scholarly journals Large-scale vortices with dynamic rotation emerged from monolayer collective motion of gliding Flavobacteria

2021 ◽  
Author(s):  
Daisuke Nakane ◽  
Shoko Odaka ◽  
Kana Suzuki ◽  
Takayuki Nishizaka
Keyword(s):  
Circular Plate ◽  
Large Scale ◽  
Collective Motion ◽  
Single Cells ◽  
Gliding Motility ◽  
Soil Bacterium ◽  
Random Orientation ◽  
Flavobacterium Johnsoniae ◽  
Collective Motions ◽  
Vortex Patterns

A collective motion of self-driven particles has been a fascinating subject in physics and biology. Sophisticated macroscopic behavior emerges through a population in thousands or millions of bacterial cells, propelling itself by flagellar rotation and its chemotactic response. Here we found a series of collective motions accompanying successive phase-transitions in a non-flagellated rod-shaped soil bacterium, Flavobacterium johnsoniae, which was driven by a surface cell movement known as gliding motility. When we spot the cells on an agar plate with a low level of nutrients, the bacterial community exhibited vortex patterns that spontaneously appeared as lattice and integrated into a large-scale circular plate. All patterns exhibit with monolayer of bacteria, which enable to visualize an individual cell with a high resolution among a wide-range pattern two-dimensionally. The single cells moved at random orientation, but the cells connected with one another showed left-turn biased trajectories in starved environment. This feature is possibly due to the collision of cells inducing a nematic alignment of dense cells as self-propelled rods. Subsequently, each vortex oscillated independently, and then transformed to the rotating mode as an independent circular plate. Notably, the rotational direction of the circular plate was counterclockwise without exception. The plates developed accompanying rotation with constant angular velocity, suggesting that the mode is an efficient strategy for bacterial survival. Importance Self-propelled bacteria propelled by flagella rotation often display highly organized dynamic patterns at high cell densities. Here we found a new mode of collective motion in non-flagellated bacteria: vortex patterns were spontaneously appeared as lattice and integrated into a large-scale circular plate comprising hundreds of thousands of cells, which exhibited unidirectional rotation in a counterclockwise manner and expanded in size on agar. A series of collective motions was driven by gliding motility of the rod-shaped soil bacterium Flavobacterium johnsoniae. In a low nutrient environment, single cells moved at random orientation while cells at high density moved together as a unitary cluster. This might be an efficient strategy for cells of this species to find nutrients.

scholarly journals Colony spreading of the gliding bacterium Flavobacterium johnsoniae in the absence of the motility adhesin SprB

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Keiko Sato ◽  
Masami Naya ◽  
Yuri Hatano ◽  
Yoshio Kondo ◽  
Mari Sato ◽  
...  
Keyword(s):  
Soft Agar ◽  
Gliding Motility ◽  
Wild Type ◽  
Initial Cell ◽  
Flavobacterium Johnsoniae ◽  
Seeking Behavior ◽  
Colony Spreading ◽  
Gliding Bacterium ◽  
Mutant Cells ◽  
Scanning Electron

AbstractColony spreading of Flavobacterium johnsoniae is shown to include gliding motility using the cell surface adhesin SprB, and is drastically affected by agar and glucose concentrations. Wild-type (WT) and ΔsprB mutant cells formed nonspreading colonies on soft agar, but spreading dendritic colonies on soft agar containing glucose. In the presence of glucose, an initial cell growth-dependent phase was followed by a secondary SprB-independent, gliding motility-dependent phase. The branching pattern of a ΔsprB colony was less complex than the pattern formed by the WT. Mesoscopic and microstructural information was obtained by atmospheric scanning electron microscopy (ASEM) and transmission EM, respectively. In the growth-dependent phase of WT colonies, dendritic tips spread rapidly by the movement of individual cells. In the following SprB-independent phase, leading tips were extended outwards by the movement of dynamic windmill-like rolling centers, and the lipoproteins were expressed more abundantly. Dark spots in WT cells during the growth-dependent spreading phase were not observed in the SprB-independent phase. Various mutations showed that the lipoproteins and the motility machinery were necessary for SprB-independent spreading. Overall, SprB-independent colony spreading is influenced by the lipoproteins, some of which are involved in the gliding machinery, and medium conditions, which together determine the nutrient-seeking behavior.

