hayes et al.

Summary: Trichuris muris, a parasitic nematode in mice, induces a strong immune response that impacts both locally within the intestines and systemically on multiple organs.

PARASITOLOGY (2021)

Article Multidisciplinary Sciences

Genome-scale metabolic network reconstruction of model animals as a platform for translational research

Hao Wang et al.

Summary: Genome-scale metabolic models (GEMs) are extensively used for analyzing mechanisms of human diseases and metabolic disorders. A unified platform of GEMs covering five major model animals was presented, providing comprehensive metabolic network coverage and revealing a potential biomarker for early diagnosis of Alzheimer's disease through integrative analysis of RNA-sequencing and proteomics data.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Biochemistry & Molecular Biology

Serotonin Signalling in Flatworms: An Immunocytochemical Localisation of 5-HT7 Type of Serotonin Receptors in Opisthorchis felineus and Hymenolepis diminuta

Natalia Kreshchenko et al.

Summary: This study investigates the localization of serotonin and 5-HT7 type serotonin receptors in larvae of parasitic flatworms using immunocytochemical methods and confocal laser scanning microscopy. The results indicate the presence of 5-HT7 immunoreactivity in specific structures of the worms, suggesting its importance in the motor control system of flatworms.

BIOMOLECULES (2021)

Article Biochemistry & Molecular Biology

PubChem in 2021: new data content and improved web interfaces

Sunghwan Kim et al.

Summary: PubChem, a popular chemical information resource, has made substantial improvements in the past two years by adding data from over 100 new sources, updating its homepage and record pages, introducing new services like the Periodic Table and Pathway pages, and creating a special data collection related to COVID-19 and SARS-CoV-2 in response to the pandemic.

NUCLEIC ACIDS RESEARCH (2021)

Letter Biotechnology & Applied Microbiology

MEMOTE for standardized genome-scale metabolic model testing

Christian Lieven et al.

NATURE BIOTECHNOLOGY (2020)

Review Parasitology

Small RNAs in parasitic nematodes - forms and functions

Collette Britton et al.

PARASITOLOGY (2020)

Article Biochemistry & Molecular Biology

An atlas of human metabolism

Jonathan L. Robinson et al.

SCIENCE SIGNALING (2020)

Article Biochemistry & Molecular Biology

Modeling tissue-relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels

Lutfu Safak Yilmaz et al.

MOLECULAR SYSTEMS BIOLOGY (2020)

Review Cell Biology

Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens

Mustafa Sertbas et al.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2020)

Article Biochemical Research Methods

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Laurent Heirendt et al.

NATURE PROTOCOLS (2019)

Article Endocrinology & Metabolism

Metabolomic profiling of the excretory-secretory products of hookworm and whipworm

Phurpa Wangchuk et al.

METABOLOMICS (2019)

Article Multidisciplinary Sciences

The major secreted protein of the whipworm parasite tethers to matrix and inhibits interleukin-13 function

Allison J. Bancroft et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

Identification of small molecule enzyme inhibitors as broad- spectrum anthelmintics

Rahul Tyagi et al.

SCIENTIFIC REPORTS (2019)

Review Biotechnology & Applied Microbiology

Current status and applications of genome-scale metabolic models

Changdai Gu et al.

GENOME BIOLOGY (2019)

Article Multidisciplinary Sciences

Manipulation of host and parasite microbiotas: Survival strategies during chronic nematode infection

Emily C. White et al.

SCIENCE ADVANCES (2018)

Article Biochemistry & Molecular Biology

Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans

Michael Witting et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2018)

Article Biochemistry & Molecular Biology

WormBase ParaSite - a comprehensive resource for helminth genomics

Kevin L. Howe et al.

MOLECULAR AND BIOCHEMICAL PARASITOLOGY (2017)

Article Parasitology

A comparison of two methods for quantifying parasitic nematode fecundity

Lauren V. Austin et al.

PARASITOLOGY RESEARCH (2017)

Article Biochemistry & Molecular Biology

ChEBI in 2016: Improved services and an expanding collection of metabolites

Janna Hastings et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Biochemistry & Molecular Biology

The role of glutathione reductase and related enzymes on cellular redox homoeostasis network

Narciso Couto et al.

FREE RADICAL BIOLOGY AND MEDICINE (2016)

Article Biochemistry & Molecular Biology

A Caenorhabditis elegans Genome-Scale Metabolic Network Model

L. Safak Yilmaz et al.

CELL SYSTEMS (2016)

Article Biochemistry & Molecular Biology

A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism

Juliane Gebauer et al.

CELL SYSTEMS (2016)

Article Biochemical Research Methods

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

The BioMart community portal: an innovative alternative to large, centralized data repositories

Damian Smedley et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Pharmacology & Pharmacy

Auranofin: Repurposing an Old Drug for a Golden New Age

Christine Roder et al.

DRUGS IN R&D (2015)

Article Infectious Diseases

Repurposing Auranofin as a Lead Candidate for Treatment of Lymphatic Filariasis and Onchocerciasis

Christina A. Bulman et al.

PLOS NEGLECTED TROPICAL DISEASES (2015)

Review Biochemistry & Molecular Biology

Thioredoxin Glutathione Reductase-Dependent Redox Networks in Platyhelminth Parasites

David L. Williams et al.

ANTIOXIDANTS & REDOX SIGNALING (2013)

Article Mathematical & Computational Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

Ali Ebrahim et al.

BMC SYSTEMS BIOLOGY (2013)

Review Immunology

Trichuris muris: a model of gastrointestinal parasite infection

Joanna E. Klementowicz et al.

SEMINARS IN IMMUNOPATHOLOGY (2012)

Article Multidisciplinary Sciences

Selenoprotein TRXR-1 and GSR-1 are essential for removal of old cuticle during molting in Caenorhabditis elegans

Jorgen Stenvall et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemical Research Methods

A protocol for generating a high-quality genome-scale metabolic reconstruction

Ines Thiele et al.

NATURE PROTOCOLS (2010)

Article Multidisciplinary Sciences

Exploitation of the Intestinal Microflora by the Parasitic Nematode Trichuris muris

K. S. Hayes et al.

SCIENCE (2010)

Article Biochemistry & Molecular Biology

Glutathione reductase and thioredoxin reductase at the crossroad:: The structure of Schistasoma mansoni thioredoxin glutathione reductase

Francesco Angelucci et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)