High-throughput top-down fabrication of uniform magnetic particles

Ion Beam Aperture Array Lithography was applied to top-down fabrication of large dense (10(8)-10(9) particles/cm(2)) arrays of uniform micron-scale particles at rates hundreds of times faster than electron beam lithography. In this process, a large array of helium ion beamlets is formed when a stencil mask containing an array of circular openings is illuminated by a broad beam of energetic (5-8 keV) ions, and is used to write arrays of specific repetitive patterns. A commercial 5-micrometer metal mesh was used as a stencil mask; the mesh size was adjusted by shrinking the stencil openings using conformal sputter-deposition of copper. Thermal evaporation from multiple sources was utilized to form magnetic particles of varied size and thickness, including alternating layers of gold and permalloy. Evaporation of permalloy layers in the presence of a magnetic field allowed creation of particles with uniform magnetic properties and pre-determined magnetization direction. The magnetic properties of the resulting particles were characterized by Vibrating Sample Magnetometry. Since the orientation of the particles on the substrate before release into suspension is known, the orientation-dependent magnetic properties of the particles could be determined.     

Bacterial adhesion to different termite flagellates: Ultrastructural and functional evidence for distinct molecular attachment modes

Summary The attachment modes of rodlike ectobiotic bacteria to the surface of two different termite flagellates were studied.Devescovina glabra was covered by laterally attached bacteria. Treatment with chemicals that disturb hydrophobic interactions and solubilize proteins removed the ectobionts. Freeze-fracture and freeze-etching electron microscopy revealed rows of intramembrane particles that occurred exclusively along the attachment sites. The adhering Gram-negative bacteria possessed an S-layer (surface layer) composed of globular protein particles. The S-layer could be removed by protein-solubilizing chemicals, e.g., urea, as shown by ultrathin-section electron microscopy. Therefore, it seems plausible that the attachment was mediated by hydrophobic interactions between the flagellate's plasma membrane and the S-layer of the bacteria. The bacteria of the second flagellate,Joenia annectens, adhered by their tips. The attachment was extremely strong. Chemicals disturbing ionic or hydrophobic bindings or solubilizing proteins did not detach the ectobionts. Globular intramembrane protein particles were preferentially found in a ringlike array at the external fracture face of the flagellate's contact sites.Abbreviations DIC differential interference contrast - EGTA ethylene glycol-bis(-aminoethyl ether) N,N,N,N-tetraacetic acid - TEM transmission electron microscope - Tween 20 polyoxyethylenesorbitan     

Interception of small particles by flocculent structures, sessile ciliates, and the basic layer of a wastewater biofilm

We investigated attachment processes of hydrophobic and hydrophilic particles (diameter = 1 microm) to mature biofilms grown on clay marbles in a sequencing batch biofilm reactor. During a treatment cycle with filtered wastewater containing different fluorescent beads, the progression of particle density in various biofilm compartments (carrier biofilm, basic biofilm layer, biofilm flocs, and sessile ciliates) was determined by flow cytometry, confocal laser scanning microscopy and automated image analysis. Particles were almost completely removed from wastewater by typical processes of particle retention: up to 58% of particles attached to clay marbles, up to 15% were associated with suspended flocs, and up to 10% were ingested by sessile ciliates. Ingestion of particles by ciliates was exceptionally high immediately after wastewater addition (1,200 particles grazer(-1) x h(-1)) and continued until approximately 14% of the water had been cleared by ciliate filter feeding. Most probably, ciliate bioturbation increases particle sorption to the basic biofilm. Backwashing of the reactor detached pieces of biofilm and thus released approximately 50% of the particles into rinsing water. Clay marbles in the upper part of the reactor were more efficiently abraded than in the lower part. No indications for selective attachment of the applied hydrophobic and hydrophilic beads were found. As a consequence of interception patterns, organisms at elevated biofilm structures are probably major profiteers of wastewater particles; among them, ciliates may be of major importance because of their highly active digestive food vacuoles.     

