Thomas Shimizu
YOU?
Author Swipe
View article: Cellular anatomy of arbuscular mycorrhizal fungi
Cellular anatomy of arbuscular mycorrhizal fungi Open
View article: Carbon-phosphorous exchange rate constrains growth of arbuscular mycorrhizal fungal networks
Carbon-phosphorous exchange rate constrains growth of arbuscular mycorrhizal fungal networks Open
Symbiotic nutrient exchange between arbuscular mycorrhizal (AM) fungi and their host plants varies widely depending on their physical, chemical, and biological environment. Yet dissecting this context dependency remains challenging because…
View article: A travelling-wave strategy for plant–fungal trade
A travelling-wave strategy for plant–fungal trade Open
For nearly 450 million years, mycorrhizal fungi have constructed networks to collect and trade nutrient resources with plant roots 1,2 . Owing to their dependence on host-derived carbon, these fungi face conflicting trade-offs in building …
View article: Nongenetic adaptation by collective migration
Nongenetic adaptation by collective migration Open
Cell populations must adjust their phenotypic composition to adapt to changing environments. One adaptation strategy is to maintain distinct phenotypic subsets within the population and to modulate their relative abundances via gene regula…
View article: The potential of strigolactones to shift competitive dynamics among two Rhizophagus irregularis strains
The potential of strigolactones to shift competitive dynamics among two Rhizophagus irregularis strains Open
Strigolactones are phytohormones that influence arbuscular mycorrhizal fungal (AMF) spore germination, pre-symbiotic hyphal branching, and metabolic rates. Historically, strigolactone effects have been tested on single AMF strains. An open…
View article: Statistics of C. elegans turning behavior reveals optimality under biasing constraints
Statistics of C. elegans turning behavior reveals optimality under biasing constraints Open
Animal locomotion is often subject to constraints arising from anatomical/physiological asymmetries. We use the nematode C. elegans as a minimal model system to ask whether such constraints might shape locomotion patterns optimized during …
View article: Statistics of C. elegans turning behavior reveals optimality under biasing constraints
Statistics of C. elegans turning behavior reveals optimality under biasing constraints Open
Animal locomotion is often subject to constraints arising from anatomical/physiological asymmetries. We use the nematode C. elegans as a minimal model system to ask whether such constraints might shape locomotion patterns optimized during …
View article: Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis
Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis Open
View article: Non-genetic adaptation by collective migration
Non-genetic adaptation by collective migration Open
Cell populations must adjust their phenotypic composition to adapt to changing environments. One adaptation strategy is to maintain distinct phenotypic subsets within the population and to modulate their relative abundances via gene regula…
View article: Large-volume cryoEM sample preparation for the investigation of the plant-microbiome interaction
Large-volume cryoEM sample preparation for the investigation of the plant-microbiome interaction Open
View article: Statistics of C. elegans turning behavior reveals optimality under biasing constraints
Statistics of C. elegans turning behavior reveals optimality under biasing constraints Open
Animal locomotion is often subject to constraints arising from anatomical/physiological asymmetries. We use the nematode C.~elegans as a minimal model system to ask whether such constraints might shape locomotion patterns optimized during …
View article: Exploring the dynamics of vascular adaptation
Exploring the dynamics of vascular adaptation Open
A combination of in toto imaging and theory suggests a new mechanism for the remodeling of veins in vascular networks.
