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PubMed1981

Immunogenetic studies on the resistance of mice to highly metastatic DBA/2 tumor cell variants. I. Effect of incompatibilities at H-2 or non-H-2 genes in normal and nude (nu/nu) mice.

The ability of two highly metastatic tumor lines of DBA/2 (H-2d) origin to metastasize in various allogeneic normal or nude (nu/nu) mouse strains was investigated. Normal mice differing from DBA/2 at either the major histocompatibility complex or at minor histocompatibility loci were both able to reject rather high subcutaneous inocula of these tumor cells. F1 hybrids between susceptible and resistant strains could not reject the metastatic tumors. This suggests that tumor rejection was dependent on the recognition of allogeneic histocompatibility antigens. Two mouse strains appeared to be selectively resistant to the establishment of tumor metastases but could not prevent the progressive tumor growth at a local site. One was a new variant subline of DBA/2, provisionally designated as DBA/2/HD, the other was C57B1/6 (nu/nu), an athymic 'nude' mouse of C57B1/6 background. 'Nude' mice of BALB/c or C3H background were more or less susceptible to these tumors and their metastases. These studies demonstrate that the establishment of tumor metastasis is greatly influenced by genetic factors of the host. Resistance to local tumor growth seemed to require the presence of mature T lymphocytes while resistance to metastasis formation could be established in T-cell-deficient nude mice of certain genetic backgrounds.

Animals↗
PubMed1995

Preliminary expansion of the resonant recognition model to incorporate multi variable analysis.

The Resonant Recognition Model (rrm) uses digital signal processing methods to investigate protein structure-function; and links the biological function of protein families to unique characteristic frequencies. The rrm originally used a single set of variables: the electron ion interaction potential (EIIP). Here the rrm has been expanded to include 242 sets of variables to analyse a sample of protein families. Despite the evident increase in complexity of the data, distinguishing patterns can be observed between the different protein families. The thus-obtained Signature Profiles (SP) indicate that proteins having similar overall functions may be identifiable and differentiated from others by their characteristic frequency signatures far more readily than with the single variable rrm spectra.

Amino Acid Sequence↗
PubMed1996

The role of MHC- and non-MHC-associated genes in determining the human immune response to malaria antigens.

Individual susceptibility to malaria infection, disease and death is influenced by host genotype, parasite virulence and a number of environmental factors including malaria-specific immunity. Immune responses are themselves determined by a combination of host genes and environmental effects. The extent to which host genotype limits the spectrum of possible immune responses may influence the outcome of infection and has consequences for vaccine design. Associations have been observed between human major histocompatibility complex (MHC) genotype and susceptibility to severe malaria, but no similar associations have been observed for mild malarial disease or for specific antibody responses to defined malaria antigens. Epidemiological studies have shown that, in practice, neither T helper cell nor antibody responses to malaria parasite are limited by host MHC genotype, but have revealed that genes lying outside the MHC may influence T cell proliferative responses. These genes have yet to be identified, but possible candidates include T cell receptor (TcR) genes, and genes involved in TcR gene rearrangements. More importantly, perhaps, longitudinal epidemiological studies have shown that the anti-malarial antibody repertoire is selective and becomes fixed in malaria-immune individuals, but is independent of host genotype. These findings suggest that the antibody repertoire may be determined, at least in part, by stochastic events. The first of these is the generation of the T and B cell repertoire, which results from random gene recombinations and somatic mutation and is thus partially independent of germline genes. Secondly, of the profusion of immunogenic peptides which are processed and presented by antigen presenting cells, a few will, by chance, interact with T and B cell surface antigen receptors of particularly high affinity. These T and B cell clones will be selected, will expand and may come to dominate the immune response, preventing the recognition of variant epitopes presented by subsequent infections-a process known as original antigenic sin or clonal imprinting. The immune response of an individual thus reflects the balance between genetic and stochastic effects. This may have important consequences for subunit vaccine development.

