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PubMed2002

Classification and phylogenetic analysis of the cAMP-dependent protein kinase regulatory subunit family.

The members of the PKA regulatory subunit family (PKA-R family) were analyzed by multiple sequence alignment and clustering based on phylogenetic tree construction. According to the phylogenetic trees generated from multiple sequence alignment of the complete sequences, the PKA-R family was divided into four subfamilies (types I to IV). Members of each subfamily were exclusively from animals (types I and II), fungi (type III), and alveolates (type IV). Application of the same methodology to the cAMP-binding domains, and subsequently to the region delimited by beta-strands 6 and 7 of the crystal structures of bovine RIalpha and rat RIIbeta (the phosphate-binding cassette; PBC), proved that this highly conserved region was enough to classify unequivocally the members of the PKA-R family. A single signature sequence, F-G-E-[LIV]-A-L-[LIMV]-x(3)-[PV]-R-[ANQV]-A, corresponding to the PBC was identified which is characteristic of the PKA-R family and is sufficient to distinguish it from other members of the cyclic nucleotide-binding protein superfamily. Specific determinants for the A and B domains of each R-subunit type were also identified. Conserved residues defining the signature motif are important for interaction with cAMP or for positioning the residues that directly interact with cAMP. Conversely, residues that define subfamilies or domain types are not conserved and are mostly located on the loop that connects alpha-helix B' and beta strand 7.

Amino Acid Sequence↗
PubMed2006

Psoriasis: genetic associations and immune system changes.

Psoriasis is a common inflammatory skin disease characterized by infiltration of inflammatory cells into the epidermis and altered keratinocyte differentiation. Psoriasis is currently thought of as a T-cell mediated 'Type-1' autoimmune disease. Gene expression changes in psoriasis lesions have been well documented, and strongly support an important role for tumor necrosis factor and interferon gamma signal pathways in its pathogenesis. The strongest genetic determinant of psoriasis identified to date lies within the class I region of the multiple histocompatibility locus antigen cluster, although its low penetrance implicates a requirement for other genetic risk factors. Multiple genome-wide linkage and an increasing number of association studies have been carried out, leading to multiple linkage peaks, and the identification of potential low risk variants. A number of these variants lie within genes encoding components of the immune system. However, the functional relationships between predisposing genetic variation is unclear, and presumably involves genetic susceptibility factors affecting both immune cell activation and keratinocyte differentiation. The interaction of environmental trigger factors with genetic effects is also not understood, but provide further evidence for the complex basis of this disease.

Animals↗
PubMed2002

Cluster of pulmonary blastomycosis in a rural community: evidence for multiple high-risk environmental foci following a sustained period of diminished precipitation.

Much of our understanding of the epidemiologic features of infection with Blastomyces dermatitidis has come from cluster and outbreak investigations which have established the association of human disease with recreational pursuits and the presence of infectious microfoci in areas of moist soil with high organic content. This report describes the clustering of eight cases of pulmonary blastomycosis without an apparent common source exposure which occurred during a 90 day period in a 96 square mile area (population 4,450) within Oconto County, Wisconsin. We conclude that multiple high-risk environmental foci may have existed following a sustained five-year period of diminished precipitation in the cluster area. A case-control study which included family and community controls concluded that multiple earth-disturbing activities engaged in by case-patients was statistically associated with illness. Lymphocyte-proliferation assays of whole blood samples detected previously unrecognized infection with B. dermatititidis among five of 32 family controls.

Adolescent↗
PubMed2001

A study of interleukin-1 cluster genes in susceptibility to and severity of multiple sclerosis.

In this explorative study, interleukin-1 (IL-1) receptor antagonist (IL-1RA; polymorphism of variable number of tandem repeats: VNTR), IL-1alpha (-889), IL-1beta (-511) and IL-1beta (+3953) polymorphisms were studied in relation to susceptibility to and severity of multiple sclerosis (MS), in 93 MS patients and 400 normal controls. No associations were found for any polymorphisms, alone or in combination. However, in our MS cohort, females were found to be IL-1RA allele 2 carriers more frequently than males (33/49 vs. 16/44, p = 0.0028). Using a cohort of 109 controls, IL-1RA allele 2 carriers were more frequently women with MS than control women (33/49 vs. 23/43, odds ratio (OR) = 2.19, 95% confidence interval (CI) 1.02-4.72, p = 0.043, P(C) = ns). The data suggest that the IL-1 cluster genes make no major contribution to MS, but the tentative association between IL-1RA allele 2 and susceptibility of MS in women warrants further studies.

Adult↗
PubMed1994

Astrocyte associations with nodes of Ranvier: ultrastructural analysis of HRP-filled astrocytes in the mouse optic nerve.

