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Characterization of freshwater natural aquatic colloids by atomic force microscopy (AFM).

Atomic force microscopy (AFM) has been used to image and quantify riverine colloids in a quantitative and relatively nonperturbing manner. Three main classes of material have been imaged including fibrils (about 10 nm in diameter and 100 nm or more in length), discrete, near-spherical, small colloids primarily below 30-50 nm in diameter, and a surface film, of at least several nanometers thickness, which coatsthe entire mica surface within 30 min of exposure to river water. Colloid structure was found to vary as a function of pH, particularly at high pH. Substantially different structures were observed at high pH values, with the loss of the near-spherical colloids possibly due to rearrangement and aggregation. In addition,film thicknesses of up to 100 nm were estimated on the silicon nitride AFM cantilever after 30 h of deposition in the same water (unperturbed and size fractionated). The observation of these surface films has important implications for understanding the mechanisms by which colloids might bind trace elements. In particular, development of surface coatings implies that binding of pollutants (at least initial surface binding) may be dominated by adsorbed surface layers.

Adsorption↗

Solid-state microstructure of poly(l-lactide) and l-lactide/meso-lactide random copolymers by atomic force microscopy (AFM).

Tapping mode atomic force microscopy was used to investigate the lamellar morphology of poly(l-lactide) and two poly(l-lactide-co-meso-lactide) random copolymers containing 3% and 6% meso-lactide. Samples were isothermally crystallized at selected temperatures, and qualitative and quantitative analyses of lamellar structure were performed using height and phase images. This is the first study of the morphology of polylactide stereocopolymers using a real-space probe, and the important effects of scanning parameters on the acquired images are described. More open spherulites with an abundance of screw dislocations between edge-on lamellar stacks were observed in samples crystallized at higher temperatures. Mean lamellar thicknesses are lower for the random copolymers compared to PLLA, particularly at lower DeltaT, in agreement with the results of our previous small-angle X-ray scattering (SAXS) experiments. Mean lamellar thicknesses derived from the current real-space examination are in good agreement with those determined previously from SAXS. Internal surfaces-from microtomed specimens-were also studied to investigate the bulk crystal morphology. Although quantitative analysis was not feasible (for reasons discussed in the text), lamellar organization similar to that seen in the surface experiments is observed at high magnifications.

Biocompatible Materials↗

Quantification of bacterial adhesion forces using atomic force microscopy (AFM).

This study demonstrated that atomic force microscopy (AFM) can be used to obtain high-resolution topographical images of bacteria, and to quantify the tip-cell interaction force and the surface elasticity. Results show that the adhesion force between the Si3N4 tip and the bacteria surface was in the range from -3.9 to -4.3 nN. On the other hand, the adhesion forces at the periphery of the cell-substratum contact surface ranged from -5.1 to -5.9 nN and those at the cell-cell interface ranged from -6.5 to -6.8 nN. The two latter forces were considerably greater than the former one, most likely due to the accumulation of extracellular polymer substance (EPS). Results also show that the elasticity varied on the cell surface.

Aluminum Silicates↗

Nanodissection and high-resolution imaging of the Rhodopseudomonas viridis photosynthetic core complex in native membranes by AFM. Atomic force microscopy.

In photosynthesis, highly organized multiprotein assemblies convert sunlight into biochemical energy with high efficiency. A challenge in structural biology is to analyze such supramolecular complexes in native membranes. Atomic force microscopy (AFM) with high lateral resolution, high signal-to-noise ratio, and the possibility to nanodissect biological samples is a unique tool to investigate multiprotein complexes at molecular resolution in situ. Here we present high-resolution AFM of the photosynthetic core complex in native Rhodopseudomonas viridis membranes. Topographs at 10-A lateral and approximately 1-A vertical resolution reveal a single reaction center (RC) surrounded by a closed ellipsoid of 16 light-harvesting (LH1) subunits. Nanodissection of the tetraheme cytochrome (4Hcyt) subunit from the RC allows demonstration that the L and M subunits exhibit an asymmetric topography intimately associated to the LH1 subunits located at the short ellipsis axis. This architecture implies a distance distribution between the antenna and the RC compared with a centered location of the RC within a circular LH1, which may influence the energy transfer within the core complex. The LH1 subunits rearrange into a circle after removal of the RC from the core complex.

Image Processing, Computer-Assisted↗

Force and Compliance Measurements on Living Cells Using Atomic Force Microscopy (AFM).

