Biomolecular force measurements and the atomic force microscope

The atomic force microscope (AFM) is a surface-sensitive instrument capable of imaging biological samples at nanometer resolution in all environments including liquids. The sensitivity of the AFM cantilever, to forces in the pico Newton range, has been exploited to measure breakaway forces between biomolecules and to measure folding-unfolding forces within single proteins. By attaching specific antibodies to cantilevers the simultaneous imaging of target antigens and identification of antigen-antibody interactions have been demonstrated.     

Amyloid under the atomic force microscope

The atomic force microscope (AFM) is a versatile instrument that can be used to image biological samples at nanometre resolution as well as to measure inter and intra-molecular forces in air and liquid environments. This review summarises the use of AFM applied to protein and peptide self-assembly systems involved in amyloid formation. The technical principles of the AFM are outlined and its advantages and disadvantages are highlighted and discussed in the context of the rapidly developing field of amyloid research.     

Atomic force microscopy: from cellular imaging to molecular manipulation

Using a sharp tip attached at the end of a soft cantilever as a probe, the atomic force microscope (AFM) explores the surface topography of biological samples bathed in physiological solutions. In the last few years, the AFM has gained popularity among biologists. This has been obtained through the improvement of the equipment and imaging techniques as well as through the development of new non-imaging applications. Biological imaging has to face a main difficulty that is the softness and the dynamics of most biological materials. Progress in understanding the AFM tip-biological samples interactions provided spectacular results in different biological fields. Recent examples of the possibilities offered by the AFM in the imaging of intact cells, isolated membranes, membrane model systems and single molecules at work are discussed in this review. Applications where the AFM tip is used as a nanotool to manipulate biomolecules and to determine intra- and intermolecular forces from single molecules are also presented.     

Application of atomic force microscopy to the study of micromechanical properties of biological materials

Atomic force microscopy (AFM) has been used to study the micromechanical properties of biological systems. Its unique ability to function both as an imaging device and force sensor with nanometer resolution in both gaseous and liquid environments has meant that AFM has provided unique insights into the mechanical behaviour of tissues, cells and single molecules. As a surface scanning device, AFM can map properties such as adhesion and the Young's modulus of surfaces. As a force sensor and nanoindentor AFM can directly measure properties such as the Young's modulus of surfaces or the binding forces of cells. As a stress-strain gauge AFM can study the stretching of single molecules or fibres and as a nanomanipulator it can dissect biological particles such as viruses or DNA strands. The present paper reviews key research that has demonstrated the versatility of AFM and how it can be exploited to study the micromechanical behaviour of biological materials.     

An octopus-bioinspired solution to movement and manipulation for soft robots

Soft robotics is a challenging and promising branch of robotics. It can drive significant improvements across various fields of traditional robotics, and contribute solutions to basic problems such as locomotion and manipulation in unstructured environments. A challenging task for soft robotics is to build and control soft robots able to exert effective forces. In recent years, biology has inspired several solutions to such complex problems. This study aims at investigating the smart solution that the Octopus vulgaris adopts to perform a crawling movement, with the same limbs used for grasping and manipulation. An ad hoc robot was designed and built taking as a reference a biological hypothesis on crawling. A silicone arm with cables embedded to replicate the functionality of the arm muscles of the octopus was built. This novel arm is capable of pushing-based locomotion and object grasping, mimicking the movements that octopuses adopt when crawling. The results support the biological observations and clearly show a suitable way to build a more complex soft robot that, with minimum control, can perform diverse tasks.     

Modeling Group Formation and Activity Patterns in Self-Organizing Collectives of Individuals

We construct and analyze a nonlocal continuum model for group formation with application to self-organizing collectives of animals in homogeneous environments. The model consists of a hyperbolic system of conservation laws, describing individual movement as a correlated random walk. The turning rates depend on three types of social forces: attraction toward other organisms, repulsion from them, and a tendency to align with neighbors. Linear analysis is used to study the role of the social interaction forces and their ranges in group formation. We demonstrate that the model can generate a wide range of patterns, including stationary pulses, traveling pulses, traveling trains, and a new type of solution that we call zigzag pulses. Moreover, numerical simulations suggest that all three social forces are required to account for the complex patterns observed in biological systems. We then use the model to study the transitions between daily animal activities that can be described by these different patterns.     