Animals↗
PubMed1996

Human intestinal Vdelta1+ lymphocytes recognize tumor cells of epithelial origin.

gammadelta T cells can be grouped into discrete subsets based upon their expression of T cell receptor (TCR) variable (V) region families, their tissue distribution, and their specificity. Vdelta2+ T cells constitute the majority of gammadelta T cells in peripheral blood whereas Vdelta1+T cells reside preferentially in skin epithelium and in the intestine. gammadelta T cells are envisioned as first line host defense mechanisms capable of providing a source of immune effector T cells and immunomodulating cytokines such as interleukin (IL) 4 or interferon (IFN) gamma. We describe here the fine specificity of three distinct gammadelta+ tumor-infiltrating lymphocytes (TIL) obtained from patients with primary or metastatic colorectal cancer, that could be readily expanded in vitro in the presence of IL-1beta and IL-7. Irrespective of donor, these individual gammadelta T cells exhibited a similar pattern of reactivity defined by recognition of autologous and allogeneic colorectal cancer cells, renal cell cancer, pancreatic cancer, and a freshly isolated explant from human intestine as measured by cytolytic T cell responses and by IFN-gamma release. In contrast, tumors of alternate histologies were not lysed, including lung cancer, squamous cell cancer, as well as the natural/lymphocyte-activated killer cell-sensitive hematopoietic cell lines T2, C1R, or Daudi. The cell line K562 was only poorly lysed when compared with colorectal cancer targets. Target cell reactivity mediated by Vdelta1+ T cells was partially blocked with Abs directed against the TCR, the beta2 or beta7 integrin chains, or fibronectin receptor. Marker analysis using flow cytometry revealed that all three gammadelta T cell lines exhibit a similar phenotype. Analysis of the gammadelta TCR junctional suggested exclusive usage of the Vdelta1/Ddelta3/Jdelta1 TCR segments with extensive (< or = 29 bp) N/P region diversity. T cell recognition of target cells did not appear to be a major histocompatibility complex restricted or to be correlated with target cell expression of heat-shock proteins. Based on the ability of some epithelial tumors, including colorectal, pancreatic, and renal cell cancers to effectively cold target inhibit the lysis of colorectal cancer cell lines by these Vdelta1+ T cell lines, we suggest that intestinal Vdelta1+ T cell lines, we suggest that intestinal Vdelta1+ T cells are capable of recognizing cell surface Ag(s) shared by tumors of epithelial origin.

Amino Acid Sequence↗
PubMed2005

Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins.

Free-flow electrophoresis (FFE) and rapid (6 min) RP-HPLC was used to fractionate human citrate-treated plasma. Prior to analysis, the six most abundant proteins in plasma were removed by immunoaffinity chromatography; both depleted plasma and the fraction containing the six abundant proteins depleted were taken for MS-based analysis. Fractionated proteins were digested with trypsin and the generated peptides were subjected to MS-based peptide sequencing. To date, 78 plasma proteins have been unambiguously identified by manual validation from 16% (15/96 FFE total fractions) of the collected FFE pools; 55 identifications were based on > or = 2 tryptic peptides and 23 using single peptides. The molecular weight range of proteins and peptides isolated by this method ranged from approximately 190 K (e.g., Complement C3 and C4) to approximately 4-6 K (e.g., CRISPP and Apolipoprotein C1). This FFE/RP-HPLC approach reveals low-abundance proteins and peptides (e.g., L-Selectin approximately 17 ng/mL and the cancer-associated SCM-recognition, immunodefense suppression, and serine protease protection peptide (CRISPP) at approximately 0.5-1 ng/mL), where CRISPP was found in association with alpha-1-antitrypsin as a non-covalent complex, in the fraction containing the depleted high-abundance proteins. In contrast to shotgun proteomic approaches, the FFE/RP-HPLC method described here allows the identification of potentially interesting peptides to be traced back to their protein of origin, and for the first time, has confirmed the "protein sponge" hypothesis where the 35 residue CRISPP polypeptide is non-covalently complexed with the major circulating plasma protein alpha-1-antitrypsin.

Amino Acid Sequence↗
PubMed1998

Crystal structure of lambda-Cro bound to a consensus operator at 3.0 A resolution.

