Computational design of microscopic swimmers and capsules: From directed motion to collective behavior

Systems of motile microscopic particles can exhibit behaviors that resemble those of living microorganisms, including cooperative motion, self-organization, and adaptability to changing environments. Using mesoscale computational modeling, we design synthetic microswimmers and microcapsules that undergo controllable, self-propelled motion in solution. Stimuli-responsive hydrogels are used to actuate the microswimmers and to enable their navigation and chemotaxing behavior. The self-propelled motion of microcapsules on solid surfaces is achieved by the release of encapsulated solutes that alter the surface adhesiveness. These signaling solutes also enable interactions among multiple microcapsules that lead to complex, cooperative behavior. Our findings provide guidelines for creating microscopic devices and machines able to autonomously move and mimic the communication and chemotaxis of biological microorganisms.     

Separation of progressive motile sperm from mouse semen using on-chip chemotaxis

We present a novel method for the separation of progressive motile sperm from non-progressive motile and immotile sperm. This separation was accomplished by inducing chemotaxis along a longitudinal chemical gradient in a microchip composed of a biocompatible polydimethysiloxane layer and a glass substrate. In a preliminary experiment using fluorescent rhodamine B as a marker, we verified that a chemical gradient was generated by diffusion within the microchannel. We used acetylcholine as a chemoattractant to evaluate the chemotactic response of sperm. We tested the response to a 1/2 to 1/64 dilution series of acetylcholine. The results of a mouse sperm chemotaxis assay showed that progressive motile sperm swam predominantly toward the outlet at an optimal chemical gradient of 0.625 (mg/ml)/mm of acetylcholine. This device provides a convenient, disposable, and high-throughput platform that could function as a progressive motile sperm sorter for potential use in intracytoplasmic sperm injection.     

Bioconvection Due to Gyrotactic Microorganisms in Couple Stress Hybrid Nanofluid Laminar Mixed Convection Incompressible Flow with Magnetic Nanoparticles and Chemical Reaction as Carrier for Targeted Drug Delivery through Porous Stretching Sheet

In this paper, the steady electrically conducting hybrid nanofluid (CuO-Cu/blood) laminar-mixed convection incompressible flow at the stagnation-point with viscous and gyrotactic microorganisms is considered. Additionally, hybrid nanofluid flow over a horizontal porous stretching sheet along with an induced magnetic field and external magnetic field effects that can be used in biomedical fields, such as in drug delivery and the flow dynamics of the microcirculatory system. This investigation can also deliver a perfect view about the mass and heat transfer behavior of blood flow in a circulatory system and various hyperthermia treatments such as the treatment of cancer. The simple partial differential equations (PDEs) are converted into a series of dimensional ordinary differential equations (ODEs), which are determined using appropriate similarities variables (HAM). The influence of the suction or injection parameter, mixed convection, Prandtl number, buoyancy ratio parameter, permeability parameter, magnetic parameter, reciprocal magnetic prandtl number, bioconvection Rayleigh number, coupled stress parameter, thermophoretic parameter, Schmidt number, inertial parameter, heat source parameter, and Brownian motion parameter on the concentration, motile microorganisms, velocity, and temperature is outlined, and we study the physical importance of the present problem graphically.     

Numerical treatment of Casson nanofluid Bioconvectional flow with heat transfer due to stretching cylinder/plate: Variable physical properties