Acoustic radiation force optical coherence elastography for evaluating mechanical properties of soft condensed matters and its biological applications

Evaluating mechanical properties of biological soft tissues and viscous mucus is challenging because of complicated dynamic behaviors. Soft condensed matter models have been successfully used to explain a number of dynamical behaviors. Here, we reported that optical coherence elastography (OCE) is capable of quantifying mechanical properties of soft condensed matters, micellar fluids. A 7.5 MHz focused transducer was utilized to generate acoustic radiation force exerted on the surface of soft condensed matters in order to produce Rayleigh waves. The waves were recorded by optical coherence tomography (OCT). The Kelvin‐Voigt model was adopted to evaluate shear modulus and loss modulus of soft condensed matters. The results reported that various concentrations of micellar fluids can provide reasonable ranges of elasticity from 65.71 to 428.78 Pa and viscosity from 0.035 to 0.283 Pa·s, which are close to ranges for actual biological samples, like mucus. OCE might be a promising tool to differentiate pathologic mucus samples from healthy cases as advanced applications in the future.     

A simple cryogenic holder for tensile testing of soft biological tissues

To overcome the difficulty of gripping soft biological materials for tensile test, a simple inexpensive cryogenic holder was developed which allows rapid (3 min) preparation of samples. It is made of 6 parts, built in a bakelite cloth, which is an excellent thermal isolant, and is used with rectangular (8x10(-2)x10(-2)x10(-2)m) samples. The holder with the sample inside is completely immersed in liquid nitrogen for 50 s. This duration allows the freezing of the sample ends on a 10(-2)m length and gives a very flat freezing surface throughout the sample cross section. The 6x10(-2)m central part of the sample remained at ambient temperature. Two parts of the holder help maintain the sample until its ends are vertically gripped in the tensile machine thus avoiding any sample deformation during this step. No pressure was applied on the frozen part of the sample by grips of the tensile machine and this avoids breaks in this region. The sample is fixed by adhesion forces (>1 kN) between its frozen parts and 2 pieces of the holder. The procedure has been successfully tested with bovine and salmon muscle samples and results show tensile breaks randomly distributed in the unfrozen region of the samples. Particular attention has been paid to obtain a very flat freezing surface so that the axial strain is equal throughout the sample and therefore any strain-related mechanical parameters can be accurately determined. The dimensions of the holder can be easily modified to fit other sample geometries and can be used with other biological materials.     

Atomic force microscopy of insulin single crystals: direct visualization of molecules and crystal growth.

Atomic force microscopy performed on single crystals of three different polymorphs of bovine insulin revealed molecularly smooth (001) layers separated by steps whose heights reflect the dimensions of a single insulin hexamer. Whereas contact mode imaging caused etching that prevented molecular-scale resolution, tapping mode imaging in solution provided molecular-scale contrast that enabled determination of lattice parameters and polymorph identification while simultaneously enabling real-time examination of growth modes and assessment of crystal quality. Crystallization proceeds layer by layer, a process in which the protein molecules assemble homoepitaxially with nearly perfect orientational and translational commensurism. Tapping mode imaging also revealed insulin aggregates attached to the (001) faces, their incorporation into growing terraces, and their role in defect formation. These observations demonstrate that tapping mode imaging is ideal for real-time in situ investigation of the crystallization of soft protein crystals of relatively small proteins such as insulin, which cannot withstand the lateral shear forces exerted by the scanning probe in conventional imaging modes.     

Forces on Biological Particles in Electric Fields

The forces exerted by electric fields on particles suspended in biological fluids are examined. Both charged particles and polarlzable bodies are treated and expressions for the current flow under the influence of an electric field are obtained.     

An artificial muscle actuator for biomimetic underwater propulsors

In this paper, we introduce the analytical framework of the modeling dynamic characteristics of a soft artificial muscle actuator for aquatic propulsor applications. The artificial muscle used for this underwater application is an ionic polymer-metal composite (IPMC) which can generate bending motion in aquatic environments. The inputs of the model are the voltages applied to multiple IPMCs, and the output can be either the shape of the actuators or the thrust force generated from the interaction between dynamic actuator motions and surrounding water. In order to determine the relationship between the input voltages and the bending moments, the simplified RC model is used, and the mechanical beam theory is used for the bending motion of IPMC actuators. Also, the hydrodynamic forces exerted on an actuator as it moves relative to the surrounding medium or water are added to the equations of motion to study the effect of actuator bending on the thrust force generation. The proposed method can be used for modeling the general bending type artificial muscle actuator in a single or segmented form operating in the water. The segmented design has more flexibility in controlling the shape of the actuator when compared with the single form, especially in generating undulatory waves. Considering an inherent nature of large deformations in the IPMC actuator, a large deflection beam model has been developed and integrated with the electrical RC model and hydrodynamic forces to develop the state space model of the actuator system. The model was validated against existing experimental data.     

