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Biomedical subjects

John R Rodgers

Publications and source records attributed to John R Rodgers.

13 recordsLinked to original sources
PubMed2006

Clostridium difficile lacks detectable superantigen activity.

Clostridium difficile colitis causes striking leukocytosis. We examined the possibility that toxins A or B, or other nontoxin products of C. difficile, act as superantigens, thereby stimulating leukocytosis. Our results failed to show major histocompatibility complex class II-dependent T lymphocyte proliferation, the hallmark of superantigen activity. Elevated white blood cell counts in C. difficile colitis are probably due to increased generation of cytokines such as interleukin-6 (IL-6) or IL-8.

Animals↗
PubMed2005

MHC class Ib molecules bridge innate and acquired immunity.

Our understanding of the classical MHC class I molecules (MHC class Ia molecules) has long focused on their extreme polymorphism. These molecules present peptides to T cells and are central to discrimination between self and non-self. By contrast, the functions of the non-polymorphic MHC class I molecules (MHC class Ib molecules) have been elusive, but emerging evidence reveals that, in addition to antigen presentation, MHC class Ib molecules are involved in immunoregulation. As we discuss here, the subset of MHC class Ib molecules that presents peptides to T cells bridges innate and acquired immunity, and this provides insights into the origins of acquired immunity.

Amino Acid Sequence↗
PubMed2004

Deficiency of CD11b or CD11d results in reduced staphylococcal enterotoxin-induced T cell response and T cell phenotypic changes.

The beta(2) integrin CD11a is involved in T cell-APC interactions, but the roles of CD11b, CD11c, and CD11d in such interactions have not been examined. To evaluate the roles of each CD11/CD18 integrin in T cell-APC interactions, we tested the ability of splenocytes of CD11-knockout (KO) mice to respond to staphylococcal enterotoxins (SEs), a commonly used superantigen. The defect in T cell proliferation with SEA was more severe in splenocytes from mice deficient in CD18, CD11b, or CD11d than in CD11a-deficient splenocytes, with a normal response in CD11c-deficient splenocytes. Mixing experiments showed that the defect of both CD11b-KO and CD11d-KO splenocytes was, unexpectedly, in T cells rather than in APC. Cytometric analysis failed to detect CD11b or CD11d on resting or activated T cells or on thymocytes of wild-type adult mice, nor did Abs directed to these integrins block responses in culture, suggesting that T cells educated in CD11b-KO or CD11d-KO mice were phenotypically altered. Consistent with this hypothesis, T cells from CD11b-KO and CD11d-KO splenocytes exhibited reduced intensity of CD3 and CD28 expression and decreased ratios of CD4/CD8 cells, and CD4(+) T cells were reduced among CD11b-KO and CD11d-KO thymocytes. CD11b and CD11d were coexpressed on a subset of early wild-type fetal thymocytes. We postulate that transient thymocyte expression of both CD11b and CD11d is nonredundantly required for normal thymocyte and T cell development, leading to phenotypic changes in T cells that result in the reduced response to SE stimulation.

Animals↗
PubMed2004

Long-term correction of ornithine transcarbamylase deficiency by WPRE-mediated overexpression using a helper-dependent adenovirus.

The urea cycle disorders (UCDs) are important models for developing gene replacement therapy for liver diseases. Long-term correction of the most common UCD, ornithine transcarbamylase (OTC) deficiency, has yet to be achieved in clinical or preclinical settings. The single human clinical trial using early-generation adenovirus (Ad) failed to show any biochemical correction. In adult OTC-deficient mice, an E1/E2-deleted Ad vector expressing the mouse OTC gene, but not the human, was only transiently therapeutic. By using post-transcriptional overexpression in the context of the less immunogenic helper-dependent adenoviral vector, we achieved metabolic correction of adult OTC-deficient mice for >6 months. Demonstrating this result were normalized orotic aciduria, normal hepatic enzyme activity, and elevated OTC RNA and protein levels in the absence of chronic hepatotoxicity. Overexpressing the human protein may have overcome two potential mechanisms accounting for poor cross-species complementation: a kinetic block at the level of mitochondrial import or a dominant negative effect by the mutant polypeptide. These data represent an important approach for treating human inborn errors of hepatocyte metabolism like the UCDs that require high-level transduction and gene expression for clinical correction.

Adenoviridae↗
PubMed2003

Cotton rat Sihi-M3 is a minimally oligomorphic Mhc I-b molecule that binds the chemotactic peptide fMLF under stringent conditions. Evidence that positive selection drives inter-species diversity of residues interacting with the termini of short peptides.

