Paul A. Wiggins
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View article: OmniSegger: A time-lapse image analysis pipeline for bacterial cells
OmniSegger: A time-lapse image analysis pipeline for bacterial cells Open
Time-lapse microscopy is a powerful tool to study the biology of bacterial cells. The development of pipelines that facilitate the automated analysis of these datasets is a long-standing goal of the field. In this paper, we describe the Om…
View article: Future Directions of the Prokaryotic Chromosome Field
Future Directions of the Prokaryotic Chromosome Field Open
In September 2023, the Biology and Physics of Prokaryotic Chromosomes meeting ran at the Lorentz Center in Leiden, The Netherlands. As part of the workshop, those in attendance developed a series of discussion points centered around curren…
View article: OmniSegger: A time-lapse image analysis pipeline for bacterial cells
OmniSegger: A time-lapse image analysis pipeline for bacterial cells Open
Time-lapse microscopy is a powerful tool for studying the cell biology of bacterial cells. The development of pipelines that facilitate the automated analysis of these datasets is a long-standing goal of the field. In this paper, we descri…
View article: Noise robustness and metabolic load determine the principles of central dogma regulation
Noise robustness and metabolic load determine the principles of central dogma regulation Open
The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light of noise? To answer this question, we build a mathematical model to explore the trade-off…
View article: Protein overabundance is driven by growth robustness
Protein overabundance is driven by growth robustness Open
Protein expression levels optimize cell fitness: Too low an expression level of essential proteins will slow growth by compromising essential processes; whereas overexpression slows growth by increasing the metabolic load. This trade-off n…
View article: Protein overabundance is driven by growth robustness
Protein overabundance is driven by growth robustness Open
Protein expression levels optimize cell fitness: Too low an expression level of essential proteins will slow growth by compromising essential processes; whereas overexpression slows growth by increasing the metabolic load. This trade-off n…
View article: Direct measure of DNA bending by quantum magnetic imaging of a nano-mechanical torque-balance
Direct measure of DNA bending by quantum magnetic imaging of a nano-mechanical torque-balance Open
DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is d…
View article: Noise robustness and metabolic load determine the principles of central dogma regulation
Noise robustness and metabolic load determine the principles of central dogma regulation Open
The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light of noise? To answer this question, we build a mathematical model to explore the trade-off…
View article: Noise robustness and metabolic load determine the principles of central dogma regulation
Noise robustness and metabolic load determine the principles of central dogma regulation Open
The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light of noise? To answer this question, we build a mathematical model to explore the trade-off…
View article: The one-message-per-cell-cycle rule: A conserved minimum transcription level for essential genes
The one-message-per-cell-cycle rule: A conserved minimum transcription level for essential genes Open
The inherent stochasticity of cellular processes leads to significant cell-to-cell variation in protein abundance. Although this noise has already been characterized and modeled, its broader implications and significance remain unclear. In…
View article: The one-message-per-cell-cycle rule: A conserved minimum transcription level for essential genes
The one-message-per-cell-cycle rule: A conserved minimum transcription level for essential genes Open
The inherent stochasticity of cellular processes leads to significant cell-to-cell variation in protein abundance. Although this noise has already been characterized and modeled, its broader implications and significance remain unclear. In…
View article: The in vivo measurement of replication fork velocity and pausing by lag-time analysis
The in vivo measurement of replication fork velocity and pausing by lag-time analysis Open
View article: Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation
Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation Open
View article: The high-resolution <i>in vivo</i> measurement of replication fork velocity and pausing by lag-time analysis
The high-resolution <i>in vivo</i> measurement of replication fork velocity and pausing by lag-time analysis Open
An important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell, where a crowded cytoplasm as …
View article: The high-resolution in vivo measurement of replication fork velocity and pausing by lag-time analysis
The high-resolution in vivo measurement of replication fork velocity and pausing by lag-time analysis Open
