Hemodynamic Evaluation of Type B Aortic Dissection Using Compressed Sensing Accelerated 4D Flow MRI.

BACKGROUND: 4D Flow MRI is a quantitative imaging technique to evaluate blood flow patterns; however, it is unclear how compressed sensing (CS) acceleration would impact aortic hemodynamic quantification in type B aortic dissection (TBAD). PURPOSE: To investigate CS-accelerated 4D Flow MRI performance compared to GRAPP-accelerated 4D Flow MRI (GRAPPA) to evaluate aortic hemodynamics in TBAD. STUDY TYPE: Prospective. POPULATION: Twelve TBAD patients, two volunteers. FIELD STRENGTH/SEQUENCE: 1.5T, 3D time-resolved cine phase-contrast gradient echo sequence. ASSESSMENT: GRAPPA (acceleration factor [R] = 2) and two CS-accelerated (R = 7.7 [CS7.7] and 10.2 [CS10.2]) 4D Flow MRI scans were acquired twice for interscan reproducibility assessment. Voxelwise kinetic energy (KE), peak velocity (PV), forward flow (FF), reverse flow (RF), and stasis were calculated. Plane-based mid-lumen flows were quantified. Imaging times were recorded. TESTS: Repeated measures analysis of variance, Pearson correlation coefficients (r), intraclass correlation coefficients (ICC). P < 0.05 indicated statistical significance. RESULTS: The KE and FF in true lumen (TL) and PV in false lumen (FL) did not show difference among three acquisition types (P = 0.818, 0.065, 0.284 respectively). The PV and stasis in TL were higher, KE, FF, and RF in FL were lower, and stasis was higher in GRAPPA compared to CS7.7 and CS10.2. The RF was lower in GRAPPA compared to CS10.2. The correlation coefficients were strong in TL (r = [0.781-0.986]), and low to strong in FL (r = [0.347-0.948]). The ICC levels demonstrated moderate to excellent interscan reproducibility (0.732-0.989). The FF and net flow in mid-descending aorta TL were significantly different between CS7.7 and CS10.2. CONCLUSION: CS-accelerated 4D Flow MRI has potential for clinical utilization with shorter scan times in TBAD. Our results suggest similar hemodynamic trends between acceleration types, but CS-acceleration impacts KE, FF, RF, and stasis more in FL. EVIDENCE LEVEL: 1 Technical Efficacy: Stage 2.

The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.

BACKGROUND: Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an increasing need for methods to interrelate phenotypic data easily and accurately from experiments in animal models with human development and disease. RESULTS: Here we present the Xenopus phenotype ontology (XPO) to annotate phenotypic data from experiments in Xenopus, one of the major vertebrate model organisms used to study gene function in development and disease. The XPO implements design patterns from the Unified Phenotype Ontology (uPheno), and the principles outlined by the Open Biological and Biomedical Ontologies (OBO Foundry) to maximize interoperability with other species and facilitate ongoing ontology management. Constructed in Web Ontology Language (OWL) the XPO combines the existing uPheno library of ontology design patterns with additional terms from the Xenopus Anatomy Ontology (XAO), the Phenotype and Trait Ontology (PATO) and the Gene Ontology (GO). The integration of these different ontologies into the XPO enables rich phenotypic curation, whilst the uPheno bridging axioms allows phenotypic data from Xenopus experiments to be related to phenotype data from other model organisms and human disease. Moreover, the simple post-composed uPheno design patterns facilitate ongoing XPO development as the generation of new terms and classes of terms can be substantially automated. CONCLUSIONS: The XPO serves as an example of current best practices to help overcome many of the inherent challenges in harmonizing phenotype data between different species. The XPO currently consists of approximately 22,000 terms and is being used to curate phenotypes by Xenbase, the Xenopus Model Organism Knowledgebase, forming a standardized corpus of genotype-phenotype data that can be directly related to other uPheno compliant resources.

Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database.

