Wake structure and hydrodynamic performance of flapping foils mimicking fish fin kinematics

Numerical simulations are used to investigate the wake structure and hydrodynamic performance of bionic flapping foils. The study is motivated by the quest to understand the fluid dynamics of fish fins and use it in the underwater propulsion. The simulations employ an immersed boundary method that makes it possible to simulate flows with complex moving boundaries on fixed Cartesian grids. A detailed analysis of the vortex topology shows that the wake of flapping foils is dominated by two sets of complex shaped vortex rings that convect at oblique angles to the wake centerline. The wake of these flapping foils is characterized by two oblique jets. Simulations are also used to examine the wake vortex and hydrodynamic performance over a range of Strouhal numbers and maximum pitch angles and the connection between the foil kinematics, vortex dynamics and force production is discussed. The results show that the variety law of the hydrodynamic performance with kinematic parameters strongly depends on the flow dynamics underlying the force production, including the orientation, interconnection and dissipation rate of the vortex rings.     

A triangular loop of domain D1 of FlgE is essential for hook assembly but not for the mechanical function

The bacterial flagellar hook is a short, curved tubular structure made of FlgE. The hook connects the basal body as a rotary motor and the filament as a helical propeller and functions as a universal joint to smoothly transmit torque produced by the motor to the filament. Salmonella FlgE consists of D0, Dc, D1 and D2 domains. Axial interactions between a triangular loop of domain D1 (D1-loop) and domain D2 are postulated to be responsible for hook supercoiling. In contrast, Bacillus FlgE lacks the D1-loop and domain D2. Here, to clarify the roles of the D1-loop and domain D2 in the mechanical function, we carried out deletion analysis of Salmonella FlgE. A deletion of the D1-loop conferred a loss-of-function phenotype whereas that of domain D2 did not. The D1-loop deletion inhibited hook polymerization. Suppressor mutations of the D1-loop deletion was located within FlgD, which acts as the hook cap to promote hook assembly. This suggests a possible interaction between the D1-loop of FlgE and FlgD. Suppressor mutant cells produced straight hooks, but retained the ability to form a flagellar bundle behind a cell body, suggesting that the loop deletion does not affect the bending flexibility of the Salmonella hook.     

Overview of Mathematical Approaches Used to Model Bacterial Chemotaxis II: Bacterial Populations

We review the application of mathematical modeling to understanding the behavior of populations of chemotactic bacteria. The application of continuum mathematical models, in particular generalized Keller–Segel models, is discussed along with attempts to incorporate the microscale (individual) behavior on the macroscale, modeling the interaction between different species of bacteria, the interaction of bacteria with their environment, and methods used to obtain experimentally verified parameter values. We allude briefly to the role of modeling pattern formation in understanding collective behavior within bacterial populations. Various aspects of each model are discussed and areas for possible future research are postulated.     

Incorporating an immersed boundary method to study thermal effects of vascular systems during tissue cryo-freezing

In this paper, the three-dimensional thermal effects of a clinically-extracted vascular tissue undergoing cryo-freezing are numerically investigated. Based on the measured experimental temperature field, the numerical results of the Pennes bioheat model combined with the boundary condition-enforced immersed boundary method (IBM) agreed well with experimental data with a maximum temperature discrepancy of 2.9 °C. For simulating the temperature profile of a tumor sited in a dominantly vascularized tissue, our model is able to capture with ease the thermal effects at specified junctions of the blood vessels. The vascular complexity and the ice-ball shape irregularity which cannot be easily quantified via clinical experiments are also analyzed and compared for both two-dimensional and three-dimensional settings with different vessel configurations and developments. For the three-dimensional numerical simulations, a n-furcated liver vessels model from a three-dimensional segmented volume using hole-making and subdivision methods is applied. A specific study revealed that the structure and complexity of the vascular network can markedly affect the tissue's freezing configuration with increasing ice-ball irregularity for greater blood vessel complexity.     

Bacterial transformation using micro-shock waves

Shock waves are one of the most competent mechanisms of energy dissipation observed in nature. We have developed a novel device to generate controlled micro-shock waves using an explosive-coated polymer tube. In this study, we harnessed these controlled micro-shock waves to develop a unique bacterial transformation method. The conditions were optimized for the maximum transformation efficiency in Escherichia coli. The maximum transformation efficiency was obtained when we used a 30 cm length polymer tube, 100 μm thick metal foil, 200 mM CaCl₂, 1 ng/μl plasmid DNA concentration, and 1 × 10⁹ cell density. The highest transformation efficiency achieved (1 × 10⁻⁵ transformants/cell) was at least 10 times greater than the previously reported ultrasound-mediated transformation (1 × 10⁻⁶ transformants/cell). This method was also successfully employed for the efficient and reproducible transformation of Pseudomonas aeruginosa and Salmonellatyphimurium. This novel method of transformation was shown to be as efficient as electroporation with the added advantage of better recovery of cells, reduced cost (40 times cheaper than a commercial electroporator), and growth phase independent transformation.     