scholarly journals Cell migration guided by long-lived spatial memory

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joseph d’Alessandro ◽  
Alex Barbier--Chebbah ◽  
Victor Cellerin ◽  
Olivier Benichou ◽  
René Marc Mège ◽  
...  
Keyword(s):  
Cell Migration ◽  
Spatial Memory ◽  
Large Scale ◽  
Single Cells ◽  
Environmental Perturbations ◽  
Motile Cells ◽  
Unicellular Organisms ◽  
Biochemical Signals ◽  
The Impact ◽  
Cell Trajectories

AbstractLiving cells actively migrate in their environment to perform key biological functions—from unicellular organisms looking for food to single cells such as fibroblasts, leukocytes or cancer cells that can shape, patrol or invade tissues. Cell migration results from complex intracellular processes that enable cell self-propulsion, and has been shown to also integrate various chemical or physical extracellular signals. While it is established that cells can modify their environment by depositing biochemical signals or mechanically remodelling the extracellular matrix, the impact of such self-induced environmental perturbations on cell trajectories at various scales remains unexplored. Here, we show that cells can retrieve their path: by confining motile cells on 1D and 2D micropatterned surfaces, we demonstrate that they leave long-lived physicochemical footprints along their way, which determine their future path. On this basis, we argue that cell trajectories belong to the general class of self-interacting random walks, and show that self-interactions can rule large scale exploration by inducing long-lived ageing, subdiffusion and anomalous first-passage statistics. Altogether, our joint experimental and theoretical approach points to a generic coupling between motile cells and their environment, which endows cells with a spatial memory of their path and can dramatically change their space exploration.

Identification of the Flavobacterium johnsoniae cysteate‐fatty acyl transferase required for capnine synthesis and for efficient gliding motility

2021 ◽  
Author(s):  
Miguel Ángel Vences‐Guzmán ◽  
Rafael Peña‐Miller ◽  
Nancy Adriana Hidalgo‐Aguilar ◽  
Maritza Lorena Vences‐Guzmán ◽  
Ziqiang Guan ◽  
...  
Keyword(s):  
Fatty Acyl ◽  
Gliding Motility ◽  
Acyl Transferase ◽  
Flavobacterium Johnsoniae

scholarly journals Cloning and Characterization of theFlavobacterium johnsoniae Gliding Motility GenesgldD and gldE

2001 ◽  
Vol 183 (14) ◽  
pp. 4167-4175 ◽  
Author(s):  
David W. Hunnicutt ◽  
Mark J. McBride
Keyword(s):  
Membrane Protein ◽  
Cytoplasmic Membrane ◽  
Sequence Similarity ◽  
Gliding Motility ◽  
Wild Type ◽  
Bacteriophage Infection ◽  
Flavobacterium Johnsoniae ◽  
Latex Spheres ◽  
Serovar Typhimurium

ABSTRACT Cells of Flavobacterium johnsoniae move over surfaces by a process known as gliding motility. The mechanism of this form of motility is not known. Cells of F. johnsoniaepropel latex spheres along their surfaces, which is thought to be a manifestation of the motility machinery. Three of the genes that are required for F. johnsoniae gliding motility,gldA, gldB, and ftsX, have recently been described. Tn4351 mutagenesis was used to identify another gene, gldD, that is needed for gliding. Tn4351-induced gldD mutants formed nonspreading colonies, and cells failed to glide. They also lacked the ability to propel latex spheres and were resistant to bacteriophages that infect wild-type cells. Introduction of wild-type gldD into the mutants restored motility, ability to propel latex spheres, and sensitivity to bacteriophage infection. gldD codes for a cytoplasmic membrane protein that does not exhibit strong sequence similarity to proteins of known function. gldE, which lies immediately upstream ofgldD, encodes another cytoplasmic membrane protein that may be involved in gliding motility. Overexpression ofgldE partially suppressed the motility defects of agldB point mutant, suggesting that GldB and GldE may interact. GldE exhibits sequence similarity to Borrelia burgdorferi TlyC and Salmonella enterica serovar Typhimurium CorC.

scholarly journals Leveraging high-powered RNA-Seq datasets to improve inference of regulatory activity in single-cell RNA-Seq data

2019 ◽  
Author(s):  
Ning Wang ◽  
Andrew E. Teschendorff
Keyword(s):  
Transcription Factors ◽  
Single Cell ◽  
Cell Fate ◽  
Regulatory Networks ◽  
Large Scale ◽  
Single Cells ◽  
Differential Expression Analysis ◽  
Dropout Rate ◽  
Rna Seq ◽  
Regulatory Activity

