SEARCH · Search PubMed

Results for “multiple clustering”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

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

At least 199 records · Page 11Linked to original sources

PubMed2001

Glycopeptide N-acetylgalactosaminyltransferase specificities for O-glycosylated sites on MUC5AC mucin motif peptides.

The recombinant proteins of the two novel UDP-N-acetylgalactosamine (GalNAc) glycopeptide:N-acetylgalactosaminyltransferases (designated gpGaNTase-T7 and gpGaNTase-T9) were assayed with O-glycosylated products obtained from the prior action of the ubiquitous transferases (GaNTase-T1 and GaNTase-T2) towards MUC5AC mucin motif peptides (GTTPSPVPTTSTTSAP and peptides with single amino acid substitutions, GTTPSAVPTTSTTSVP and GTTPSPVPTTSITSVP, that are a reflection of mucin molecule polymorphism). gpGaNTase-T9 is known to be expressed differentially and more abundantly than gpGaNTase-T7 in some tissues; the results of in vitro glycosylation also indicates a difference in acceptor substrate specificities between the gpGaNTase isoforms. With the use of capillary electrophoresis, MS and Edman degradation, our study suggests that, in the O-glycosylation of mucin-type proteins, approach and recognition signalling by gpGaNTase-T7 and gpGaNTase-T9 depend largely on the peptide's primary structure (for example the presence of multiple clusters of hydroxy amino acids and the number of GalNAc residues attached to the peptide backbone). O-glycosylation in terms of sites of attachment seems to be less random than previously described and, if sequential reactions are ordered throughout the Golgi stack, the complete O-glycosylation of the mucin molecules seems to be finely tuned to respond to specific damage to, or attack on, epithelia.

Amino Acid Sequence↗

PubMed2003

Establishment, characterization, and long-term maintenance of cultures of human fetal hepatocytes.

Cultured human hepatocytes have broad research and clinical applications; however, the difficulties in culturing rodent and human hepatocytes are well known. These problems include the rapid loss of the hepatocytic phenotype in primary culture and the limited replicating capacity of the cultured cells. We describe the establishment of serum-free primary cultures of human fetal hepatocytes (HFHs) that retain hepatocytic morphology and gene expression patterns for several months and maintain sufficient proliferative activity to permit subculturing for at least 2 passages. Initially, HFH cultures contained 2 main cell types that morphologically resembled large and small hepatocytes. The fetal hepatocytes expressed alpha-fetoprotein (AFP), cytokeratin (CK) 19, albumin, and other hepatic proteins. Treatment of the cultures with oncostatin M (OSM) increased cell size and enhanced cell differentiation and formation of bile canaliculi, probably through an effect on hepatocyte nuclear factor (HNF) 4alpha. Approximately 1 month after plating, multiple clusters of very small cells became apparent in the cultures. These cells had very few organelles and are referred to as blast-like cells. Flow cytometric analysis of these cells showed that they express oval cell/stem cell markers such as CD90 (Thy-1), CD34, and OV-6 but do not stain with antibodies to beta(2)-microglobulin. HFH cultures maintained for 9 to 12 months produced grossly visible organoids containing ductular structures that stained for CK18, CK19, and AFP. In conclusion, HFH cultures, which might contain a population of hepatic stem cells, constitute an excellent tool for a variety of studies with human hepatocytes, including the mechanisms of viral infection.

Biomarkers↗

PubMed1988

Appalachian spring: variations on ancient gastro-entero-pancreatic themes in New World mammals.

Studies of guinea pig genomic and/or cDNA clones encoding the gastro-entero-pancreatic (GEP) hormones--insulin, glucagon and pancreatic polypeptide--as well as portions of the insulin receptor, are described. Multiple clustered substitutions (localized rapid mutation acceptance) altering the biological properties of both insulin and glucagon have been revealed, but this does not appear to be the case with either pancreatic polypeptide or those regions of guinea pig insulin receptor cDNAs that have been examined thus far. These findings suggest that novel selective pressures operative in the New World environment, in which these animals evolved in isolation from Old World mammalian species, have led to altered solutions to problems related to the regulation of growth and carbohydrate metabolism.

Americas↗

PubMed2001

Complete genome sequence of Caulobacter crescentus.