The structure of the Cro protein from bacteriophage lambda in complex with a 19 base-pair DNA duplex that includes the 17 base-pair consensus operator has been determined at 3.0 A resolution. The structure confirms the large changes in the protein and DNA seen previously in a crystallographically distinct low-resolution structure of the complex and, for the first time, reveals the detailed interactions between the side-chains of the protein and the base-pairs of the operator. Relative to the crystal structure of the free protein, the subunits of Cro rotate 53 degrees with respect to each other on binding DNA. At the same time the DNA is bent by 40 degrees through the 19 base-pairs. The intersubunit connection includes a region within the protein core that is structurally reminiscent of the "ball and socket" motif seen in the immunoglobulins and T-cell receptors. The crystal structure of the Cro complex is consistent with virtually all available biochemical and related data. Some of the interactions between Cro and DNA proposed on the basis of model-building are now seen to be correct, but many are different. Tests of the original model by mutagenesis and biochemical analysis corrected some but not all of the errors. Within the limitations of the crystallographic resolution it appears that operator recognition is achieved almost entirely by direct hydrogen-bonding and van der Waals contacts between the protein and the exposed bases within the major groove of the DNA. The discrimination of Cro between the operators OR3 and OR1, which differ in sequence at just three positions, is inferred to result from a combination of small differences, both favorable and unfavorable. A van der Waals contact at one of the positions is of primary importance, while the other two provide smaller, indirect effects. Direct hydrogen bonding is not utilized in this distinction.

Bacteriophage lambda↗
PubMed2002

DNA modifications by antitumor platinum and ruthenium compounds: their recognition and repair.

The development of metal-based antitumor drugs has been stimulated by the clinical success of cis-diamminedichloroplatinum(II) (cisplatin) and its analogs and by the clinical trials of other platinum and ruthenium complexes with activity against resistant tumors and reduced toxicity including orally available platinum drugs. Broadening the spectrum of antitumor drugs depends on understanding existing agents with a view toward developing new modes of attack. It is therefore of great interest to understand the details of molecular and biochemical mechanisms underlying the biological efficacy of platinum and other transition-metal compounds. There is a large body of experimental evidence that the success of platinum complexes in killing tumor cells results from their ability to form various types of covalent adducts on DNA; thus, the research of DNA interactions of metal-based antitumor drugs has predominated. The present review summarizes current knowledge on DNA modifications by platinum and ruthenium complexes, their recognition by specific proteins, and repair. It also provides strong support for the view that either platinum or ruthenium drugs, which bind to DNA in a fundamentally different manner from that of 'classical' cisplatin, have altered pharmacological properties. The present article also demonstrates that this concept has already led to the synthesis of several new unconventional platinum or ruthenium antitumor compounds that violate the original structure-activity relationships.

Amino Acid Sequence↗
PubMed1987

Reactivity of anti-HLA class I polymorphic monoclonal antibodies with normal human skin.

In this work the reactivity of 16 monoclonal antibodies raised against different HLA class I specificities was tested with human skin of healthy donors of known HLA typing. By indirect immunofluorescence, six antibodies reacted strongly with keratinocytes carrying the corresponding alloantigens. The reactivity of 3 other antibodies which was weak or absent using indirect immunofluorescence, was enhanced by various amplification systems such as avidin-biotin-peroxidase method, biotin-streptavidin-fluorescein complex and especially preliminary trypsin treatment that revealed alloantigens masked in the epidermis. The immunostaining of 4 antibodies was negative regardless of the method used. Some of the antibodies we tested cross-reacted with cytoplasmic antigens of keratinocytes. This study has allowed to select a battery of monoclonal antibodies which can specifically detect alloantigens on keratinocytes and will be useful for the recognition the cell origin in allografting experiments.

Antibodies, Monoclonal↗
PubMed1995

Local connected fractal dimensions and lacunarity analyses of 60 degrees fluorescein angiograms.

