SEARCH · PubMed Health

Results for “reverse engineering”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources

PubMed2006

Construction of a complete rabbit cornea substitute using a fibrin-agarose scaffold.

PURPOSE: To construct a full-thickness biological substitute of the rabbit cornea by tissue engineering. METHODS: Ten rabbit corneas were surgically excised, and the three main cell types of the cornea (epithelial, stromal, and endothelial cells) were cultured. Genetic profiling of the cultured cells was performed by RT-PCR for the genes COL8 and KRT12. To develop an organotypic rabbit cornea equivalent, we used a sequential culture technique on porous culture inserts. First, endothelial cells were seeded on the base of the inserts. Then, a stroma substitute made of cultured keratocytes entrapped in a gel of human fibrin and 0.1% agarose was developed. Finally, cultured corneal epithelial cells were grown on the surface of the scaffold. Stratification of the epithelial cell layer was promoted by using an air-liquid culture technique. Corneal substitutes were analyzed by light and electron microscopy. RESULTS: All three types of corneal cells were efficiently cultured in the laboratory, expanded, and used to construct a full-thickness cornea substitute. Gene expression analyses confirmed that cultured endothelial cells expressed the COL8 gene, whereas epithelial cells expressed KRT12. Microscopic evaluation of the cornea substitutes demonstrated that epithelial cells tended to form a normal stratified layer and that stromal keratocytes proliferated rapidly in the stromal substitute. The endothelial monolayer exhibited a pattern similar to a normal corneal endothelium. CONCLUSIONS: These findings suggest that development of a full-thickness rabbit cornea model is possible in the laboratory and may open new avenues for research.

Animals↗

PubMed2007

Three-dimensional cartilage tissue engineering using adult stem cells from osteoarthritis patients.

OBJECTIVE: To determine whether it is possible to engineer 3-dimensional hyaline cartilage using mesenchymal stem cells derived from the bone marrow (BMSCs) of patients with osteoarthritis (OA). METHODS: Expanded BMSCs derived from patients with hip OA were seeded onto polyglycolic acid scaffolds and differentiated using transforming growth factor beta3 in the presence or absence of parathyroid hormone-related protein (PTHrP) to regulate hypertrophy. Micromass pellet cultures were established using the same cells for comparison. At the end of culture, the constructs or pellets were processed for messenger RNA (mRNA) analysis by quantitative real-time reverse transcription-polymerase chain reaction. Matrix proteins were analyzed using specific assays. RESULTS: Cartilage constructs engineered from BMSCs were at least 5 times the weight of equivalent pellet cultures. Histologic, mRNA, and biochemical analyses of the constructs showed extensive synthesis of proteoglycan and type II collagen but only low levels of type I collagen. The protein content was almost identical to that of cartilage engineered from bovine nasal chondrocytes. Analysis of type X collagen mRNA revealed a high level of mRNA in chondrogenic constructs compared with that in undifferentiated BMSCs, indicating an increased risk of hypertrophy in the tissue-engineered cells. However, the inclusion of PTHrP at a dose of 1 microM or 10 microM during the culture period resulted in significant suppression of type X collagen mRNA expression and a significant decrease in alkaline phosphatase activity, without any loss of the cartilage-specific matrix proteins. CONCLUSION: Three-dimensional hyaline cartilage can be engineered using BMSCs from patients with OA. This method could thus be used for the repair of cartilage lesions.

Adult↗

PubMed2006

Long-term mechanical loading of chondrocyte-chitosan biocomposites in vitro enhanced their proteoglycan and collagen content.

One major problem in cartilage tissue engineering is the insufficient biochemical composition of the generated biocomposites. The aim of this study was to improve the collagen and proteoglycan deposition in tissue engineering constructs by application of long-term mechanical loading in culture. Chondrocyte-seeded chitosan biocomposites revealed a homogenous cell distribution, high viability (>95%) and maintenance of a rounded cell shape typical for chondrocytes over 3 weeks of load-free culture. Cyclic compression of chitosan biocomposites (0.1 Hz, amplitude 5-15%, 45 min on and 315 min off) was applied after two different preculture times (3, 21 days) for 3 weeks. At day 42 this resulted in enhanced mRNA levels for aggrecan and a significantly higher specific proteoglycan (5-fold, p<0.0002) and collagen type II (2-fold, p<0.02) deposition compared to unloaded controls. In sum, the chitosan scaffold was highly attractive for cartilage tissue engineering approaches and mechanical loading allowed to further improve the biochemical composition of these biocomposites.