The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic environment, coordinates the cell division cycle and multiple cell differentiation events. With the annotated genome sequence, a full description of the genetic network that controls bacterial differentiation, cell growth, and cell cycle progression is within reach. Two-component signal transduction proteins are known to play a significant role in cell cycle progression. Genome analysis revealed that the C. crescentus genome encodes a significantly higher number of these signaling proteins (105) than any bacterial genome sequenced thus far. Another regulatory mechanism involved in cell cycle progression is DNA methylation. The occurrence of the recognition sequence for an essential DNA methylating enzyme that is required for cell cycle regulation is severely limited and shows a bias to intergenic regions. The genome contains multiple clusters of genes encoding proteins essential for survival in a nutrient poor habitat. Included are those involved in chemotaxis, outer membrane channel function, degradation of aromatic ring compounds, and the breakdown of plant-derived carbon sources, in addition to many extracytoplasmic function sigma factors, providing the organism with the ability to respond to a wide range of environmental fluctuations. C. crescentus is, to our knowledge, the first free-living alpha-class proteobacterium to be sequenced and will serve as a foundation for exploring the biology of this group of bacteria, which includes the obligate endosymbiont and human pathogen Rickettsia prowazekii, the plant pathogen Agrobacterium tumefaciens, and the bovine and human pathogen Brucella abortus.

Adaptation, Biological↗

PubMed1988

Deletion of transfected oncogenes from NIH 3T3 transformants by inhibitors of poly(ADP-ribose) polymerase.

a1-1 cells, a transformant line obtained by transfection of NIH 3T3 cells with human c-Ha-rasT24 (hc-Ha-rasT24), were converted to morphologically normal flat cells following a 2-week culture in the presence of benzamide (BA), an inhibitor of poly(ADP-ribose) polymerase [ADP-ribosyltransferase (polymerizing); EC 2.4.2.30]. Concomitant with these morphological changes was the loss of the exogenous hc-Ha-rasT24 sequence. When cells were cultured without transfer, multiple clusters of flat revertant cells surrounded by transformed cells within single colonies of a1-1 cells were observed. This, together with the slow growth rate of flat cells in the presence of BA, indicated that flat revertants were induced rather than selected by BA. Flat cells isolated from mixed colonies completely lost the exogenous and amplified hc-Ha-rasT24 gene. In contrast, the endogenous mouse c-Ha-ras in flat revertant cells was not lost during culture with BA. Similarly, the endogenous hc-Ha-rasT24 in human bladder carcinoma T24 cells was not affected by BA. By using various chemicals, it was suggested that inhibition of poly(ADP-ribose) polymerase induces an efficient and specific loss of the exogenous transforming genes including Ki-ras, N-ras, c-raf, and ret-II.

Animals↗

PubMed1996

Verbal learning subtypes in traumatic brain injury: a replication.

Traumatic brain injury (TBI) has been associated with memory impairments, but the severity and qualitative aspects of such impairment do not appear homogeneous across patients. This study sought to replicate an earlier investigation that found distinct verbal learning subtypes in TBI using the California Verbal Learning Test (CVLT). CVLT data from 88 acute rehabilitation inpatients with mild, moderate, and severe traumatic brain injuries were analyzed with multiple cluster analytic techniques. Cluster analyses yielded five learning subtypes, three of which appeared similar to the subtypes previously identified as Active, Disorganized, and Passive subtypes, and two that appeared similar to the Deficient subgroup. Traumatic brain injury appears to be characterized by heterogeneous, but fairly reliable, verbal learning subtypes that can be detected early postinjury.

Adolescent↗

PubMed1995

Generation of immunoglobulin light chain gene diversity in Raja erinacea is not associated with somatic rearrangement, an exception to a central paradigm of B cell immunity.