We describe the use of atomic force microscopy (AFM) in studies of cell adhesion and cell compliance. Our studies use the interaction between leukocyte function associated antigen-1 (LFA-1)/intercellular adhesion molecule-1 (ICAM-1) as a model system. The forces required to unbind a single LFA-1/ICAM-1 bond were measured at different loading rates. This data was used to determine the dynamic strength of the LFA-1/ICAM-1 complex and characterize the activation potential that this complex overcomes during its breakage. Force measurements acquired at the multiple- bond level provided insight about the mechanism of cell adhesion. In addition, the AFM was used as a microindenter to determine the mechanical properties of cells. The applications of these methods are described using data from a previous study.

Journal Article↗

Visual representation by atomic force microscopy (AFM) of tomato spotted wilt virus ribonucleoproteins.

Atomic force microscopy (AFM) allows the observation of biological material without fixation procedures. Here we present AFM images of ribonucleoproteins (nucleocapsids) derived from a plant infecting RNA virus (tomato spotted wilt virus, TSWV), which have been recorded in contact mode. The nucleocapsids, prepared from systemically infected leaves of tobacco, were spreaded on a glass surface and dried in air, and appeared as regularly formed rings, resembling the proposed pseudocircular and panhandle structure of encapsidated genomic RNA. Average values between 1300 and 2200 nm of nucleocapsid lengths could be related to dimensions estimated by electron microscopy, thereby validating a filamentous configuration of the TSWV ribonucleoproteins. However, to our knowledge regular, ring-like forms of ribonucleoproteins have not been obtained by electron microscopy, which rather showed an amorphous structure of the virus particles. Hence, the AFM approach provides a starting point for further detailed studies on TSWV ribonucleoprotein complexes.

Centrifugation, Density Gradient↗

A multi-wall carbon nanotube (MWCNT) relocation technique for atomic force microscopy (AFM) samples.

A simple relocation technique for atomic force microscopy (AFM), which takes advantage of multi-wall carbon nanotube (MWCNT), is used for investigating repeatedly the imaging of some specific species on the whole substrate with a high relocation accuracy of tens of nanometers. As an example of the application of this technique, TappingMode AFM ex situ study of the morphology transition induced by solvent treatment in a triblock copolymer thin film has been carried out.

Journal Article↗

Aspects of the physical chemistry of polymers, biomaterials and mineralised tissues investigated with atomic force microscopy (AFM).

Beyond being merely a tool for measuring surface topography, atomic force microscopy (AFM) has made significant contributions to various scientific areas dealing with physical chemistry processes. This paper presents aspects of the physical chemistry at surfaces and interfaces of polymers, biomaterials and tissues investigated with AFM. Selected examples presented include surface induced self-assembly of polymer blends, copolymer interfacial reinforcement of immiscible homopolymers, protein adsorption on biomaterials and erosion of mineralised human tissues. In these areas, AFM is a useful and versatile tool to study structural or dynamic sample properties including thermodynamically driven surface evolution of polymer surfaces, lateral surface composition of interfaces, adsorption processes, and the metrology of demineralisation phenomena.

Journal Article↗

A relocated technique of atomic force microscopy (AFM) samples and its application in molecular biology.

A kind of simple atomic force microscopy (AFM) relocated technique, which takes advantage of homemade sample locator system, is used for investigating repeatedly imaging of some specific species on the whole substrate (over 1 x 1 cm2) with resolution about 400 nm. As applications of this sample locator system, single extended DNA molecules and plasmid DNA network are shown in different AFM operational modes: tapping mode and contact mode with different tips after the substrates have been moved.

Aluminum Silicates↗

Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr3+ ions: VCD and AFM evidence of DNA condensation.

The interaction of natural calf thymus DNA with Cr(3+) ions was studied at room temperature by means of vibrational CD (VCD) and infrared absorption (ir) spectroscopy, and atomic force microscopy (AFM). Cr(3+) ion binding mainly to N(7) (G) and to phosphate groups was demonstrated. Psi-type VCD spectra resembling electronic CD (ECD) spectra, which appear during psi-type DNA condensation, were observed. These spectra are characterized mainly by an anomalous, severalfold increase of VCD intensity. Such anomalous VCD spectra were assigned to DNA condensation with formation of large and dense particles of a size comparable to the wavelength of the probing ir beam and possessing large-scale helicity. Atomic force microscopy confirmed DNA condensation by Cr(3+) ions and the formation of tight DNA particles responsible for the psi-type VCD spectra. Upon increasing the Cr(3+) ion concentration the shape of the condensates changed from loose flower-like structures to highly packed dense spheres. No DNA denaturation was seen even at the highest concentration of Cr(3+) ions studied. The secondary structure of DNA remained in a B-form before and after the condensation. VCD and ir as well as AFM proved to be an effective combination for investigating DNA condensation. In addition to the ability of VCD to determine DNA condensation, VCD and ir can in the same experiment provide unambiguous information about the secondary structure of DNA contained in the condensed particles.

