Shear-reversible clusters of HIV-1 in solution: stabilized by antibodies, dispersed by mucin.

The phenomenon of reversible clustering is expected to further nuance HIV immune stealth because virus surfaces can escape interaction with antibodies (Abs) by hiding temporarily within clusters. It is well known that mucin reduces HIV virulence, and the current perspective is that mucin aggregates HIV-1 to reduce infections. Our findings, however, suggest that mucin is dispersing HIV clusters.

Shells of compacted DNA as nanocontainers transporting proteins in multiplexed delivery.

Polyethyleneimine (PEI) polymers are known to compact DNA strands into spheroid, toroid, or rod structures. A formulation with mannose-grafted PEI (PEIm), however, was reported to compact DNA into ~100 nm spheroids that indented like thin-walled pressurized shells. The goal of the study is to understand why mannose bristles divert the traditional pathway of PEI-DNA compaction to produce shell-like structures, and to manipulate the process so that proteins can be packed into the core of the assembling shells for co-delivering DNA and proteins into cells.

Establishing Rules for Self-Adhesion and Aggregation of -Glycan Sugars Using Virus Glycan Shields.

The surfaces of cells and pathogens are covered with short polymers of sugars known as glycans. Complex -glycans have a core of three mannose sugars with distal repeats of -acetylglucosamine and galactose sugars terminating with sialic acid (SA). Long-range tough and short-range brittle self-adhesions were observed between SA and mannose residues, respectively, in ill-defined artificial monolayers.

Complex-type N-glycans on VSV-G pseudotyped HIV exhibit 'tough' sialic and 'brittle' mannose self-adhesions.

The complex-type glycan shields of eukaryotic cells have a core layer of mannose residues buried under tiers of sugars that end with sialic acid (SA) residues. We investigate if the self-latching of mannose residues, earlier reported in pure monolayer studies, also manifests in the setting of a complex-type glycan shield. Would distal SA residues impede access to the mannose core? The interactions of mannobiose-, SA-, and lactose-coated probes with the complex-type VSV-G glycan shield on an HIV pseudovirus were studied with force-spectroscopy and gold-nanoparticle solutions.

Capturing 3D large-strain Euler-bending filament dynamics in fibrous media simulations; sample case of compression collapse in dendritic actin network.

Cytoskeletal networks to transmission towers are comprised of slender elements. Slender filaments bend and buckle more easily than stretch. Therefore a deforming network is expected to exhaust all possible bending-based modes before engaging filament stretch.

Microscale mapping of extracellular matrix elasticity of mouse joint cartilage: an approach to extracting bulk elasticity of soft matter with surface roughness.

Cartilage is composed of cells and an extracellular matrix, the latter being a composite of a collagen mesh interpenetrated by proteoglycans responsible for tissue osmotic swelling. The matrix composition and structure vary through the tissue depth. Mapping such variability requires tissue sectioning to gain access.

Mannose Surfaces Exhibit Self-Latching, Water Structuring, and Resilience to Chaotropes: Implications for Pathogen Virulence.

Several viral and fungal pathogens, including HIV, SARS, Dengue, Ebola, and Cryptococcus neoformans, display a preponderance of mannose residues on their surface, particularly during the infection cycle or in harsh environments. The innate immune system, on the other hand, abounds in mannose receptors which recognize mannose residues on pathogens and trigger their phagocytosis. We pose the question if there is an advantage for pathogens to display mannose on their surface, despite these residues being recognized by the immune system.

An engineering design approach to systems biology.

Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact.

Unusual Salt and pH Induced Changes in Polyethylenimine Solutions.

Linear PEI is a cationic polymer commonly used for complexing DNA into nanoparticles for cell-transfection and gene-therapy applications. The polymer has closely-spaced amines with weak-base protonation capacity, and a hydrophobic backbone that is kept unaggregated by intra-chain repulsion. As a result, in solution PEI exhibits multiple buffering mechanisms, and polyelectrolyte states that shift between aggregated and free forms.

DNA nanoparticles with core-shell morphology.

Mannobiose-modified polyethylenimines (PEI) are used in gene therapy to generate nanoparticles of DNA that can be targeted to the antigen-presenting cells of the immune system. We report that the sugar modification alters the DNA organization within the nanoparticles from homogenous to shell-like packing. The depth-dependent packing of DNA within the nanoparticles was probed using AFM nano-indentation.

Structural mechanism for alteration of collagen gel mechanics by glutaraldehyde crosslinking.

