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1. Evaluation of bone formation on orthopedic implant surfaces using an ex-vivo bone bioreactor system

   https://doi.org/10.1038/s41598-021-02070-z  

   Dua, Rupak; Jones, Hugh; Noble, Philip C. (December 2021, Scientific Reports)

   Abstract Recent advances in materials and manufacturing processes have allowed the fabrication of intricate implant surfaces to facilitate bony attachment. However, refinement and evaluation of these new design strategies are hindered by the cost and complications of animal studies, particularly during early iterations in the development process. To address this problem, we have previously constructed and validated an ex-vivo bone bioreactor culture system that can maintain the viability of bone samples for an extended period ex-vivo. In this study, we investigated the mineralization of a titanium wire mesh scaffold under both static and dynamic culturing using our ex vivo bioreactor system. Thirty-six cancellous bone cores were harvested from bovine metatarsals at the time of slaughter and divided into five groups under the following conditions: Group 1) Isolated bone cores placed in static culture, Group 2) Unloaded bone cores placed in static culture in contact with a fiber-mesh metallic scaffold, Group 3) Bone cores placed in contact with a fiber-mesh metallic scaffold under the constant pressure of 150 kPa, Group 4) Bone core placed in contact with a fiber-mesh metallic scaffold and exposed to cyclic loading with continuous perfusion flow of media within the ex-vivo culture system and Group 5) Bone core evaluated on Day 0 to serve as a positive control for comparison with all other groups at weeks 4 and 7. Bone samples within Groups 1–4 were incubated for 4 and 7 weeks and then evaluated using histological examination (H&E) and the Live-Dead assay (Life Technologies). Matrix deposits on the metallic scaffolds were examined with scanning electron microscopy (SEM), while the chemical composition of the matrix was measured using energy-dispersive x-ray spectroscopy (EDX). We found that the viability of bone cores was maintained after seven weeks of loading in our ex vivo system. In addition, SEM images revealed crystallite-like structures on the dynamically loaded metal coupons (Group 4), corresponding to the initial stages of mineralization. EDX results further confirmed the presence of carbon at the interface and calcium phosphates in the matrix. We conclude that a bone bioreactor can be used as an alternate tool for in-vivo bone ingrowth studies of new implant surfaces or coatings. 

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2. A New Approach to In Vivo Transformation of Killer T Cells

   https://doi.org/10.1016/j.jmb.2025.169369  

   Rodriguez, Noe; Hofmann, Christian; Yang, Otto O; Gelbart, William M (August 2025, Journal of Molecular Biology)

   Chimeric antigen receptor (CAR) T cell therapy is a relatively new and powerful way of transforming T cells with receptors needed to recognize and kill diseased cells. Traditionally, it involves extraction of T cells from a patient, ex vivo transformation of them with CARs, expansion, and subsequent re-infusion into the patient. Recent developments aim to avoid this lengthy, costly patient-specific procedure by using var- ious viral and non-viral vector particles for direct in vivo delivery of CAR-encoding genes. In this paper we highlight several fundamental connections between in vitro and in vivo aspects of this process. We dis- cuss the proposed use of in vitro-reconstituted virus-like particles (VLPs), prepared from purified CAR- encoding mRNA and viral capsid protein, and functionalized with a T cell-targeting antibody. We compare and contrast these particles – and their use as gene vectors – with the several modalities currently employed that involve in cellulo generation of lentiviral or AAV vectors or in vitro complexation of nucleic acids with cationic polymers or lipid vesicles. We report the unique stoichiometric preciseness and ther- modynamic stability of VLPs formed from anti-HIV-glycoprotein CAR-encoding mRNA and the capsid pro- tein from a plant virus, and quantify the extent to which these monodisperse spherical VLPs are RNase resistant and lead to strong CAR expression in T cells. Further, in vitro cell-killing experiments are pro- posed, in which these CAR VLP-transformed T cells are mixed with HIV-infected cells, to be followed by in vivo experiments involving injection of the particles into HIV-infected humanized mice. 

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3. Uncovering in vivo biochemical patterns from time-series metabolic dynamics

   https://doi.org/10.1371/journal.pone.0268394  

   Wu, Yue; Judge, Michael T.; Edison, Arthur S.; Arnold, Jonathan (May 2022, PLOS ONE)

   Millet, Oscar (Ed.)