PURPOSE: The retinal vascular tree exhibits fractal characteristics. These findings relate to the mechanisms involved in the vascularization process and to the objective morphologic characterization of retinal vessels using fractal analysis. Although normal retinas show uniform patterns of blood vessels, in pathologic retinas with central vein or artery occlusions, the patterns are irregular. Because the generalized box fractal dimension fails to differentiate successfully between normal and abnormal retinal vessels in 60 degrees fluorescein angiograms, the authors have further investigated this problem using the local connected fractal dimension (alpha). METHODS: The authors studied 24 digitized 60 degrees fluorescein angiograms of patients with normal retinas and 5 angiograms of patients with central retinal vein or artery occlusion. The pointwise method estimated the local complexity of the angiogram within a finite window centered on those pixels that belong to the retinal vessels. Color-coded dimensional images of the angiograms were constructed by plotting the pixels forming the object with a color that corresponded to specific values of alpha +/- delta alpha. RESULTS: The color-coded representation allowed recognition of areas with increased or decreased local angiogram complexity. The alpha distributions showed differences between normal and pathologic retinas, which overcomes problems encountered when using the methods of calculating the generalized fractal dimensions. A multivariate linear discriminant function using parameters from the alpha distribution and a further fractal parameter--lacunarity--reclassified 23 of the 24 normal and 4 of the 5 pathologic angiograms in their original groups (total: 92.1% correct). CONCLUSIONS: This methodology may be used for automatic detection and objective characterization of local retinal vessel abnormalities.

Discriminant Analysis↗
PubMed1996

A functionally significant allelic polymorphism in a T cell receptor V beta gene segment.

The effect of an allelic polymorphism in the BV1S1 gene segment on recognition of major histocompatibility complex (MHC)-peptide complexes by a specific T cell receptor (TCR) was studied using RBL 2H3 cells transfected with TCR-CD3 zeta chimeric receptors. An HLA-A2-restricted human immunodeficiency virus (HIV) pol-specific cytotoxic T lymphocyte (CTL) clone utilizing the BV1S1A2 gene in combination with AV2S1A2 was identified and the extracellular domains of the TCR were fused to CD3 zeta. In degranulation assays RBL 2H3 transfectants expressing this receptor maintained the specificity of the parental CTL clone. The allelic variant BV1S1A1N1 containing a glutamine for histidine substitution at position 48 in the loop of the second complementarity-determining region was generated by site-directed mutagenesis. Transfection of this molecule as a CD3 zeta chimera together with the original AV2S1A2 CD3 zeta molecule resulted in cell surface expression of both chains but a loss of recognition of HLA-A2 HIV pol peptide-pulsed targets. The effect of this polymorphism on MHC-peptide recognition supports current models of TCR MHC-peptide interaction and provides evidence for a functional role for polymorphism in the TCRV genes.

Alleles↗
PubMed2001

Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase.

Glutamyl-tRNA synthetases (GluRSs) are divided into two distinct types, with regard to the presence or absence of glutaminyl-tRNA synthetase (GlnRS) in the genetic translation systems. In the original 19-synthetase systems lacking GlnRS, the 'non-discriminating' GluRS glutamylates both tRNAGlu and tRNAGln. In contrast, in the evolved 20-synthetase systems with GlnRS, the 'discriminating' GluRS aminoacylates only tRNAGlu. Here we report the 2.4 A resolution crystal structure of a 'discriminating' GluRS.tRNAGlu complex from Thermus thermophilus. The GluRS recognizes the tRNAGlu anticodon bases via two alpha-helical domains, maintaining the base stacking. We show that the discrimination between the Glu and Gln anticodons (34YUC36 and 34YUG36, respectively) is achieved by a single arginine residue (Arg 358). The mutation of Arg 358 to Gln resulted in a GluRS that does not discriminate between the Glu and Gln anticodons. This change mimics the reverse course of GluRS evolution from anticodon 'non-dicsriminating' to 'discriminating'.

Anticodon↗
PubMed1994

Structural and functional characterisation of the signal recognition particle-specific 54 kDa protein (SRP54) of tomato.

