[Competitive risk and Markov chains: a short description of the additive model].
Explore the source record for details and available documents.
Markov Chains↗
SEARCH · PubMed Health
Results for “Addition chains”
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.
Diagnosis, surveillance, and epidemiologic evaluation of viral infections in pediatric cardiac transplant recipients with the use of the polymerase chain reaction.
BACKGROUND: Viral infections, particularly those caused by cytomegalovirus, are a major cause of postoperative morbidity and mortality in heart transplant recipients. These infections have classically been diagnosed by history, physical examination, peripheral viral cultures, and serologic studies. These methods are often time-consuming and lack sensitivity. Positive viral cultures from the heart are rarely obtained, and viral myocarditis and acute cellular rejection are unable to be differentiated histologically. We have therefore used the polymerse chain reaction to diagnose possible viral infection in pediatric heart transplant recipients with findings consistent with acute unexplained rejection. METHODS: Polymerase chain reaction was used as an aid to diagnose cytomegalovirus infection of cardiac tissue obtained by right ventricular endomyocardial biopsy and follow its long-term course. In addition, polymerase chain reaction was used to diagnose infection of the heart by other viruses in patients with clinical and histologic evidence of rejection, especially those with unexplained late rejection or chronic rejection. Polymerase chain reaction primers were designed to amplify nucleic acid sequences from cytomegalovirus, parvovirus, adenovirus, herpes simplex virus, Epstein-Barr virus, and the RNA viruses of the Enterovirus family. RESULTS: Forty patients underwent serial right ventricular endomyocardial biopsy (129 samples) for rejection surveillance with positive results obtained in 41 samples (32%) from 21 patients. Viral genome amplified included cytomegalovirus in 16 samples, adenovirus in 14, enterovirus in 6, parvovirus in 3, and herpes simplex virus in 2. In 13 of the 21 patients positive for viral genome (62%), endomyocardial biopsy histologic scores were consistent with multifocal moderate to severe rejection (Internal Society for Heart and Lung Transplantation scores of 3A or greater). CONCLUSIONS: Polymerase chain reactions may be used as a rapid and sensitive method to evaluate postoperative viral infections in heart transplant recipients, especially in those with late-onset rejection or chronic rejection. Polymerase chain reaction may also be useful in the serial analysis of cytomegalovirus status in transplant recipients. The use of multiple viral primers improves the diagnostic evaluation of these patients and may lead to a better understanding of the epidemiologic characteristics of posttransplantation viral infections and the cause of late or chronic rejection.
Adenoviruses, Human↗
Nested polymerase chain reaction-based HLA class II typing for the unique identification of formalin-fixed and paraffin-embedded tissue.
Human leukocyte antigen (HLA) genotyping is routinely performed prior to organ transplantation using peripheral blood leukocyte-derived DNA. In addition, polymerase chain reaction (PCR)-based methods have permitted HLA genotyping using DNA extracted from formalin-fixed and paraffin-embedded tissue, with proven applications in HLA-disease association studies and surgical biopsy identification. The utility of current techniques may be limited by the poor yield of intact DNA from such paraffin biopsies. This paper describes a new nested PCR-based HLA class II genotyping method which reliably detects HLA DRB alleles within DNA extracted from even extremely small paraffin biopsies. This method comprises initial PCR amplification of exon II sequences of the HLA DRB1, 3, 4, and 5 genes using generic PCR primers. Identification of the HLA DRB1 alleles and detection of the DRB3, 4, and 5 genes is then performed using a series of separate individual second-round PCR reactions, each of which contains PCR primer pairs detecting a single HLA DRB allele or group of alleles (PCR-SSP). The ability of this method to detect 19 individual HLA DRB1 alleles or groups of alleles, covering all common DRB1 specificities, was confirmed via concordant results when compared with 'direct' (single amplification step) PCR-SSP analysis of one cell line-derived and nine peripheral blood-derived DNA samples, and with five DNA samples extracted from paraffin biopsies. The technique was then successfully applied to 11 further paraffin biopsy-derived DNA samples, of which ten were untypable by 'direct' PCR-SSP analysis, from five cases in which doubt existed as to the individual origin of the tissues.