PurposeThe purpose of the current framework is to scrutinize the two-dimensional flow and heat transfer of Casson nanofluid over cylinder/plate along with impacts of thermophoresis and Brownian motion effects. Also, the effects of exponential thermal sink/source, bioconvection, and motile microorganisms are taken.Methodology/ApproachThe resulting non-linear equations (PDEs) are reformed into nonlinear ODEs by using appropriate similarity variables. The resultant non-linear (ODEs) were numerically evaluated by the use of the Bvp4c package in the mathematical solver MATLAB.FindingsThe numerical and graphical illustration regarding outcomes represents the performance of flow-involved physical parameters on velocity, temperature, concentration, and microorganism profiles. Additionally, the skin friction coefficient, local Nusselt number, local Sherwood number, and local microorganism density number are computed numerically for the current presented system. We noted that the velocity profile diminishes for the rising estimations of magnetic and mixed convection parameters. The Prandtl number corresponds with the declining performance of the temperature profile observed. The enhancement in the values of the Solutal Biot number and Brownian motion parameter increased in the concentration profile.OriginalityIn specific, this framework focuses on the rising heat transfer of Casson nanofluid with bioconvection by using a shooting mathematical model. The novel approach of the presented study is the use of motile microorganisms with exponential thermal sink/source in a Casson nano-fluid through a cylinder/plate. A presented study performed first time in the author’s opinion. Understanding the flow characteristics and behaviors of these nanofluids is crucial for the scientific community in the developing subject of nanofluids.     

VIDEO DATA ACQUISITION FOR MOVEMENT RESPONSES IN INDIVIDUAL ORGANISMS

Abstract— We describe a simple approach for the semiautomatic acquisition of data from video recordings of movement responses of microorganisms. For a sessile microorganism like Phycomyces blakesleeanus , we describe an angle transducer consisting of a precision rolary potentiometer and a transparent ruler. This device is placed in front of a video monitor during playback from a time-lapse video recorder. The experimenter maintains the ruler parallel to the image of the upper region of the bending sporangiophore; a voltage proportional to the bending angle is directed to a strip-chart recorder. The chart provides a continuous and precise graph of the bending angle as a function of time, so that the latency, bending rate, and other parameters may be readily measured. For motile microorganisms, such as Euglena gracilis , paths from video recordings are traced onto acetate sheets during playback. A rotary and a linear potentiometer convert the angle and length of successive path elements into analog voltages which are transmitted by analog-to-digital converters to a microcomputer for subsequent statistical and mathematical treatment. The general approaches presented here should be applicable to the study of movement responses of many types of organisms.     

Numerical investigation on bioconvection flow of Oldroyd-B nanofluid with nonlinear thermal radiation and motile microorganisms over rotating disk

Journal of Thermal Analysis and Calorimetry - In this paper, the mechanism of radiative Oldroyd-B nanofluid flow over a rotating disk with activation energy and motile microorganisms is examined....     

Lensless imaging for simultaneous microfluidic sperm monitoring and sorting

5.3 million American couples of reproductive age (9%) are affected by infertility, among which male factors account for up to 50% of cases, which necessitates the identification of parameters defining sperm quality, including sperm count and motility. In vitro fertilization (IVF) with or without intra cytoplasmic sperm injection (ICSI) has become the most widely used assisted reproductive technology (ART) in modern clinical practice to overcome male infertility challenges. One of the obstacles of IVF and ICSI lies in identifying and isolating the most motile and presumably healthiest sperm from semen samples that have low sperm counts (oligozoospermia) and/or low sperm motility (oligospermaesthenia). Microfluidic systems have shown potential to sort sperm with flow systems. However, the small field of view (FOV) of conventional microscopes commonly used to image sperm motion presents challenges in tracking a large number of sperm cells simultaneously. To address this challenge, we have integrated a lensless charge-coupled device (CCD) with a microfluidic chip to enable wide FOV and automatic recording as the sperm move inside a microfluidic channel. The integrated system enables the sorting and tracking of a population of sperm that have been placed in a microfluidic channel. This channel can be monitored in both horizontal and vertical configuration similar to a swim-up column method used clinically. Sperm motilities can be quantified by tracing the shadow paths for individual sperm. Moreover, as the sperm are sorted by swimming from the inlet towards the outlet of a microfluidic channel, motile sperm that reach the outlet can be extracted from the channel at the end of the process. This technology can lead to methods to evaluate each sperm individually in terms of motility response in a wide field of view, which could prove especially useful, when working with oligozoospermic or oligospermaesthenic samples, in which the most motile sperm need to be isolated from a pool of small number of sperm.     