Two representative genes for the 54 kDa protein subunit of the signal recognition particle (SRP54) of tomato were cloned. It was shown that both genes are expressed in the tomato cv. Rentita. SRP54 is encoded by nine exons distributed over 10 kb of genomic sequence. The amino acid sequences deduced for the two SRP54 genes are 92% identical and the calculated protein size is 55 kDa. Like the homologous proteins isolated from other eukaryotes, the tomato SRP54 is evidently divided into two domains. As deduced from sequence motif identity, the N-terminally located G-domain can be assumed to have GTPase activity. The C-terminal part of the protein is methionine rich (14% methionine) and represents the M-domain. In in vitro binding experiments, SRP54 of tomato was able to attach to the 7S RNA of tomato, its natural binding partner in the SRP. This interaction can only take place in a trimeric complex consisting of 7S RNA, SRP54 and SRP19. The latter protein subunit of the SRP complex is assumed to induce a conformational change in the 7S RNA. The human SRP19 was able to mediate the binding of the tomato SRP54 to the 7S RNA, irrespective of whether this latter originated from tomato or man.

Amino Acid Sequence↗
PubMed1993

The I-Ab-restricted alloresponse of D10.G4.1 T cells is based on the recognition of an endogenous peptide.

The alloreactivity of T cells is thought to be based on the cross-reactive recognition of allogeneic major histocompatibility complex (MHC) molecules which have bound peptides derived from self antigens or, in the case of cultured T cells, from serum components. While studying the processing requirements of conalbumin (CA) that is recognized by D10.G4.1 T cells in combination with I-Ak molecules we also analysed the cross-reactive stimulation of clone D10.G4.1 T cells by allogeneic, I-Ab expressing stimulator cells which is shown here to be CD4 dependent. In order to distinguish between an endogenous or exogenous origin of a peptide that is presumably co-recognized with I-Ab different types of stimulatory/antigen-presenting cells (APC) were treated with drugs that are known to influence the processing and/or presentation of antigens. It was found that the alloreactive response of D10.G4.1 cells was abolished if the APC were treated with brefeldin A or inhibitors of protein biosynthesis. Under the same conditions neither the CA-specific response of D10.G4.1 cells nor the activation of control T cells by ovalbumin (OVA) or insulin was affected. On the other hand, the use of lysosomotropic agents or inhibitors of glycoprotein trimming had no influence on the ability of the APC to induce the alloresponse of D10.G4.1 cells, whilst the presentation of CA and other protein antigens by the APC was prevented. In addition, treatment of APC with pronase to remove surface MHC molecules or acidic buffer to remove peptides from the binding groove of MHC class II molecules at the surface of APC strongly diminished their ability to induce an alloresponse. However, this capacity was restored by incubating the APC for 2 hr in serum-free medium. These data indicate that the alloreactive response of D10.G4.1 cells is based on the recognition of newly synthesized endogenous peptide(s) in combination with I-Ab.

Acids↗
PubMed2002

A protein-domain microarray identifies novel protein-protein interactions.

Protein domains mediate protein-protein interactions through binding to short peptide motifs in their corresponding ligands. These peptide recognition modules are critical for the assembly of multiprotein complexes. We have arrayed glutathione S-transferase (GST) fusion proteins, with a focus on protein interaction domains, on to nitrocellulose-coated glass slides to generate a protein-domain chip. Arrayed protein-interacting modules included WW (a domain with two conserved tryptophans), SH3 (Src homology 3), SH2, 14.3.3, FHA (forkhead-associated), PDZ (a domain originally identified in PSD-95, DLG and ZO-1 proteins), PH (pleckstrin homology) and FF (a domain with two conserved phenylalanines) domains. Here we demonstrate, using peptides, that the arrayed domains retain their binding integrity. Furthermore, we show that the protein-domain chip can 'fish' proteins out of a total cell lysate; these domain-bound proteins can then be detected on the chip with a specific antibody, thus producing an interaction map for a cellular protein of interest. Using this approach we have confirmed the domain-binding profile of the signalling molecule Sam68 (Src-associated during mitosis 68), and have identified a new binding profile for the core small nuclear ribonucleoprotein SmB'. This protein-domain chip not only identifies potential binding partners for proteins, but also promises to recognize qualitative differences in protein ligands (caused by post-translational modification), thus getting at the heart of signal transduction pathways.

Amino Acid Sequence↗
PubMed1985

Immunoprecipitation of antigen-associated [32P]-labelled nucleic acids from Crohn's disease mesenteric lymph nodes.