Animals↗

Ultrastructural pathology of varicocele spermatozoa by using atomic force microscopy (AFM).

Ultrastructural investigation of pathological spermatozoa of patients having varicocele (grades I and III) in its natural environment (without fixation, dehydration, embedding, sectioning, etc.) was carried out by using Atomic Force Microscope (AFM) in tapping mode. This is a unique technique to examine the topographical structure with precision and to obtain 3-D images. It revealed structural alterations caused by the presence of varicocele. Not only neckpieces and flagella were defective, but also the head; particularly, dimensions and heights are altered.

Case-Control Studies↗

Fine mapping of inherent flexibility variation along DNA molecules: validation by atomic force microscopy (AFM) in buffer.

Curvature and flexibility are structural properties of central importance to genome function. However, due to the difficulties in finding suitable experimental conditions, methods for studying one without the interference of the other have proven to be difficult. We propose a new approach that provides a measure of inherent flexibility of DNA by taking advantage of two powerful techniques, X-ray crystallography and nuclear magnetic resonance. Both techniques are able to detect local curvature on DNA fragments but, while the first analyzes DNA in the solid state, the second works on DNA in solution. Comparison of the two data sets allowed us to calculate the relative contribution to flexibility of the three rotations and three translations, which relate successive base pair planes for the ten different dinucleotide steps. These values were then used to compute the variation of flexibility along a given nucleotide sequence. This allowed us to validate the method experimentally through comparisons with maps of local fluctuations in DNA molecule trajectory constructed from atomic force microscopy imaging in solution. We conclude that the six dinucleotide-step parameters defined here provide a powerful tool for the exploration of DNA structure and, consequently will make an important contribution to our understanding of DNA-sequence-dependent biological processes.

Base Sequence↗

Purification of the recombinant hepatitis B virus core antigen (rHBcAg) produced in the yeast Saccharomyces cerevisiae and comparative observation of its particles by transmission electron microscopy (TEM) and atomic force microscopy (AFM).

Hepatitis B virus core antigen (HBcAg) gene (C gene) was expressed in Saccharomyces cerevisiae and the products (rHBcAg or core particles) were purified from a crude lysate of the yeast by three steps: Sephrose CL-4B chromatography, Sucrose step-gradient ultracentrifugation and CsCl-isopycnic ultracentrifugation. It has been observed that HBcAg was synthesized in yeast cells as a particle consisting of polypeptides with a molecular weight of 21.5 kDa (p21.5). Results of ELISA test and density analysis of CsCl-isopycnic ultracentrifugation indicated that the purified products (rHBcAg particles) with HBcAg antigenicity mainly located at the densities of 1.27 and 1.40 g ml(-1), respectively. Observation and analysis of the purified rHBcAg products by TEM indicated that rHBcAg peptides could mainly self-assemble into two size classes of core particles. The larger particles were approximately 30.1 nm and the smaller were approximately 21.5 nm in mean diameter. Further observation and analysis of the same rHBcAg (core) particles by AFM also indicated that rHBcAg (core) particles were similar to the native HBcAg (core) particles from infected human hepatocytes and mainly composed of two size classes of partides core. The larger particles were approximately 31.3 nm and the smaller were approximately 22.5 nm in mean diameter which was similar to the results obtained by TEM. All results from both TEM and AFM suggested that core particles (capsids) produced in S. cerevisiae possessed dimorphism.

Genes, Viral↗

Visualization of chromatin folding patterns in chicken erythrocytes by atomic force microscopy (AFM).

The organization of the higher order structure of chromatin in chicken erythrocytes has been examined with tapping-mode scanning force microscopy under conditions close to their native environment. Reproducible high-resolution AFM images of chromatin compaction at several levels can be demonstrated. An extended beads-on-astring (width of approximately 15-20 nm, height of approximately 2-3 nm for each individual nucleosome) can be consistently observed. Furthermore, superbeads (width of approximately 40 nm, height of approximately 7 nm) are demonstrated. Visualization of the solenoid conformation at the level of 30 nm chromatin fiber is attained either by using AFM or by using electron microscopy. In addition, tightly coiled chromatin fibers (approximately 50-60 nm and approximately 90-110 nm) can be revealed. Our data suggest that the chromatin in the interphase nucleus of chicken erythrocyte represents a high-order conformation and AFM provides useful high-resolution structural information concerning the folding pattern of interphase chromatin fibers.