Membrane structure of nonactivated and activated human blood platelets as revealed by freeze-fracture: evidence for particle redistribution during platelet contraction

The distribution of intramembrane particles of nonactivated and activated human blood platelets was studied by freeze-fracture under various experimental conditions to see whether morphological evidence for a structural coupling between the platelet actomyosin system and the fibrin network in a retracting clot could be established. Membrane particles were evenly distributed in nonactivated platelets; the total number (E + P faces) was approximately 1,500/micrometers 2 of membrane, and there were two to three times more particles present on the E face than on the P face. Transformation of discoid platelets to "spiny spheres" by cooling did not change the particle distribution. Platelet activation and aggregation by serum or ADP caused no change in membrane particle density or distribution. Particle distribution was not changed in Ca2+-activated platelets fixed immediately before fibrin formation, but after fibrin formation and during clot retraction, particles were sometimes most frequent on the P face and tended to form distinct clusters, and aggregates of E face pits were observed. Blood platelets contain contractile proteins that are distinct as filaments in platelets in retracting clots. We suggest that the redistribution of particles seen in activated platelets during clot retraction reflects the esablishment of mechanical transmembrane links between the platelet actomyosin system and the fibrin net. The P-face particle clusters may represent sites of force transmission between actin filaments bonded to the inside of the membrane and the fibrin network at the outside. Thus, whereas membrane particles may not be directly involved in the attachment of actin filaments to membranes, the transmission of the force of the contractile system to an exterior substrate apparently involves the intramembrane particles.     

A freeze-fracture study of the body wall of adult, in utero larvae and infective-stage larvae of Trichinella (Nematoda)

The surface layers of the cuticle, the hypodermal membranes and the muscle membranes of the adult, the in utero larvae and the infective-stage larvae of the nematode Trichinella spiralis have been studied by means of the freeze-fracturing technique. The surface of the cuticle of both adults and larvae fractures in ways different from membranes of internal cells. The surface coat on top of the epicuticle is probably the layer that changes antigenically. Reticulate ridges, with associated particles, on the E face of the outer hypodermal membrane of the adult are probably sites of attachment of the hypodermis to the cuticle. Longitudinally arranged ridges, with associated particles, of the outer hypodermal membrane are probably points of attachment to the cuticle in the in utero and infective larvae. Rectilinear arrays of particles are present on the P face of the inner hypodermal membrane and the P face of the muscle membrane adjacent to the hypodermis of adults and larvae and probably play a role in adhesion of the muscle membrane to the hypodermis. Particle-free areas of membrane lie external to the Z bundles of the muscle cell and are similar to the sites of attachment of Z lines in insect muscles.     

Square arrays and their role in ridge formation in human lens fibers

Square arrays in human lens fibers were studied with freeze-fracture and thin-section TEM. In superficial fibers a number of patches of square array particles in the P face and pits in the E face are found in the smooth membrane. In the deeper cortex and the nucleus, fiber cells have undulating membranes and many ridges. Numerous patches of the particles (P face) are distributed in the concave regions, and the pits (E face) in the convex areas of the bumpy membrane. In most ridges, patches of the particles occur at regular intervals in the "valley" portion, while the pits are on the "crest" portion of ridges. Also, continuous square arrays having the same "valley" location as the regularly arranged patches are found in areas with extensive ridge patterns. The overlapping of the outer portions of two adjacent square arrays is found on the sides between the "crest" and the "valley" of the ridges. Structurally, square arrays are located in a nonjunctional part of the membrane; in an orthogonal crystalline arrangement; and with a particle size of about 6 nm and center-center spacing about 6.4 nm. They are structurally different from gap junctions found in the lens fibers. Thin-section studies reveal two types of cellular contacts: thin pentalamellar structures (about 12-13 nm in overall thickness) associated with the ridge patterns are believed to be square arrays; thick heptalamellar structures (about 16-17 nm in overall thickness) with a narrow gap in between the two central laminae are believed to be gap junctions. This study strongly suggests that square arrays are specifically involved in ridge formation in human lens fibers.     