Defining A Global Map of Functional Group-based 3D Ligand-binding Motifs

Uncovering conserved 3D protein–ligand binding patterns on the basis of functional groups (FGs) shared by a variety of small molecules can greatly expand our knowledge of protein–ligand interactions. Despite that conserved binding patterns for a few commonly used FGs have been reported in the literature, large-scale identification and evaluation of FG-based 3D binding motifs are still lacking. Here, we propose a computational method, Automatic FG-based Three-dimensional Motif Extractor (AFTME), for automatic mapping of 3D motifs to different FGs of a specific ligand. Applying our method to 233 naturally-occurring ligands, we define 481 FG-binding motifs that are highly conserved across different ligand-binding pockets. Systematic analysis further reveals four main classes of binding motifs corresponding to distinct sets of FGs. Combinations of FG-binding motifs facilitate the binding of proteins to a wide spectrum of ligands with various binding affinities. Finally, we show that our FG–motif map can be used to nominate FGs that potentially bind to specific drug targets, thus providing useful insights and guidance for rational design of small-molecule drugs.     

Overview of Mathematical Approaches Used to Model Bacterial Chemotaxis I: The Single Cell

Mathematical modeling of bacterial chemotaxis systems has been influential and insightful in helping to understand experimental observations. We provide here a comprehensive overview of the range of mathematical approaches used for modeling, within a single bacterium, chemotactic processes caused by changes to external gradients in its environment. Specific areas of the bacterial system which have been studied and modeled are discussed in detail, including the modeling of adaptation in response to attractant gradients, the intracellular phosphorylation cascade, membrane receptor clustering, and spatial modeling of intracellular protein signal transduction. The importance of producing robust models that address adaptation, gain, and sensitivity are also discussed. This review highlights that while mathematical modeling has aided in understanding bacterial chemotaxis on the individual cell scale and guiding experimental design, no single model succeeds in robustly describing all of the basic elements of the cell. We conclude by discussing the importance of this and the future of modeling in this area.     

人SP-B蛋白转基因小鼠及细菌性肺炎模型的构建

目的:构建携带人SP-B蛋白+1580 SNP不同等位基因的转基因小鼠并进行细菌性肺炎模型的造模。方法:利用受精卵原核注射技术将hSP-B基因整合至小鼠染色体上获得F0代小鼠,将其与mSP-B基因敲除鼠进行交配,逐步去除转基因小鼠体内m SP-B基因。利用PCR技术鉴定小鼠基因型,通过测序确定+1580位点的等位基因。将铜绿假单胞菌经支气管灌注接种至小鼠肺内进行细菌性肺炎造模,对照组注射等量灭菌生理盐水。结果:F2代小鼠只表达人SP-B蛋白而不表达鼠SP-B蛋白,蛋白表达量与人肺内含量相近,即为构建成功的转基因小鼠。3个小鼠家系+1580位点等位基因为T,1个家系为C。细菌接种(1×10~6CFU/mouse)后24小时,小鼠肺泡内炎症渗出明显,大量中性粒细胞浸润,SP-B蛋白含量明显降低,但不同等位基因间在此条件下无明显差异。结果:成功构建只表达人SP-B蛋白的转基因小鼠模型,细菌性肺炎模型造模成功,为今后进一步研究人SP-B蛋白的生理功能及+1580基因多态性与肺疾病的关系提供了有力的工具。     

Remote Magnetic Actuation of Micrometric Probes for in situ 3D Mapping of Bacterial Biofilm Physical Properties

