4.6 Article

Metabolomic Profiling of the Responses of Planktonic and Biofilm Vibrio cholerae to Silver Nanoparticles

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。
Review Biophysics

Multivariate analysis of NMR-based metabolomic data

Julia Debik et al.

Summary: Nuclear magnetic resonance (NMR) spectroscopy allows for simultaneous detection of a wide range of metabolites and lipids, which are often highly correlated. In metabolomic studies, latent-variable-based methods and machine learning methods are widely used to take into account the complex metabolic networks and achieve optimal biological insight.

NMR IN BIOMEDICINE (2022)

Article Microbiology

Surviving in the Brine: A Multi-Omics Approach for Understanding the Physiology of the Halophile Fungus Aspergillus sydowii at Saturated NaCl Concentration

Irina Jimenez-Gomez et al.

Summary: This study used a multi-omics approach to compare Aspergillus sydowii at saturated NaCl concentration to optimal salinity. The analysis revealed differentially expressed genes involved in metabolism and signal transduction. The study also found that amino acid metabolism was reprogrammed and non-coding RNAs and transcription factors played important roles in the transcriptomic response to high NaCl stress. Metabolomic analyses showed more complex and unknown metabolites at saturated NaCl concentration.

FRONTIERS IN MICROBIOLOGY (2022)

Article Multidisciplinary Sciences

Multi-omics study identifies novel signatures of DNA/RNA, amino acid, peptide, and lipid metabolism by simulated diabetes on coronary endothelial cells

Aldo Moreno-Ulloa et al.

Summary: Coronary artery endothelial cells (CAEC) play an important role in the development of cardiovascular disease, and dysfunction of CAEC is associated with type 2 diabetes mellitus (T2DM). This study characterized the molecular changes in cultured bovine CAEC subjected to a diabetic environment and identified specific perturbations in metabolite and peptide levels. The findings provide insights into the mechanisms underlying cardiovascular disease in patients with T2DM.

SCIENTIFIC REPORTS (2022)

Article Biotechnology & Applied Microbiology

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra

Kai Duehrkop et al.

Summary: CANOPUS is a computational tool that uses a deep neural network to predict compound classes from fragmentation spectra, even for compounds lacking reference data. In evaluation, CANOPUS showed high prediction performance and outperformed other baseline methods. It has broad utility in investigating chemical diversity in plants and discovering natural products, providing biological insights at the compound class level.

NATURE BIOTECHNOLOGY (2021)

Article Chemistry, Analytical

Biogenic Silver Nanoparticles: Synthesis and Application as Antibacterial and Antifungal Agents

Artem Rozhin et al.

Summary: The review discusses the current methods for the synthesis of biogenic silver nanoparticles using plant extracts, fungi, and microorganisms. It compares the physico-morphological, antibacterial, and antifungal properties of these nanoparticles with those obtained through chemical synthesis, highlighting the self-assembly process of the biogenic silver nanoparticles.

MICROMACHINES (2021)

Review Chemistry, Multidisciplinary

Nanoantibiotics: Functions and Properties at the Nanoscale to Combat Antibiotic Resistance

M. Mustafa Mamun et al.

Summary: Nanoantibiotics, encapsulating antibiotic molecules with engineered nanoparticles or artificially synthesized pure antibiotics, can restore drug efficacy and counteract antibiotic resistant bacteria through multi-dimensional attacks. With nanoscale functionalities, NPs deliver antibiotics at high concentrations, breaking down bacteria physically and interfering with critical molecules in bacterial processes. Utilizing the physical and chemical properties of NPs, nAbts epitomize a potential Trojan horse strategy to circumvent antibiotic resistance mechanisms.

FRONTIERS IN CHEMISTRY (2021)

Article Biochemistry & Molecular Biology

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights

Zhiqiang Pang et al.

Summary: MetaboAnalyst version 5.0 has been introduced to facilitate comprehensive metabolomics data analysis and interpretation, with the aim of narrowing the gap from raw data to functional insights. Three new modules have been developed to assist in this goal, along with various other new functions and improvements in interface, graphics, and codebase. Users can now easily switch between compatible modules for a streamlined data analysis experience.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

MolDiscovery: learning mass spectrometry fragmentation of small molecules

Liu Cao et al.

Summary: molDiscovery is a mass spectral database search method that improves efficiency and accuracy of small molecule identification by learning a probabilistic model to match small molecules with their mass spectra. It identifies six times more unique small molecules than previous methods based on a search of over 8 million spectra from the Global Natural Product Social molecular networking infrastructure. The method uses an algorithm to generate mass spectrometry fragmentations to match small molecules with their mass spectra.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Upregulation of virulence genes promotes Vibrio cholerae biofilm hyperinfectivity

A. L. Gallego-Hernandez et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Chemistry, Multidisciplinary

Antimicrobial Metal Nanomaterials: From Passive to Stimuli-Activated Applications

Samuel Cheeseman et al.

ADVANCED SCIENCE (2020)

Article Biochemical Research Methods

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Allegra T. Aron et al.

NATURE PROTOCOLS (2020)

Article Computer Science, Artificial Intelligence

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC

Marcus Ludwig et al.