Microbial diversity in biodeteriorated monuments as studied by denaturing gradient gel electrophoresis

Studies of the microorganisms living on cultural assets and their potential damaging effects begin with an understanding of the microbial diversity present in such samples. Recently, molecular techniques have started to attract considerable interest since they do not require the culture of microorganisms in order to detect their presence. The basic protocol followed during microbial diversity analysis on cultural heritage assets utilizes electrophoretic techniques for separating highly homologous sequences. At present, Denaturing Gradient Gel Electrophoresis (DGGE) is the most frequently reported technique for separating DNA fragments during microbial diversity studies of art objects. In this report, we describe DGGE profiling techniques, show the most common applications, and present some examples of their use in microbial diversity studies on cultural heritage.     

基于微流控芯片的细菌趋化性检测研究进展

细菌趋化性是指有运动能力的细菌对环境化学物质梯度产生响应,趋向某些化学诱导剂或避开某些化学驱避剂的移动行为,是微生物适应环境变化而生存的一种基本属性.研究细菌趋化性对于利用细菌治理环境、控制病原菌侵染机体以及开发微生物工业项目等方面都具有重要意义.微流控芯片可以实现对细菌趋化性的定性与定量检测,与传统的检测方法相比,可以更好地对细菌的微环境进行控制,有较高的灵敏度.近年来,基于微流控技术检测细菌趋化性研究得到了飞速发展.本文从微流控芯片的结构、工作方式及主要应用3个方面对近年出现的微流控趋化性检测装置进行了介绍和评述.     

Double-diffusivity heat generation effects on bioconvection process embedded in a vertical porous surface with variable fluid properties

Journal of Thermal Analysis and Calorimetry - The present paper concerns the bioconvective flow, mass and heat transfer including motile microorganisms on a vertical surface saturated with porous...     

Bioconvective Homann flow of tangent hyperbolic nanofluid due to spiraling disk with convective and zero mas flux constraints

The phenomenon of bioconvection in nanomaterials presents novel applications in the biotechnology, biofuels, enzymes, biomedical engineering and energy systems. Current exploration explores the applications of bioconvection in Homann flow of nanofluid due to spiraling of disk theoretically. The generalized model namely tangent hyperbolic fluid is used to predicts the rheological and thermal impact. The stability of nanofluid is ensured with interaction of motile microorganisms. The Boungrino nanofluid model with thermophoresis and Brownian motion features is used to perform the analysis The thermal distribution of nanofluids is proceeded by utilizing the zero mass thermal constraints. The similarity variables are introduced in order to estimating the dimensionless formulation. The Keller Box method with higher efficiency is imposed with implicit finite difference numerical algorithm. The main observations reveal that with enhancing the radial velocity and azimuthal velocity decreases with increasing sparling angle. For highly viscous case, a decrement in the azimuthal velocity has been observed.     

Electrochemical Motion Tracking of Microorganisms Using a Large-Scale-Integration-Based Amperometric Device

Motion tracking of microorganisms is useful to investigate the effects of chemical or physical stimulation on their biological functions. Herein, we describe a novel electrochemical imaging method for motion tracking of microorganisms using a large-scale integration (LSI)-based amperometric device. The device consists of 400 electrochemical sensors with a pitch of 250 μm. A convection flow caused by the motion of microorganisms supplies redox species to the sensors and increases their electrochemical responses. Thus, the flow is converted to electrochemical signals, enabling the electrochemical motion tracking of the microorganisms. As a proof of concept, capillary vibration was monitored. Finally, the method was applied to monitoring the motion of Daphnia magna. The motions of these microorganisms were clearly tracked based on the electrochemical oxidation of [Fe(CN)₆]⁴⁻ and reduction of O₂.     

Electrochemical Motion Tracking of Microorganisms Using a Large‐Scale‐Integration‐Based Amperometric Device

Motion tracking of microorganisms is useful to investigate the effects of chemical or physical stimulation on their biological functions. Herein, we describe a novel electrochemical imaging method for motion tracking of microorganisms using a large‐scale integration (LSI)‐based amperometric device. The device consists of 400 electrochemical sensors with a pitch of 250 μm. A convection flow caused by the motion of microorganisms supplies redox species to the sensors and increases their electrochemical responses. Thus, the flow is converted to electrochemical signals, enabling the electrochemical motion tracking of the microorganisms. As a proof of concept, capillary vibration was monitored. Finally, the method was applied to monitoring the motion of Daphnia magna . The motions of these microorganisms were clearly tracked based on the electrochemical oxidation of [Fe(CN)₆]⁴⁻ and reduction of O₂.     

