Related papers: Image-based physical characterization of magnetota…
Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap…
Motility is a fundamental survival strategy of bacteria to navigate porous environments. Swimming cells thrive in quiescent wetlands and sediments at the bottom of the marine water column, where they mediate many essential biogeochemical…
Organic material in anoxic sediment represents a globally significant carbon reservoir that acts to stabilize Earth's atmospheric composition. The dynamics by which microbes organize to consume this material remain poorly understood. Here…
Bacterial flagellar swarming enables dense microbial populations to migrate collectively across surfaces, often resulting in emergent, coordinated behaviors. However, probing the underlying energetics of swarming at the single cluster level…
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the…
Information processing in the mammalian brain relies on a careful regulation of the membrane potential dynamics of its constituent neurons, which propagates across the neuronal tissue via electrical signalling. We recently reported the…
Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large…
Purpose: Antimicrobial resistance is a major global health concern, affecting hospital admissions and treatment success. This study aims to introduce an experimental setup for monitoring bacterial activity over time using image-based…
The transport of heat and solutes by vertically migrating aggregations of plankton has long been explored as a potentially important source of ocean mixing. However, direct evidence of enhanced mixing due to these migrations remains…
The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
We experimentally study the emergence of collective bacterial swimming, a phenomenon often referred to as bacterial turbulence. A phase diagram of the flow of 3D E. coli suspensions spanned by bacterial concentration, the swimming speed of…
Morphological traits are physical characteristics of biological organisms that provide vital clues on how organisms interact with their environment. Yet extracting these traits remains a slow, expert-driven process, limiting their use in…
To enhance research on multimodal knowledge base and multimodal information processing, we propose a new task called multimodal entity tagging (MET) with a multimodal knowledge base (MKB). We also develop a dataset for the problem using an…
Active matter comprises individual units that convert energy into mechanical motion. In many examples, such as bacterial systems and biofilament assays, constituent units are elongated and can give rise to local nematic orientational order.…
We study the chemotaxis of a population of genetically identical swimming bacteria undergoing run and tumble dynamics driven by stochastic switching between clockwise and counterclockwise rotation of the flagellar rotary system.…
Bacteria can chemotactically migrate up attractant gradients by controlling run-and-tumble motility patterns. In addition to this well-known chemotactic behaviour, several soil and marine bacterial species perform chemokinesis: they adjust…
Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many…
Cell tracking is a ubiquitous image analysis task in live-cell microscopy. Unlike multiple object tracking (MOT) for natural images, cell tracking typically involves hundreds of similar-looking objects that can divide in each frame, making…
Molecular dynamics is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to molecular dynamics, by replacing the…