Xenbase (www.xenbase.org) is a knowledge base for researchers and biomedical scientists that employ the amphibian Xenopus as a model organism in biomedical research to gain a deeper understanding of developmental and disease processes. Through expert curation and automated data provisioning from various sources Xenbase strives to integrate the body of knowledge on Xenopus genomics and biology together with the visualization of biologically significant interactions. Most current studies utilize next generation sequencing (NGS) but until now the results of different experiments were difficult to compare and not integrated with other Xenbase content. Xenbase has developed a suite of tools, interfaces and data processing pipelines that transforms NCBI Gene Expression Omnibus (GEO) NGS content into deeply integrated gene expression and chromatin data, mapping all aligned reads to the most recent genome builds. This content can be queried and visualized via multiple tools and also provides the basis for future automated 'gene expression as a phenotype' and gene regulatory network analyses.

Xenbase: a genomic, epigenomic and transcriptomic model organism database.

Xenbase (www.xenbase.org) is an online resource for researchers utilizing Xenopus laevis and Xenopus tropicalis, and for biomedical scientists seeking access to data generated with these model systems. Content is aggregated from a variety of external resources and also generated by in-house curation of scientific literature and bioinformatic analyses. Over the past two years many new types of content have been added along with new tools and functionalities to reflect the impact of high-throughput sequencing. These include new genomes for both supported species (each with chromosome scale assemblies), new genome annotations, genome segmentation, dynamic and interactive visualization for RNA-Seq data, updated ChIP-Seq mapping, GO terms, protein interaction data, ORFeome support, and improved connectivity to other biomedical and bioinformatic resources.

Heterogeneity is key to hydrogel-based cartilage tissue regeneration.

Degradable hydrogels have been developed to provide initial mechanical support to encapsulated cells while facilitating the growth of neo-tissues. When cells are encapsulated within degradable hydrogels, the process of neo-tissue growth is complicated by the coupled phenomena of transport of large extracellular matrix macromolecules and the rate of hydrogel degradation. If hydrogel degradation is too slow, neo-tissue growth is hindered, whereas if it is too fast, complete loss of mechanical integrity can occur. Therefore, there is a need for effective modelling techniques to predict hydrogel designs based on the growth parameters of the neo-tissue. In this article, hydrolytically degradable hydrogels are investigated due to their promise in tissue engineering. A key output of the model focuses on the ability of the construct to maintain overall structural integrity as the construct transitions from a pure hydrogel to engineered neo-tissue. We show that heterogeneity in cross-link density and cell distribution is the key to this successful transition and ultimately to achieve tissue growth. Specifically, we find that optimally large regions of weak cross-linking around cells in the hydrogel and well-connected and dense cell clusters create the optimum conditions needed for neo-tissue growth while maintaining structural integrity. Experimental observations using cartilage cells encapsulated in a hydrolytically degradable hydrogel are compared with model predictions to show the potential of the proposed model.

Determination of the Polymer-Solvent Interaction Parameter for PEG Hydrogels in Water: Application of a Self Learning Algorithm.

Concentrating on the case of poly(ethylene glycol) hydrogels, this paper introduces a methodology that enables a natural integration between the development of a so-called mechanistic model and experimental data relating material's processing to response. In a nutshell, we develop a data-driven modeling component that is able to learn and indirectly infer its own parameters and structure by observing experimental data. Using this method, we investigate the relationship between processing conditions, microstructure and chemistry (cross-link density and polymer-solvent interactions) and response (swelling and elasticity) of non-degradable and degradable PEG hydrogels. We show that the method not only enables the determination of the polymer-solvent interaction parameter, but also it predicts that this parameter, among others, varies with processing conditions and degradation. The proposed methodology therefore offers a new approach that accounts for subtle changes in the hydrogel processing.

Associations between 3D-based Left Atrial Volumetric and Blood Flow Parameters in a Single-Site Cohort of the Multi-Ethnic Study of Atherosclerosis.