The methods of immunoselection and electrophoretic analysis of [32P]-labelled nucleic acids have been applied to the problem of defining Crohn's disease (CD) specific antigen associated DNA or RNA, with the intention of identifying a presumptive aetiological microbial agent. Mesenteric lymph node derived cells from CD and control gastrointestinal disease cases were cultured in vitro with [32P] orthophosphate after mitogenic stimulation with phytohaemaglutinin and pokeweed mitogen. Total cell lysates were immunoprecipitated with CD and control serum IgG fractions and immune complexes recovered with pansorbin. Antigen associated [32P]-labelled nucleic acids were phenol/chloroform extracted and analysed by electrophoresis on polyacrylamide and agarose gels. No immunoprecipitated nucleic acid specific to CD tissues could be detected and no differences in antigen recognition between CD and control serum IgG were observed. No evidence was obtained for nucleic acid containing antigens either of the autoimmune type or of possible viral or microbial origin in CD mesenteric lymph nodes.

Antigen-Antibody Reactions↗
PubMed1993

Coding coenzyme handles: a hypothesis for the origin of the genetic code.

The coding coenzyme handle hypothesis suggests that useful coding preceded translation. Early adapters, the ancestors of present-day anticodons, were charged with amino acids acting as coenzymes of ribozymes in a metabolically complex RNA world. The ancestral aminoacyl-adapter synthetases could have been similar to present-day self-splicing tRNA introns. A codon-anticodon-discriminator base complex embedded in these synthetases could have played an important role in amino acid recognition. Extension of the genetic code proceeded through the take-over of nonsense codons by novel amino acids, related to already coded ones either through precursor-product relationship or physicochemical similarity. The hypothesis is open for experimental tests.

Amino Acyl-tRNA Synthetases↗
PubMed2006

Does the signal for the activation of T cells originate from the antigen-presenting cell or the effector T-helper?

The present view is that the antigen-presenting cell (APC) processes and presents simultaneously on its surface several different antigens that are displayed randomly (with respect to their being Self or Nonself) as peptide-MHC complexes. The naive T-cell interacting with its ligand on the APC is activated by "co-stimulation," the first step on the pathway to effectors. This view ignores the requirement for associative recognition of antigen (ARA) in mediating both the Self-Nonself discrimination and the regulation of effector class. The introduction of ARA as a requirement for these two decision functions highlights a critical role for the effector T-helper (eTh) and necessitates rethinking the contribution of the APC.

Animals↗
PubMed2004

Electrocardiographic recognition of the epicardial origin of ventricular tachycardias.

BACKGROUND: Some ventricular tachycardias (VTs) originating from the epicardium are not suitable for endocardial radiofrequency ablation and require an epicardial approach. The aim of this study was to define the ECG characteristics that may identify an epicardial origin of VTs. METHODS AND RESULTS: We analyzed the 12-lead ECG recordings during epicardial and endocardial left ventricular pacing in 9 patients to verify the hypothesis that the epicardial origin of the ventricular activation widens the initial part of the QRS complex. Then, we analyzed the ECG pattern in 14 VTs successfully ablated from the epicardium after a failed endocardial approach (group A), in 27 VTs successfully ablated from the endocardium (group B), and in 28 additional VTs that could not be ablated from the endocardium (group C). Four distinct intervals of ventricular activation were defined and measured: (1) the pseudodelta wave, (2) the intrinsicoid deflection time in V2, (3) the shortest RS complex, and (4) the QRS complex. VTs from groups A and C showed a significantly longer pseudodelta wave, intrinsicoid deflection time, and RS complex duration compared with VTs of group B. There was no difference between groups A and C. A pseudodelta wave of > or =34 ms has a sensitivity of 83% and a specificity of 95%, an intrinsicoid deflection time of > or =85 ms has a sensitivity of 87% and a specificity of 90%, and an RS complex duration of > or =121 ms has a sensitivity of 76% and a specificity of 85% in identifying an epicardial origin of the VTs. CONCLUSIONS: ECG suggests VTs originating from the epicardium and those with an unsuccessful radiofrequency ablation from the endocardium.

Cardiac Pacing, Artificial↗