In all vertebrate species examined to date, rearrangement and somatic modification of gene segmental elements that encode portions of the antigen-combining sites of immunoglobulins are integral components of the generation of antibody diversity. In the phylogenetically primitive cartilaginous fishes, gene segments encoding immunoglobulin heavy and light chain loci are arranged in multiple clusters, in which segmental elements are separated by only 300-400 bp. In some cases, segmental elements are joined in the germline of nonlymphoid cells (joined genes). Both genomic library screening and direct amplification of genomic DNA have been used to characterize at least 89 different type I light chain gene clusters in the skate, Raja. Analyses of predicted nucleotide sequences and predicted peptide structures are consistent with the distribution of genes into different sequence groups. Predicted amino acid sequence differences are preferentially distributed in complementarity-determining versus framework regions, and replacement-type substitutions exceed neutral substitutions. When specific germline sequences are related to the sequences of individual cDNAs, it is apparent that the joined genes are expressed and are potentially somatically mutated. No evidence was found for the presence of any type I light chain gene in Raja that is not germline joined. The type I light chain gene clusters in Raja appear to represent a novel gene system in which combinatorial and junctional diversity are absent.

Amino Acid Sequence↗

PubMed1997

Three-dimensional reconstruction of port wine stain vascular anatomy from serial histological sections.

Port wine stains (PWSs) treated with a flashlamp-pumped pulsed dye laser show a variability in clinical response that is incompletely understood. To identify any vascular structure that might adversely affect treatment response, we obtained a three-dimensional reconstruction of the vascular anatomy of a non-responsive, light-purple superficial PWS on the forearm. The reconstructed PWS consisted of multiple clusters of small diameter (10-50 microns) blood vessels. We propose that this and similar structures, which have not been identified in the literature, have limited the efficacy of laser therapy. Further study is required to clarify the role of vessel clusters for laser treatment of PWSs, and the corresponding dosimetry necessary to clear non-responsive lesions. We expect that three-dimensional reconstruction of PWS vascular anatomy will provide the basis for (i) accurate PWS classification, (ii) guidance for selection of more effective laser dosimetry, and (iii) a standard against which to assess non-invasive diagnostic imaging techniques.

Adult↗

PubMed2005

Risk factors for sexually transmitted disease among rural-to-urban migrants in China: implications for HIV/sexually transmitted disease prevention.

The objective of the study was to identify risk factors associated with sexually transmitted diseases (STDs) among rural-to-urban migrants in Beijing in 2002. Migrants with STDs consisted of 432 migrants who sought STD care in two public STD clinics. Migrants without STDs included 892 migrants recruited from 10 occupational clusters. Multiple logistic regression was used for data analysis. Compared to migrants without STDs, migrants with STDs were more likely to report having engaged in commercial sex (selling or buying sex) (odds ratio [OR] = 2.70, 95% confidence interval [CI]: 1.71-4.25), multiple sex partners in the previous month (OR = 6.50, 95% CI: 3.73-11.32) and higher perceived HIV-related stigma (OR = 1.89, 95% CI: 1.30-2.75). Being a migrant with an STD was also associated with female gender (OR = 4.10, 95% CI: 2.89-5.82), higher education (OR = 2.92, 95% CI: 1.40-6.06), and higher monthly salary (OR = 1.68. 95% CI: 1.23-2.29). Migrants with STDs visited their hometowns more frequently and had more stable jobs than migrants without STDs. Approximately 10% of the migrants with STDs and 7.7% of the migrants without STDs always used condoms. This study suggests that among migrants, acquisition of an STD is associated with higher participation in risk behaviors as would be expected, but also with higher perceived stigma, education, stable jobs, salary, and with female gender. Appropriate behavioral intervention programs are advocated to reduce the risk and stigma among the special population.

Adult↗

PubMed2003

Thymine-rich single-stranded DNA activates Mcm4/6/7 helicase on Y-fork and bubble-like substrates.

The presence of multiple clusters of runs of asymmetric adenine or thymine is a feature commonly found in eukaryotic replication origins. Here we report that the helicase and ATPase activities of the mammalian Mcm4/6/7 complex are activated specifically by thymine stretches. The Mcm helicase is specifically activated by a synthetic bubble structure which mimics an activated replication origin, as well as by a Y-fork structure, provided that a single-stranded DNA region of sufficient length is present in the unwound segment or 3' tail, respectively, and that it carries clusters of thymines. Sequences derived from the human lamin B2 origin can serve as a potent activator for the Mcm helicase, and substitution of its thymine clusters with guanine leads to loss of this activation. At the fork, Mcm displays marked processivity, expected for a replicative helicase. These findings lead us to propose that selective activation by stretches of thymine sequences of a fraction of Mcm helicases loaded onto chromatin may be the determinant for selection of initiation sites on mammalian genomes.