Adult↗
Regulated expression of PDGF A-chain mRNA in human saphenous vein smooth muscle cells.
Platelet-derived growth factor (PDGF) may be an important regulator of vascular smooth muscle cell (SMC) replication and migration in vivo. Platelets, macrophages, endothelial cells, and SMC are all potential sources of PDGF in the vessel wall. In this study, we have examined the regulation of PDGF gene expression using human SMC cultured in vitro. These cells express transcripts encoding the PDGF A-chain, but not the B-chain. The addition of serum, phorbol ester, acidic fibroblast growth factor, transforming growth factor-beta, or tumor necrosis factor-alpha to serum-starved SMC increased PDGF A-chain mRNA levels. The cytokines interleukin-1 and -6 had no detectable effect. These results indicate that SMC present at sites of injury or inflammation may express elevated levels of PDGF-AA, which could act locally in an autocrine or paracrine manner.
Cells, Cultured↗
Diversity of light chain variable region sequences among rabbit antibodies elicited by the same antigens.
We report the complete variable region sequences of three homogeneous rabbit antibody light chains and the partial sequences of five others. Wehn these are compared to other published rabbit light chain sequences, two regions of markedly increased variability are revealed, which are homologous in position to the first and third hypervariable regions of murine and human myeloma light chains. In addition, there is increased variability among the first three residues at the aminoterminal end. A hypervariable region homologous to that identified at positions 50 to 56 in myeloma light chains is not present in these rabbit antibody light chains. The available three-dimensional models of Fab fragments based on x-ray crystallography indicate that neither the amino-terminal portion of the light chain nor the region homologous to positions 50 to 56 forms a part of the combining site. Comparison of the hypervariable regions among six light chains from antibodies to Type III pneumococcal polysaccharide and among four from antibodies to Type VIII pneumococcal polysaccharide suggests that a large number of different sequences may be found in antibodies specific for these relatively simple antigens. Certain residues outside of the hypervariable regions are invariant in the rabbit light chains and correspond to residues that are required for proper chain folding in human and murine myeloma light chains, indicating that the general conformation of myeloma light chains is the same as that of light chains of elicited antibodies.
Amino Acid Sequence↗
Conformational dynamics of a metallomesogen studied by 2H-NMR spectroscopy
In this work we present a quantitative analysis of both quadrupolar splittings and deuterium Zeeman and quadrupolar spin-lattice relaxation times reported in the literature for two isotopomers of Azpac, an acetylacetonate derivative of the cyclopalladated 4, 4'-bis(hexyloxy) azoxybenzene. Azpac-d(4) is deuterated at the aromatic rings and Azpac-d(26) is deuterated on the alkoxy chains. The additive potential method is used to model the splittings, while the derived spectral densities are interpreted using the decoupled model in conjunction with the Nordio model. The two side chains are assumed to be noninteracting and identical in their conformations in order to limit the size of the transition rate matrix needed to describe correlated internal bond rotations in the chains. Rotational diffusion constants and internal jump rate constants are derived for this metallomesogen.
Journal Article↗
A major part of platelet-derived growth factor purified from human platelets is a heterodimer of one A and one B chain.
Platelet-derived growth factor, PDGF, purified from human platelets is a disulfide-bonded dimer consisting of two homologous polypeptide chains denoted A and B; it has not been known whether it is a heterodimer or a mixture of homodimers. We present here evidence that a major part of PDGF has a heterodimer structure. A highly homogeneous, 31-kDa PDGF was purified in the presence of protease inhibitors and shown to contain both chains by means of immunoprecipitations with peptide antisera specific for the A and B chains, respectively. The susceptibility of PDGF to mild acid treatment and its chromatographic behavior in reversed-phase high performance liquid chromatography and immobilized metal ion affinity chromatography, as compared to A and B chain homodimers, is consistent with a heterodimer structure. Analysis of PDGF purified according to our routine, large scale procedure revealed the major part to have a heterodimer structure. In addition, B chain homodimers were also found. With the demonstration that a major part of PDGF purified from human platelets occurs as a heterodimer, all three dimeric forms of PDGF have been identified. The following nomenclature to distinguish the various forms is suggested: PDGF-AA, a homodimer of A chains; PDGF-AB, a heterodimer; PDGF-BB, a homodimer of B chains; PDGF, any dimeric form of A or B chains.