Purpose To investigate associations between left atrial volume (LAV) and function with impaired three-dimensional hemodynamics from four-dimensional flow MRI. Materials and Methods A subcohort of participants from the Multi-Ethnic Study of Atherosclerosis from Northwestern University underwent prospective 1.5-T cardiac MRI including whole-heart four-dimensional flow and short-axis cine imaging between 2019 and 2020. Four-dimensional flow MRI analysis included manual three-dimensional segmentations of the LA and LA appendage (LAA), which were used to quantify LA and LAA peak velocity and blood stasis (% voxels < 0.1 m/sec). Short-axis cine data were used to delineate LA contours on all cardiac time points, and the resulting three-dimensional-based LAVs were extracted for calculation of LA emptying fractions (LAEFtotal, LAEFactive, LAEFpassive). Stepwise multivariable linear models were calculated for each flow parameter (LA stasis, LA peak velocity, LAA stasis, LAA peak velocity) to determine associations with LAV and LAEF. Results This study included 158 participants (mean age, 73 years ± 7 [SD]; 83 [52.5%] female and 75 [47.4%] male participants). In multivariable models, a 1-unit increase of LAEFtotal was associated with decreased LA stasis (ß coefficient, -0.47%; P < .001), while increased LAEFactive was associated with increased LA peak velocity (ß coefficient, 0.21 cm/sec; P < .001). Furthermore, increased minimum LAV indexed was most associated with impaired LAA flow (higher LAA stasis [ß coefficient, 0.65%; P < .001] and lower LAA peak velocity [ß coefficient, -0.35 cm/sec; P < .001]). Conclusion Higher minimum LAV and reduced LA function were associated with impaired flow characteristics in the LA and LAA. LAV assessment might therefore be a surrogate measure for LA and LAA flow abnormalities. Keywords: Atherosclerosis, Left Atrial Volume, Left Atrial Blood Flow, 4D Flow MRI Supplemental material is available for this article. © RSNA, 2024.

Echinobase: a resource to support the echinoderm research community.

Echinobase (www.echinobase.org) is a model organism knowledgebase serving as a resource for the community that studies echinoderms, a phylum of marine invertebrates that includes sea urchins and sea stars. Echinoderms have been important experimental models for over 100 years and continue to make important contributions to environmental, evolutionary, and developmental studies, including research on developmental gene regulatory networks. As a centralized resource, Echinobase hosts genomes and collects functional genomic data, reagents, literature, and other information for the community. This third-generation site is based on the Xenbase knowledgebase design and utilizes gene-centric pages to minimize the time and effort required to access genomic information. Summary gene pages display gene symbols and names, functional data, links to the JBrowse genome browser, and orthology to other organisms and reagents, and tabs from the Summary gene page contain more detailed information concerning mRNAs, proteins, diseases, and protein-protein interactions. The gene pages also display 1:1 orthologs between the fully supported species Strongylocentrotus purpuratus (purple sea urchin), Lytechinus variegatus (green sea urchin), Patiria miniata (bat star), and Acanthaster planci (crown-of-thorns sea star). JBrowse tracks are available for visualization of functional genomic data from both fully supported species and the partially supported species Anneissia japonica (feather star), Asterias rubens (sugar star), and L. pictus (painted sea urchin). Echinobase serves a vital role by providing researchers with annotated genomes including orthology, functional genomic data aligned to the genomes, and curated reagents and data. The Echinoderm Anatomical Ontology provides a framework for standardizing developmental data across the phylum, and knowledgebase content is formatted to be findable, accessible, interoperable, and reusable by the research community.

Computational Design of Phosphotriesterase Improves V-Agent Degradation Efficiency.

Organophosphates (OPs) are a class of neurotoxic acetylcholinesterase inhibitors including widely used pesticides as well as nerve agents such as VX and VR. Current treatment of these toxins relies on reactivating acetylcholinesterase, which remains ineffective. Enzymatic scavengers are of interest for their ability to degrade OPs systemically before they reach their target. Here we describe a library of computationally designed variants of phosphotriesterase (PTE), an enzyme that is known to break down OPs. The mutations G208D, F104A, K77A, A80V, H254G, and I274N broadly improve catalytic efficiency of VX and VR hydrolysis without impacting the structure of the enzyme. The mutation I106 A improves catalysis of VR and L271E abolishes activity, likely due to disruptions of PTE's structure. This study elucidates the importance of these residues and contributes to the design of enzymatic OP scavengers with improved efficiency.

