AIMC Topic: Gram-Negative Bacteria
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DeeplyEssential: a deep neural network for predicting essential genes in microbes.
BMC bioinformatics
Sep 30, 2020
BACKGROUND: Essential genes are those genes that are critical for the survival of an organism. The prediction of essential genes in bacteria can provide targets for the design of novel antibiotic compounds or antimicrobial strategies.
Use of Chou's 5-steps rule to predict the subcellular localization of gram-negative and gram-positive bacterial proteins by multi-label learning based on gene ontology annotation and profile alignment.
Journal of integrative bioinformatics
Jun 29, 2020
To date, many proteins generated by large-scale genome sequencing projects are still uncharacterized and subject to intensive investigations by both experimental and computational means. Knowledge of protein subcellular localization (SCL) is of key i...
Fast Pathogen Identification Using Single-Cell Matrix-Assisted Laser Desorption/Ionization-Aerosol Time-of-Flight Mass Spectrometry Data and Deep Learning Methods.
Analytical chemistry
May 11, 2020
In diagnostics of infectious diseases, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) can be applied for the identification of pathogenic microorganisms. However, to achieve a trustworthy identification fr...
ACNNT3: Attention-CNN Framework for Prediction of Sequence-Based Bacterial Type III Secreted Effectors.
Computational and mathematical methods in medicine
Apr 3, 2020
The type III secretion system (T3SS) is a special protein delivery system in Gram-negative bacteria which delivers T3SS-secreted effectors (T3SEs) to host cells causing pathological changes. Numerous experiments have verified that T3SEs play importan...
Estimating the association between antibiotic exposure and colonization with extended-spectrum β-lactamase-producing Gram-negative bacteria using machine learning methods: a multicentre, prospective cohort study.
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
May 23, 2019
OBJECTIVES: The aim of the study was to measure the impact of antibiotic exposure on the acquisition of colonization with extended-spectrum β-lactamase-producing Gram-negative bacteria (ESBL-GNB) accounting for individual- and group-level confounding...
In vitro colonic fermentation of Mexican "taco" from corn-tortilla and black beans in a Simulator of Human Microbial Ecosystem (SHIME®) system.
Food research international (Ottawa, Ont.)
Jun 2, 2018
A Mexican staple food prepared with corn "tortilla" (Zea mays L.) and common beans (Phaseolus vulgaris L.) is named as "taco". It was fermented in an in vitro colonic Simulator of Human Microbial Ecosystem (SHIME®) to evaluate the effect in short cha...
Predictive Model of Linear Antimicrobial Peptides Active against Gram-Negative Bacteria.
Journal of chemical information and modeling
May 11, 2018
Antimicrobial peptides (AMPs) have been identified as a potential new class of anti-infectives for drug development. There are a lot of computational methods that try to predict AMPs. Most of them can only predict if a peptide will show any antimicro...
Accurate prediction of Gram-negative bacterial secreted protein types by fusing multiple statistical features from PSI-BLAST profile.
SAR and QSAR in environmental research
Apr 24, 2018
Gram-negative bacterial secreted proteins play different roles in invaded eukaryotic cells and cause various diseases. Prediction of Gram-negative bacterial secreted protein types is a meaningful and challenging task. In this paper, we develop a mult...
In vitro activity of eravacycline against 2213 Gram-negative and 2424 Gram-positive bacterial pathogens isolated in Canadian hospital laboratories: CANWARD surveillance study 2014-2015.
Diagnostic microbiology and infectious disease
Dec 22, 2017
Gram-negative (n=2213) and Gram-positive (n=2424) pathogens isolated from patients in 13 Canadian hospitals in 2014 and 2015 were tested for in vitro susceptibility to eravacycline and comparators using the Clinical and Laboratory Standards Institute...
An evidence of C16 fatty acid methyl esters extracted from microalga for effective antimicrobial and antioxidant property.
Microbial pathogenesis
Dec 22, 2017
Fatty acid methyl esters (FAME) derived from lipids of microalgae is known to have wide bio-functional materials including antimicrobials. FAME is an ideal super-curator and superior anti-pathogenic. The present study evaluated the efficiency of FAME...
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