Nellie: automated organelle segmentation, tracking and hierarchical feature extraction in 2D/3D live-cell microscopy.

Cellular organelles undergo constant morphological changes and dynamic interactions that are fundamental to cell homeostasis, stress responses and disease progression. Despite their importance, quantifying organelle morphology and motility remains challenging due to their complex architectures, rapid movements and the technical limitations of existing analysis tools. Here we introduce Nellie, an automated and unbiased pipeline for segmentation, tracking and feature extraction of diverse intracellular structures.

High-throughput screening for improved microbial cell factories, perspective and promise.

High-throughput screening is a critical part of any industrial strain engineering effort, helping ensure the lowest cost product is produced in the shortest amount of time. Small-scale testing that correlates to manufacturing scale allows rapid strain development with confidence that engineering changes are relevant at-scale. In this review, the current state of high-throughput screening, the technological advances for the next generation strain screening pipeline, and options for implementation are reviewed.

An Oil-Free Picodrop Bioassay Platform for Synthetic Biology.

Droplet microfluidics enables massively-parallel analysis of single cells, biomolecules, and chemicals, making it valuable for high-throughput screens. However, many hydrophobic analytes are soluble in carrier oils, preventing their quantitative analysis with the method. We apply Printed Droplet Microfluidics to construct defined reactions with chemicals and cells incubated under air on an open array.

Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment.

Antibiotic resistance arising via chromosomal mutations is typically specific to a particular antibiotic or class of antibiotics. We have identified mutations in genes encoding ribosomal components in that confer resistance to several structurally and mechanistically unrelated classes of antibiotics and enhance survival following heat shock and membrane stress. These mutations affect ribosome assembly and cause large-scale transcriptomic and proteomic changes, including the downregulation of the catalase KatG, an activating enzyme required for isoniazid sensitivity, and upregulation of WhiB7, a transcription factor involved in innate antibiotic resistance.