scholarly journals Formation, collective motion, and merging of macroscopic bacterial aggregates

2021 ◽  
Author(s):  
James Q Boedicker ◽  
George Courcoutbetis ◽  
Manasi Gangan ◽  
Sean Lim ◽  
Xiaokan Guo ◽  
...  
Keyword(s):  
Cell Density ◽  
Collective Motion ◽  
Aggregate Size ◽  
Enterobacter Cloacae ◽  
Soft Agar ◽  
Culture Dish ◽  
Directed Movement ◽  
Collective Behaviors ◽  
Chemical Gradients ◽  
Bacterial Aggregates

Chemotactic bacteria form emergent spatial patterns of variable cell density within cultures that are initially spatially uniform. These patterns are the result of chemical gradients that are created from the directed movement and metabolic activity of billions of cells. A recent study on pattern formation in wild bacterial isolates has revealed unique collective behaviors of the bacteria Enterobacter cloacae . As in other bacteria species, Enterobacter cloacae form macroscopic aggregates. Once formed, these bacterial clusters can migrate several millimeters, sometimes resulting in the merging of two or more clusters. To better understand these phenomena, we examine the formation and dynamics of thousands of bacterial clusters that form within a 22 cm square culture dish filled with soft agar over two days. At the macroscale, the aggregates display spatial order at short length scales, and the migration of cell clusters is superdiffusive, with a merging acceleration that is correlated with aggregate size. At the microscale, aggregates are composed of immotile cells surrounded by low density regions of motile cells. The collective movement of the aggregates is the result of an asymmetric flux of bacteria at the boundary. An agent based model is developed to examine how these phenomena are the result of both chemotactic movement and a change in motility at high cell density. These results identify and characterize a new mechanism for collective bacterial motility driven by a transient, density-dependent change in motility.

scholarly journals Formation, collective motion, and merging of macroscopic bacterial aggregates

2022 ◽  
Vol 18 (1) ◽  
pp. e1009153
Author(s):  
George Courcoubetis ◽  
Manasi S. Gangan ◽  
Sean Lim ◽  
Xiaokan Guo ◽  
Stephan Haas ◽  
...  
Keyword(s):  
Cell Density ◽  
Collective Motion ◽  
Bacterial Species ◽  
Aggregate Size ◽  
Enterobacter Cloacae ◽  
Soft Agar ◽  
Culture Dish ◽  
Directed Movement ◽  
Collective Behaviors ◽  
Bacterial Aggregates

Chemotactic bacteria form emergent spatial patterns of variable cell density within cultures that are initially spatially uniform. These patterns are the result of chemical gradients that are created from the directed movement and metabolic activity of billions of cells. A recent study on pattern formation in wild bacterial isolates has revealed unique collective behaviors of the bacteria Enterobacter cloacae. As in other bacterial species, Enterobacter cloacae form macroscopic aggregates. Once formed, these bacterial clusters can migrate several millimeters, sometimes resulting in the merging of two or more clusters. To better understand these phenomena, we examine the formation and dynamics of thousands of bacterial clusters that form within a 22 cm square culture dish filled with soft agar over two days. At the macroscale, the aggregates display spatial order at short length scales, and the migration of cell clusters is superdiffusive, with a merging acceleration that is correlated with aggregate size. At the microscale, aggregates are composed of immotile cells surrounded by low density regions of motile cells. The collective movement of the aggregates is the result of an asymmetric flux of bacteria at the boundary. An agent-based model is developed to examine how these phenomena are the result of both chemotactic movement and a change in motility at high cell density. These results identify and characterize a new mechanism for collective bacterial motility driven by a transient, density-dependent change in motility.

scholarly journals An Algorithm for Global Optimization Inspired by Collective Animal Behavior

2012 ◽  
Vol 2012 ◽  
pp. 1-24 ◽  
Author(s):  
Erik Cuevas ◽  
Mauricio González ◽  
Daniel Zaldivar ◽  
Marco Pérez-Cisneros ◽  
Guillermo García
Keyword(s):  
Global Optimization ◽  
Animal Behavior ◽  
Food Source ◽  
Collective Motion ◽  
Global Optimum ◽  
Migration Routes ◽  
Collective Behaviors ◽  
Biological Laws ◽  
Harvesting Efficiency ◽  
Collective Animal Behavior