Animals↗

PubMed2005

Reconstruction of 3D stacked-up structures by rat small hepatocytes on microporous membranes.

The three-dimensional (3D) culture of hepatocytes is essential for the reconstruction of functional hepatic tissues in vitro. In the present experiment, we developed a 3D-culture method in order to reconstruct hepatic cordlike structures by stacking up two-dimensional (2D) tissues composed of rat small hepatocytes (SHs), which are hepatic progenitor cells. Pairs of membranes were prepared and the cells were separately cultured on each membrane. After the SH colonies had developed, one membrane was inverted on top of the other to form an SH bilayer. Thereafter, we investigated whether the stacked cells were organized into differentiated tissues. In the 3D stacked-up structures, bile canaliculi (BC) started to form and gradually developed into anastomosing networks. Transmission electron microscopy revealed that the SHs of the upper and lower layers adhered to one another, and that BC formed between them. Bile canalicular proteins localized on the lumina of the tubular structures. Furthermore, the cells within the structures exhibited mRNA transcription of the hepatic-differentiation markers and maintained a relatively high level of albumin secretion. We conclude that highly differentiated 3D tissues, including functional BC, can be reconstructed by stacking up layers of SHs. This 3D stacked-up culture is useful for the reconstruction of tissue-engineered livers.

Albumins↗

PubMed2002

Polymer/alginate amalgam for cartilage-tissue engineering.

Marrow stroma-derived cells (MSC) are highly proliferative, multipotential cells that have been considered as ideal candidate cells for autologous tissue engineering applications. In this study, we have characterized the chondrogenic potential of human MSCs in both a PLA/alginate amalgam and pure PLA macrostructure as model three-dimensional constructs to support both chondrogenic differentiation and proliferation following TGF-beta treatment. MSCs were seeded in experimental groups that consisted of PLA-loaded constructs and PLA/alginate amalgams with and without recombinant human TGF-beta1. Chondrogenesis of the PLA and the PLA/alginate amalgam cultures was assessed at weekly intervals by histology, immunohistochemistry, scanning electron microscopy, sulfate incorporation, and RT-PCR. Chondrogenic differentiation occurs within a polymeric macrostructure with TGF-beta1 treatment as indicated by histological, immunohistochemical, sulfate incorporation, and gene expression profiles. This macrostructure can be further encased in an alginate gel/solution to optimize cell shape and to confine growth factors and cells within the polymer construct, while the polymeric scaffold provides appropriate mechanical/tissue support. The stable three-dimensional PLA/alginate amalgam represents a novel candidate system of mesenchymal chondrogenesis, which is amendable to investigation of mechanical and biological factors that normally modulate cartilage development and formation as well as a potential tissue engineering construct for cartilage repair.

Alginates↗

PubMedDate not supplied

Symposium on Metrology and Standards for Cell Signaling: Impact on Tissue Engineering, National Institute for Standards and Technology, October 14-15, 2003.

The Symposium on Metrology and Standards for Cell Signaling: Impact on Tissue Engineering, was cosponsored by the National Institute for Standards and Technology (NIST) and ASTM International, and was held at the NIST on October 14 and 15, 2003. The purpose of the symposium was to discuss the role of standards and quantitative measurements of cellular responses for the field of tissue engineering. Accurate and quantitative measurements, reference materials, and standards are needed to facilitate the understanding and control of cell responses to materials, culture media, and the in vivo environment. Speakers included government researchers from the NIST, the Food and Drug Administration, and the National Cancer Institute; vice presidents, chief executive officers, and directors of research from companies; and academic researchers in engineering, medicine, and cell biology. The metrology needs identified include quantitative assays of cell signaling pathways, bioinformatics that will allow consolidation of these complex data and permit correlative parameters to be identified, well-characterized standardized cell lines against which responses in other cells can be compared, and reference materials for use in control experiments.

Cell Culture Techniques↗

PubMed2006

Bone regeneration on computer-designed nano-fibrous scaffolds.