Emergent Swarming States in Active Particles System with Opposite Anisotropic Interactions

From the organization of animal flocks to the emergence of swarming behaviors in bacterial suspension, populations of motile organisms at all scales display coherent collective motion. Recent studies showed that the anisotropic interaction between active particles plays a key role in the phase behaviors. Here we investigate the collective behaviors of based-active Janus particles that experience an anisotropic interaction of which the orientation is opposite to the direction of active force by using Langevin dynamics simulations in two dimensional space. Interestingly, the system shows emergence of collective swarming states upon increasing the total area fraction of particles, which is not observed in systems without anisotropic interaction or activity. The threshold for emergence of swarming states decreases as particle activity or interaction strength increases. We have also performed basic kinetic analysis to reproduce the essential features of the simulation results. Our results demonstrate that anisotropic interactions at the individual level are sufficient to set homogeneous active particles into stable directed motion.     

Hydrogels with Dynamically Controllable Mechanics and Biochemistry for 3D Cell Culture Platforms

Many cell-matrix interaction studies have proved that dynamic changes in the extracellular matrix(ECM)are crucial to maintain cellular properties and behaviors.Thus,developing materials that can recapitulate the dynamic attributes of the ECM is highly desired for threedimensional(3 D)cell culture platforms.To this end,we sought to develop a hydrogel system that would enable dynamic and reversible turning of its mechanical and biochemical properties,thus facilitating the control of cell culture to imitate the natural ECM.Herein,a hydrogel with dynamic mechanics and a biochemistry based on an addition-fragmentation chain transfer(AFCT)reaction was constructed.Thiol-modified hyaluronic acid(HA)and allyl sulfide-modifiedε-poly-L-lysine(EPL)were synthesized to form hydrogels,which were non-swellable and biocompatible.The reversible modulus of the hydrogel was first achieved through the AFCT reaction;the modulus can also be regulated stepwise by changing the dose of UVA irradiation.Dynamic patterning of fluorescent markers in the hydrogel was also realized.Therefore,this dynamically controllable hydrogel has great potential as a 3 D cell culture platform for tissue engineering applications.     

Synthetic electrically driven colloids: A platform for understanding collective behavior in soft matter

The collective motion of synthetic active colloids is an emerging area of research in soft matter physics and is important both as a platform for fundamental studies ranging from non-equilibrium statistical mechanics to the basic principles of self-organization, emergent phenomena, and assembly underlying life, as well as applications in biomedicine and metamaterials. The potentially transformative nature of the field over the next decade and beyond is a topic of critical research importance. Electrokinetic active colloids represent an extremely flexible platform for the investigation and modulation of collective behavior in active matter. Here, we review progress in the past five years in electrokinetic active systems and related topics in active matter with important fundamental research and applicative potential to be investigated using electrokinetic systems.     

A Rapid and Simple Method for Preparing an Insoluble Substrate for Screening of Microbial Xylanase

Several types of enzymes, including cellulases and xylanases, are required to degrade hemicelluloses and cellulose, which are major components of lignocellulosic biomass. Such degradative processes can be used to produce various useful industrial biomaterials. Screening methods for detecting polysaccharide-degrading microorganisms include the use of dye-labeled substrates in growth medium and culture plate staining techniques. However, the preparation of screening plates, which typically involves chemical cross-linking to synthesize a dye-labeled substrate, is a complicated and time-consuming process. Moreover, such commercial substrates are very expensive, costing tenfold more than the natural xylan. Staining methods are also problematic because they may damage relevant microorganisms and are associated with contamination of colonies of desirable organisms with adjacent unwanted bacteria. In the present study, we describe a sonication method for the simple and rapid preparation of an insoluble substrate that can be used to screen for xylanase-expressing bacteria in microbial populations. Using this new method, we have successfully isolated a novel xylanase gene from a xylolytic microorganism termed Xyl02-KBRB and Xyl14-KBRB in the bovine rumen.     