A metaheuristic algorithm for global optimization called the collective animal behavior (CAB) is introduced. Animal groups, such as schools of fish, flocks of birds, swarms of locusts, and herds of wildebeest, exhibit a variety of behaviors including swarming about a food source, milling around a central locations, or migrating over large distances in aligned groups. These collective behaviors are often advantageous to groups, allowing them to increase their harvesting efficiency, to follow better migration routes, to improve their aerodynamic, and to avoid predation. In the proposed algorithm, the searcher agents emulate a group of animals which interact with each other based on the biological laws of collective motion. The proposed method has been compared to other well-known optimization algorithms. The results show good performance of the proposed method when searching for a global optimum of several benchmark functions.

Discontinuous and continuous transitions of collective behaviors in living systems

2021 ◽  
Author(s):  
Xu Li ◽  
Tingting Xue ◽  
Yu Sun ◽  
Jingfang Fan ◽  
Hui Li ◽  
...  
Keyword(s):  
Cognitive Abilities ◽  
Collective Motion ◽  
Finite Size ◽  
Continuous Phase ◽  
Living System ◽  
Living Systems ◽  
Finite Size Scaling ◽  
Continuous Transition ◽  
Collective Behaviors ◽  
Large Groups

Abstract Living systems are full of astonishing diversity and complexity of life. Despite differences in the length scales and cognitive abilities of these systems, collective motion of large groups of individuals can emerge. It is of great importance to seek for the fundamental principles of collective motion, such as phase transitions and their natures. Via an eigen microstate approach, we have found a discontinuous transition of density and a continuous transition of velocity in the Vicsek models of collective motion, which are identified by the finite-size scaling form of order-parameter. At strong noise, living systems behave like gas. With the decrease of noise, the interactions between the particles of a living system become stronger and make them come closer. The living system experiences then a discontinuous gas-liquid like transition of density. The even stronger interactions at smaller noise make the velocity directions of particles become ordered and there is a continuous phase transition of collective motion in addition.

Effects of Qingre Huatan Huoxue prescription on biological characteristics and cell cycle proteins of esophageal cancer stem cells.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e16052-e16052
Author(s):  
Fuchun Si
Keyword(s):  
Cell Cycle ◽  
Stem Cells ◽  
Flow Cytometry ◽  
Esophageal Cancer ◽  
Soft Agar ◽  
Biological Characteristics ◽  
Culture Dish ◽  
Serum Free ◽  
Mtt Method ◽  
Expression Rate

e16052 Background: Esophageal cancer (EC) stem cells characterized with immature differentiation, high invasion, high tumorigenesis and other biological characteristics, which are the root of the occurrence, development, recurrence, metastasis of EC. In this study, its purpose is to select and identify EC stem cells from serum-free cultured EC9706 cells, explore the effect of Chinese herbal prescription and its separated prescriptions on the biological characteristics of EC9706 stem cells, and to reveal the cytological and molecular mechanisms of Chinese herbal prescription anti-cancer. Methods: Firstly, MTT method was applied to explore the serum-free culture conditions of EC9706 stem cells in diameter of 60 mm low adhesion culture dish, at the same time, applying flow cytometry to identify the p75NTR mark ratio of each passage of cell to screenEC9706 stem cells. Next, Plotting the growth curve of EC9706 stem cells, detecting the proliferation inhibition rate EC9706 stem cells by cisplatin, soft agar clone formation, cell cycle to identify the characteristics of EC9706 stem cells by MTT method, soft agar assay, flow cytometry. Then applying MTT method and orthogonal test to screen and optimize Qingre Huatan Huoxue prescription (QHHP), using flow cytometry and western blot to test the effects of QHHP and its separated prescriptions on EC9706 stem cells appraisal indicators and Cell Cycle Proteins. Results: EC9706 cells with concentration of 8×104 cells/dish inoculateed on diameter of 60mm low adhesion culture dish, with adding 5 ml DMEM/F12 medium, a daily supplement of 20ng EGF, 10ng bFGF, per 10 to 14 days to passage one generation. After 5 generations of cell passage, the expression rate of p75NTR was 4-5%, was selected as the experimental object.EC9706 stem cells with the biological characteristics of slower adhesive growth, stronger cisplatin resistance, higher soft agar clone formation and p75NTR expression rate than that of EC9706 cells, and The cell cycle distribution was concentrated in the G0/G1 phase. 6 Chinese herbs were screened out ( Coptis coptidis, Rhizoma officinalis, Cucurbita pedicle, Toona bark, Cantharidopsis cantharidis, Augustia japonica) and compose QHHP. QHHP and its separated prescriptions could change the morphology, colony formation ability and cycle distribution of EC9706 stem cells in serum-free culture condition, which were related to the BMI1/CyclinB1 signaling pathway. Conclusions: Serum-free cell culture is a method to enrich stem cell-like cells in EC9706 cells. Qingre Huatan Huoxue prescription and its separated prescriptions inhibited the proliferation of EC9706 stem cells and change esophageal cancer stem cells characters. The mechanism of QHHP and its separated prescriptions on stem cells in EC9706 cells was related to BMI1 /CyclinB1 signaling pathway.