The ability to control architectural features in tissue engineering scaffolds is critical to the success of neo-tissue regeneration. In this work, reverse solid freeform fabrication and thermal phase separation of poly(L-lactic acid) (PLLA) solutions were used to create three-dimensional nano-fibrous (NF) scaffolds with complex geometries on the macro- and micro-scales. This approach allows for the fabrication of NF matrices while having precise control of internal pore size and structure, as well as external scaffold shape including architectures generated from computed-tomography scans and histological sections. In vitro cell cultivation experiments with MC3T3-E1 pre-osteoblasts were performed on NF scaffolds and on similarly designed solid-walled (SW) scaffolds that did not have nano-fibers. Proliferation studies showed significantly more cells on NF scaffolds after 7 d. In differentiation studies, the NF scaffolds displayed more uniform matrix and mineral production throughout. Real-time PCR also showed significantly higher expression of osteocalcin and bone sialoprotein mRNAs after 2 and 6 weeks in the NF scaffolds. Expression of type I collagen mRNA was lower in NF scaffolds which possibly indicates quicker differentiation on the NF substrate. In summary, we controlled the geometry of NF PLLA scaffolds at multiple size scales, and the in vitro results showed that these NF scaffolds were advantageous to control scaffolds for bone tissue engineering.

3T3 Cells↗

PubMed2006

Combining enabling techniques in organic synthesis: continuous flow processes with heterogenized catalysts.

The concepts article describes enabling techniques (solid-phase assisted synthesis, new reactor design, microwave irradiation and new solvents) in organic chemistry and emphasizes the combination of several of them for creating new synthetic technology platforms. Particular focus is put on the combination of immobilized catalysts as well as biocatalysts with continuous flow processes. In this context, the PASSflow continuous flow technique fulfils both chemical as well as chemical engineering requirements. It combines reactor design with optimized, monolithic solid phases as well as reversible immobilization techniques for performing small as well as large scale synthesis with heterogenized catalysts under continuous flow conditions.

Journal Article↗

PubMed2025

Targeted Forward Genetics: Saturating Mutational Analyses of Specific Target Loci Within the Genome.

Precise allele replacement by homologous recombination (also known as "gene targeting" or "genome editing") allows scientists to engineer altered DNA sequences, insertions, or deletions at specific locations in the genome. Such reverse genetics provides powerful tools to elucidate the structure and function of regulatory DNA elements, genes, RNAs, and proteins within their natural, endogenous context. Here, we describe in detail the methodology for Targeted Forward Genetics (TFG), which supports population-scale, saturating screens of allele replacements spanning thousands of base pairs at a specific target locus in the genome. The overall approach and detailed protocols, developed for the fission yeast Schizosaccharomyces pombe, are extensible to other organisms in which gene targeting is feasible.

Schizosaccharomyces↗

PubMed2004

Chondrosarcoma cell differentiation.

A mixed population of lymphocytes from a healthy donor co-existed with an established culture of allogeneic chondrosarcoma cells, during which time the tumor cells changed from malignantly transformed to benign fibroblast-like morphology; from multilayered to a monolayered growth pattern; lost their potency to grow in colonies in soft agar; and showed signs of senescence. A discussion of possible molecular mechanisms for this event is offered. If there are as yet undiscovered lymphokines that can induce reversal of the malignant geno/phenotype, the cognate gene(s) should be cloned for genetic engineering and for the mass production of the corresponding molecular mediators for clinical trials.

Cell Differentiation↗

PubMed2006

Interaction of dermal fibroblasts with electrospun composite polymer scaffolds prepared from dextran and poly lactide-co-glycolide.

A highly porous electrospun scaffold was prepared by physically blending Dextran and poly lactide-co-glycolide (PLGA). The interaction between dermal fibroblasts and the Dextran/PLGA scaffold such as viability, proliferation, attachment, migration, extracellular matrix deposition, cytoskeleton organization and the functional gene expressions were characterized. The results indicated that cells interacted favorably with the scaffold. Moreover, cells migrated into the highly porous three dimensional matrix of the scaffold and organized into dense multi-layered structures that resembled dermal structure. The results of collagen gel assay also revealed that gel contraction was enhanced by the presence of the scaffold. The additional mechanical strength provided by the scaffold could enhance the binding of the seeded fibroblasts. These findings suggested that Dextran/PLGA scaffold can potentially be useful in enhancing the healing of chronic or trauma wounds.