Xenbase: key features and resources of the Xenopus model organism knowledgebase.

Xenbase (https://www.xenbase.org/), the Xenopus model organism knowledgebase, is a web-accessible resource that integrates the diverse genomic and biological data from research on the laboratory frogs Xenopus laevis and Xenopus tropicalis. The goal of Xenbase is to accelerate discovery and empower Xenopus research, to enhance the impact of Xenopus research data, and to facilitate the dissemination of these data. Xenbase also enhances the value of Xenopus data through high-quality curation, data integration, providing bioinformatics tools optimized for Xenopus experiments, and linking Xenopus data to human data, and other model organisms. Xenbase also plays an indispensable role in making Xenopus data interoperable and accessible to the broader biomedical community in accordance with FAIR principles. Xenbase provides annotated data updates to organizations such as NCBI, UniProtKB, Ensembl, the Gene Ontology consortium, and most recently, the Alliance of Genomic Resources, a common clearing house for data from humans and model organisms. This article provides a brief overview of key and recently added features of Xenbase. New features include processing of Xenopus high-throughput sequencing data from the NCBI Gene Expression Omnibus; curation of anatomical, physiological, and expression phenotypes with the newly created Xenopus Phenotype Ontology; Xenopus Gene Ontology annotations; new anatomical drawings of the Normal Table of Xenopus development; and integration of the latest Xenopus laevis v10.1 genome annotations. Finally, we highlight areas for future development at Xenbase as we continue to support the Xenopus research community.

Protein Based Biomaterials for Therapeutic and Diagnostic Applications.

Proteins are some of the most versatile and studied macromolecules with extensive biomedical applications. The natural and biological origin of proteins offer such materials several advantages over their synthetic counterparts, such as innate bioactivity, recognition by cells and reduced immunogenic potential. Furthermore, proteins can be easily functionalized by altering their primary amino acid sequence and can often be further self-assembled into higher order structures either spontaneously or under specific environmental conditions. This review will feature the recent advances in protein-based biomaterials in the delivery of therapeutic cargo such as small molecules, genetic material, proteins, and cells. First, we will discuss the ways in which secondary structural motifs, the building blocks of more complex proteins, have unique properties that enable them to be useful for therapeutic delivery. Next, supramolecular assemblies, such as fibers, nanoparticles, and hydrogels, made from these building blocks that are engineered to behave in a cohesive manner, are discussed. Finally, we will cover additional modifications to protein materials that impart environmental responsiveness to materials. This includes the emerging field of protein molecular robots, and relatedly, protein-based theranostic materials that combine therapeutic potential with modern imaging modalities, including near-infrared fluorescence spectroscopy (NIRF), single-photo emission computed tomography/computed tomography (SPECT/CT), positron emission tomography (PET), magnetic resonance imaging (MRI), and ultrasound/photoacoustic imaging (US/PAI).

Risk factors and patterns of recurrence after sentinel lymph node biopsy for thin melanoma.

While having a thin melanoma (defined as AJCC 8 T1 stage tumor ≤ 1.0 mm) with negative sentinel lymph node biopsy (SLNB) provides an excellent prognosis, some patients still develop recurrence and die. To determine risk factors for any recurrence (local/in-transit, nodal, distant) in thin melanoma patients with negative SLNB and assess survival outcomes. Retrospective review of thin melanomas with negative SLNB from 1999 to 2018 was performed. Two hundred and nine patients were identified. Clinicopathologic characteristics of the primary melanoma were collected. Patterns of recurrence for local/in-transit, nodal or distant recurrence and survival outcomes were analyzed. Eighteen patients (8.6%) developed recurrence: 3 (1.9%) local/in-transit, 4 (2.9%) regional/nodal, and 11 (5.3%) distant recurrence during a median follow-up time of 62 months. A multivariate Cox regression model showed that head and neck site (HR 3.52), ulceration (HR 10.8), and mitotic rate (HR 1.39) were significant risk factors for recurrence. Median time to first recurrence was 49 months. Patients with recurrence had a significantly worse 5 year overall survival than those without recurrence (82.2 vs 99.2%). A retrospective single center study and limited sample size. Did not factor in possible false negative SLNBs when calculating hazard ratios. For thin melanoma patients with negative SLNB, heightened surveillance is warranted for those with ulceration, primary tumor location on the head or neck, and elevated mitotic rate.