Nanostructure Processed on Culture Plate Improves Cell Adhesion

2011 ◽  
Author(s):  
Lisa Suganuma ◽  
Hiromichi Fujie ◽  
Hiroki Sudama ◽  
Yoshihide Sato ◽  
Norimasa Nakamura ◽  
...  
Keyword(s):  
Tensile Strength ◽  
Cell Adhesion ◽  
Cell Density ◽  
Soft Tissues ◽  
High Cell Density ◽  
Morphological Observation ◽  
Density Condition ◽  
Culture Dish ◽  
Engineering Technique ◽  
Tissue Engineering Technique

Ligaments and tendons have superior functions, but their healing capacities are limited. We have been developing a novel tissue-engineering technique for the repair of ligaments and tendons which involve stem cell-based self-assembled tissues (scSAT) derived from synovium[1]. For biological reconstruction of soft tissues, it is required for the scSAT to have high tensile strength. Our previous study indicted that, when the scSAT was cultured under high cell density condition, the tensile strength of the scSAT become higher than that cultured under low density condition[2]. However, the scSAT had a significant tendency to detach naturally from the culture dish with increasing cell density. Therefore, we expect that the mechanical property of the scSAT improves by enhancing the cell adhesion to culture plates. Previous studies suggested that nanostructure processed on culture dish affected cell adhesion [3, 4]. In the present study, nanostructure was processed on a silicon wafer using a nanoprocessing technology, and the structure was replicated to a polydimethylsiloxane (PDMS) plate. Human synovium-derived mesenchymal stem cells were cultured on the plate, and cell adhesion and morphological observation were performed.

scholarly journals Conformational shifts in a chemoreceptor helical hairpin control kinase signaling in Escherichia coli

2019 ◽  
Vol 116 (31) ◽  
pp. 15651-15660
Author(s):  
Qun Gao ◽  
Anchun Cheng ◽  
John S. Parkinson
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Salt Bridge ◽  
Soft Agar ◽  
Side Chain ◽  
Wild Type ◽  
Chemical Gradients ◽  
Helical Hairpin ◽  
Mutant Receptors ◽  
Activity Dependent

Motile Escherichia coli cells use chemoreceptor signaling arrays to track chemical gradients with exquisite precision. Highly conserved residues in the cytoplasmic hairpin tip of chemoreceptor molecules promote assembly of trimer-based signaling complexes and modulate the activity of their CheA kinase partners. To explore hairpin tip output states in the serine receptor Tsr, we characterized the signaling consequences of amino acid replacements at the salt-bridge residue pair E385-R388. All mutant receptors assembled trimers and signaling complexes, but most failed to support serine chemotaxis in soft agar assays. Small side-chain replacements at either residue produced OFF- or ON-shifted outputs that responded to serine stimuli in wild-type fashion, suggesting that these receptors, like the wild-type, operate as two-state signaling devices. Larger aliphatic or aromatic side chains caused slow or partial kinase control responses that proved dependent on the connections between core signaling units that promote array cooperativity. In a mutant lacking one of two key adapter-kinase contacts (interface 2), those mutant receptors exhibited more wild-type behaviors. Lastly, mutant receptors with charged amino acid replacements assembled signaling complexes that were locked in kinase-ON (E385K|R) or kinase-OFF (R388D|E) output. The hairpin tips of mutant receptors with these more aberrant signaling properties probably have nonnative structures or dynamic behaviors. Our results suggest that chemoeffector stimuli and adaptational modifications influence the cooperative connections between core signaling units. This array remodeling process may involve activity-dependent changes in the relative strengths of interface 1 and 2 interactions between the CheW and CheA.P5 components of receptor core signaling complexes.