AbstractInferring the activity of transcription factors in single cells is a key task to improve our understanding of development and complex genetic diseases. This task is, however, challenging due to the relatively large dropout rate and noisy nature of single-cell RNA-Seq data. Here we present a novel statistical inference framework called SCIRA (Single Cell Inference of Regulatory Activity), which leverages the power of large-scale bulk RNA-Seq datasets to infer high-quality tissue-specific regulatory networks, from which regulatory activity estimates in single cells can be subsequently obtained. We show that SCIRA can correctly infer regulatory activity of transcription factors affected by high technical dropouts. In particular, SCIRA can improve sensitivity by as much as 70% compared to differential expression analysis and current state-of-the-art methods. Importantly, SCIRA can reveal novel regulators of cell-fate in tissue-development, even for cell-types that only make up 5% of the tissue, and can identify key novel tumor suppressor genes in cancer at single cell resolution. In summary, SCIRA will be an invaluable tool for single-cell studies aiming to accurately map activity patterns of key transcription factors during development, and how these are altered in disease.

scholarly journals Assessing the measurement transfer function of single-cell RNA sequencing

2016 ◽  
Author(s):  
Hannah R. Dueck ◽  
Rizi Ai ◽  
Adrian Camarena ◽  
Bo Ding ◽  
Reymundo Dominguez ◽  
...  
Keyword(s):  
Transfer Function ◽  
Single Cell ◽  
Rna Sequencing ◽  
Large Scale ◽  
Transfer Functions ◽  
Single Cells ◽  
Biological Information ◽  
Gene Detection ◽  
Single Cell Rna Sequencing ◽  
Scale Control

AbstractRecently, measurement of RNA at single cell resolution has yielded surprising insights. Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of single cell methods and the factors governing their performance are still poorly known. Here, we conducted a large-scale control experiment to assess the transfer function of three scRNA-seq methods and factors modulating the function. All three methods detected greater than 70% of the expected number of genes and had a 50% probability of detecting genes with abundance greater than 2 to 4 molecules. Despite the small number of molecules, sequencing depth significantly affected gene detection. While biases in detection and quantification were qualitatively similar across methods, the degree of bias differed, consistent with differences in molecular protocol. Measurement reliability increased with expression level for all methods and we conservatively estimate the measurement transfer functions to be linear above ~5-10 molecules. Based on these extensive control studies, we propose that RNA-seq of single cells has come of age, yielding quantitative biological information.

scholarly journals Characterization of CRISPR/Cas9 RANKL knockout mesenchymal stem cell clones based on single-cell printing technology and emulsion coupling assay as a low-cellularity workflow for single-cell cloning

2020 ◽  
Author(s):  
Tobias Groß ◽  
Csaba Jeney ◽  
Darius Halm ◽  
Günter Finkenzeller ◽  
G. Björn Stark ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Line ◽  
Large Scale ◽  
Single Cells ◽  
Protein Detection ◽  
Cell Line Development ◽  
Cell Printing ◽  
Cell Clones ◽  
The University

AbstractThe homogeneity of the genetically modified single-cells is a necessity for many applications such as cell line development, gene therapy, and tissue engineering and in particular for regenerative medical applications. The lack of tools to effectively isolate and characterize CRISPR/Cas9 engineered cells is considered as a significant bottleneck in these applications. Especially the incompatibility of protein detection technologies to confirm protein expression changes without a preconditional large-scale clonal expansion, creates a gridlock in many applications. To ameliorate the characterization of engineered cells, we propose an improved workflow, including single-cell printing/isolation technology based on fluorescent properties with high yield, a genomic edit screen (surveyor assay), mRNA rtPCR assessing altered gene expression and a versatile protein detection tool called emulsion-coupling to deliver a high-content, unified single-cell workflow. The workflow was exemplified by engineering and functionally validating RANKL knockout immortalized mesenchymal stem cells showing altered bone formation capacity of these cells. The resulting workflow is economical, without the requirement of large-scale clonal expansions of the cells with overall cloning efficiency above 30% of CRISPR/Cas9 edited cells. Nevertheless, as the single-cell clones are comprehensively characterized at an early, highly parallel phase of the development of cells including DNA, RNA, and protein levels, the workflow delivers a higher number of successfully edited cells for further characterization, lowering the chance of late failures in the development process.Author summaryI completed my undergraduate degree in biochemistry at the University of Ulm and finished my master's degree in pharmaceutical biotechnology at the University of Ulm and University of applied science of Biberach with a focus on biotechnology, toxicology and molecular biology. For my master thesis, I went to the University of Freiburg to the department of microsystems engineering, where I developed a novel workflow for cell line development. I stayed at the institute for my doctorate, but changed my scientific focus to the development of the emulsion coupling technology, which is a powerful tool for the quantitative and highly parallel measurement of protein and protein interactions. I am generally interested in being involved in the development of innovative molecular biological methods that can be used to gain new insights about biological issues. I am particularly curious to unravel the complex and often poorly understood protein interaction pathways that are the cornerstone of understanding cellular functionality and are a fundamental necessity to describe life mechanistically.