The leading model for class I-b evolution suggests non-polymorphic I-b genes evolve by gene duplication from polymorphic I-a genes. We recently found N-formyl peptide-specific orthologs of the class I-b gene H2-M3 in the rodent subfamily Sigmodontinae. To test if sigmodont M3 is a I-b gene, we sequenced M3 from wild cotton rats ( Sigmodon hispidus) diverse at the class II locus, Sihi-DQA. These haplotypes carry a single allele of M3 that closely resembles H2-M3. However, peptide-binding assays showed that cotton rat M3 bound the chemotactic N-formylpeptide fMLF better than did rat or mouse M3. The Ala116-->Lys substitution in cotton rat M3 might enhance binding of fMLF and is one of eight residues of M3 that interact with ligand residues P3 and P4 and that are positively selected, with a d(N) /d(S) ratio of 1.8. Thus, M3 is a class I-b gene in both sigmodontine and murine murids, but positive selection operates on a small subset of residues in the traditionally defined antigen recognition site.

Amino Acid Sequence↗
PubMed2003

Hyperconservation of the N-formyl peptide binding site of M3: evidence that M3 is an old eutherian molecule with conserved recognition of a pathogen-associated molecular pattern.

The mouse MHC class I-b molecule H2-M3 has unique specificity for N-formyl peptides, derived from bacteria (and mitochondria), and is thus a pathogen-associated molecular pattern recognition receptor (PRR). To test whether M3 was selected for this PRR function, we studied M3 sequences from diverse murid species of murine genera Mus, Rattus, Apodemus, Diplothrix, Hybomys, Mastomys, and Tokudaia and of sigmodontine genera Sigmodon and PEROMYSCUS: We found that M3 is highly conserved, and the 10 residues coordinating the N-formyl group are almost invariant. The ratio of nonsynonymous and synonymous substitution rates suggests the Ag recognition site of M3, unlike the Ag recognition site of class I-a molecules, is under strong negative (purifying) selection and has been for at least 50-65 million years. Consistent with this, M3 alpha1alpha2 domains from Rattus norvegicus and Sigmodon hispidus and from the "null" allele H2-M3(b) specifically bound N-formyl peptides. The pattern of nucleotide substitution in M3 suggests M3 arose rapidly from murid I-a precursors by an evolutionary leap ("saltation"), perhaps involving intense selective pressure from bacterial pathogens. Alternatively, M3 arose more slowly but prior to the radiation of eutherian (placental) mammals. Older dates for the emergence of M3, and the accepted antiquity of CD1, suggest that primordial class I MHC molecules could have evolved originally as monomorphic PRR, presenting pathogen-associated molecular patterns. Such MHC PRR molecules could have been preadaptations for the evolution of acquired immunity during the early vertebrate radiation.

Amino Acid Sequence↗
PubMed2002

The role of T cell antagonism and original antigenic sin in genetic immunization.

To counter highly mutable pathogens like HIV-1, a number of vaccines are being developed to deliver multiple mutant forms of viral Ags to provoke multivalent antiviral CTLs. However, it is uncertain whether such multiple mutant epitope vaccines will generate the diverse CTL responses desired or will instead create immune interference. To characterize the role of immune interference by mutant epitopes in this process, we have tested a "worst case" scenario in which the immunodominant epitope of OVA (SIINFEKL) and its in vitro TCR antagonist (SIINFEDL) have been used to genetically immunize C57BL/6 mice. We demonstrate here that sequential delivery of these mutant epitopes provokes original antigenic sin in CD8 T cells as demonstrated by attenuation of CTLs, intracellular IFN-gamma production, and MHC I peptide-tetramer staining. By contrast, simultaneous exposure of the immune system to this agonist/antagonist pair not only fails to generate T cell antagonism in vivo, but also avoids original antigenic sin. These observations suggest that simultaneous immunization with vaccines containing mutant epitopes, even T cell antagonists, can indeed generate a diverse array of T cell responses and that at least some immune interference can be avoided by delivering mutant Ags to the immune system simultaneously.

Animals↗
PubMed2002

Hyperconservation of the putative antigen recognition site of the MHC class I-b molecule TL in the subfamily Murinae: evidence that thymus leukemia antigen is an ancient mammalian gene.