Force microscopy imaging of individual protein molecules with sub-pico Newton force sensitivity

The capability of atomic force microscopes (AFM) to generate atomic or nanoscale resolution images of surfaces has deeply transformed the study of materials. However, high resolution imaging of biological systems has proved more difficult than obtaining atomic resolution images of crystalline surfaces. In many cases, the forces exerted by the tip on the molecules (1-10 nN) either displace them laterally or break the noncovalent bonds that hold the biomolecules together. Here, we apply a force microscope concept based on the simultaneous excitation of the first two flexural modes of the cantilever. The coupling of the modes generated by the tip-molecule forces enables imaging under the application of forces ( approximately 35 pN) which are smaller than those needed to break noncovalent bonds. With this instrument we have resolved the intramolecular structure of antibodies in monomer and pentameric forms. Furthermore, the instrument has a force sensitivity of 0.2 pN which enables the identification of compositional changes along the protein fragments.     

Incorporating fundamental laws of biology and physics into population ecology: the metaphysiological approach

Models commonly used in population ecology have somewhat vague and often misleading connections with physical and biological processes connecting organisms with their environments. The metaphysiological modelling approach offers a conceptual framework that is consistent with basic laws and enables integration across levels of organization from cells to ecosystems. This perspective accommodates the intrinsically disequilibrial nature of biological systems in changing environments, as well as adaptive responses to these changes. More attention needs to be paid to factors governing mortality losses rather than the functional or intake response alone. Models need to be based more firmly on underlying biophysical processes in order to serve as reliable guides to conservation action in novel environments.     

A Submersible,Off-Axis Holographic Microscope for Detection of Microbial Motility and Morphology in Aqueous and Icy Environments

Sea ice is an analog environment for several of astrobiology’s near-term targets: Mars, Europa, Enceladus, and perhaps other Jovian or Saturnian moons. Microorganisms, both eukaryotic and prokaryotic, remain active within brine channels inside the ice, making it unnecessary to penetrate through to liquid water below in order to detect life. We have developed a submersible digital holographic microscope (DHM) that is capable of resolving individual bacterial cells, and demonstrated its utility for immediately imaging samples taken directly from sea ice at several locations near Nuuk, Greenland. In all samples, the appearance and motility of eukaryotes were conclusive signs of life. The appearance of prokaryotic cells alone was not sufficient to confirm life, but when prokaryotic motility occurred, it was rapid and conclusive. Warming the samples to above-freezing temperatures or supplementing with serine increased the number of motile cells and the speed of motility; supplementing with serine also stimulated chemotaxis. These results show that DHM is a useful technique for detection of active organisms in extreme environments, and that motility may be used as a biosignature in the liquid brines that persist in ice. These findings have important implications for the design of missions to icy environments and suggest ways in which DHM imaging may be integrated with chemical life-detection suites in order to create more conclusive life detection packages.     

Atomic force microscopy: from cell imaging to molecular manipulation

The atomic force microscope (AFM) allows to explore the surface of biological samples bathed in physiological solutions, with vertical and horizontal resolutions ranging from nanometers to angstr?ms. Complex biological structures as well as single molecules can be observed and recent examples of the possibilities offered by the AFM in the imaging of intact cells, isolated membranes, membrane model systems and single molecules are discussed in this review. Applications where the AFM tip is used as a nanotool to manipulate biomolecules and to determine intra and intermolecular forces from single molecules are also presented.     

TopCount coupled to ultra-performance liquid chromatography for the profiling of radiolabeled drug metabolites in complex biological samples

The recent commercial availability of small particle packed columns (<2microm) and associated instrumentation capable of withstanding the high pressures of such columns, has lead to an increase in the application of so called ultra-performance liquid chromatography (UPLC). It has recently been shown that the improved efficiency, resolution and peak capacity of these columns, when coupled to mass spectrometry, provides particular benefit for the identification of drug metabolites in complex biological samples. In this work, the ability of TopCount, a microplate scintillation counter, to act as a suitable radiodetection system for ultra-performance liquid chromatography methods is tested. TopCount, has innumerable benefits over more traditional on-line radioactivity flow detection methods, when dealing with the narrow peak widths and small peak volumes associated with the enhanced efficiency of sub-2microm columns. The system is tested for robustness and sensitivity, and then used to undertake successful metabolite profiling of actual samples, and the data compared to traditional HPLC with on-line radioactivity flow detector.     