Actins↗

PubMedDate not supplied

Stem cell regeneration of the nucleus pulposus.

Low back pain due to disc degeneration is one of the largest health problems faced in this nation when judged by lost work time and direct as well as indirect costs. Many experimental methods are being explored to treat or to reverse the effect of disc degeneration. This article reviews the strategy of a tissue engineering approach to disc regeneration. Mesenchymal stem cells (MSC) such as those obtained from marrow stroma when exposed to the appropriate microenvironment (hypoxia, growth factor, three dimensional culture) differentiate into nucleus pulposus-like cells. These then may be candidates for transplantation and nucleus repopulation. While the work is in its infancy, there is significant optimism that next steps will lead to organ culture models of disc degeneration and regeneration, and ultimately to in vivo rescue of degenerating discs with stem cell treatment.

Humans↗

PubMed2004

Characterization of a DNA vaccine expressing a human immunodeficiency virus-like particle.

An ideal human immunodeficiency virus type-1 (HIV-1) vaccine will most likely need to elicit cross-reactive neutralizing antibodies and a strong cell-mediated immune response against multiple HIV-1 antigens to confer protection against challenge. In this study, DNA vaccines were constructed to express virally regulated human immunodeficiency virus-like particles (VLP) to elicit broad-spectrum immune responses to multiple HIV-1 antigens. VLPs were efficiently produced using sequences encoding gag and pol gene products from an X4 isolate and sequences encoding for tat, rev, vpu, and env from R5 or R5X4 isolates. The integrase, vpr, vif, and nef genes were deleted. In addition, the long terminal repeats (LTRs) were removed and transcription of the VLP insert was driven by the addition of the cytomegalovirus immediate-early (CMV-IE) promoter. A second generation of VLP vaccine plasmids was constructed with mutations engineered into the VLP DNA to produce particles deficient in activities associated with viral reverse transcriptase and protease. Primate cell lines, transiently transfected with DNA, efficiently secreted VLP into the supernatant that banded within a sucrose gradient at densities similar to infectious virions. In addition, these particles incorporated Env on the particle surface that bound soluble human CD4. These VLPs provide a safe and efficient strategy for presenting multiple HIV-1 antigens, expressed from a single insert, to the immune system in a structure that mimics the infectious virion.

AIDS Vaccines↗

PubMed1996

T cell receptor (TCR) recognition of MHC class I variants: intermolecular second-site reversion provides evidence for peptide/MHC conformational variation.

We investigated mechanistic differences in antigen presentation between murine MHC class I variants H-2K(b) and H-2K(bm)8. H-2K(bm)8 differs from H-2K(b) by four residues at the floor of the peptide-binding site, affecting its B pocket which interacts with the second (P2) residue of the peptide. The rest of the molecule, including the T cell receptor (TCR)-contacting residues, is identical to H-2K(b). Due to this variation, CTLs that recognize the ovalbumin 257-264 and HSV gB 498-505 peptides on H-2K(b) cannot recognize them on H-2K(bm)8. This could be due to impaired peptide binding or an altered peptide: K(bm)8 conformation. Peptide binding studies ruled out the first explanation. Molecular modeling indicated that the most obvious consequence of amino acid variation between peptide/H-2K(b) and peptide/H-2K(bm)8 complexes would be a loss of the conserved hydrogen bond network in the B pocket of the latter. This could cause conformational variation of bound peptides. Intermolecular second-site reversion was used to test this hypothesis: P2-substituted OVA and HSV peptides, engineered to restore the hydrogen bond network of the B pocket, were the only ones which restored CTL recognition. These results provide a molecular understanding of peptide/MHC conformational variation.

Amino Acid Sequence↗

PubMed2004

Heparanase gene silencing, tumor invasiveness, angiogenesis, and metastasis.