Bacterial adhesion and growth on interfaces lead to the formation of three-dimensional heterogeneous structures so-called biofilms. The cells dwelling in these structures are held together by physical interactions mediated by a network of extracellular polymeric substances. Bacterial biofilms impact many human activities and the understanding of their properties is crucial for a better control of their development — maintenance or eradication — depending on their adverse or beneficial outcome. This paper describes a novel methodology aiming to measure in situ the local physical properties of the biofilm that had been, until now, examined only from a macroscopic and homogeneous material perspective. The experiment described here involves introducing magnetic particles into a growing biofilm to seed local probes that can be remotely actuated without disturbing the structural properties of the biofilm. Dedicated magnetic tweezers were developed to exert a defined force on each particle embedded in the biofilm. The setup is mounted on the stage of a microscope to enable the recording of time-lapse images of the particle-pulling period. The particle trajectories are then extracted from the pulling sequence and the local viscoelastic parameters are derived from each particle displacement curve, thereby providing the 3D-spatial distribution of the parameters. Gaining insights into the biofilm mechanical profile is essential from an engineer''s point of view for biofilm control purposes but also from a fundamental perspective to clarify the relationship between the architectural properties and the specific biology of these structures.     

二维细胞运动模型的数值模拟

研究了一个二维细胞运动模型,该模型是个动边界问题．我们运用运动网格的有限元算法对此模型进行了数值模拟,数值结果表明,细胞最终收敛到固定形状,并且以固定速度向前运动．     

Flow within models of the vertebrate embryonic heart

Vertebrate cardiogenesis is believed to be partially regulated by fluid forces imposed by blood flow in addition to myocardial activity and other epigenetic factors. To understand the flow field within the embryonic heart, numerical simulations using the immersed boundary method were performed on a series of models that represent simplified versions of some of the early morphological stages of heart development. The results of the numerical study were validated using flow visualization experiments conducted on equivalent dynamically scaled physical models. The chamber and cardiac cushion (or valve) depths in the models were varied, and Reynolds numbers ranging from 0.01 to 1000 corresponding to the scale of the early heart tube to the adult heart were considered. The observed results showed that vortex formation within the chambers occurred for Reynolds numbers on the order of 1-10. This transition to vortical flow appears to be highly sensitive to the chamber and cushion depths within the model. These fluid dynamic events could be important to induce shear sensing at the endothelial surface layer which is thought to be a part of regulating the proper morphological development and functionality of the valves.     

A Computational Study of the Development of Epithelial Acini: I. Sufficient Conditions for the Formation of a Hollow Structure

Normal hollow epithelial acini are 3-dimensional culture structures that resemble the architecture and functions of normal breast glands and lobules. This experimental model enables in vitro investigations of genotypic and molecular abnormalities associated with epithelial cancers. However, the way in which the acinar structure is formed is not yet completely understood. Gaining more information about consecutive stages of acini development—starting from a single cell that gives rise to a cluster of randomly oriented cells, followed by cell differentiation that leads to a layer of polarised cells enclosing the hollow lumen—will provide insight into the transformations of eukaryotic cells that are necessary for their successful arrangement into an epithelium. In this paper, we introduce a two-dimensional single-cell-based model representing the cross section of a typical acinus. Using this model, we investigate mechanisms that lead to the unpolarised cell growth, cell polarisation, stabilisation of the acinar structure and maintenance of the hollow lumen and discuss the sufficient conditions for each stage of acinar formation. In the follow-up paper (Rejniak and Anderson, A computational study of the development of epithelial acini. II. Necessary conditions for structure and lumen stability), we investigate what morphological changes are observable in the growing acini when some assumptions of this model are relaxed.     

A Bacterial Iron Exporter for Maintenance of Iron Homeostasis

Nutritional iron acquisition by bacteria is well described, but almost nothing is known about bacterial iron export even though it is likely to be an important homeostatic mechanism. Here, we show that Bradyrhizobium japonicum MbfA (Blr7895) is an inner membrane protein expressed in cells specifically under high iron conditions. MbfA contains an N-terminal ferritin-like domain (FLD) and a C-terminal domain homologous to the eukaryotic vacuolar membrane Fe²⁺/Mn²⁺ transporter CCC1. An mbfA deletion mutant is severely defective in iron export activity, contains >2-fold more intracellular iron than the parent strain, and displays an aberrant iron-dependent gene expression phenotype. B. japonicum is highly resistant to iron and H₂O₂ stresses, and MbfA contributes substantially to this as determined by phenotypes of the mbfA mutant strain. The N-terminal FLD was localized to the cytoplasmic side of the inner membrane. Substitution mutations in the putative iron-binding amino acid residues E20A and E107A within the N-terminal FLD abrogate iron export activity and stress response function. Purified soluble FLD oxidizes ferrous iron (Fe²⁺) to incorporate ferric iron (Fe³⁺) in a 2:1 iron:protein ratio, which does not occur in the E20A/E107A mutant. The FLD fragment is a dimer in solution, implying that the MbfA exporter functions as a dimer. MbfA belongs to a protein family found in numerous prokaryotic genera. The findings strongly suggest that iron export plays an important role in bacterial iron homeostasis.     