Lithographically Fabricated 10-Micron Scale Autonomous Motors

2008 ◽  
Vol 1135 ◽  
Author(s):  
Yang Wang ◽  
Shih-to Fei ◽  
Vincent H. Crespi ◽  
Ayusman Sen ◽  
Thomas E. Mallouk
Keyword(s):  
Catalytic Reactions ◽  
Free Standing ◽  
Propulsion Systems ◽  
Directed Movement ◽  
Rotational Movement ◽  
Chemical Gradients ◽  
Micro Particles ◽  
Rotary Motors ◽  
Micro Machine ◽  
Complex Movement

ABSTRACTSelf-propulsion and directed movement of nano- and micro-particles can in principle provide novel components for applications in microrobotics and MEMS. Our research involves the design of catalytic propulsion systems and the control of colloidal movement based on this principle. We have designed autonomous nanomotors that mimic biological motors by using catalytic reactions to generate forces derived from chemical gradients. Through architectural control of bimetallic catalytic particles, we have recently developed systems that undergo more complex movement. For example, we have constructed 10-micron scale rotary motors by contact lithography. In these chiral motors, bimetallic Au-Pt patterns are free-standing and move in the pattern predicted by theory. These studies demonstrate that by designing the proper architecture, one can tailor the pattern of movement to specific applications, such as changing from translational to rotational movement. The potential for elaboration of these designs to more complex micro-machine assemblies is discussed.

scholarly journals Collective behavior emerges from genetically controlled simple behavioral motifs in zebrafish

2021 ◽  
Author(s):  
Ariel C. Aspiras ◽  
Roy Harpaz ◽  
Sydney Chambule ◽  
Sierra Tseng ◽  
Florian Engert ◽  
...  
Keyword(s):  
Larval Stage ◽  
Visual Motion ◽  
Collective Motion ◽  
Group Behavior ◽  
Visual Responses ◽  
Animal Groups ◽  
Collective Behaviors ◽  
Early Larval Stage ◽  
Model Simulations ◽  
Species Survival

AbstractSince Darwin, coordinated movement of animal groups has been believed to be essential to species survival, but it is not understood how changes in the genetic makeup of individuals might alter behavior of the collective. Here we find that even at the early larval stage, zebrafish regulate their proximity and alignment with each other. Two simple visual responses, one that measures relative visual field occupancy and the other global visual motion, suffice to account for the group behavior that emerges. We analyze how mutations in genes known to affect social behavior of humans perturb these simple reflexes in larval zebrafish and thereby affect their collective behaviors. We use model simulations to show that changes in reflexive responses of individual mutant animals predict well the distinctive collective patterns that emerge in a group. Hence group behaviors reflect in part genetically defined primitive sensorimotor “motifs”, which are evident even in young larvae.Long AbstractCoordinated movement of animal groups is essential to species survival. It is not clear whether there are simple interactions among the individuals that account for group behaviors, nor when they arise during development. Zebrafish at the early larval stage do not manifest obvious tendencies to form groups, but we find here that they have already established mechanisms to regulate proximity and alignment with respect to their neighbors, which are the two key ingredients of shoaling and schooling. Specifically, we show that two basic reflexes are sufficient to explain a large part of emerging collective behaviors. First, young larvae repel away from regions of high visual clutter, leading to a dispersal of the group. At later developmental stages, this dispersal reflex shifts to attraction and aggregation behaviors. Second, larvae display a strong tendency to move along with whole field motion stimuli, a well-described behavior known as the optomotor reflex (OMR). When applied to individuals swimming within a group, this reflex leads to an emergence of mutual alignment between close neighbors and induces collective motion of the whole group. The combined developmental maturation of both reflexes can then explain emergent shoaling and schooling behavior.In order to probe the link between single genetic mutations and emergent collective motion, we select fish with mutations in genes orthologous to those associated with human behavioral disorders and find that these mutations affect the primitive visuomotor behaviors at a very young age and persist over development. We then use model simulations to show that the phenotypic manifestations of these mutations are predictive of changes in the emergent collective behaviors of mutant animals. Indeed, models based solely on these two primitive motor reflexes can synergistically account for a large fraction of the distinctive emergent group behaviors across ages and genetic backgrounds. Our results indicate that complex interactions among individuals in a group are built upon genetically defined primitive sensorimotor “motifs”, which are evident even in young larvae at a time when the nervous system is far less complex and more directly accessible to detailed analysis.