   System biology relies on holistic biomolecule measurements, and untangling biochemical networks requires time-series metabolomics profiling. With current metabolomic approaches, time-series measurements can be taken for hundreds of metabolic features, which decode underlying metabolic regulation. Such a metabolomic dataset is untargeted with most features unannotated and inaccessible to statistical analysis and computational modeling. The high dimensionality of the metabolic space also causes mechanistic modeling to be rather cumbersome computationally. We implemented a faster exploratory workflow to visualize and extract chemical and biochemical dependencies. Time-series metabolic features (about 300 for each dataset) were extracted by Ridge Tracking-based Extract (RTExtract) on measurements from continuous in vivo monitoring of metabolism by NMR (CIVM-NMR) in Neurospora crassa under different conditions. The metabolic profiles were then smoothed and projected into lower dimensions, enabling a comparison of metabolic trends in the cultures. Next, we expanded incomplete metabolite annotation using a correlation network. Lastly, we uncovered meaningful metabolic clusters by estimating dependencies between smoothed metabolic profiles. We thus sidestepped the processes of time-consuming mechanistic modeling, difficult global optimization, and labor-intensive annotation. Multiple clusters guided insights into central energy metabolism and membrane synthesis. Dense connections with glucose 1-phosphate indicated its central position in metabolism in N . crassa . Our approach was benchmarked on simulated random network dynamics and provides a novel exploratory approach to analyzing high-dimensional metabolic dynamics. 

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4. Quantitative NMR-Based Biomedical Metabolomics: Current Status and Applications

   https://doi.org/10.3390/molecules25215128  

   Crook, Alexandra A.; Powers, Robert (November 2020, Molecules)

   null (Ed.)

   Nuclear Magnetic Resonance (NMR) spectroscopy is a quantitative analytical tool commonly utilized for metabolomics analysis. Quantitative NMR (qNMR) is a field of NMR spectroscopy dedicated to the measurement of analytes through signal intensity and its linear relationship with analyte concentration. Metabolomics-based NMR exploits this quantitative relationship to identify and measure biomarkers within complex biological samples such as serum, plasma, and urine. In this review of quantitative NMR-based metabolomics, the advancements and limitations of current techniques for metabolite quantification will be evaluated as well as the applications of qNMR in biomedical metabolomics. While qNMR is limited by sensitivity and dynamic range, the simple method development, minimal sample derivatization, and the simultaneous qualitative and quantitative information provide a unique landscape for biomedical metabolomics, which is not available to other techniques. Furthermore, the non-destructive nature of NMR-based metabolomics allows for multidimensional analysis of biomarkers that facilitates unambiguous assignment and quantification of metabolites in complex biofluids. 

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5. Microrheology of Pseudomonas aeruginosa biofilms grown in wound beds

   https://doi.org/10.1038/s41522-022-00311-1  

   Rahman, Minhaz Ur; Fleming, Derek F.; Wang, Liyun; Rumbaugh, Kendra P.; Gordon, Vernita D.; Christopher, Gordon F. (December 2022, npj Biofilms and Microbiomes)

   Abstract A new technique was used to measure the viscoelasticity of in vivo Pseudomonas aeruginosa biofilms. This was done through ex vivo microrheology measurements of in vivo biofilms excised from mouse wound beds. To our knowledge, this is the first time that the mechanics of in vivo biofilms have been measured. In vivo results are then compared to typical in vitro measurements. Biofilms grown in vivo are more relatively elastic than those grown in a wound-like medium in vitro but exhibited similar compliance. Using various genetically mutated P. aeruginosa strains, it is observed that the contributions of the exopolysaccharides Pel, Psl, and alginate to biofilm viscoelasticity were different for the biofilms grown in vitro and in vivo. In vitro experiments with collagen containing medium suggest this likely arises from the incorporation of host material, most notably collagen, into the matrix of the biofilm when it is grown in vivo. Taken together with earlier studies that examined the in vitro effects of collagen on mechanical properties, we conclude that collagen may, in some cases, be the dominant contributor to biofilm viscoelasticity in vivo. 

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