Soft collagenous tissues that are loaded in vivo undergo crosslinking during aging and wound healing. Bioprosthetic tissues implanted in vivo are also commonly crosslinked with glutaraldehyde (GA). While crosslinking changes the mechanical properties of the tissue, the nature of the mechanical changes and the underlying microstructural mechanism are poorly understood.

Aggrecan, an unusual polyelectrolyte: review of solution behavior and physiological implications.

Aggrecan is a high-molecular-weight, bottlebrush-shaped, negatively charged biopolymer that forms supermolecular complexes with hyaluronic acid. In the extracellular matrix of cartilage, aggrecan-hyaluronic acid complexes are interspersed in a collagen meshwork and provide the osmotic properties required to resist deswelling under compressive load. In this review we compile aggrecan solution behavior from different experimental techniques, and discuss them in the context of concentration regimes that were identified in osmotic pressure experiments.

Structure and biological activity of pathogen-like synthetic nanomedicines.

Unlabelled: Here we characterize the structure, stability and intracellular mode of action of DermaVir nanomedicine that is under clinical development for the treatment of HIV/AIDS. This nanomedicine comprises pathogen-like pDNA/PEIm nanoparticles (NPs) having the structure and function resembling spherical viruses that naturally evolved to deliver nucleic acids to the cells. Atomic force microscopy demonstrated spherical 100 - 200 nm NPs with a smooth polymer surface protecting the pDNA in the core.

Probing Interactions between Aggrecan and Mica Surface by the Atomic Force Microscopy.

Aggrecan is a bottlebrush shaped macromolecule found in the extracellular matrix of cartilage. The negatively charged glycosaminoglycan (GAG) chains attached to its protein backbone give aggrecan molecules a high charge density, which is essential for exerting high osmotic swelling pressure and resisting compression under external load. In solution aggrecan assemblies are insensitive to the presence of calcium ions, and show distinct osmotic pressure versus concentration regimes.

Averaged implicit hydrodynamic model of semiflexible filaments.

We introduce a method to incorporate hydrodynamic interaction in a model of semiflexible filament dynamics. Hydrodynamic screening and other hydrodynamic interaction effects lead to nonuniform drag along even a rigid filament, and cause bending fluctuations in semiflexible filaments, in addition to the nonuniform Brownian forces. We develop our hydrodynamics model from a string-of-beads idealization of filaments, and capture hydrodynamic interaction by Stokes superposition of the solvent flow around beads.

Rods-on-string idealization captures semiflexible filament dynamics.

We present an approach to modeling the two-dimensional Brownian dynamics of semiflexible filaments in the worm-model description as uniform, isotropic, and continuously flexible. Experimental observations increasingly show that the mechanical behavior of semiflexible filament networks departs from conventional knowledge. A force-balance-based dynamic simulation of the filament networks has multiple advantages as an approach to understanding their anomalous mechanics.

Collagen fiber alignment does not explain mechanical anisotropy in fibroblast populated collagen gels.

Many load-bearing soft tissues exhibit mechanical anisotropy. In order to understand the behavior of natural tissues and to create tissue engineered replacements, quantitative relationships must be developed between the tissue structures and their mechanical behavior. We used a novel collagen gel system to test the hypothesis that collagen fiber alignment is the primary mechanism for the mechanical anisotropy we have reported in structurally anisotropic gels.

Deterministic material-based averaging theory model of collagen gel micromechanics.

Mechanics of collagen gels, like that of many tissues, is governed by events occurring on a length scale much smaller than the functional scale of the material. To deal with the challenge of incorporating deterministic micromechanics into a continuous macroscopic model, we have developed an averaging-theory-based modeling framework for collagen gels. The averaging volume, which is constructed around each integration point in a macroscopic finite-element model, is assumed to experience boundary deformations homogeneous with the macroscopic deformation field, and a micromechanical problem is solved to determine the average stress at the integration point.

Affine versus non-affine fibril kinematics in collagen networks: theoretical studies of network behavior.

The microstructure of tissues and tissue equivalents (TEs) plays a critical role in determining the mechanical properties thereof. One of the key challenges in constitutive modeling of TEs is incorporating the kinematics at both the macroscopic and the microscopic scale. Models of fibrous microstructure commonly assume fibrils to move homogeneously, that is affine with the macroscopic deformation.

Microstructural mechanics of collagen gels in confined compression: poroelasticity, viscoelasticity, and collapse.

Background: Collagen gels are important as platforms for in vitro study of cell behavior and as prototypical bioartificial tissues, but their mechanical behavior, particularly on the microscopic scale, is still poorly understood.

Method Of Approach: Collagen gels were studied in step (10% strain in 0.05 s) and ramp (0.