View article: Optimal inference of molecular interaction dynamics in FRET microscopy
Optimal inference of molecular interaction dynamics in FRET microscopy Open
Intensity-based time-lapse fluorescence resonance energy transfer (FRET) microscopy has been a major tool for investigating cellular processes, converting otherwise unobservable molecular interactions into fluorescence time series. However…
View article: Signal Integration and Adaptive Sensory Diversity Tuning in<i>Escherichia coli</i>Chemotaxis
Signal Integration and Adaptive Sensory Diversity Tuning in<i>Escherichia coli</i>Chemotaxis Open
Summary In uncertain environments, phenotypic diversity can be advantageous for survival. However, as the environmental uncertainty decreases, the relative advantage of having diverse phenotypes decreases. Here, we show how populations of …
View article: Near-critical tuning of cooperativity revealed by spontaneous switching in a protein signalling array
Near-critical tuning of cooperativity revealed by spontaneous switching in a protein signalling array Open
Dynamic properties of allosteric complexes are crucial for cellular information processing. However, direct observations of allosteric switches have been limited to compact molecular assemblies. Here, we report in vivo FRET measurements of…
View article: Optimal inference of molecular interactions in live FRET imaging
Optimal inference of molecular interactions in live FRET imaging Open
Intensity-based live-cell fluorescence resonance energy transfer (FRET) imaging converts otherwise unobservable molecular interactions inside cells into fluorescence time-series signals. However, inferring the degree of molecular interacti…
View article: Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit
Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit Open
Theory suggests that relatives will cooperate more, and compete less, because of an increased benefit for shared genes. In symbiotic partnerships, hosts may benefit from interacting with highly related symbionts because there is less confl…
View article: Data belonging to: Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit
Data belonging to: Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit Open
Dataset beloning to the publication: "Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit" in Ecology letters (2021). R script used to analyse the data in the .csv fi…
View article: Data belonging to: Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit
Data belonging to: Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit Open
Dataset beloning to the publication: "Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit" in Ecology letters (2021). R script used to analyse the data in the .csv fi…
View article: HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein
HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein Open
The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelli…
View article: Author response for "Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit"
Author response for "Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit" Open
View article: Adaptive tuning of cell sensory diversity without changes in gene expression
Adaptive tuning of cell sensory diversity without changes in gene expression Open
Cell populations can switch strategies between bet-hedging and adaptive tracking using only posttranslational processes.
View article: Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit
Decreasing relatedness among mycorrhizal fungi in a shared plant network increases fungal network size but not plant benefit Open
Relatives are expected to cooperate more and compete less. In symbiotic partnerships, hosts may benefit from interacting with highly-related symbionts because there is less conflict. This has been difficult to test empirically. We used the…
View article: Temporal tracking of quantum-dot apatite across in vitro mycorrhizal networks shows how host demand can influence fungal nutrient transfer strategies
Temporal tracking of quantum-dot apatite across in vitro mycorrhizal networks shows how host demand can influence fungal nutrient transfer strategies Open
Arbuscular mycorrhizal fungi function as conduits for underground nutrient transport. While the fungal partner is dependent on the plant host for its carbon (C) needs, the amount of nutrients that the fungus allocates to hosts can vary wit…
View article: Functional modules from variable genes: Leveraging percolation to analyze noisy, high-dimensional data
Functional modules from variable genes: Leveraging percolation to analyze noisy, high-dimensional data Open
While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise -- expression counts can differ strongly across samples due to …
View article: Functional modules from variable genes: Leveraging percolation to analyze noisy, high-dimensional data
Functional modules from variable genes: Leveraging percolation to analyze noisy, high-dimensional data Open
While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise — expression counts can differ strongly across samples due to v…
View article: Modelling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behaviour across species
Modelling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behaviour across species Open
A quantitative understanding of organism-level behaviour requires predictive models that can capture the richness of behavioural phenotypes, yet are simple enough to connect with underlying mechanistic processes. Here, we investigate the m…
View article: Mycorrhizal Fungi Respond to Resource Inequality by Moving Phosphorus from Rich to Poor Patches across Networks
Mycorrhizal Fungi Respond to Resource Inequality by Moving Phosphorus from Rich to Poor Patches across Networks Open
View article: Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome
Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome Open
View article: Modeling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behavior across species
Modeling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behavior across species Open
A quantitative understanding of organism-level behavior requires predictive models that can capture the richness of behavioral phenotypes, yet are simple enough to connect with underlying mechanistic processes. Here we investigate the moti…