Particle Assemblies in the Plasma Membrane of Tetrahymena: Relationship to Cell Surface Topography and Cellular Morphogenesis1

During a freeze-fracture electron microscopical study of the plasma membrane of Tetrahymena, several different types of organized particle assemblies were observed. Three of these were found only on the protoplasmic face and were localized in the anterior-ventral region of the cell. These consisted of plate-like arrays composed of 4–25 triplet rows of small 3–4 nm particles; long, paired linear arrays localized at the tops of cortical ridges and composed of 7–8 nm particles; and elongated tetragonal arrays located in the grooves between ridges and composed of approximately 10 nm particles. The distribution of these arrays is consistent with roles in cellular morphogenesis, chemoreception, or cell-cell pairing during conjugation. In addition, a unique particle track associated with the cytoproct (anal pore) was observed in the external face of the plasma membrane. Furthermore, the protoplasmic face of the plasma membrane is characterized by a high density of particles organized into localized microarrays, consisting of small paracrystals or strings, which exhibit a loose higher-order patterning most evident toward the anterior end of the cell. Particle distributions on the protoplasmic face do not appear to be significantly altered by conditions that cause clumping of alveolar membrane particles. Taken together, these observations are consistent with the idea that the proteins of the plasma membrane are highly ordered and relatively immobile and that the structure of the plasma membrane is regionally differentiated.     

Gold nanoparticle-protein arrays improve resolution for cryo-electron microscopy

Cryo-electron microscopy single particle analysis shows limited resolution due to poor alignment precision of noisy images taken under low electron exposure. Certain advantages can be obtained by assembling proteins into two-dimensional (2D) arrays since protein particles are locked into repetitive orientation, thus improving alignment precision. We present a labeling method to prepare protein 2D arrays using gold nanoparticles (NPs) interconnecting genetic tag sites on proteins. As an example, mycobacterium tuberculosis 20S proteasomes tagged with 6x-histidine were assembled into 2D arrays using 3.9-nm Au NPs functionalized with nickel-nitrilotriacetic acid. The averaged top-view images from the array particles showed higher resolution (by 6-8A) compared to analysis of single particles. The correct 7-fold symmetry was also evident by using array particles whereas it was not clear by analysis of a comparable number of single particles. The applicability of this labeling method for three-dimensional reconstruction of biological macromolecules is discussed.     

Interception of Small Particles by Flocculent Structures, Sessile Ciliates, and the Basic Layer of a Wastewater Biofilm

We investigated attachment processes of hydrophobic and hydrophilic particles (diameter = 1 μm) to mature biofilms grown on clay marbles in a sequencing batch biofilm reactor. During a treatment cycle with filtered wastewater containing different fluorescent beads, the progression of particle density in various biofilm compartments (carrier biofilm, basic biofilm layer, biofilm flocs, and sessile ciliates) was determined by flow cytometry, confocal laser scanning microscopy and automated image analysis. Particles were almost completely removed from wastewater by typical processes of particle retention: up to 58% of particles attached to clay marbles, up to 15% were associated with suspended flocs, and up to 10% were ingested by sessile ciliates. Ingestion of particles by ciliates was exceptionally high immediately after wastewater addition (1,200 particles grazer⁻¹ h⁻¹) and continued until approximately 14% of the water had been cleared by ciliate filter feeding. Most probably, ciliate bioturbation increases particle sorption to the basic biofilm. Backwashing of the reactor detached pieces of biofilm and thus released approximately 50% of the particles into rinsing water. Clay marbles in the upper part of the reactor were more efficiently abraded than in the lower part. No indications for selective attachment of the applied hydrophobic and hydrophilic beads were found. As a consequence of interception patterns, organisms at elevated biofilm structures are probably major profiteers of wastewater particles; among them, ciliates may be of major importance because of their highly active digestive food vacuoles.     