Adenosine Triphosphatases↗

PubMed1984

Internal micronuclear DNA regions which include sequences homologous to macronuclear telomeres are deleted during development in Tetrahymena.

C4A2 repeats are present in multiple clusters in both the macronucleus and micronucleus of Tetrahymena. Although the macronucleus is generated from the micronucleus after sexual conjugation, the repeats are telomeric sequences in the macronucleus but are internally located in the micronucleus (1). This study investigates the fate of the sequences adjacent to the micronuclear C4A2 repeats. Southern blot analyses of 21 C4A2-containing micronuclear clones show that extensive elimination of the adjacent sequences occurs during the formation of the macronucleus. Comparison of one C4A2-containing micronuclear clone with its derived macronuclear segment indicates that approximately 4.5 kb of DNA, which includes the C4A2 repeats and adjacent sequences on both sides is deleted from the macronucleus. The two regions adjoining the deletion are joined together to form a contiguous segment in the macronucleus. This excision of C4A2 repeats and surrounding sequences and the rejoining of the retained segments is probably the mechanism by which all or most of the other C4A2 adjacent sequences are eliminated.

Animals↗

PubMed2004

The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms.

Currently, the Genomic Threading Database (GTD) contains structural assignments for the proteins encoded within the genomes of nine eukaryotes and 101 prokaryotes. Structural annotations are carried out using a modified version of GenTHREADER, a reliable fold recognition method. The Gen THREADER annotation jobs are distributed across multiple clusters of processors using grid technology and the predictions are deposited in a relational database accessible via a web interface at http://bioinf.cs.ucl.ac.uk/GTD. Using this system, up to 84% of proteins encoded within a genome can be confidently assigned to known folds with 72% of the residues aligned. On average in the GTD, 64% of proteins encoded within a genome are confidently assigned to known folds and 58% of the residues are aligned to structures.

Animals↗

PubMed1991

Plasmacytoid monocytes in Jessner's lymphocytic infiltration of the skin. A valuable clue for the diagnosis.

Plasmacytoid monocytes (PCMs) are mononuclear cells of monocyte/macrophage origin with peculiar plasmacytoid features on electron microscopy. This cell type is largely unknown in dermatopathology, probably due to standard fixation procedures. The authors provide a detailed histopathologic, immunohistochemical, and electron-microscopic study of PCMs in Jessner's lymphocytic infiltration of the skin (LIS). PCMs occurred in 58% of all biopsy specimens from 75 patients with LIS in single or multiple clusters within the dermal infiltrates. Recognition of this cell type was important for differential diagnostic reasons because PCMs did not occur in polymorphic light eruption. In discoid lupus erythematosus, PCMs were present in only 7.3% of 110 biopsy specimens. PCMs are probably involved in the activation, proliferation, and differentiation of T-lymphocytes. Their origin and function are discussed and a special role in the homing of lymphocytes into the skin is suggested.

Diagnosis, Differential↗

PubMed2002

Oscillations by symmetry breaking in homogeneous networks with electrical coupling.

In many biological systems, the electrical coupling of nonoscillating cells generates synchronized membrane potential oscillations. This work describes a dynamical mechanism in which the electrical coupling of identical nonoscillating cells destabilizes the homogeneous fixed point and leads to network oscillations via a Hopf bifurcation. Each cell is described by a passive membrane potential and additional internal variables. The dynamics of the internal variables, in isolation, is oscillatory, but their interaction with the membrane potential damps the oscillations and therefore constructs nonoscillatory cells. The electrical coupling reveals the oscillatory nature of the internal variables and generates network oscillations. This mechanism is analyzed near the bifurcation point, where the spatial structure of the membrane potential oscillations is determined by the network architecture and in the limit of strong coupling, where the membrane potentials of all cells oscillate in-phase and multiple cluster states dominate the dynamics. In particular, we have derived an asymptotic behavior for the spatial fluctuations in the limit of strong coupling in fully connected networks and in a one-dimensional lattice architecture.

Journal Article↗

PubMed2004

Number of spanning clusters at the high-dimensional percolation thresholds.

