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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

FIRM image analysis: A machine learning workflow for quantifying extracellular matrix components from electron microscopy images

The extracellular matrix (ECM) is a complex network of biomolecules that plays an integral role in the structure, processes, and signaling mechanisms of cells and tissues. Identifying and quantifying changes in these matrix components provides insight into the mechanisms behind specific tissue remodeling processes; however, quantifying these changes is challenging due to difficult imaging conditions, complexity of the ECM, and the subtlety of these changes. Current imaging techniques allow us to visualize these critical remodeling events and developments in image analysis have employed a combination of analysis software and machine learning techniques to improve the efficiency and accuracy with which features are measured. Although image analysis has seen much improvement in recent years, there has been no technique developed to address ambiguity in feature edges in electron microscopy images. Presented here is a new machine learning-based workflow for the analysis of microscopy images named FIRM (Feature Identification from Raw Microscopy) that uses a random forest classifier to identify ECM features of interest and generate binary segmentation masks for quantification with ImageJ-FIJI. FIRM performed with an F1 score of 0.794 and greater than 80% accuracy for number and size of features detected. FIRM had similar deviation from the ground truth in the number of identified fibrils, fibril size, and size distributions when compared to human analyses. The results suggest that FIRM performs as well as manual analysis and requires a fraction of the time. This analysis technique is more efficient, eliminates user bias, and can be easily optimized to identify a variety of features, making it useful for any discipline requiring image analysis.

Science & Technology - Other Topics↗
DOE OSTI2021

Phenotypical modifications of immune cells are enhanced by extracellular matrix

Immune cells not only constitute tumour microenvironment but they may even affect disease prognosis as a result of dual functional roles that they may play in tumour tissues. Two frequently used established immune cell lines (lymphocytic Jurkat and monocytic THP-1) were used to test whether microenvironmental factors, especially molecular components of extracellular matrix, can shape the phenotype of immune cells. Proliferation, morphological and phenotypical analyses were applied to compare behaviour of the immune cells, typically cultured as suspensions in culture medium, with their behaviour in collagen type I-based and Matrigel-based 3D cultures. Density of both immune cell types in routine suspension cultures affected their subsequent proliferation in extracellular matrices. THP-1 cells appeared to be more sensitive to their surrounding microenvironment as judged from extracellular matrix type-dependent changes in their cell doubling times and from slight increase in their diameters in both extracellular matrix-containing cell cultures. Moreover, even chemically uninduced monocytic THP-1 cells were present in a minor fraction as CD68 positive cell population in collagen type I matrix indicating their partial differentiation to macrophages. Observed modifications of immune cells by microenvironmental factors may have profound implications for their roles in healthy and pathological tissues.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Exploring the Interplay between Polyphenols and Lysyl Oxidase Enzymes for Maintaining Extracellular Matrix Homeostasis

Collagen, the most abundant structural protein found in mammals, plays a vital role as a constituent of the extracellular matrix (ECM) that surrounds cells. Collagen fibrils are strengthened through the formation of covalent cross-links, which involve complex enzymatic and non-enzymatic reactions. Lysyl oxidase (LOX) is responsible for catalyzing the oxidative deamination of lysine and hydroxylysine residues, resulting in the production of aldehydes, allysine, and hydroxyallysine. These intermediates undergo spontaneous condensation reactions, leading to the formation of immature cross-links, which are the initial step in the development of mature covalent cross-links. Additionally, non-enzymatic glycation contributes to the formation of abnormal cross-linking in collagen fibrils. During glycation, specific lysine and arginine residues in collagen are modified by reducing sugars, leading to the creation of Advanced Glycation End-products (AGEs). These AGEs have been associated with changes in the mechanical properties of collagen fibers. Interestingly, various studies have reported that plant polyphenols possess amine oxidase-like activity and can act as potent inhibitors of protein glycation. This review article focuses on compiling the literature describing polyphenols with amine oxidase-like activity and antiglycation properties. Specifically, we explore the molecular mechanisms by which specific flavonoids impact or protect the normal collagen cross-linking process. Furthermore, we discuss how these dual activities can be harnessed to generate properly cross-linked collagen molecules, thereby promoting the stabilization of highly organized collagen fibrils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cadherin 11 Promotes Immunosuppression and Extracellular Matrix Deposition to Support Growth of Pancreatic Tumors and Resistance to Gemcitabine in Mice