Ultrastructure of the membrane attachment sites of the extrusomes of Ciliophrys marina and Heterophrys marina (Actinopoda)

Summary The actinopods Ciliophrys marina and Heterophrys marina both have membrane bounded extrusomes attached to their cellular and axopodial membranes. The extrusomes of C. marina, the muciferous bodies, are fairly simple in structure and contain a homogeneous osmiophilic substance. Their attachment site is characterized by a rectangular array of freeze fracture particles in the cell membrane. The extrusomes of H. marina, the conicysts, are more complex and contain a two-part osmiophilic body. The attachment site of conicysts is characterized by a rosette of 8 freeze fracture particles very similar to the 9-particle rosette found at the mucocyst attachment sites in Tetrahymena. Furthermore, intracytoplasmic bridges connect the conicyst and cell membrane faces, and a specialized fibrillar structure is found on the cell membrane in the region of conicyst attachment. The various possible roles for such particle arrays are discussed and their presence in virtually all extrusomes is predicted.Supported by USPHS GM01021 and HL13849     

Magnetic targeting of mechanosensors in bone cells for tissue engineering applications

Mechanical signalling plays a pivotal role in maintaining bone cell function and remodelling of the skeleton. Our previous work has highlighted the potential role of mechano-induction in tissue engineering applications. In particular, we have highlighted the potential for using magnetic particle techniques for tissue engineering applications. Previous studies have shown that manipulation of integrin attached magnetic particles leads to changes in intracellular calcium signalling within osteoblasts. However, due to the phenomenon of particle internalisation, previous studies have typically focused on short-term stimulation experiments performed within 1-2 h of particle attachment. For tissue engineering applications, bone tissue growth occurs over a period of 3-5 weeks. To date, no study has investigated the cellular responses elicited from osteoblasts over time following stimulation with internalised magnetic particles. Here, we demonstrate the long-term biocompatibility of 4.5 microm RGD-coated particles with osteoblasts up to 21 days in culture, and detail a time course of responses elicited from osteoblasts following mechanical stimulation with integrin attached magnetic particles (<2h post attachment) and internalised particles (>48h post attachment). Mechanical manipulation of both integrin attached and internalised particles were found to induce intracellular calcium signalling. It is concluded that magnetic particles offer a tool for applying controlled mechanical forces to osteoblasts, and can be used to stimulate intracellular calcium signalling over prolonged periods of time. Magnetic particle technology presents a potentially valuable tool for tissue engineering which permits the delivery of highly localised mechano-inductive forces directly to cells.     

Manipulation of microparticles for construction of array patterns by negative dielectrophoresis using multilayered array and grid electrodes

In this study, a useful method was developed to fabricate array patterns of microparticles not on electrode surfaces, but on arbitrary surfaces, using negative‐dielectrophoresis (n‐DEP). First, electrodes were designed and electric field simulations were performed to manipulate microparticles toward target areas. Based on the simulation results, multilayered array and grid (MLAG) electrodes, consisting of array electrodes surrounded by insulated regions and a grid electrode, were fabricated for the formation of localized, non‐uniform electric fields. The MLAG electrode was mounted to a target substrate in a face‐to‐face configuration with a spacer. When an AC voltage (4.60 V_rms and 1 MHz) was applied to the MLAG electrode, array patterns of 6 and 20 µm diameter microparticles were rapidly fabricated on the target substrate with ease. The results suggest that MLAG electrodes can be widely applied for the fabrication of biochips including cell arrays. Biotechnol. Bioeng. 2009; 104: 709–718 © 2009 Wiley Periodicals, Inc.     

Cell walls,plasma membranes,and dictyosomes during zygote maturation ofClosterium ehrenbergii

Summary The cell wall formation and its correlation with the plasma membrane and dictyosome were investigated by an electron microscope in the zygote cells ofClosterium ehrenbergii. During zygote maturation, six wall layers were formed outside the plasma membrane. Wall layer III was the thickest layer and consisted of microfibril bundles. Dictyosomes produced flat vesicles during formation of wall layer III. Hexagonal arrays of rosette particles appeared in the plasma membrane in this period, thus confirming the simultaneous occurrence of flat vesicles and hexagonal particle arrays in the formation of microfibril bundles even at different stages of the life cycle. Wall layer VI was second in thickness and consisted of single microfibrils. Neither flat vesicles nor hexagonal particle arrays were observed during formation of this layer.     