Baseline 4D Flow-Derived in vivo Hemodynamic Parameters Stratify Descending Aortic Dissection Patients With Enlarging Aortas.

Purpose: The purpose of our study was to assess the value of true lumen and false lumen hemodynamics compared to aortic morphological measurements for predicting adverse-aorta related outcomes (AARO) and aortic growth in patients with type B aortic dissection (TBAD). Materials and Methods: Using an IRB approved protocol, we retrospectively identified patients with descending aorta (DAo) dissection at a large tertiary center. Inclusion criteria includes known TBAD with ≥ 6 months of clinical follow-up after initial presentation for TBAD or after ascending aorta intervention for patients with repaired type A dissection with residual type B aortic dissection (rTAAD). Patients with prior descending aorta intervention were excluded. The FL and TL of each patient were manually segmented from 4D flow MRI data, and 3D parametric maps of aortic hemodynamics were generated. Groups were divided based on (1) presence vs. absence of AARO and (2) growth rate ≥ vs. < 3 mm/year. True and false lumen kinetic energy (KE), stasis, peak velocity (PV), reverse/forward flow (RF/FF), FL to TL KE ratio, as well as index aortic diameter were compared between groups using the Mann-Whitney U or independent t-test. Results: A total of n = 51 patients (age: 58.4 ± 15.0 years, M/F: 31/20) were included for analysis of AARO. This group contained n = 26 patients with TBAD and n = 25 patients with rTAAD. In the overall cohort, AARO patients had larger baseline diameters, lower FL-RF, FL stasis, TL-KE, TL-FF and TL-PV. Among patients with de novo TBAD, those with AAROs had larger baseline diameter, lower FL stasis and TL-PV. In both the overall cohort and in the subgroup of de novo TBAD, subjects with aortic growth ≥ 3mm/year, patients had a higher KE ratio. Conclusion: Our study suggests that 4D flow MRI is a promising tool for TBAD evaluation that can provide information beyond traditional MRA or CTA. 4D flow has the potential to become an integral aspect of TBAD work-up, as hemodynamic assessment may allow earlier identification of at-risk patients who could benefit from earlier intervention.

Utilization of a cloud-based radiology analytics platform to monitor imaging volumes at a large tertiary center.

Rationale and objective: In this study, we evaluate the ability of a novel cloud-based radiology analytics platform to continuously monitor imaging volumes at a large tertiary center following institutional protocol and policy changes. Materials and methods: We evaluated response to environmental factors through the lens of the COVID-19 pandemic. Analysis involved 11 CT/18 MR imaging systems at a large tertiary center. A vendor neutral, cloud-based analytics tool (CBRAP) was used to retrospectively collect information via DICOM headers on imaging exams between Oct. 2019 to Aug. 2021. Exams were stratified by modality (CT or MRI) and organized by body region. Pre-pandemic scan volumes (Oct 2019-Feb. 2010) were compared with volumes during/after two waves of COVID-19 in Illinois (Mar. to May 2020 & Oct. to Dec. 2020) using a t-test or Mann-Whitney U test. Results: The CBRAP was able to analyze 169,530 CT and 110,837 MR images, providing a detailed snapshot of baseline and post-pandemic CT and MR imaging across the radiology enterprise at our tertiary center. The CBRAP allowed for further subdivision in its reporting, showing monthly trends in average scan volumes specifically in the head, abdomen, spine, MSK, thorax, neck, GU system, or breast. Conclusion: The CBRAP retrieved data for 300,000 + imaging exams across multiple modalities at a large tertiary center in a highly populated, urban environment. The ability to analyze large imaging volumes across multiple waves of COVID-19 and evaluate quality-improvement endeavors/imaging protocol changes displays the usefulness of the CBRAP as an advanced imaging analytics tool.