Antigen-Antibody Complex↗
The abundance of additional N-acetyllactosamine units in N-linked tetraantennary oligosaccharides of human Tamm-Horsfall glycoprotein is a donor-specific feature.
Previously, treatment of Tamm-Horsfall glycoprotein (THp) from different donors with endo-beta-galactosidase has been shown to liberate a tetra- and a Sd(a)-active pentasaccharide, concluding the presence of N-linked carbohydrate chains containing additional N -acetyllactosamine units. These type of oligosaccharides were not found in a detailed structure elucidation of the carbohydrate moiety of THp of one male donor, suggesting a donor-specific feature for these type of structures. Therefore, THp was isolated from four healthy male donors and each subjected to endo-beta-galactosidase treatment in order to release these tetra- and Sd(a)-active pentasaccharide. Differences were observed in the total amount of released tetra- and Sda-active pentasaccharide of the used donors (42, 470, 478, 718 microg/100 mg THp), indicating that the presence of repeating N-acetyllactosamine units incorporated into the N-glycan moiety of THp is donor specific. Furthermore, a higher expression of the Sd(a) determinant on antennae which display N-acetyllactosamine elongation was observed, suggesting a better accessibility for the beta-N-acetylgalactosaminyltransferase. In order to characterize the N-glycans containing repeating N-acetyllactosamine units, carbohydrate chains were enzymatically released from THp and isolated. The tetraantennary fraction, which accounts for more than 33% of the total carbohydrate moiety of THp, was used to isolate oligosaccharides containing additional N -acetyllactosamine units. Five N-linked tetraantennary oligosaccharides containing a repeating N-acetyllactosamine unit were identified, varying from structures bearing four Sd(a) determinants to structures containing no Sd(a) determinant (see below). One compound was used in order to specify the branch location of the additional N-acetyllactosamine unit, and it appeared that only the Gal-6' and Gal-8' residues were occupied by a repeating N -acetyllactosamine unit.
Amino Sugars↗
Roles of alpha 114 and beta 87 amino acid residues in the polymerization of hemoglobin S: implications for gene therapy.
Three novel recombinant mutants of sickle hemoglobin (Hb S, beta 6Glu-->Val) have been constructed to assess the role of proline at alpha 114 and threonine at beta 87 in the polymerization of deoxygenated Hb S. Using the hemoglobin expression system (pHE2) designed in our laboratory, four plasmids were expressed separately in Escherichia coli to produce the four recombinant hemoglobins: r Hb S (beta 6Glu-->Val); r Hb S-Chiapas (beta 6Glu-->Val, alpha 114Pro-->Arg); r Hb S-D-Ibadan (beta 6Glu-->Val, beta 87Thr-->Lys); and r Hb S-Chiapas-D-Ibadan (beta 6Glu-->Val, alpha 114Pro-->Arg, beta 87Thr-->Lys). The structural features of these four recombinant hemoglobins were analyzed by proton nuclear magnetic resonance spectroscopy, and were found to be similar to those of human normal adult hemoglobin (Hb A) under identical conditions. The recombinant hemoglobins were further investigated by measuring the oxygen-binding properties, which were found to be comparable to those of Hb A. Delay-time gelation studies of the three mutants of r Hb S were carried out in 1.8 M potassium phosphate (pH 7.34) by a temperature jump from 4 degrees C to 30 degrees C and an increase in delay time over that of r Hb S was observed, as well as an overall decrease in the polymerization of these three mutants of Hb S. A more detailed and quantitative investigation has also been carried out to determine the equilibrium solubility (Csat) in 0.1 M potassium phosphate (pH 7.35) at 25 degrees C of the three Hb S mutants as well as of mixtures of these mutants with Hb S versus mixtures of fetal hemoglobin (Hb F) and Hb A with Hb S. The inhibition of polymerization demonstrated in these experiments suggests that the interactions involving the two amino acid residues alpha 114Pro and beta 87Thr are very important to the formation of Hb S polymer, and modification of these amino acids results in an anti-sickling potential. Of particular interest is the inhibitory effect of alpha 114Pro-->Arg, which offers a novel opportunity to use an alpha-chain construct, in addition to a beta-chain construct in the same vector, in gene therapy for sickle cell anemia, with the objective of modifying a larger number of hemoglobin tetramers at a given level of expression.
