Our genomes influence nearly every aspect of human biology-from molecular and cellular functions to phenotypes in health and disease. Studying the differences in DNA sequence between individuals (genomic variation) could reveal previously unknown mechanisms of human biology, uncover the basis of genetic predispositions to diseases, and guide the development of new diagnostic tools and therapeutic agents. Yet, understanding how genomic variation alters genome function to influence phenotype has proved challenging. To unlock these insights, we need a systematic and comprehensive catalogue of genome function and the molecular and cellular effects of genomic variants. Towards this goal, the Impact of Genomic Variation on Function (IGVF) Consortium will combine approaches in single-cell mapping, genomic perturbations and predictive modelling to investigate the relationships among genomic variation, genome function and phenotypes. IGVF will create maps across hundreds of cell types and states describing how coding variants alter protein activity, how noncoding variants change the regulation of gene expression, and how such effects connect through gene-regulatory and protein-interaction networks. These experimental data, computational predictions and accompanying standards and pipelines will be integrated into an open resource that will catalyse community efforts to explore how our genomes influence biology and disease across populations.

Metastasis driven by cancer cell migration is the leading cause of cancer-related deaths. It involves significant changes in the organization of the cytoskeleton, which includes the actin microfilaments and the vimentin intermediate filaments. Understanding how these filament change cells from normal to invasive offers insights that can be used to improve cancer diagnosis and therapy. We have developed a computational, transparent, large-scale and imaging-based pipeline, that can distinguish between normal human cells and their isogenically matched, oncogenically transformed, invasive and metastasizing counterparts, based on the spatial organization of actin and vimentin filaments in the cell cytoplasm. Due to the intricacy of these subcellular structures, manual annotation is not trivial to automate. We used established deep learning methods and our new multi-attention channel architecture. To ensure a high level of interpretability of the network, which is crucial for the application area, we developed an interpretable global explainable approach correlating the weighted geometric mean of the total cell images and their local GradCam scores. The methods offer detailed, objective and measurable understanding of how different components of the cytoskeleton contribute to metastasis, insights that can be used for future development of novel diagnostic tools, such as a nanometer level, vimentin filament-based biomarker for digital pathology, and for new treatments that significantly can increase patient survival.

In this study, we report the preparation and characterization of water-stable films with UV-shielding and good mechanical properties, exploiting the synergistic effect of regenerated silk fibroin and bamboo-derived cellulose. Silk fibroin (SF)/bamboo (B) hybrid films are achieved by solubilizing both silk and bamboo fibers in formic acid with added CaCl2. Infrared spectroscopy indicates that SF, when combined with bamboo, undergoes a conformational transition, providing evidence of an increase in SF crystallinity. Exploiting the intrinsic absorption of SF in the ultraviolet region, UV-Vis spectroscopy was used to assess the glass transition temperature (Tg) of SF/B films, showing a decrease in Tg by increasing the SF content. The addition of 10 wt% SF to the B matrix improved the elastic modulus by about 10% while conserving the strain at break with respect to the neat B films, increasing the UV shielding properties, while water absorption suggested the material\'s hydrophilic and swelling capacity even after one month. The hybrid films showed, under solar irradiation, a photoprotective behavior on keratinocyte human cells by increasing cellular viability. These findings may find potential applications in functional fabrics.

Large-scale drug discovery and repurposing is challenging. Identifying the mechanism of action (MOA) is crucial, yet current approaches are costly and low-throughput. Here we present an approach for MOA identification by profiling changes in mitochondrial phenotypes. By temporally imaging mitochondrial morphology and membrane potential, we established a pipeline for monitoring time-resolved mitochondrial images, resulting in a dataset comprising 570,096 single-cell images of cells exposed to 1,068 United States Food and Drug Administration-approved drugs. A deep learning model named MitoReID, using a re-identification (ReID) framework and an Inflated 3D ResNet backbone, was developed. It achieved 76.32% Rank-1 and 65.92% mean average precision on the testing set and successfully identified the MOAs for six untrained drugs on the basis of mitochondrial phenotype. Furthermore, MitoReID identified cyclooxygenase-2 inhibition as the MOA of the natural compound epicatechin in tea, which was successfully validated in vitro. Our approach thus provides an automated and cost-effective alternative for target identification that could accelerate large-scale drug discovery and repurposing.

The confocal laser scanning microscope allows the visualization of intracellular structures in greater detail than a widefield fluorescence microscope. Immunofluorescence (IF) techniques make use of the inherent ability of antibodies to bind to specific epitopes of specific proteins. Tagging these antibodies with an easily visualized molecule, e.g., a fluorophore, enables imaging in the fluorescence microscope. This is, however, a localization technique and will only give information about where certain proteins are; it does not provide the ultrastructural context provided by the transmission electron microscope. It also relies heavily on the accuracy and binding affinity of individual primary antibodies. Despite this, it is a commonly used, robust, and adaptable technique. In this chapter, we use a long-established IF protocol from our laboratory to locate EHDV proteins in a monolayer of infected cultured cells.