Animals↗

Expression of HBcAg mutant with long internal deletion in Saccharomyces cerevisiae and observation of its self-assembly particles by atomic force microscopy (AFM).

An internally truncated C gene of adr hepatitis B virus core antigen with long internal deletion (aa81-aa116) (DeltaHBcAg with 36aa truncation) was expressed in Saccharomyces cerevisiae and the products (DeltarHBcAg) were purified from a crude lysate of the yeast by three steps: Sephrose CL-4B chromatography, sucrose step-gradient ultracentrifugation and CsCl-isopycnic ultracentrifugation. Results of ELISA test and density analysis of CsCl-isopycnic ultracentrifugation indicated that the purified products (DeltarHBcAg protein) with HBeAg antigenicity mainly located at the densities of 1.23 g ml-1. Observation and analysis of the purified DeltarHBcAg products by AFM indicated that the DeltarHBcAg (core) protein produced in S. cerevisiae could self-assemble into three or more size classes of core particles which exhibited a polymorphous distribution of DeltarHBcAg (core) particles. These different size classes of core particles mainly centred on the range whose mean diameter was from 10 nm to 48 nm, especially on the position of 11 nm, 15.6 nm and the range from 27 nm to 41 nm, respectively. Furthermore, the most number of core particles mainly centred on the range whose mean diameter was from 27 nm to 41 nm. These results above indicated that the truncated internal long fragment (aa81-aa116) probably had no effect on self-assembly of the HBcAg core particles which implied the internal length fragment (aa81-aa116) was not the sole domain for self-assembly of HBcAg dimer or the truncated HBcAg protein subunit formed the fresh interactive domain with each other. These initial results above by AFM analysis were very important for further research on the self-assembly, ultrastructure, subunit interaction and core internal deletion mutant (CIDM) function of HBcAg core particles.

Amino Acid Sequence↗

Self assembly of epicuticular waxes on living plant surfaces imaged by atomic force microscopy (AFM).

The cuticle of terrestrial vascular plants and some bryophytes is covered with a complex mixture of lipids, usually called epicuticular waxes. Self-assembly processes of wax molecules lead to crystalline three-dimensional micro- and nanostructures that emerge from an underlying wax film. This paper presents the first AFM study on wax regeneration on the surfaces of living plants and the very early stages of wax crystal formation at the molecular level. Wax formation was analysed on the leaves of Euphorbia lathyris, Galanthus nivalis, and Ipheion uniflorum. Immediately after wax removal, regeneration of a wax film began, consisting of individual layers of, typically, 3-5 nm thickness. Subsequently, several different stages of crystal growth could be distinguished, and different patterns of wax regeneration as well as considerable variation in regeneration speed were found.

Euphorbia↗

Interaction forces, deformation and nano-rheology of emulsion droplets as determined by colloid probe AFM.

Atomic force microscopy (AFM) has been used to determine the interaction forces between a spherical silica probe and immobilised colloidal droplets of polydimethylsiloxane (PDMS) in aqueous solution. Under mildly alkaline conditions where PDMS droplets and the silica probe are both negatively charged, a repulsive force is evident that increases less rapidly on surface approach than expected for electrical double layer interaction of rigid particles. The departure from hard-sphere behaviour enables the extent of droplet deformation to be determined and by varying the extent of internal cross-linking within the PDMS droplets, the influence of bulk rheology and interfacial tension on droplet deformation and nano-rheology has been isolated. For highly cross-linked droplets, the extent of deformation is controlled by the bulk rheology rather than the droplet's interfacial properties. Upon retraction of the surfaces, force curve hysteresis is observed and is due to the viscoelastic response of the PDMS. The extent of hysteresis is dependent on the rate of approach/retraction and the loading force, and has been theoretically fitted to obtain nano-rheological parameters, which describe the droplet relaxation processes. For liquid-like droplets, with a low level of cross-linking, no force curve hysteresis is observed and the elastic deformation may be described by a single spring constant. The spring constant is proportional to the surface tension (as controlled by surfactant adsorption) and the reciprocal of the droplet radius, i.e. the Laplace pressure exclusively controls droplet deformation. These colloid probe AFM studies offer due insight into the deformation and interaction of emulsion droplets and have implications when considering the stability, adhesion and processing of emulsions.

Journal Article↗