Alterations in Chloroplast Thylakoids during Cold Acclimation

Freeze-fracture electron microscopy reveals a decreased particle concentration on the inner fracture face of acclimated thylakoids, suggestive of some alteration(s) in the hydrophobic region. Sonic oscillation causes a reversal of the altered particle concentration in acclimated thylakoids and suggests that increases in unsaturation of fatty acids can, at most, account for only part of the altered particle concentration. The particles on the inner fracture face of acclimated thylakoids are of one size group (+/- 140 A) as compared to two size groups (+/- 100 A and +/- 165 A) for nonacclimated thylakoids. The paracrystalline array might be associated with the acclimated state of thylakoids. Nonacclimated thylakoids require 50 mm sucrose for maximum protection of light-dependent proton uptake, while acclimated thylakoids require 25 mm sucrose, and the protection afforded acclimated thylakoids during a freeze-thaw cycle is greater. Sucrose is required for alterations in acclimated thylakoids to be manifested. Apparently increased hardiness is not only associated with changes in cellular environment but also alterations in membranes.     

Unexpected binding motifs for subnucleosomal particles revealed by atomic force microscopy

The structure of individual nucleosomes organized within reconstituted 208-12 arrays at different levels of compaction was examined by tapping mode atomic force microscopy in air and liquid. Reconstitution at lower histone octamer to DNA weight ratios showed an extended beads-on-a-string morphology with less than the expected maximum of 12 nucleosome core particles per array, each particle located in the most favored positioning site. A correlation of the contour lengths of these arrays with the number of observed particles revealed two distinct populations of particles, one with approximately 50 nm of bound DNA and a second population with approximately 25 nm. The measured nucleosome center-to-center distances indicate that this approximately 25 nm is not necessarily symmetrically bound about the dyad axis, but can also correspond to DNA bound from either the entry or exit point of the particle to a location at or close to the dyad axis. An assessment of particle heights suggests that particles wrapping approximately 25 nm of DNA are most likely to be subnucleosomal particles, which lack either one or both H2A-H2B dimers. At a higher reconstitution ratio, folded compact arrays fully populated with 12 nucleosome core particles, were observed. Liquid measurements demonstrated dynamic movements of DNA loops protruding from these folded arrays.     

Performance of antibody microarrays fabricated by either DNA-directed immobilization, direct spotting, or streptavidin-biotin attachment: a comparative study

Antibody microarrays have the potential to revolutionize protein diagnostics. The major problems in the fabrication of antibody arrays, however, concern the reproducibility and homogeneity of the attachment of the proteins on the solid substrate. We here compare the DNA-directed immobilization (DDI) method with two conventional strategies for immobilization of antibodies on glass substrates. DDI is based on the self-assembly of semisynthetic DNA-streptavidin conjugates which converts an array of DNA oligomers into an antibody microarray. DDI was compared with direct spotting of antibodies on chemically activated glass slides and with immobilization of biotinylated antibodies on streptavidin-coated slides. The immobilized antibodies were used as capture reagents in a two-sided (sandwich) immunoassay for the quantification of rabbit IgG as a model antigen. Detection limits down to 0.001nM (150 pg/mL) were attained with all three array formats; however, DDI and direct spotting of the antibodies led to the highest fluorescence intensities. DDI led to the best spot homogeneity and intra- and interexperimental reproducibility. Moreover, DDI allowed highly economical use of antibody materials; that is, at least 100-fold less antibody is needed for preparing an array by DDI instead of by direct spotting. Taking into account the greater versatility and convenience of handling of the self-assembly approach, this study demonstrates that DDI is an advantageous alternative for generating versatile and robust protein arrays.     

