Autoencoder neural networks enable low dimensional structure analyses of microbial growth dynamics

Y Baig, HR Ma, H Xu, L You - Nature Communications, 2023 - nature.com
The ability to effectively represent microbiome dynamics is a crucial challenge in their
quantitative analysis and engineering. By using autoencoder neural networks, we show that …

Land use alters bacterial growth dynamics in soil

CJ Wattenburger, DH Buckley - Environmental Microbiology, 2023 - Wiley Online Library
Microbial growth and mortality are major determinants of soil carbon cycling. We measured
in situ growth dynamics of individual bacterial taxa in cropped and successional soils in …

AMiGA: software for automated analysis of microbial growth assays

FS Midani, J Collins, RA Britton - Msystems, 2021 - Am Soc Microbiol
The analysis of microbial growth is one of the central methods in the field of microbiology.
Microbial growth dynamics can be characterized by meaningful parameters, including …

Private benefit of β-lactamase dictates selection dynamics of combination antibiotic treatment

HR Ma, HZ Xu, K Kim, DJ Anderson, L You - Nature Communications, 2024 - nature.com
Abstract β-lactam antibiotics have been prescribed for most bacterial infections since their
discovery. However, resistance to β-lactams, mediated by β-lactamase (Bla) enzymes such …

Drug-dependent growth curve reshaping reveals mechanisms of antifungal resistance in Saccharomyces cerevisiae

L Guinn, E Lo, G Balázsi - Communications Biology, 2022 - nature.com
Microbial drug resistance is an emerging global challenge. Current drug resistance assays
tend to be simplistic, ignoring complexities of resistance manifestations and mechanisms …

Identification and characterization of a potential strain for the production of polyhydroxyalkanoate from glycerol

M Xue, R Huang, W Liu, J Cheng, Y Liu… - Frontiers in …, 2024 - frontiersin.org
While poly (3-hydroxybutyrate)(PHB) holds promise as a bioplastic, its commercial utilization
has been hampered by the high cost of raw materials. However, glycerol emerges as a …

Comparative Genomics Identifies Conserved and Variable TAL Effectors in African Strains of the Cotton Pathogen Xanthomonas citri pv. malvacearum

AL Pérez-Quintero, LM Rodriguez-R… - …, 2023 - Am Phytopath Society
Strains of Xanthomonas citri pv. malvacearum cause bacterial blight of cotton, a potentially
serious threat to cotton production worldwide, including in sub-Saharan countries …

Machine learning establishes single-cell calcium dynamics as an early indicator of antibiotic response

CT Meyer, MP Jewell, EJ Miller, JM Kralj - Microorganisms, 2021 - mdpi.com
Changes in bacterial physiology necessarily precede cell death in response to antibiotics.
Herein we investigate the early disruption of Ca2+ homeostasis as a marker for antibiotic …

Culture of attenuated Salmonella Typhimurium VNP20009 in animal-product-free media does not alter schwannoma growth control

SG Ahmed, G Oliva, M Shao, JJ Mekalanos… - Human Vaccines & …, 2023 - Taylor & Francis
Schwannomas are slow-growing benign peripheral nerve sheath tumors derived from
Schwann-lineage cells that develop in association with NF2-related schwannomatosis (NF2) …

Genome sequence of the plant-growth-promoting bacterium Bacillus velezensis EU07

Ö Baysal, DJ Studholme… - Access …, 2024 - microbiologyresearch.org
Many Gram-positive spore-forming rhizobacteria of the genus Bacillus show potential as
biocontrol biopesticides agricultural that promise improved sustainability and ecologically …