Enhancing organophosphate hydrolase efficacy via protein engineering and immobilization strategies.

Organophosphorus compounds (OPs), developed as pesticides and chemical warfare agents, are extremely toxic chemicals that pose a public health risk. Of the different detoxification strategies, organophosphate-hydrolyzing enzymes have attracted much attention, providing a potential route for detoxifying those exposed to OPs. Phosphotriesterase (PTE), also known as organophosphate hydrolase (OPH), is one such enzyme that has been extensively studied as a catalytic bioscavenger. In this review, we will discuss the protein engineering of PTE aimed toward improving the activity and stability of the enzyme. In order to make enzyme utilization in OP detoxification more favorable, enzyme immobilization provides an effective means to increase enzyme activity and stability. Here, we present several such strategies that enhance the storage and operational stability of PTE/OPH.

Cell encapsulation spatially alters crosslink density of poly(ethylene glycol) hydrogels formed from free-radical polymerizations.

Photopolymerizable poly(ethylene glycol) (PEG) hydrogels are a promising platform for chondrocyte encapsulation and cartilage tissue engineering. This study demonstrates that during the process of encapsulation, chondrocytes alter the formation of PEG hydrogels leading to a reduction in the bulk and local hydrogel crosslink density. Freshly isolated chondrocytes were shown to interact with hydrogel precursors, in part through thiol-mediated events between dithiol crosslinkers and cell surface free thiols, depleting crosslinker concentration and causing a reduction in the bulk hydrogel crosslink density. This effect was more pronounced with increasing cell density at the time of encapsulation. Encapsulation of chondrocytes in fluorescently labeled hydrogels exhibited a gradient in hydrogel density around the cell, which was abrogated by treatment of the cells with the antioxidant estradiol prior to encapsulation. This gradient led to spatial variations in the degradation behavior of a hydrolytically degradable PEG hydrogel, creating regions devoid of hydrogel surrounding cells. Collectively, findings from this study indicate that the antioxidant defense mechanisms in chondrocytes alter the resultant properties of PEG hydrogels formed by free-radical polymerizations. These interactions will have a significant impact on tissue engineering, affecting the local microenvironment around cells and how tissue grows within the hydrogels. STATEMENT OF SIGNIFICANCE: Cell encapsulations in synthetic hydrogels formed by free-radical polymerizations offer numerous benefits for tissue engineering. Herein, we studied cartilage cells and identified that during encapsulation, cells interfered with hydrogel formation through two distinct mechanisms. Thiol-mediated events between monomers led to monomer depletion and a lower crosslinked hydrogel. Cells' antioxidant defense mechanisms interfered with free-radicals and inhibited hydrogel formation near the cell. These cell-mediated effects led to softer hydrogels and created unique hydrogel degradations patterns causing rapid degradation around the cells. The latter has benefits for tissue engineering, where these regions provide space for tissue growth. Overall, this study demonstrates that cells play a key role in how the hydrogel structure forms when cells are present.

An in vitro and in vivo comparison of cartilage growth in chondrocyte-laden matrix metalloproteinase-sensitive poly(ethylene glycol) hydrogels with localized transforming growth factor ß3.

