J. Elf

Automatic Culture-free Detection of Bacteria from Blood for Rapid Sepsis Diagnostics

This paper develops a method to rapidly detect bacteria in blood using smart centrifugation, microfluidic trapping, and deep learning for sepsis diagnostics.

One-day phenotypic drug susceptibility testing for Mycobacterium tuberculosis variant bovis BCG using single-cell imaging and a deep neural network

This study uses single-cell imaging and a deep neural network to rapidly assess drug susceptibility in Mycobacterium tuberculosis variant bovis BCG, achieving results in under 12 hours.

Pooled optical screening in bacteria using chromosomally expressed barcodes

The paper develops a method for in situ genotyping of bacterial libraries using chromosomally expressed barcodes to measure intracellular maturation times of red fluorescent proteins.

Three-dimensional localization of fluorescent proteins in living Escherichia coli

This paper develops a method for accurate 3D localization of fluorescent proteins in living E. coli using mother-machine devices and deep learning, revealing distinct nucleoid locus distributions.

Real-time pooled optical screening with single-cell isolation capability.

This paper introduces a method for real-time pooled optical screening with single-cell isolation using optical tweezers and 3D microfluidics.

The Escherichia coli chromosome moves to the replisome

This study uses fluorescence microscopy to show that Escherichia coli replisomes are stationary and chromosomal loci move toward them during replication.

Antibiotic perseverance increases the risk of resistance development

The paper uses single-cell imaging to study antibiotic resistance in E. coli and finds that growth perseverance increases resistance development.

Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization

This paper develops a method for sub-millisecond 3D tracking of single molecules in E. coli using cross-entropy minimization and achieves high precision with a new PSF positioning technique.

Rapid antibiotic susceptibility testing and species identification for mixed infections

This paper presents a method for rapid antibiotic susceptibility testing and species identification in mixed infections using microfluidic chips and in situ FISH.

The coordination of replication initiation with growth rate in Escherichia coli

This study investigates how Escherichia coli coordinates replication initiation with growth rate by analyzing replisome tracking and mutant data, finding that DnaA-ATP and RIDA play key roles.

Sequence specificity in DNA binding is determined by association rather than dissociation

The paper derives an equation linking association and dissociation rates in DNA-protein binding and tests it using LacI and dCas9, showing sequence specificity is determined by recognition efficiency, not dissociation rates.

Live cell imaging reveals that RecA finds homologous DNA by reduced dimensionality search

The paper uses live cell imaging to show that RecA filaments in E. coli find homologous DNA through a two-dimensional search mechanism, completing DSB repair within 15 minutes.

Mechanism of DNA surface exploration and operator bypassing during target search

This study uses SMCT-FCS to show LacI slides on DNA, bypassing target sequences by hopping out of the DNA groove, revealing a speed-accuracy trade-off in target search.

A time-resolved imaging-based CRISPRi screening method

This paper introduces a CRISPRi screening method combining time-lapse imaging and microfluidic devices to study gene knockdown effects on E. coli cell cycle dynamics.

Direct observation of rotation-coupled protein diffusion along DNA on the microsecond timescale

This study measures the rotation-coupled diffusion of LacI along DNA, finding it moves ~50 base pairs per revolution, supporting a facilitated diffusion model.