Adult↗
T-cell receptor gene rearrangement and its expression in human myeloid leukemia cell lines.
ML cell lines (ML-1, -2, and -3) were derived from the cells of a patient with acute myelocytic leukemia preceded by a T-cell malignant lymphoma. A deletion of chromosome 11 (11q-) was common to the affected cells in both neoplastic phases. We report here that the three ML cell lines have DNA rearrangements of the T-cell receptor (TcR)-beta and gamma-chain genes in addition to immunoglobulin heavy-chain gene rearrangement, though they do not have TcR gene messages. The findings presented here indicate that ML cell lines could be used as models for the elucidation of the bilineal nature of hematopoietic neoplastic cells, though they have a biphenotypic (myelomonocytic/T-cell) marker expression.
Blotting, Northern↗
Molecular analysis of the genes for human class II antigens of the major histocompatibility complex.
Different cDNA clones have been isolated that encode each of the three chains of HLA-DR antigens: alpha, intermediate and beta, as well as another beta chain, most likely DC. Whereas the DR alpha and intermediate chains seem encoded by single genes, the DR and DC beta chains are most likely encoded by multiple genes; furthermore, their polymorphism can be readily detected by restriction analysis of cellular DNA. Several genomic DNA clones were isolated for the DR and DC beta chain genes and for the intermediate chain gene. The sum of all distinct cDNA clones and genomic DNA clones for HLA-DR beta chains, isolated from a heterozygous cell line, represent five genes. This implies the existence of at least three nonallelic DR beta chain genes in addition to the DC beta chain genes. The complete sequence of one of the DR beta chains is presented. A genomic DNA clone for a DR beta chain was transferred into mouse L cells and found to be expressed into RNA of the same size as DR beta mRNA. The finding, among the genes for class II antigens, of multiple genes for the beta chain of HLA-DR, distinct from those of other known subregions such as DC, emphasizes the importance of gene transfer experiments, where individual genes can be expressed and tested for their functional role in the immune response.
Alleles↗
Reversed-phase liquid chromatography as a tool in the determination of the hydrophilicity/hydrophobicity of amino acid side-chains at a ligand-receptor interface in the presence of different aqueous environments. I. Effect of varying receptor hydrophobicity.
We have developed further a chromatographic model for studying the hydrophobic interactions which characterize the way a ligand binds to its receptor. This model is based on observing the retention behaviour of de novo designed model 18-residue amphipathic alpha-helical peptides (representing the hydrophobic binding domain of a ligand) on reversed-phase packings by varying hydrophobicity (representing a receptor protein with a hydrophobic binding pocket). Mutants of the "native" peptide ligand (which contains seven Leu residues in its non-polar face) were designed by replacing one residue in the center of the extremely non-polar face of the amphipathic alpha-helix. Through reversed-phase liquid chromatography of these peptides at pH 2.0 on cyano and C18 columns, we have demonstrated how an increase in receptor hydrophobicity (represented by an increase in column stationary phase hydrophobicity; cyano --> C18) significantly enhances hydrophilicity of polar amino acid side-chains at the ligand-receptor interface while moderately enhancing the hydrophobicity of non-polar side-chains. The addition of salt (100 mM sodium perchlorate) to the aqueous environment surrounding the binding site of receptor and ligand was also shown to have a profound effect on side-chain hydrophilicity/hydrophobicity in the binding interface. This effect was particularly dramatic for the positively charged side-chains Arg, Lys and His, whose significant enhancement of hydrophobicity in the presence of the cyano column contrasted with their increase in hydrophilicity in the presence of the considerably more hydrophobic C18 stationary phase. Our results have major implications to understanding the influence of hydrophobic and aqueous environment on hydrophilicity/hydrophobicity of amino acid side-chains and the role side-chains play in the folding and stability of proteins.