An important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell, where a crowded cytoplasm as …
View article: Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase
Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase Open
View article: Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation
Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation Open
Advances in microscopy hold great promise for allowing quantitative and precise readouts of morphological and molecular phenomena at the single cell level in bacteria. However, the potential of this approach is ultimately limited by the av…
View article: Characterizing stochastic cell cycle dynamics in exponential growth
Characterizing stochastic cell cycle dynamics in exponential growth Open
Two powerful and complementary experimental approaches are commonly used to study the cell cycle and cell biology: One class of experiments characterizes the statistics (or demographics) of an unsynchronized exponentially-growing populatio…
View article: Genome-wide protein-DNA interaction site mapping using a double strand DNA-specific cytosine deaminase
Genome-wide protein-DNA interaction site mapping using a double strand DNA-specific cytosine deaminase Open
DNA–protein interactions (DPIs) are central to such fundamental cellular processes as transcription and chromosome maintenance and organization. The spatiotemporal dynamics of these interactions dictate their functional consequences; there…
View article: Wide-Field Dynamic Magnetic Microscopy Using Double-Double Quantum Driving of a Diamond Defect Ensemble
Wide-Field Dynamic Magnetic Microscopy Using Double-Double Quantum Driving of a Diamond Defect Ensemble Open
Wide-field magnetometry can be realized by imaging the optically-detected magnetic resonance of diamond nitrogen vacancy (NV) center ensembles. However, NV ensemble inhomogeneities significantly limit the magnetic-field sensitivity of thes…
View article: An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations
An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations Open
When bacterial cells come in contact, antagonism mediated by the delivery of toxins frequently ensues. The potential for such encounters to have long-term beneficial consequences in recipient cells has not been investigated. Here, we exami…
View article: Author response: An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations
Author response: An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations Open
View article: An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations
An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations Open
When bacterial cells come in contact, antagonism mediated by the delivery of toxins frequently ensues. The potential for such encounters to have long-term beneficial consequences in recipient cells has not been investigated. Here we examin…
View article: Mitigation of sensor inhomogeneities to speed up diamond-based wide-field magnetic imaging
Mitigation of sensor inhomogeneities to speed up diamond-based wide-field magnetic imaging Open
Wide-field magnetometry can be realized by imaging the optically-detected magnetic resonance of diamond nitrogen vacancy (NV) center ensembles. However, sensor inhomogeneities significantly limit the magnetic field sensitivity of these mea…
View article: Essential gene deletions producing gigantic bacteria
Essential gene deletions producing gigantic bacteria Open
To characterize the consequences of eliminating essential functions needed for peptidoglycan synthesis, we generated deletion mutations of Acinetobacter baylyi by natural transformation and visualized the resulting microcolonies of dead ce…
View article: Correspondence between thermodynamics and inference
Correspondence between thermodynamics and inference Open
We expand upon a natural analogy between Bayesian statistics and statistical physics in which sample size corresponds to inverse temperature. This analogy motivates the definition of two novel statistical quantities: a learning capacity an…
View article: The Observation Protein Position and Orientation Dynamics using an Unbleachable Probe
The Observation Protein Position and Orientation Dynamics using an Unbleachable Probe Open
View article: Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins
Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins Open
View article: Type VI Secretion System Dynamics Reveals a Novel Secretion Mechanism in Pseudomonas aeruginosa
Type VI Secretion System Dynamics Reveals a Novel Secretion Mechanism in Pseudomonas aeruginosa Open
The type VI secretion system (T6SS) inhibits the growth of neighboring bacterial cells through a contact-mediated mechanism. Here, we describe a detailed characterization of the protein localization dynamics in the Pseudomonas aeruginosa T…
View article: Noise in a phosphorelay drives stochastic entry into sporulation in <i>Bacillus subtilis</i>
Noise in a phosphorelay drives stochastic entry into sporulation in <i>Bacillus subtilis</i> Open