"Classical" MHC class I (I-a) genes are extraordinarily polymorphic, but "nonclassical" MHC class I (I-b) genes are monomorphic or oligomorphic. Although diversifying (positive) Darwinian selection is thought to explain the origin and maintenance of MHC class I-a polymorphisms, genetic mechanisms underlying MHC class I-b evolution are uncertain. In one extreme model, MHC class I-b loci are derived by gene duplication from MHC class I-a alleles but rapidly drift into functional obsolescence and are eventually deleted. In this model, extant MHC class I-b genes are relatively young, tend to be dysfunctional or pseudogenic, and orthologies are restricted to close taxa. An alternative model proposed that the mouse MHC class I-b gene thymus leukemia Ag (TL) arose approximately 100 million years ago, near the time of the mammalian radiation. To determine the mode of evolution of TL, we cloned TL from genomic DNA of 11 species of subfamily Murinae: Every sample we tested contained TL, suggesting this molecule has been maintained throughout murine evolution. The sequence similarity of TL orthologs ranged from 85-99% and was inversely proportional to taxonomic distance. The sequences showed high conservation throughout the entire extracellular domains with exceptional conservation in the putative Ag recognition site. Our results strengthen the hypotheses that TL has evolved a specialized function and represents an ancient MHC class I-b gene.

Amino Acid Sequence↗
PubMed2002

Symmetry-general ab initio computation of physical properties using quantum software integrated with crystal structure databases: results and perspectives.

The timely integration of crystal structure databases, such as CRYSTMET, ICSD etc., with quantum software, like VASP, OresteS, ElectrA etc., allows ab initio cell and structure optimization on existing pure-phase compounds to be performed seamlessly with just a few mouse clicks. Application to the optimization of rough structure models, and possibly new atomic arrangements, is detailed. The ability to reproduce observed cell data can lead to an assessment of the intrinsic plausibility of a structure model, even without a competing model. The accuracy of optimized atom positions is analogous to that from routine powder studies. Recently, the ab initio symmetry-general least-squares extraction of the coefficients of the elastic tensor for pure-phase materials using data from corresponding entries in crystal structure databases was automated. A selection of highly encouraging results is presented, stressing the complementarity of simulation and experiment. Additional physical properties also appear to be computable using existing quantum software under the guidance of an automation scheme designed following the above automation for the elastic tensor. This possibility creates the exciting perspective of mining crystal structure databases for new materials with combinations of physical properties that were never measured before. Crystal structure databases can accordingly be expected to become the cornerstone of materials science research within a very few years, adding immense practical value to the archived structure data.

Journal Article↗
PubMed2002

CRYSTMET: a database of the structures and powder patterns of metals and intermetallics.

CRYSTMET is a database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) and associated bibliographic, chemical and physical information. Also included are simulated powder diffraction patterns for all of the entries. The database currently contains almost 70,000 entries and covers the literature exhaustively from 1922 to the present. The database is available on CD-ROM with search/analysis software for use on personal computers. This software can be used with any database in the appropriate format; currently CRYSTMET and the ICSD databases are available. This paper describes the database content, the procedures used in its construction, the software made available to the user and a number of potential uses for the data.

Journal Article↗
PubMed2002

Enhancement of transgene expression by combining glucocorticoids and anti-mitotic agents during transient transfection using DNA-cationic liposomes.

The anti-mitotic drugs colchicine and paclitaxel increase transfection efficiency of cationic liposomes. Using combined lipid-mediated transfection with anti-mitotic agents for gene therapy of cancer has been limited due to the likely development of multi-drug resistance (MDR). We treated human cancer cell lines and normal liver cells with glucocorticoids in combination with the antimitotics paclitaxel or colchicine before transient, cationic lipid-mediated transfection. Colchicine and paclitaxel each enhanced transgene expression in several cell lines. Moreover, glucocorticoid, combined with paclitaxel or colchicine, significantly increased reporter gene expression above that seen in cells treated with each drug alone. P-glycoprotein (PGP), a drug exporter encoded by ABCB1, exports both paclitaxel and colchicine. To determine the influence of PGP in colchicine- or paclitaxel-mediated enhancement of transgene expression, cells were treated with a histone deacetylase inhibitor, trichostatin A (TSA), known to induce ABCB1 expression, before treatment with colchicine or paclitaxel. TSA significantly reduced colchicine-mediated increases in reporter gene expression. Addition of glucocorticoid to colchicine pretreatment significantly attenuated TSA-mediated inhibition of colchicine-induced increases in transgene expression. TSA accelerated and glucocorticoid blocked export of rhodamine 123, a molecule known to be exported by PGP. The glucocorticoid/paclitaxel combination also increased reporter gene expression in BE(2)C cells, which constitutively express high levels of PGP. Thus, the degree of enhancement of transgene expression mediated by these anti-mitotics seems to be dependent on PGP activity. Glucocorticoids augment colchicine- or paclitaxel-mediated enhancement of transgene expression most likely by reducing drug egress through PGP.

ATP Binding Cassette Transporter, Subfamily B, Mem↗