Virus isolation is used to assist in the diagnosis and confirmation of viral infections. Successful isolation of a virus is highly dependent upon the quality of starting material. Here we describe the preparation and isolation of epizootic hemorrhagic disease virus (EHDV) from blood and tissue samples in tissue culture flasks (TCFs) through the inoculation of susceptible cell lines including Vero, BHK, and KC cells.

Gallium is a tri-valent p-block metal that closely mimics tri-valent iron. Gallium is internalized into cells via transferrin receptor-mediated endocytosis. Both Ga-67 and Ga-68 are radionuclides that can be radiolabeled to various bioactive compounds for clinical imaging procedures to visualize tumors and sites of inflammation. High-dose ascorbate (pharmacological ascorbate) is an emergent glioblastoma therapy that enhances cancer cell-killing through iron-metabolic perturbations. We hypothesized that pharmacological ascorbate treatments might alter Ga-67 uptake in glioblastoma cells. We evaluated the in vitro ability of pharmacological ascorbate to alter gallium uptake in patient-derived glioblastoma cells with variable genetic backgrounds by co-incubating cells with Ga-67 ± pharmacological ascorbate. Surprisingly, we observed increased basal gallium uptake in the glioblastoma cells compared to normal human astrocytes. Further, pharmacological ascorbate treatment stimulated gallium uptake in glioblastoma cells while not affecting uptake in normal human astrocytes. This effect appears to be related to transient increases in transferrin receptor expression. Finally, pharmacological ascorbate treatment appears to stimulate gallium uptake in an iron metabolism-dependent manner. Further mechanistic experiments are required to evaluate the translational utility of ascorbate to impact gallium tumor imaging.

Secondary healing of fractured bones requires an application of an appropriate fixator. In general, steel or titanium devices are used mostly. However, in recent years, composite structures arise as an attractive alternative due to high strength to weight ratio and other advantages like, for example, radiolucency. According to Food and Drug Administration (FDA), the only unidirectionally reinforced composite allowed to be implanted in human bodies is carbon fiber (CF)-reinforced poly-ether-ether-ketone (PEEK). In this work, the healing process of long bone assembled with CF/PEEK plates with cross- and angle-ply lay-up configurations is studied in the framework of finite element method. The healing is simulated by making use of the mechanoregulation model basing on the Prendergast theory. Cells transformation is determined by the octahedral shear strain and interstitial fluid velocity. The process runs iteratively assuming single load cycle each day. The fracture is subjected to axial and transverse forces. In the computations, the Abaqus program is used. It is shown that the angle-ply lamination scheme of CF/PEEK composite seems to provide better conditions for the transformation of the soft callus into the bone tissue.

Congenital heart disease (CHD) is the most common birth defect, requiring invasive surgery often before a child\'s first birthday. Current materials used during CHD surgery lack the ability to grow, remodel, and regenerate. To solve those limitations, 3D bioprinting is an emerging tool with the capability to create tailored constructs based on patients\' own imaging data with the ability to grow and remodel once implanted in children with CHD. It has the potential to integrate multiple bioinks with several cell types and biomolecules within 3D-bioprinted constructs that exhibit good structural fidelity, stability, and mechanical integrity. This review gives an overview of CHD and recent advancements in 3D bioprinting technologies with potential use in the treatment of CHD. Moreover, the selection of appropriate biomaterials based on their chemical, physical, and biological properties that are further manipulated to suit their application are also discussed. An introduction to bioink formulations composed of various biomaterials with emphasis on multiple cell types and biomolecules is briefly overviewed. Vasculogenesis and angiogenesis of prefabricated 3D-bioprinted structures and novel 4D printing technology are also summarized. Finally, we discuss several restrictions and our perspective on future directions in 3D bioprinting technologies in the treatment of CHD.

OBJECTIVE: Meniscus progenitor cells (MPCs) have been identified as promising candidates for meniscus regeneration, and it is crucial for us to understand meniscus injury repair mechanism at the cellular level. In this study, we investigate the biological properties of MPCs isolated from different species using the differential adhesion to fibronectin (DAF) technique. We aim to characterize MPCs in different species and evaluate the feasibility of these models for future meniscal investigation.
METHODS: MPCs were isolated from freshly digested meniscus from rat, rabbit, goat, and human cells using DAF. Biological properties, including proliferation, colony-forming, multilineage differentiation, and migration abilities, were compared in MPCs and their corresponding mixed meniscus cell (MCs) population in each species.
RESULTS: MPCs were successfully isolated by the DAF technique in all species. Rat MPCs appeared cobblestone-like, rabbit MPCs were more polygonal, goat MPCs had a spindle-shaped morphology, human MPCs appear more fibroblast-like. Compared with MCs, isolated MPCs showed progenitor cell characteristics, including multilineage differentiation ability and MSC (mesenchymal stem cells) markers (CD166, CD90, CD44, Stro-1) expression. They also highly expressed fibronectin receptors CD49e and CD49c. MPCs also showed greater proliferation capacity and retained colony-forming ability. Except for goat MPCs showed greater migration abilities than MCs, no significant differences were found in the migration ability between MPCs and MCs in other species.
CONCLUSIONS: Our study shows that DAF is an effective method for isolating MPCs from rat, rabbit, goat, and human. MPCs in these species demonstrated similar characteristics, including greater proliferation ability and better chondrogenic potential.