While matrix-assisted autologous chondrocyte implantation has emerged as a promising therapy to treat focal chondral defects, matrices that support regeneration of hyaline cartilage remain challenging. The goal of this work was to investigate the potential of a matrix metalloproteinase (MMP)-sensitive poly(ethylene glycol) (PEG) hydrogel containing the tethered growth factor, transforming growth factor ß3 (TGF-ß3), and compare cartilage regeneration in vitro and in vivo. The in vitro environment comprised chemically-defined medium while the in vivo environment utilized the subcutaneous implant model in athymic mice. Porcine chondrocytes were isolated and expanded in 2D culture for 10 days prior to encapsulation. The presence of tethered TGF-ß3 reduced cell spreading. Chondrocyte-laden hydrogels were analyzed for total sulfated glycosaminoglycan and collagen contents, MMP activity, and spatial deposition of aggrecan, decorin, biglycan, and collagens type II and I. The total amount of extracellular matrix (ECM) deposited in the hydrogel constructs was similar in vitro and in vivo. However, the in vitro environment was not able to support long-term culture up to 64 days of the engineered cartilage leading to the eventual breakdown of aggrecan. The in vivo environment, on the other hand, led to more elaborate ECM, which correlated with higher MMP activity, and an overall higher quality of engineered tissue that was rich in aggrecan, decorin, biglycan and collagen type II with minimal collagen type I. Overall, the MMP-sensitive PEG hydrogel containing tethered TGF-ß3 is a promising matrix for hyaline cartilage regeneration in vivo. STATEMENT OF SIGNIFICANCE: Regenerating hyaline cartilage remains a significant clinical challenge. The resultant repair tissue is often fibrocartilage, which long-term cannot be sustained. The goal of this study was to investigate the potential of a synthetic hydrogel matrix containing peptide crosslinks that can be degraded by enzymes secreted by encapsulated cartilage cells (i.e., chondrocytes) and tethered growth factors, specifically TGF-ß3, to provide localized chondrogenic cues to the cells. This hydrogel led to hyaline cartilage-like tissue growth in vitro and in vivo, with minimal formation of fibrocartilage. However, the tissue formed in vitro, could not be maintained long-term. In vivo this hydrogel shows great promise as a potential matrix for use in regenerating hyaline cartilage.

Xenbase: Facilitating the Use of Xenopus to Model Human Disease.

At a fundamental level most genes, signaling pathways, biological functions and organ systems are highly conserved between man and all vertebrate species. Leveraging this conservation, researchers are increasingly using the experimental advantages of the amphibian Xenopus to model human disease. The online Xenopus resource, Xenbase, enables human disease modeling by curating the Xenopus literature published in PubMed and integrating these Xenopus data with orthologous human genes, anatomy, and more recently with links to the Online Mendelian Inheritance in Man resource (OMIM) and the Human Disease Ontology (DO). Here we review how Xenbase supports disease modeling and report on a meta-analysis of the published Xenopus research providing an overview of the different types of diseases being modeled in Xenopus and the variety of experimental approaches being used. Text mining of over 50,000 Xenopus research articles imported into Xenbase from PubMed identified approximately 1,000 putative disease- modeling articles. These articles were manually assessed and annotated with disease ontologies, which were then used to classify papers based on disease type. We found that Xenopus is being used to study a diverse array of disease with three main experimental approaches: cell-free egg extracts to study fundamental aspects of cellular and molecular biology, oocytes to study ion transport and channel physiology and embryo experiments focused on congenital diseases. We integrated these data into Xenbase Disease Pages to allow easy navigation to disease information on external databases. Results of this analysis will equip Xenopus researchers with a suite of experimental approaches available to model or dissect a pathological process. Ideally clinicians and basic researchers will use this information to foster collaborations necessary to interrogate the development and treatment of human diseases.

Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.

Xenbase is the Xenopus model organism database ( www.xenbase.org ), a web-accessible resource that integrates the diverse genomic and biological data for Xenopus research. It hosts a variety of content including current and archived genomes for both X. laevis and X. tropicalis, bioinformatic tools for comparative genetic analyses including BLAST and GBrowse, annotated Xenopus literature, and catalogs of reagents including antibodies, ORFeome clones, morpholinos, and transgenic lines. Xenbase compiles gene-specific pages which include manually curated gene expression images, functional information including gene ontology (GO), disease associations, and links to other major data sources such as NCBI:Entrez, UniProtKB, and Ensembl. We also maintain the Xenopus Anatomy Ontology (XAO) which describes anatomy throughout embryonic development. This chapter provides a full description of the many features of Xenbase, and offers a guide on how to use various tools to perform a variety of common tasks such as identifying nucleic acid or protein sequences, finding gene expression patterns for specific genes, stages or tissues, identifying literature on a specific gene or tissue, locating useful reagents and downloading our extensive content, including Xenopus gene-Human gene disease mapping files.