BACKGROUND: Heparanase is an endoglycosidase that degrades heparan sulfate, the main polysaccharide constituent of the extracellular matrix and basement membrane. Expression of the heparanase gene is associated with the invasive, angiogenic, and metastatic potential of diverse malignant tumors and cell lines. We used gene-silencing strategies to evaluate the role of heparanase in malignancy and to explore the therapeutic potential of its specific targeting. METHODS: We designed plasmid vectors to express hammerhead ribozymes or small interfering RNAs (siRNAs) directed against the human or mouse heparanase mRNAs. Human breast carcinoma (MDA-MB-435) and mouse lymphoma (Eb) and melanoma (B16-BL6) tumor cell lines, which have naturally high levels of endogenous heparanase or have been genetically engineered to overexpress heparanase, were transfected with anti-heparanase ribozyme or siRNA. Semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) and measurements of enzymatic activity were used to confirm the efficient silencing of heparanase gene expression. Cells transfected with the anti-heparanase ribozyme and siRNA vectors were tested for invasiveness in vitro and metastatic dissemination in animal models of experimental and spontaneous metastasis. RESULTS: Compared with cells transfected with control constructs, cells transfected with the anti-heparanase ribozyme or siRNA vectors had profoundly reduced invasion and adhesion in vitro, regardless of cell type, and expressed less heparanase. In vivo, tumors produced by cells transfected with the anti-heparanase ribozyme and siRNA vectors were less vascularized and less metastatic than tumors produced by cells transfected with the control vectors. Mice injected with cells transfected with the anti-heparanase ribozyme and siRNA vectors lived longer than mice injected with control cells. CONCLUSIONS: The association of reduced levels of heparanase and altered tumorigenic properties in cells with anti-heparanase ribozyme- or siRNA-mediated gene-silencing vectors suggests that heparanase is important in cancer progression. Heparanase gene silencing has potential use as a target for anticancer drug development.

Angiogenesis Inducing Agents↗

PubMed2024

DNA-guided CRISPR/Cas12 for RNA targeting.

CRISPR-Cas nucleases are transforming genome editing, RNA editing, and diagnostics but have been limited to RNA-guided systems. We present ΨDNA, a DNA-based guide for Cas12 enzymes, engineered for specific and efficient RNA targeting. ΨDNA mimics a crRNA but with a reverse orientation, enabling stable Cas12-RNA assembly and activating trans-cleavage without RNA components. ΨDNAs are effective in sensing short and long RNAs and demonstrated 100% accuracy for detecting HCV RNA in clinical samples. We discovered that ΨDNAs can guide certain Cas12 enzymes for RNA targeting in cells, enhancing mRNA degradation via ribosome stalling and enabling multiplex knockdown of multiple RNA transcripts. This study establishes ΨDNA as a robust alternative to RNA guides, augmenting the potential of CRISPR-Cas12 for diagnostic applications and targeted RNA modulation in cellular environments.

Journal Article↗

PubMed2002

Reverse genetics demonstrates that proteolytic processing of the Ebola virus glycoprotein is not essential for replication in cell culture.

Ebola virus, a prime example of an emerging pathogen, causes fatal hemorrhagic fever in humans and in nonhuman primates. Identification of major determinants of Ebola virus pathogenicity has been hampered by the lack of effective strategies for experimental mutagenesis. Here we exploit a reverse genetics system that allows the generation of Ebola virus from cloned cDNA to engineer a mutant Ebola virus with an altered furin recognition motif in the glycoprotein (GP). When expressed in cells, the GP of the wild type, but not of the mutant, virus was cleaved into GP1 and GP2. Although posttranslational furin-mediated cleavage of GP was thought to be an essential step in Ebola virus infection, generation of a viable mutant Ebola virus lacking a furin recognition motif in the GP cleavage site demonstrates that GP cleavage is not essential for replication of Ebola virus in cell culture.

Animals↗

PubMed2004

Differential Behavior Between Isolated and Aggregated Rabbit Auricular Chondrocytes on Plastic Surfaces.

A knowledge of the behavior of chondrocytes in culture is relevant for tissue engineering. Chondrocytes dedifferentiate to a fibroblast-like phenotype on plastic surfaces. Dedifferentiation is reversible if these cells are then cultured in suspension. In this report a description is given of how when chondrocyte aggregates formed in suspension are next seeded on plastic, most of them attach as round or polygonal cells. This morphological differentiation, with synthesis of type II collagen, is stable for long culture periods. This simple method can be of use as a model for studies of chondrocyte behavior on plastic. The results indicate that in addition to culture conditions, such as cell isolation method or cell density, chondrocyte behavior on plastic depends on the presence of aggregates.

Journal Article↗