Non-Labeled Cell Tracking Velocimetry for Biological Flows

2007 ◽  
Author(s):  
Chang-Beom Kim ◽  
Edward Steager ◽  
Min Jun Kim
Keyword(s):  
Velocity Field ◽  
Cell Tracking ◽  
Collective Motion ◽  
Agar Plate ◽  
Soft Agar ◽  
Spatially Correlated ◽  
Time Period ◽  
Entire Flow ◽  
Cell Tracking Velocimetry ◽  
Short Time

A tracking algorithm was developed to study the velocity field of flagellated bacteria, Serratia marcescens, swarming on a soft agar plate. Average velocities for local regions regularly arranged over the entire flow field were investigated rather than those for individual bacterium. The velocity field of the bacteria typically featured the combination of curvilinear translation and vortex modes. They repeated these patterns for a short time period, forming several groups and dissipating. To further investigate the flow patterns generated by the collective motion of the swarming bacteria, the velocity field on the swarm was spatially correlated.

scholarly journals Bioelectronics-on-a-chip for cardio myoblast proliferation enhancement using electric field stimulation

2020 ◽  
Vol 24 (1) ◽  
Author(s):  
Ángel Aragón ◽  
María Cebro-Márquez ◽  
Eliseo Perez ◽  
Antonio Pazos ◽  
Ricardo Lage ◽  
...  
Keyword(s):  
Cell Culture ◽  
Electric Field ◽  
Cell Density ◽  
Electric Circuit ◽  
Field Stimulation ◽  
Culture Chamber ◽  
Culture Dish ◽  
Electric Field Stimulation ◽  
Myoblast Proliferation ◽  
A Cell

Abstract Background Cardio myoblast generation from conventional approaches is laborious and time-consuming. We present a bioelectronics on-a-chip for stimulating cells cardio myoblast proliferation during culture. Method The bioelectronics chip fabrication methodology involves two different process. In the first step, an aluminum layer of 200 nm is deposited over a soda-lime glass substrate using physical vapor deposition and selectively removed using a Q-switched Nd:YVO4 laser to create the electric tracks. To perform the experiments, we developed a biochip composed of a cell culture chamber fabricated with polydimethylsiloxane (PDMS) with a glass coverslip or a cell culture dish placed over the electric circuit tracks. By using such a glass cover slip or cell culture dish we avoid any toxic reactions caused by electrodes in the culture or may be degraded by electrochemical reactions with the cell medium, which is crucial to determine the effective cell-device coupling. Results The chip was used to study the effect of electric field stimulation of Rat ventricular cardiomyoblasts cells (H9c2). Results shows a remarkable increase in the number of H9c2 cells for the stimulated samples, where after 72 h the cell density double the cell density of control samples. Conclusions Cell proliferation of Rat ventricular cardiomyoblasts cells (H9c2) using the bioelectronics-on-a-chip was enhanced upon the electrical stimulation. The dependence on the geometrical characteristics of the electric circuit on the peak value and homogeneity of the electric field generated are analyzed and proper parameters to ensure a homogeneous electric field at the cell culture chamber are obtained. It can also be observed a high dependence of the electric field on the geometry of the electrostimulator circuit tracks and envisage the potential applications on electrophysiology studies, monitoring and modulate cellular behavior through the application of electric fields.

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