Pancreatic ductal adenocarcinomas (PDACs) are characterized by fibrosis and an abundance of cancer-associated fibroblasts (CAFs). Here, we investigated strategies to disrupt interactions among CAFs, the immune system, and cancer cells, focusing on adhesion molecule CDH11, which has been associated with other fibrotic disorders and is expressed by activated fibroblasts. We compared levels of CDH11 messenger RNA in human pancreatitis and pancreatic cancer tissues and cells with normal pancreas, and measured levels of CDH11 protein in human and mouse pancreatic lesions and normal tissues. We crossed p48-Cre;LSL-Kras G12D/+ ;LSL-Trp53 R172H/+ (KPC) mice with CDH11-knockout mice and measured survival times of offspring. Pancreata were collected and analyzed by histology, immunohistochemistry, and (single-cell) RNA sequencing; RNA and proteins were identified by imaging mass cytometry. Some mice were given injections of PD1 antibody or gemcitabine and survival was monitored. Pancreatic cancer cells from KPC mice were subcutaneously injected into Cdh11 +/+ and Cdh11 –/– mice and tumor growth was monitored. Pancreatic cancer cells (mT3) from KPC mice (C57BL/6), were subcutaneously injected into Cdh11 +/+ (C57BL/6J) mice and mice were given injections of antibody against CDH11, gemcitabine, or small molecule inhibitor of CDH11 (SD133) and tumor growth was monitored. Levels of CDH11 messenger RNA and protein were significantly higher in CAFs than in pancreatic cancer epithelial cells, human or mouse pancreatic cancer cell lines, or immune cells. KPC/Cdh11 +/– and KPC/Cdh11 –/– mice survived significantly longer than KPC/Cdh11 +/+ mice. Markers of stromal activation entirely surrounded pancreatic intraepithelial neoplasias in KPC/Cdh11 +/+ mice and incompletely in KPC/Cdh11 +/– and KPC/Cdh11 –/– mice, whose lesions also contained fewer FOXP3 + cells in the tumor center. Compared with pancreatic tumors in KPC/Cdh11 +/+ mice, tumors of KPC/Cdh11 +/– mice had increased markers of antigen processing and presentation; more lymphocytes and associated cytokines; decreased extracellular matrix components; and reductions in markers and cytokines associated with immunosuppression. Administration of the PD1 antibody did not prolong survival of KPC mice with 0, 1, or 2 alleles of Cdh11. Gemcitabine extended survival of KPC/Cdh11 +/– and KPC/Cdh11 –/– mice only or reduced subcutaneous tumor growth in mT3 engrafted Cdh11 +/+ mice when given in combination with the CDH11 antibody. A small molecule inhibitor of CDH11 reduced growth of pre-established mT3 subcutaneous tumors only if T and B cells were present in mice. Knockout or inhibition of CDH11, which is expressed by CAFs in the pancreatic tumor stroma, reduces growth of pancreatic tumors, increases their response to gemcitabine, and significantly extends survival of mice. CDH11 promotes immunosuppression and extracellular matrix deposition, and might be developed as a therapeutic target for pancreatic cancer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Artificial extracellular matrix scaffolds of mobile molecules enhance maturation of human stem cell-derived neurons

Human induced pluripotent stem cell (hiPSC) technologies offer a unique resource for modeling neurological diseases. However, iPSC models are fraught with technical limitations including abnormal aggregation and inefficient maturation of differentiated neurons. These problems are in part due to the absence of synergistic cues of the native extracellular matrix (ECM). We report on the use of three artificial ECMs based on peptide amphiphile (PA) supramolecular nanofibers. All nanofibers display the laminin-derived IKVAV signal on their surface but differ in the nature of their non-bioactive domains. Here, we find that nanofibers with greater intensity of internal supramolecular motion have enhanced bioactivity toward hiPSC-derived motor and cortical neurons. Proteomic, biochemical, and functional assays reveal that highly mobile PA scaffolds caused enhanced β1-integrin pathway activation, reduced aggregation, increased arborization, and matured electrophysiological activity of neurons. Our work highlights the importance of designing biomimetic ECMs to study the development, function, and dysfunction of human neurons.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Combining stretching and gallic acid to decrease inflammation indices and promote extracellular matrix production in osteoarthritic human articular chondrocytes

Osteoarthritis (OA) patients undergo cartilage degradation and experience painful joint swelling. OA symptoms are caused by inflammatory molecules and the upregulation of catabolic genes leading to the breakdown of cartilage extracellular matrix (ECM). Here, we investigate the effects of gallic acid (GA) and mechanical stretching on the expression of anabolic and catabolic genes and restoring ECM production by osteoarthritic human articular chondrocytes (hAChs) cultured in monolayers. hAChs were seeded onto conventional plates or silicone chambers with or without 100 μM GA. A 5% cyclic tensile strain (CTS) was applied to the silicone chambers and the deposition of collagen and glycosaminoglycan, and gene expressions of collagen types II (COL2A1), XI (COL11A2), I (COL1A1), and X (COL10A1), and matrix metalloproteinases (MMP-1 and MMP-13) as inflammation markers, were quantified. CTS and GA acted synergistically to promote the deposition of collagen and glycosaminoglycan in the ECM by 14- and 7-fold, respectively. Furthermore, the synergistic stimuli selectively upregulated the expression of cartilage-specific proteins, COL11A2 by 7-fold, and COL2A1 by 47-fold, and, in contrast, downregulated the expression of MMP-1 by 2.5-fold and MMP-13 by 125-fold. GA supplementation with CTS is a promising approach for restoring osteoarthritic hAChs ECM production ability making them suitable for complex tissue engineering applications.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Structure of the polysaccharide sheath from the B race of the green microalga Botryococcus braunii