Biohybrid bacterial microswimmers with metal-organic framework exoskeletons enable cytoprotection and active drug delivery in a harsh environment

The inspiring idea of using motile bacteria as bioengines to create biohybrid microswimmers has been realized by integrating functionalized cargos with bacteria recently. However, existing pernicious factors in ambient conditions, such as enzymes, may attack bacterial microsystems when they are executing tasks. Here, a versatile bacterial microswimmer system with cytoprotective metal-organic framework (MOF) exoskeletons is reported, capable of protecting the bioengine from enzyme degradation. Zeolitic imidazolate framework-8 (ZIF-8) nanoparticles (NPs) are fully coated on the surface of motile bacteria (Escherichia coli MG1655) through tannic acid (TA) complexation. The ZIF-8 wrapping is demonstrated with negligible influence on bacterial motility under optimized conditions. Moreover, ZIF-8@E. coli microswimmers still maintain their shapes and motion performance in the presence of lysozyme, verifying the effective preservation of formed ZIF-8 exoskeletons on the bacterial surface. Coupling with the drug loading capacity of ZIF-8, Doxorubicin (DOX)-loaded ZIF-8@E. coli microsystems retain their effective propulsion after being treated with lysozyme, enabling the accelerated crossing through the Transwell membrane and improving anticancer efficacy compared with passive drugs. The fabricated bacterial microswimmers were also verified with chemotactic motion and prolonged retention time in the mouse bladder, holding great potential to design an active medical platform with improved therapeutic efficacy for targeted disease treatment, such as bladder cancer. Combining bacteria with MOFs generates multifunctional biohybrid microswimmers with capabilities of cytoprotection and active drug delivery. Such design facilitates the development of active biosystems to apply in harsh environments and meets rigorous requirements in clinical biomedical applications.     

Attachment of motile bacterial cells to prealigned holed microarrays

Construction of biomotors is an exciting area of scientific research that holds great promise for the development of new technologies with broad potential applications in areas such as the energy industry and medicine. Herein, we demonstrate the fabrication of prealigned microarrays of motile Escherichia coli bacterial cells on SiOx substrates. To prepare these arrays, holed surfaces with a gold layer on the bottom of the holes were utilized. The attachment of bacteria to the holes was achieved via nonspecific interactions using poly-l-lysine hydrobromide (PLL). Our data suggest that a single motile bacterial cell can be selectively attached to an individual hole on a surface and bacterial cell binding can be controlled by altering the pH, with the greatest occupancy occurring at pH 7.8. Cells attached to hole arrays remained motile for at least 4 h. These data indicate that holed surface structures provide a promising footprint for the attachment of motile bacterial cells to form high-density site-specific functional bacterial microarrays.     

Automated Microbial Library Generation Using the Bioinformatics Platform IDBac

Libraries of microorganisms have served as a cornerstone of therapeutic drug discovery, though the continued re-isolation of known natural product chemical entities has remained a significant obstacle to discovery efforts. A major contributing factor to this redundancy is the duplication of bacterial taxa in a library, which can be mitigated through the use of a variety of DNA sequencing strategies and/or mass spectrometry-informed bioinformatics platforms so that the library is created with minimal phylogenetic, and thus minimal natural product overlap. IDBac is a MALDI-TOF mass spectrometry-based bioinformatics platform used to assess overlap within collections of environmental bacterial isolates. It allows environmental isolate redundancy to be reduced while considering both phylogeny and natural product production. However, manually selecting isolates for addition to a library during this process was time intensive and left to the researcher’s discretion. Here, we developed an algorithm that automates the prioritization of hundreds to thousands of environmental microorganisms in IDBac. The algorithm performs iterative reduction of natural product mass feature overlap within groups of isolates that share high homology of protein mass features. Employing this automation serves to minimize human bias and greatly increase efficiency in the microbial strain prioritization process.