scholarly journals Cell migration driven by long-lived spatial memory

2021 ◽  
Author(s):  
Joseph d’Alessandro ◽  
Alex Barbier-Chebbah ◽  
Victor Cellerin ◽  
Olivier Bénichou ◽  
René-Marc Mège ◽  
...  
Keyword(s):  
Cell Migration ◽  
Spatial Memory ◽  
Large Scale ◽  
Single Cells ◽  
Environmental Perturbations ◽  
Motile Cells ◽  
Unicellular Organisms ◽  
Biochemical Signals ◽  
The Impact ◽  
Cell Trajectories

Many living cells actively migrate in their environment to perform key biological functions – from unicellular organisms looking for food to single cells such as fibroblasts, leukocytes or cancer cells that can shape, patrol or invade tissues. Cell migration results from complex intracellular processes that enable cell self-propulsion 1,2, and has been shown to also integrate various chemical or physical extracellular signals 3,4,5. While it is established that cells can modify their environment by depositing biochemical signals or mechanically remodeling the extracellular matrix, the impact of such self-induced environmental perturbations on cell trajectories at various scales remains unexplored. Here, we show that cells remember their path: by confining cells on 1D and 2D micropatterned surfaces, we demonstrate that motile cells leave long-lived physicochemical footprints along their way, which determine their future path. On this basis, we argue that cell trajectories belong to the general class of self-interacting random walks, and show that self-interactions can rule large scale exploration by inducing long-lived ageing, subdiffusion and anomalous first-passage statistics. Altogether, our joint experimental and theoretical approach points to a generic coupling between motile cells and their environment, which endows cells with a spatial memory of their path and can dramatically change their space exploration.

scholarly journals Flavobacterium johnsoniae Gliding Motility Genes Identified by mariner Mutagenesis

2005 ◽  
Vol 187 (20) ◽  
pp. 6943-6952 ◽  
Author(s):  
Timothy F. Braun ◽  
Manjeet K. Khubbar ◽  
Daad A. Saffarini ◽  
Mark J. McBride
Keyword(s):  
Complete Loss ◽  
Gliding Motility ◽  
Wild Type ◽  
Flavobacterium Johnsoniae ◽  
Chemically Induced

ABSTRACT Cells of Flavobacterium johnsoniae glide rapidly over surfaces. The mechanism of F. johnsoniae gliding motility is not known. Eight gld genes required for gliding motility have been described. Disruption of any of these genes results in complete loss of gliding motility, deficiency in chitin utilization, and resistance to bacteriophages that infect wild-type cells. Two modified mariner transposons, HimarEm1 and HimarEm2, were constructed to allow the identification of additional motility genes. HimarEm1 and HimarEm2 each transposed in F. johnsoniae, and nonmotile mutants were identified and analyzed. Four novel motility genes, gldK, gldL, gldM, and gldN, were identified. GldK is similar in sequence to the lipoprotein GldJ, which is required for gliding. GldL, GldM, and GldN are not similar in sequence to proteins of known function. Cells with mutations in gldK, gldL, gldM, and gldN were defective in motility and chitin utilization and were resistant to bacteriophages that infect wild-type cells. Introduction of gldA, gldB, gldD, gldFG, gldH, gldI, and gldJ and the region spanning gldK, gldL, gldM, and gldN individually into 50 spontaneous and chemically induced nonmotile mutants restored motility to each of them, suggesting that few additional F. johnsoniae gld genes remain to be identified.

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