Freeze-Fracture Study of the Bloodstream Form of Trypanosoma brucei gambiense

The ultrastructure of Trypanosoma brucei gambiense was investigated by the freeze-fracture method. Three different regions of the continuous plasma membrane; cell body proper, flagellar pocket, and flagellum were compared in density and distribution of the intramembranous particles (IMP's). The IMP-density was highest in the flagellar pocket membrane and lowest in flagellum. Intra membranous particles of the cell body membrane were distributed uniformly on both the protoplasmic (P) and exoplasmic (E) faces. On the P face of the flagellar membrane, a single row of IMP-clusters was seen along the juncture of the flagllum to the cell body. Since the spacing of the IMP-clusters was almost equal to the spacing of the paired rivet structures observed in thin section, these clusters likely are related to the junction of flagellum and cell body. At the neck of the flagellar pocket, several linear arrays of IMP's were found on the P face of the flagellar membrane, while on the E face rows of depressions were seen. At the flagellar base, the clusters of IMP's were only seen on the P face. On the flagellar pocket membrane, particle-rich depressions and linear particle arrays were also found on the P face, while on the E face such special particle arrangements were not recognized. These particle-rich depressions may correspond to the sites of pinocytosis of the bloodstream forms which have been demonstrated in thin sections.     

Helical crystallization on lipid nanotubes: streptavidin as a model protein

In this study, we use streptavidin (SA) as a model system to study helical protein array formation on lipid nanotubes, an alternative to 2D studies on lipid monolayers. We demonstrate that wild-type and a mutant form of SA form helical arrays on biotinylated lipid nanotubes. 3D maps from helical arrays of wild-type and mutant SA were reconstructed using two different approaches: Fourier-Bessel methods and an iterative single particle algorithm. The maps show that wild-type and mutant streptavidin molecules order differently. The molecular packing arrangements of SA on the surface of the lipid nanotubes differ from previously reported lattice packing of SA on biotinylated monolayers. Helical crystallization on lipid nanotubes presents an alternative platform to explore fundamentals of protein ordering, intermolecular protein interaction and phase behavior. We demonstrate that lipid nanotubes offer a robust and reproducible substrate for forming helical protein arrays which present a means for studying protein structure and structure-function relationships.     

Regular arrays of intramembranous particles in the plasmalemma of guard cell and mesophyll cell protoplasts of Vicia faba

Freeze fractures of the plasmalemma membranes of guard-cell and mesophyll protoplasts of Vicia faba demonstrate that the inner monolayer of the plasmalemma is compartmentalized into areas with distinct, highly organized structures. Between areas of intramembranous particles dispersed randomly on a relatively smooth fracture face, membrane domains showing an extremely regular planar, hexagonal array of particles are interspersed. The dimensions of these hexagonal lattices are about 0.5 m in diameter, the center-to-center spacing is about 22 nm, and the particle size is about 9 nm. The particle in the hexagonal arrays are accompanied by complementary pits in the opposite monolayer fracture of the plasmalemma membrane.The freeze-fracture preparation was performed by using an improved Leybold Bioetch device which provides a sufficiently high cooling rate and allows the omission of cryoprotectants, like glycerol.Presented by H. Schnabl on the Workshop on Plant Membrane Transport, Toronto, Canada, July 1979     

Arrays of plasma-membrane “rosettes” involved in cellulose microfibril formation of Spirogyra

The cell-wall structure and plasma-membrane particle arrangement during cell wall formation of the filamentous chlorophycean alga Spirogyra sp. was investigated with the freeze-fracture technique. The cell wall consists of a thick outer slime layer and a multilayered inner wall with ribbon-like microfibrils. This inner wall shows three differing orientations of microfibrils: random orientation on its outside, followed by axial bundles of parallel microfibrils, and several internal layers of bands of mostly five to six parallel associated microfibrils with transverse to oblique orientation. The extraplasmatic fracture face of the plasma membrane shows microfibril imprints, relatively few particles, and “terminal complexes” arranged in a hexagonal package at the end of the imprint of a microfibril band. The plasmatic fracture face of the plasma membrane is rich in particles. In places, it reveals hexagonal arrays of “rosettes”. These rosettes are best demonstrable with the double-replica technique. These findings on rosette arrays of the zygnematacean alga Spirogyra are compared in detail with the published data on the desmidiacean algae Micrasterias and Closterium.