A scaling theory is used to derive the dependence of the average number k of spanning clusters at threshold on the lattice size L. This number should become independent of L for dimensions d<6 and vary as ln L at d=6 . The predictions for d>6 depend on the boundary conditions, and the results there may vary between L(d-6) and L0. While simulations in six dimensions are consistent with this prediction [after including corrections of order ln(ln L)], in five dimensions the average number of spanning clusters still increases as ln L even up to L=201 . However, the histogram P(k) of the spanning cluster multiplicity does scale as a function of kX(L), with X(L) =1+const/L, indicating that for sufficiently large L the average k will approach a finite value: a fit of the five-dimensional multiplicity data with a constant plus a simple linear correction to scaling reproduces the data very well. Numerical simulations for d>6 and for d=4 are also presented.

Journal Article↗

PubMed1999

The starch-debranching enzymes isoamylase and pullulanase are both involved in amylopectin biosynthesis in rice endosperm

The activities of the two types of starch debranching enzymes, isoamylase and pullulanase, were greatly reduced in endosperms of allelic sugary-1 mutants of rice (Oryza sativa), with the decrease more pronounced for isoamylase than for pullulanase. However, the decrease in isoamylase activity was not related to the magnitude of the sugary phenotype (the proportion of the phytoglycogen region of the endosperm), as observed with pullulanase. In the moderately mutated line EM-5, the pullulanase activity was markedly lower in the phytoglycogen region than in the starch region, and isoamylase activity was extremely low or completely lost in the whole endosperm tissue. These results suggest that both debranching enzymes are involved in amylopectin biosynthesis in rice endosperm. We presume that isoamylase plays a predominant role in amylopectin synthesis, but pullulanase is also essential or can compensate for the role of isoamylase in the construction of the amylopectin multiple-cluster structure. It is highly possible that isoamylase was modified in some sugary-1 mutants such as EM-273 and EM-5, since it was present in significant and trace amounts, respectively, in these mutants but was apparently inactive. The results show that the Sugary-1 gene encodes the isoamylase gene of the rice genome.

Journal Article↗

PubMed2004

Distance-preserving projection of high-dimensional data for nonlinear dimensionality reduction.

A distance-preserving method is presented to map high-dimensional data sequentially to low-dimensional space. It preserves exact distances of each data point to its nearest neighbor and to some other near neighbors. Intrinsic dimensionality of data is estimated by examining the preservation of interpoint distances. The method has no user-selectable parameter. It can successfully project data when the data points are spread among multiple clusters. Results of experiments show its usefulness in projecting high-dimensional data.

Algorithms↗

PubMed2005

Interphase molecular cytogenetic screening for chromosomal abnormalities of prognostic significance in childhood acute lymphoblastic leukaemia: a UK Cancer Cytogenetics Group Study.

Summary Interphase fluorescence in situ hybridization (iFISH) was used independently to reveal chromosomal abnormalities of prognostic importance in a large, consecutive series of children (n = 2367) with acute lymphoblastic leukaemia (ALL). The fusions, TEL/AML1 and BCR/ABL, and rearrangements of the MLL gene occurred at frequencies of 22% (n = 447/2027) (25% in B-lineage ALL), 2% (n = 43/2027) and 2% (n = 47/2016) respectively. There was considerable variation in iFISH signal patterns both between and within patient samples. The TEL/AML1 probe showed the highest incidence of variation (59%, n = 524/884), which included 38 (2%) patients with clustered, multiple copies of AML1. We were thus able to define amplification of AML1 as a new recurrent abnormality in ALL, associated with a poor prognosis. Amplification involving the ABL gene, a rare recurrent abnormality confined to T ALL patients, was identified for the first time. The use of centromeric probes revealed significant hidden high hyperdiploidy of 33% and 59%, respectively, in patients with normal (n = 21/64) or failed (n = 32/54) cytogenetic results. The iFISH contributed significantly to the high success rate of 91% (n = 2114/2323) and the remarkable abnormality detection rate of 89% (n = 1879/2114). This study highlights the importance of iFISH as a complementary tool to cytogenetics in routine screening for significant chromosomal abnormalities in ALL.

Adolescent↗