The green microalga Botryococcus braunii forms a colony of cells held together by an intricate extracellular matrix. This extracellular matrix also acts as a storage location for liquid hydrocarbons initially produced inside the cells. These hydrocarbons can be used as feedstocks to produce transportation fuels. In the B race of B. braunii, the extracellular matrix is composed of several elements: a cross-linked hydrocarbon network filled with the liquid hydrocarbons, a retaining wall to hold the hydrocarbons in the extracellular matrix, an arabinogalactan polysaccharide fibrillar sheath that extends outward from the retaining wall, and a single protein known as polysaccharide associated protein is found at the base of the polysaccharide fibers where they connect to the retaining wall. During growth, colonies of the B race of B. braunii shed fragments of the retaining wall with polysaccharide fibrils attached into the media. Here we describe the isolation and structural analysis of these polysaccharides using a series of chemical degradations in combination with glycosyl residue composition and linkage analysis, as well as 2-dimensional nuclear magnetic resonance spectroscopy. The results demonstrate that the polysaccharide is highly branched, consisting of a galactan backbone with short branches comprised of Dgalactopyranose, L-arabinofuranose, 4-O-methyl-D-glucopyranuronic acid, and 6-deoxy-D-altropyranose. To our knowledge, this is the first description of 6-deoxyaltrose in algae or plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Construction of extracellular matrix-based 3D hydrogel and its effects on cardiomyocytes

Highlights: • SOD and Triton X-100 could efficiently decellularize cells to get cardiac ECM. • Main proteins of cECM were fibronectin, collagen, elastin, fibrillin, laminin, etc. • 75% cECM-containing 3D hydrogel promoted cell proliferation and anti-apoptosis. • cECM3DH facilitated the differentiation of ESCs into CMs. • APcECM3DH was more conducive to NCM and ESC-derived CM maturation. Some discoveries resulted from 2-dimensional (2D) cultured cardiac cells have been disqualified in animal testing and later clinical trials. Extracellular matrix (ECM) plays a vital role in cardiac homeostasis, cardiac ECM (cECM)-based 3D cell cultures can mimics the physiological and pathological conditions in vivo closely, it is hopeful of addressing this challenge. Construction of cECM-based 3-dimensional (3D) hydrogel (cECM3DH) and its effects on cell behaviors were studied here. The results indicated that cellular compartments could be efficiently removed from heart tissue via sodium dodecyl sulfonate (SDS)- and Triton X-100-mediated decellularization, remaining the natural fibrous network structure and major proteins. 3D hydrogel consisted of 1 × 10{sup 7} cells/mL cells and 75% cECM could promote the proliferation and anti-apoptosis ability of human embryonic kidney (HEK)-293T cells. 0.25% trypsin or 0.20% collagenase was suitable to retrieve these cells from 3D hydrogel for further researches. Compared with 2D culture system, cECM3DH could significantly increase the proportion of GATA 4{sup +} cardiomyocytes (CMs) derived from heart tissue of neonatal mouse or induced differentiation of embryonic stem cells (ESCs) (P < 0.05) The expression levels of mature genes including cTnT, JCN, CaV1.2, MYL2, CASQ2, NCX1, and Cx43 of these CMs in adult pig cECM-based 3D hydrogel (APcECM3DH) were significantly higher than that in 2D culture system and in newborn piglet cECM-based 3D hydrogel (NPcECM3DH), respectively (P < 0.05). Therefore, cECM3DH supports the generation of primary CMs and ESC-derived CMs, APcECM3DH was more conducive to promoting CM maturation, which contributes to building 3D model for pathogenesis exploration, drug screening, and regenerative medicine of heart diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Protein–protein interactions between tenascin-R and RPTPζ/phosphacan are critical to maintain the architecture of perineuronal nets

Neural plasticity, the ability to alter the structure and function of neural circuits, varies throughout the age of an individual. The end of the hyperplastic period in the central nervous system coincides with the appearance of honeycomb-like structures called perineuronal nets (PNNs) that surround a subset of neurons. PNNs are a condensed form of neural extracellular matrix that include the glycosaminoglycan hyaluronan and extracellular matrix proteins such as aggrecan and tenascin-R (TNR). PNNs are key regulators of developmental neural plasticity and cognitive functions, yet our current understanding of the molecular interactions that help assemble them remains limited. Disruption of Ptprz1, the gene encoding the receptor protein tyrosine phosphatase RPTPζ, altered the appearance of nets from a reticulated structure to puncta on the surface of cortical neuron bodies in adult mice. The structural alterations mirror those found in Tnr -/- mice, and TNR is absent from the net structures that form in dissociated cultures of Ptprz1 -/- cortical neurons. These findings raised the possibility that TNR and RPTPζ cooperate to promote the assembly of PNNs. Here, we show that TNR associates with the RPTPζ ectodomain and provide a structural basis for these interactions. Furthermore, we show that RPTPζ forms an identical complex with tenascin-C, a homolog of TNR that also regulates neural plasticity. Finally, we demonstrate that mutating residues at the RPTPζ–TNR interface impairs the formation of PNNs in dissociated neuronal cultures. Overall, this work sets the stage for analyzing the roles of protein–protein interactions that underpin the formation of nets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