Amino Acids↗
High-molecular weight HPMA copolymer-adriamycin conjugates.
High-molecular weight (branched) water-soluble N-(2-hydroxypropyl)methacrylamide (HPMA) copolymers containing lysosomally degradable oligopeptide crosslinks were synthesized by radical copolymerization of HPMA and newly designed crosslinking agents, N(2), N(5)-bis(N-methacryloylglycylphenylalanylleucylglycyl)ornithine s with different modification of the carboxy group. The length of the primary chain was controlled by the addition of a chain transfer agent, 3-mercaptopropionic acid. A polymerizable derivative of the anticancer drug adriamycin (ADR), N-methacryloylglycylphenylalanylleucylglycyl adriamycin, was added to some polymerization mixtures. This resulted in high-molecular weight, branched, water-soluble HPMA copolymers containing oligopeptide sequences in the crosslinks as well as in side-chains terminated in ADR. The degradability of the crosslinks as well as the release of ADR by lysosomal enzymes isolated from rat liver were investigated.
3-Mercaptopropionic Acid↗
Searching for patterns of amino acids in 3D protein structures.
This paper describes the program ASSAM, which has been developed to search for patterns of amino acid side-chains in the 3D structures in the Protein Data Bank. ASSAM represents an amino acid by a vector drawn from the main chain towards the functional part of the amino acid and then computes a graph representation of a protein in which the individual side-chain vectors are the nodes and the intervector distances are the edges. The presence of a query pattern in a Protein Data Bank structure can then be searched for by means of a subgraph isomorphism algorithm. Recent enhancements to ASSAM allow searches to include the following: the main-chain structure in addition to the side-chains; the secondary structure and solvent accessibility of side-chains; allowable distances from a known binding-site; disulfide bridges; and improved generic and wild-card queries. The effectiveness of these approaches is demonstrated by extensive searches of the Protein Data Bank for typical 3D query patterns.
Algorithms↗
Molecular analysis of the IL-2 receptor beta chain gene expressed in human tumor cells.
Interleukin-2 (IL-2) is recognized as a T cell growth factor. We have previously reported that human carcinoma cell lines are inhibited in growth by exogenous IL-2, which binds to the IL-2 receptor beta (IL-2Rbeta) chain ubiquitously expressed on the surface of tumor cells. A possibility was considered that IL-2Rbeta on carcinomas responsible for negative signaling was different from that expressed on hematopoietic cells. To investigate this possibility, mRNA for the IL-2Rbeta chain was amplified and compared in carcinoma and lymphoid cells. Using RT-PCR with pairs of sense-antisense oligonucleotide primers specific for the various regions of extracellular, transmembrane and intracellular domains of the IL-2Rbeta chain, we amplified mRNA obtained from three human carcinoma cell lines and human lymphoid cells as controls. The identity of the amplicons was confirmed by Southern analysis with the 32P-labeled cDNA probe coding for the entire span of the IL-2Rbeta chain. In addition, genomic DNA obtained from the tumor cell lines was sequenced to examine the possibility that a mutation is present in the gene coding for the intracellular IL-2Rbeta chain domain. No mutations or deletions were detected. The message for all three domains of the beta chain was identical in tumor cells and in normal lymphoid cells used as controls. Also, by Western blot and northern analyses no differences between IL-2Rbeta chain in tumors vs that expressed in lymphoid cells were demonstrable. The IL-2Rgamma chain, which participates in IL-2/IL-2R signaling pathway, was expressed in tumor cells. Expression of JAK1 transcripts in these cells was comparable to that in lymphocytes. However, RT-PCR analysis identified differences in expression of JAK3 splice variants (B and M) in tumor cells. These differences may be responsible for altered downstream signaling by IL-2. Overall, our data indicate that the same IL-2/IL-2R pathway is operative in human carcinomas and in normal epithelial or lymphoid cells.
