Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria

Hol, Felix J H; Dekker, Cees

doi:10.1126/science.1251821

Cited by 170 publications

(130 citation statements)

References 113 publications

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“…With life spans of hundreds of years, this question is hard to investigate empirically for tropical trees. Bacteria, however, with well-defined characteristics and a short generation time, have shown to be interesting model systems for testing questions of species coexistence (Hol and Dekker 2014;Kerr et al 2002). And the answer is no, intransitivity all by itself does not necessarily lead to coexistence.…”

Section: Tests With Bacterial Communities: Rock-paper-scissor Dynamicmentioning

confidence: 99%

Chance, Variation and the Nature of Causality in Ecological Communities

Kroon

Jongejans

2016

The Frontiers Collection

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Chance is pervasive in nature. Erratic events such as storms and fires can cause major damage to an ecosystem. Rare successful long distance dispersal events like a viable seed landing in just the right habitat can form the stepping stone for range expansion of a plant species. Illustrated with two examples we argue that in ecology chance events are scale-dependent. We show how random stochastic variation in species interactions may result in relative stability at a higher community level. In other systems the reverse may take place, in which deterministic interactions result in unpredictable chaotic dynamics. Analysing the processes and dynamics at these different scales has led to an increasing mechanistic understanding of the variation in ecological communities in space and time. Unambiguous identification of cause and effect relations from this work is of the greatest importance, as many ecosystems in the world are not amenable to experimentation. This work should form the scientific basis for identifying the threats to ecosystems and defining proper conservation and mitigation measures.

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Section: Tests With Bacterial Communities: Rock-paper-scissor Dynamicmentioning

confidence: 99%

Chance, Variation and the Nature of Causality in Ecological Communities

Kroon

Jongejans

2016

The Frontiers Collection

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“…However, there are advantages to smaller-scale platforms that reduce medium consumption, precisely control the cell environment, and automate analysis. In addition, significant advances have been made in the development of microfluidic systems for cell biology (30)(31)(32)(33). Of particular importance to this work, precise fluid handling on microfluidic devices provides more control over the microenvironment of the cells (34,35).…”

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confidence: 99%

Short-Stalked Prosthecomicrobium hirschii Cells Have a Caulobacter-Like Cell Cycle

et al. 2016

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The dimorphic alphaproteobacterium Prosthecomicrobium hirschii has both short-stalked and long-stalked morphotypes. Notably, these morphologies do not arise from transitions in a cell cycle. Instead, the maternal cell morphology is typically reproduced in daughter cells, which results in microcolonies of a single cell type. In this work, we further characterized the shortstalked cells and found that these cells have a Caulobacter-like life cycle in which cell division leads to the generation of two morphologically distinct daughter cells. Using a microfluidic device and total internal reflection fluorescence (TIRF) microscopy, we observed that motile short-stalked cells attach to a surface by means of a polar adhesin. Cells attached at their poles elongate and ultimately release motile daughter cells. Robust biofilm growth occurs in the microfluidic device, enabling the collection of synchronous motile cells and downstream analysis of cell growth and attachment. Analysis of a draft P. hirschii genome sequence indicates the presence of CtrA-dependent cell cycle regulation. This characterization of P. hirschii will enable future studies on the mechanisms underlying complex morphologies and polymorphic cell cycles. IMPORTANCEBacterial cell shape plays a critical role in regulating important behaviors, such as attachment to surfaces, motility, predation, and cellular differentiation; however, most studies on these behaviors focus on bacteria with relatively simple morphologies, such as rods and spheres. Notably, complex morphologies abound throughout the bacteria, with striking examples, such as P. hirschii, found within the stalked Alphaproteobacteria. P. hirschii is an outstanding candidate for studies of complex morphology generation and polymorphic cell cycles. Here, the cell cycle and genome of P. hirschii are characterized. This work sets the stage for future studies of the impact of complex cell shapes on bacterial behaviors. The Alphaproteobacteria comprise a diverse group of bacteria, including important pathogens of animals (Brucella spp. and Rickettsia spp.) and plants (Agrobacterium spp.), plant symbionts (Rhizobium spp., Sinorhizobium spp., and Mesorhizobium spp.), photosynthetic bacteria (Rhodobacter spp.), freshwater bacteria (Caulobacter spp.), and marine bacteria (Hyphomonas spp.). Despite the diverse habitats and lifestyles of these bacteria, many alphaproteobacterial species have a characteristic life cycle that culminates in asymmetric cell division (1-4). Caulobacter crescentus has served as a model bacterial system for the study of cell cycle regulation, and decades of research have provided insights into the mechanism underlying the precise cell cycle control that allows

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“…For instance, microfluidic channels ( Figure 1D) may be used to contain, and provide nutrients to, populations of engineered cells [38]. These microfluidic chips allow ease of imaging [39] while keeping the contained cells in a prolonged exponential growth phase [38]. Additionally, streptavidin functionalized microparticles can bind to a biotinylated fluorophore eliciting a measurable fluorescent response ( Figure 1E).…”

Section: Resultsmentioning

confidence: 99%

Modeling information exchange between living and artificial cells

et al. 2017

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Background: The tools of synthetic biology have enabled researchers to explore multiple scientific phenomena by directly engineering signaling pathways within living cells and artificial protocells. Here, we explored the potential for engineered living cells themselves to assemble signaling pathways for non-living protocells. This analysis serves as a preliminary investigation into a potential origin of processes that may be utilized by complex living systems. Specifically, we suggest that if living cells can be engineered to direct the assembly of genetic signaling pathways from genetic biomaterials in their environment, then insight can be gained into how naturally occurring living systems might behave similarly.Methods: To this end, we have modeled and simulated a system consisting of engineered cells that control the assembly of DNA monomers on microparticle scaffolds. These DNA monomers encode genetic circuits, and therefore, these microparticles can then be encapsulated with minimal transcription and translation systems to direct protocell phenotype. The modeled system relies on multiple previously established synthetic systems and then links these together to demonstrate system feasibility.Results: In this specific model, engineered cells are induced to synthesize biotin, which competes with biotinylated, circuit-encoding DNA monomers for an avidinized-microparticle scaffold. We demonstrate that multiple synthetic motifs can be controlled in this way and can be tuned by manipulating parameters such as inducer and DNA concentrations. Conclusions:We expect that this system will provide insight into the origin of living systems as well as serve as a tool for engineering living cells that assemble complex biomaterials in their environment.

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Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria

Cited by 170 publications

References 113 publications

Chance, Variation and the Nature of Causality in Ecological Communities

Chance, Variation and the Nature of Causality in Ecological Communities

Short-Stalked Prosthecomicrobium hirschii Cells Have a Caulobacter-Like Cell Cycle

Modeling information exchange between living and artificial cells

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