A 3D Architectural and Process-based Model of Maize Development

A 3D architectural and process-based model of maize developmentwas implemented on the basis of the L-system software Graphtal,interfaced with physical models computing microclimate distributedon the 3D canopy structure. In a first step, we incorporatedin the software Graphtal additional functions that enable bi-directionalcommunication with external modules. A simple model for distributedphotosynthetically active radiation and the model for apex temperatureby Cellieret al. (Agricultural and Forest Meteorology63: 35–54,1993) were interfaced with Graphtal. In a second step we developeda L-system model for maize, where production rules for growthand development of organs are based on the current state ofknowledge of maize development as a function of temperature.Visual representation of the plant is based on the geometricalmodel of leaf shape by Prévot, Aries and Monestiez (Agronomie11:491–503, 1991). Finally, various data sets were used toevaluate the physiological aspects and the geometrical representation.It is concluded that environmental L-systems are a convenienttool to integrate biophysical processes from organ to canopylevel, and provide a framework to model growth of individualplants in relation to local conditions and ability to foragefor resources. However, progress is needed to improve both theknowledge of physiological processes at the organ level andthe calculation of physical environmental parameters; some directionsfor future research are proposed.Copyright 1998 Annals of BotanyCompany Growth model; 3D plant architecture;Zea maysL.; corn; temperature; L-system modelling; developmental physiology; virtual plant.     

Numerical design of a microfluidic chip for probing mechanical properties of cells

Microfluidic chips have been widely used to probe the mechanical properties of cells, which are recognized as a promising label-free biomarker for some diseases. In our previous work (Ye et al., 2018), we have studied the relationships between the transit time and the mechanical properties of a cell flowing through a microchannel with a single constriction, which potentially forms a basis for a microfluidic chip to measure cell’s mechanical properties. Here, we investigate this microfluidic chip design and examine its potential in performances. We first develop the simultaneous dependence of the transit time on both the shear and bending moduli of a cell, and then examine the chip sensitivity with respect to the cell mechanical properties while serializing a single constriction along the flow direction. After that, we study the effect of the flow velocity on the transit time, and also test the chip’s ability to identify heterogeneous cells with different mechanical properties. The results show that the microfluidic chip designed is capable of identifying heterogeneous cells, even when only one unhealthy cell is included. The serialization of chip can greatly increase the chip sensitivity with respect to the mechanical properties of cells. The flow with a higher velocity helps in not only promoting the chip throughput, but also in providing more accurate transit time measurements, because the cell prefers a symmetric deformation under a high velocity.     

A Model for Bacterial Colonization of Sinking Aggregates

Sinking aggregates provide important nutrient-rich environments for marine bacteria. Quantifying the rate at which motile bacteria colonize such aggregations is important in understanding the microbial loop in the pelagic food web. In this paper, a simple analytical model is presented to predict the rate at which bacteria undergoing a random walk encounter a sinking aggregate. The model incorporates the flow field generated by the sinking aggregate, the swimming behavior of the bacteria, and the interaction of the flow with the swimming behavior. An expression for the encounter rate is computed in the limit of large Péclet number when the random walk can be approximated by a diffusion process. Comparison with an individual-based numerical simulation is also given.     

A protein-protein interaction in magnetosomes: TPR protein MamA interacts with an Mms6 protein

Magnetosomes are membrane-enveloped bacterial organelles containing nano-sized magnetic particles, and function as a cellular magnetic sensor, which assist the cells to navigate and swim along the geomagnetic field. Localized with each magnetosome is a suite of proteins involved in the synthesis, maintenance and functionalization of the organelle, however the detailed molecular organization of the proteins in magnetosomes is unresolved. MamA is one of the most abundant magnetosome-associated proteins and is anchored to the magnetosome vesicles through protein-protein interactions, but the identity of the protein that interacts with MamA is undetermined. In this study, we found that MamA binds to a magnetosome membrane protein Mms6. Two different molecular masses of Mms6, 14.5-kDa and 6.0-kDa, were associated with the magnetosomes. Using affinity chromatography, we identified that the 14.5-kDa Mms6 interacts with MamA, and the interaction was further confirmed by pull-down, immunoprecipitation and size-exclusion chromatography assays. Prior to this, Mms6 was assumed to be strictly involved with biomineralizing magnetite; however, these results suggest that Mms6 has an additional responsibility, binding to MamA.