Carcinoma, Renal Cell↗
Functional glycosylation sites of the rat luteinizing hormone receptor required for ligand binding.
The contribution of N-linked glycosylation to the ligand binding activity of the rat luteinizing hormone receptor (LHR) was studied in wild-type and mutant LHR expressed in mammalian (COS1) cells and overexpressed in insect (Sf9) cells. The binding affinities of the holoreceptor and its truncated splice variant (form B) lacking the transmembrane domain were equivalent in both cell lines. Tunicamycin-treated transfected Sf9 cells expressed a carbohydrate-free LH receptor that lacked hormone binding activity. Functional carbohydrate chains essential for binding activity were localized to glycosylation sites at Asn-173 and Asn-152. Glycosidase treatment of the double mutant N173Q/N152Q revealed the presence of at least one additional carbohydrate chain at Asn-269, Asn-277, or Asn-291 that does not contribute to hormone binding. Asn-77 was not glycosylated, but its mutation to Gln reduced hormone binding. LHR expressed in insect cells contained only high mannose carbohydrate chains, and those located at Asn-173 and Asn-152 were sufficient for high-affinity hormone binding. Enzymatic cleavage of glycosyl chains indicated that only the proximal N-acetylglucosamine residue, which is common to high mannose and complex carbohydrate forms, is necessary for acquisition of the high affinity conformation of the receptor. The carbohydrate chains of the LHR appear to be involved in intramolecular folding of the nascent receptor rather than in its interaction with the hormone.
Alternative Splicing↗
Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. I. Chemical synthesis of various reporter group-labeled 2'-deoxyribonucleoside-5'-triphosphates.
Fluorescent-labeled DNA is generated through enzymatic incorporation of fluorophore-linked 2'-deoxyribonucleoside-5'-triphosphates (dNTPs) by DNA polymerases. We describe the synthesis of a variety of dye-labeled dNTPs. Amino-linker-modified 5'-triphosphates of all four naturally occurring nucleobases were used as precursors. Commercially available dyes were coupled to the amino function of the side chain. In addition, we attached novel fluorophore derivatives. The labeled products were obtained in at least 96% purity after HPLC purification. Enzymatic incorporation into DNA and subsequent extension of the modified DNA chain were studied. Vent(R) exo- DNA polymerase and a defined template-primer system were used to analyze each dye-labeled dNTP derivative. Our data suggest that the incorporation efficiency depends on the selected dye, the nucleobase or a combination of both.
DNA↗
Chain molecules at high densities at interfaces.
We have reviewed the general principles of interfacial constraint on highly concentrated polymers near sharp interfaces. First, chains are constrained by their inability to penetrate the boundary. Second, at high concentration, polymers are also constrained by interactions with neighboring chains. Third, one additional constraint depends on the chain length: (a) for long chains, a symmetry condition arises from the indistinguishability of segments k and k + 1, whereas (b) for shorter molecules, wherein the segments are distinguishable, the length of the chains is fixed. Subject to these restraints, chains at equilibrium will be configured to maximize their entropy, and hence their configurational disorder. The physical properties of chains at interfaces are often quite different from those of bulk polymers. In most such systems, the conformational ordering is dissipated within only 5-10 A from the interface, but some physical properties depend on effects that are propagated over much longer distances. The currently available theory is found to be in quite good general agreement with a large number of conformational and mixing properties of polymers at interfaces, in semicrystalline polymers, in alkane crystals, in stationary phases used in reversed-phase liquid chromatography, and in amphiphilic aggregates including bilayer membranes and micelles.
Chemical Phenomena↗