NATURE MACHINE INTELLIGENCE (2020)

Review Medicine, Research & Experimental

Silver nanoparticles: Synthesis, medical applications and biosafety

Li Xu et al.

THERANOSTICS (2020)

Article Biochemical Research Methods

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

Kai Duhrkop et al.

NATURE METHODS (2019)

Review Public, Environmental & Occupational Health

Antibiotics versus biofilm: an emerging battleground in microbial communities

Divakar Sharma et al.

ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL (2019)

Review Engineering, Biomedical

Molecular mechanisms of polymyxin resistance and detection of mcr genes

Patrik Mlynarcik et al.

BIOMEDICAL PAPERS-OLOMOUC (2019)

Article Engineering, Biomedical

Antibacterial Activity of Silver Nanoparticles: Structural Effects

Shaoheng Tang et al.

ADVANCED HEALTHCARE MATERIALS (2018)

Review Medicine, General & Internal

Cholera

John D. Clemens et al.

LANCET (2017)

Review Biotechnology & Applied Microbiology

Metal nanoparticles: understanding the mechanisms behind antibacterial activity

Yael N. Slavin et al.

JOURNAL OF NANOBIOTECHNOLOGY (2017)

Article Biochemical Research Methods

UpSetR: an R package for the visualization of intersecting sets and their properties

Jake R. Conway et al.

BIOINFORMATICS (2017)

Article Chemistry, Analytical

MZmine 2 Data-Preprocessing To Enhance Molecular Networking Reliability

Florent Olivon et al.

ANALYTICAL CHEMISTRY (2017)

Article Multidisciplinary Sciences

Synthesis and Complete Antimicrobial Characterization of CEOBACTER, an Ag-Based Nanocomposite

O. E. Jaime-Acuna et al.

PLOS ONE (2016)

Article Chemistry, Multidisciplinary

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

Yannick Djoumbou Feunang et al.

JOURNAL OF CHEMINFORMATICS (2016)

Review Infectious Diseases

Vibrio cholerae Biofilms and Cholera Pathogenesis

Anisia J. Silva et al.

PLOS NEGLECTED TROPICAL DISEASES (2016)

Review Infectious Diseases

Biofilm-specific antibiotic tolerance and resistance

I. Olsen

EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES (2015)

Review Microbiology

Living in the matrix: assembly and control of Vibrio cholerae biofilms

Jennifer K. Teschler et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Article Multidisciplinary Sciences

Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation

Kai Papenfort et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

Kai Duehrkop et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Microbiology

Antimicrobial Tolerance in Biofilms

Philip S. Stewart

MICROBIOLOGY SPECTRUM (2015)

Review Infectious Diseases

Antimicrobial susceptibility testing in biofilm-growing bacteria

M. D. Macia et al.

CLINICAL MICROBIOLOGY AND INFECTION (2014)

Editorial Material Engineering, Environmental

Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence

Emma L. Schymanski et al.

ENVIRONMENTAL SCIENCE & TECHNOLOGY (2014)

Article Endocrinology & Metabolism

Global metabolomics characterization of bacteria: pre-analytical treatments and profiling

Ivano Bertini et al.

METABOLOMICS (2014)

Article Biotechnology & Applied Microbiology

Anti-biofilm activity of silver nanoparticles against different microorganisms

Fidel Martinez-Gutierrez et al.

BIOFOULING (2013)

Article Chemistry, Multidisciplinary

Biofilm-inactivating activity of silver nanoparticles: A comparison with silver ions

Hee-Jin Park et al.

JOURNAL OF INDUSTRIAL AND ENGINEERING CHEMISTRY (2013)

Article Biochemical Research Methods

Proteomic analysis of Mycobacterium tuberculosis isolates resistant to kanamycin and amikacin

Bhavnesh Kumar et al.

JOURNAL OF PROTEOMICS (2013)

Review Chemistry, Multidisciplinary

Nanoantibiotics: A new paradigm for treating infectious diseases using nanomaterials in the antibiotics resistant era

Ae Jung Huh et al.

JOURNAL OF CONTROLLED RELEASE (2011)

Article Biochemical Research Methods

Differences in Metabolism between the Biofilm and Planktonic Response to Metal Stress

Sean C. Booth et al.

JOURNAL OF PROTEOME RESEARCH (2011)

Review Toxicology

Nanosilver: A nanoproduct in medical application

X. Chen et al.

TOXICOLOGY LETTERS (2008)

Review Biotechnology & Applied Microbiology

Understanding biofilm resistance to antibacterial agents

D Davies

NATURE REVIEWS DRUG DISCOVERY (2003)

Review Microbiology

Molecular basis of bacterial outer membrane permeability revisited

H Nikaido

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2003)

Article Chemistry, Physical

Shape effects in plasmon resonance of individual colloidal silver nanoparticles

JJ Mock et al.

JOURNAL OF CHEMICAL PHYSICS (2002)

Review Microbiology

Riddle of biofilm resistance

K Lewis

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2001)

Review Biochemistry & Molecular Biology

Mechanisms of biofilm resistance to antimicrobial agents

TFC Mah et al.

TRENDS IN MICROBIOLOGY (2001)

Review Multidisciplinary Sciences

Molecular mechanisms that confer antibacterial drug resistance

C Walsh

NATURE (2000)