Imaging soft samples with the atomic force microscope: gelatin in water and propanol.

We have imaged mica coated with thin gelatin films in water, propanol, and mixtures of these two liquids by atomic force microscopy (AFM). The elastic modulus (Young's modulus) can be tuned from 20 kPa to more than 0.1 GPa depending on the ratio of propanol to water. The resolution is best in pure propanol, on the order of 20 nm, and becomes worse for the softer samples. The degradation in resolution can be understood by considering the elastic indentation of the gelatin caused by the AFM tip. This indentation becomes larger and thus the contact area becomes larger the softer the sample is. Therefore this study may be used to estimate the resolution to be expected with an AFM on other soft samples, such as cells. Nondestructive imaging was possible only by imaging at forces < 1 nN. This was difficult to achieve in contact mode because of drift in the zero load deflection of the cantilever, supposedly caused by temperature drift, but straightforward in tapping mode.     

Three-Dimensional Balance of Cortical Tension and Axial Contractility Enables Fast Amoeboid Migration

Fast amoeboid migration requires cells to apply mechanical forces on their surroundings via transient adhesions. However, the role these forces play in controlling cell migration speed remains largely unknown. We used three-dimensional force microscopy to measure the three-dimensional forces exerted by chemotaxing Dictyostelium cells, and examined wild-type cells as well as mutants with defects in contractility, internal F-actin crosslinking, and cortical integrity. We showed that cells pull on their substrate adhesions using two distinct, yet interconnected mechanisms: axial actomyosin contractility and cortical tension. We found that the migration speed increases when axial contractility overcomes cortical tension to produce the cell shape changes needed for locomotion. We demonstrated that the three-dimensional pulling forces generated by both mechanisms are internally balanced by an increase in cytoplasmic pressure that allows cells to push on their substrate without adhering to it, and which may be relevant for amoeboid migration in complex three-dimensional environments.     

High-resolution micromechanical measurement in real time of forces exerted by living cells

The aim of this study was to compare uniaxial traction forces exerted by different cell types using a novel sensor design and to test the dependence of measured forces on cytoskeletal integrity. The sensor design detects forces generated between 2 contact points by cells spanning a gap. The magnitude of these forces varied according to cell type and were dependent on cytoskeletal integrity. The response time for drug-induced cytoskeletal disruption also varied between cell types: dermal fibroblasts exerted the greatest forces and had the slowest drug response times; EBV-transformed epithelial cells also had slow cytoskeletal depolymerisation times but exerted the lowest forces overall. Conversely, lung epithelial tumor cells exerted low forces but had the fastest depolymerisation drug response. These results provide proof of principle for a new design of force-measurement sensor based on optical interferometry, an approach that can be used to study cytoskeletal dynamics in real time.     

Force platform for rats measures fore and hind forces concurrently

Animal models are commonly used to test the efficacy of impact loading regimens on bone strength. We designed an inexpensive force platform to concurrently measure the separate peak vertical impact forces produced by the fore and hindfeet of immature F-344 rats when dropped onto the platform. The force platform consisted of three load cells placed in a triangular pattern under a flat plate. Rats were dropped from heights of 30, 45 and 60 cm onto the platform so that they landed on all four feet concurrently. The peak vertical impact forces produced by the feet of the rats were measured using a sampling frequency of 100 kHz. The location of each foot at landing relative to the load cells, and the force received by each load cell were combined in a series of static equations to solve for the vertical impact forces produced by the fore and hindfeet. The forces produced by feet when rats stood on the single platform were similarly determined. The forces exerted separately by the fore and hindfeet of young rats when landing on the plate as a ratio to standing forces were then calculated. Rats when standing bore more weight on their hindfeet but landed with more weight on their forefeet, which provides rationale for the greater response to landing forces of bones in the forelimbs than those in the hindlimbs. This system provided a useful method to simultaneously measure peak vertical impact forces in fore and hindfeet in rats.