Differential Contributions of Conformation Extension and Domain Unfolding to Properties of Fibronectin Nanotextiles

Fibronectin (FN) textiles are built as nanometer-thick fabrics. When uniaxially loaded, these fabrics exhibit a distinct threshold between elastic and plastic deformation with increasing stretch. Fabric mechanics are modeled using an eight-chain network and two-state model, revealing that elastic properties of FN depend on conformational extension of the protein and that plastic deformation depends on domain unfolding. Our results suggest how the molecular architecture of a molecule can be exploited for designer mechanical properties of a bulk material.Engineering and Applied Science

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Abstract: Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, management, and analysis. In this perspective, we present AnVIL, describe its ecosystem and interoperability with other platforms, and highlight how this platform and associated initiatives contribute to improved genomic data sharing efforts. The AnVIL is a federated cloud platform designed to manage and store genomics and related data, enable population-scale analysis, and facilitate collaboration through the sharing of data, code, and analysis results. By inverting the traditional model of data sharing, the AnVIL eliminates the need for data movement while also adding security measures for active threat detection and monitoring and provides scalable, shared computing resources for any researcher. We describe the core data management and analysis components of the AnVIL, which currently consists of Terra, Gen3, Galaxy, RStudio/Bioconductor, Dockstore, and Jupyter, and describe several flagship genomics datasets available within the AnVIL. We continue to extend and innovate the AnVIL ecosystem by implementing new capabilities, including mechanisms for interoperability and responsible data sharing, while streamlining access management. The AnVIL opens many new opportunities for analysis, collaboration, and data sharing that are needed to drive research and to make discoveries through the joint analysis of hundreds of thousands to millions of genomes along with associated clinical and molecular data types

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

Data from: Collagen network strengthening following cyclic tensile loading

The bulk mechanical properties of tissues are highly tuned to the physiological loads they experience and reflect the hierarchical structure and mechanical properties of their constituent parts. A thorough understanding of the processes involved in tissue adaptation is required to develop multi-scale computational models of tissue remodelling. While extracellular matrix (ECM) remodelling is partly due to the changing cellular metabolic activity, there may also be mechanically directed changes in ECM nano/microscale organization which lead to mechanical tuning. The thermal and enzymatic stability of collagen, which is the principal load-bearing biopolymer in vertebrates, have been shown to be enhanced by force suggesting that collagen has an active role in ECM mechanical properties. Here, we ask how changes in the mechanical properties of a collagen-based material are reflected by alterations in the micro/nanoscale collagen network following cyclic loading. Surprisingly, we observed significantly higher tensile stiffness and ultimate tensile strength, roughly analogous to the effect of work hardening, in the absence of network realignment and alterations to the fibril area fraction. The data suggest that mechanical loading induces stabilizing changes internal to the fibrils themselves or in the fibril–fibril interactions. If such a cell-independent strengthening effect is operational in vivo, then it would be an important consideration in any multiscale computational approach to ECM growth and remodelling

TEM Images

Compressed file containing TEM images of en face and transverse section of dense disorganized collagen substrate after cyclic loadin

MechanicalTestingData

Compressed file containing raw force data of the cyclic loading experiments

Differential Contributions of Conformation Extension and Domain Unfolding to Properties of Fibronectin Nanotextiles

Fibronectin (FN) textiles are built as nanometer-thick fabrics. When uniaxially loaded, these fabrics exhibit a distinct threshold between elastic and plastic deformation with increasing stretch. Fabric mechanics are modeled using an eight-chain network and two-state model, revealing that elastic properties of FN depend on conformational extension of the protein and that plastic deformation depends on domain unfolding. Our results suggest how the molecular architecture of a molecule can be exploited for designer mechanical properties of a bulk material

Design and Performance of an Optically Accessible, Low-Volume, Mechanobioreactor for Long-Term Study of Living Constructs

Currently available bioreactor systems used by tissue engineers permit either direct, high-magnification observation of cell behavior or application of mechanical loads to growing tissue constructs, but not both simultaneously. Further, in most loading bioreactors, the volume of the dead space is not minimized to reduce the cost associated with perfusion media, exogenous stimulatory/inhibitory agents, proteases, and label. We have designed, developed, and tested a bioreactor that simultaneously satisfies the combined requirements of providing (i) controlled tensile mechanical stimulation, (ii) direct high-magnification imaging capability, and (iii) low dead-space volume. This novel mechanostimulatory (uniaxial tensile loading) bioreactor operates on an inverted microscope and permits continuous optical access (up to 600×) to a loaded, growing construct for extended periods of time (weeks). The reactor employs an adjustable reaction chamber in which the dead space can be reduced to <2 mL. The device has been used to cultivate our human primary corneal fibroblast-derived, tissue-engineered system for up to 14 days. Using the instrument we have successfully recorded (i) the process of fibroblasts populating, growing to confluence, and stratifying on different substrates; (ii) recorded complex and organized cell sheet motions; and (iii) recorded the behavior of a subpopulation of what appear to be degradative/catabolic cells within our fibroblast culture. The device is capable of providing detailed, long-term, dynamic images of mechanically stimulated cell/matrix interaction that have not been observed previously