Astrocytes are implicated in the function of nodes of Ranvier because their perinodal processes form contacts with the axonal membrane at nodes. We have filled astrocytes iontophoretically with horseradish peroxidase in the intact mouse optic nerve to resolve the precise relationship between perinodal processes and astrocyte three dimensional structure. We confirm that nodal contacts were formed either by single processes which almost completely enveloped nodes, or by delicate, finger-like projections from larger processes which made discrete nodal contacts. A single perinodal process can form multiple contacts with a node and nodes were contacted by processes from more than one astrocyte. Perinodal processes emanated from larger processes, which terminated as end-feet on blood vessels and at the pia, as well as collateral branches which subsequently ended at nodes; these latter may specifically subserve nodes. Perinodal contacts were also formed directly by the soma and cytoplasmic expansions of the cell body. Both primary processes and collateral branches formed multiple associations with nodes which often appeared in clusters. Thus, all astrocytes formed multiple contacts with nodes, blood vessels and the subpial glia limitans. We conclude that perinodal processes are not formed by a specialized astrocyte in the mouse optic nerve.

Animals↗
PubMed1993

Alterations in luteinizing hormone secretory activity in women with insulin-dependent diabetes mellitus and secondary amenorrhea.

To investigate hypothalamic and/or pituitary abnormalities in women with poorly controlled insulin-dependent diabetes mellitus (IDDM) and secondary amenorrhea, we measured serum LH every 10 min for 24 h and for 2 additional h after the administration of exogenous GnRH in 8 women with IDDM and amenorrhea and compared these to data from 15 eumenorrheic nondiabetic women. LH pulses were characterized by the pulse detection algorithm Cluster, and secretory episodes were evaluated using the multiple parameter deconvolution procedure Deconv. Cluster analysis revealed fewer LH pulses per 24 h (14.3 +/- 1.2 vs. 19.9 +/- 0.6; P < 0.001; mean +/- SEM), a greater peak width (63 +/- 4.9 vs. 44 +/- 2.2 min; P < 0.01), and greater peak area (136 +/- 17 vs. 89 +/- 13 IU/L.min; P < 0.01) in the diabetic women. Analysis with Deconv revealed fewer LH secretory episodes per 24 h in the diabetic women (14.4 +/- 0.9 vs. 20.4 +/- 0.5; P < 0.001) and no statistical difference in LH half-lives. The IDDM women responded to a 10-micrograms GnRH bolus with LH pulses of larger total (51 +/- 15.9 vs. 15 +/- 1.4 IU/L; P < 0.01) and incremental (29 +/- 7.6 vs. 9 +/- 1.2; P < 0.001) amplitude. In summary, we observed that amenorrheic diabetic women have fewer LH pulses/secretory episodes than normal women. However, they respond well to exogenous GnRH, suggesting that compromise of the GnRH pulse generator, rather than pituitary dysfunction, is responsible for their menstrual dysfunction.

Adult↗
PubMed1984

Multiplication of Musa from excised stem tips.

Rapidly multiplying cultures were established from excised shoot tips of two dessert banana clones ('Philippine Lacatan' and 'Grande Naine') and two plantain clones ('Pelipita' and 'Saba'). Apices cultured on semi-solid media produced single shoots while apices placed in liquid media produced shoot clusters. Individual shoots were induced to form multiple shoot clusters by longitudinally splitting the shoot through the apex. Shoot multiplication was stimulated maximally by 5 mg l-1 benzylaminopurine. Rooted plants were produced by treating shoots with auxins. Growth rates based on increase in f. wt of the four clones were compared. During a 4-week culture period 'Pelipita' showed a fivefold increase in f. wt while 'Grande Naine', 'Philippine Lacatan' and 'Saba' showed increases exceeding tenfold.

Adenine↗
PubMed1991

Clinical and microbiological patterns of adults with periodontitis.

Although current data suggest that periodontitis may actually be multiple diseases each with varying responses to therapy, little evidence exists to support this theory in adult patients. This report describes the design and initial findings of a longitudinal field trial involving the diagnosis and treatment of adult and refractory periodontitis patients in private practice. Adult patients (N = 221) who met specific clinical criteria were selected from the private practices of 22 periodontists. Clinical characteristics were recorded and subgingival plaque samples were sent to microbiology laboratories at either UCLA or The University of Texas Health Science Center at San Antonio (UTHSCSA). Samples were processed according to protocols standardized between the 2 centers. Five different combinations of the initial clinical and microbial findings were evaluated for patterns in the data by means of cluster analysis. Plaque, bleeding on probing, bone loss scores, probing depth distributions, and microbial findings produced multiple cluster solutions. Solutions involving 6 clusters explained 39.4% to 76.4% of the variation between patients and produced ratios for variation between clusters to variation within clusters of 5.2 to 15.3. The optimal cluster solution incorporated both clinical and microbial findings, with some clusters characterized by high plaque and moderate bleeding on probing and bone loss, whereas others had low plaque but high bleeding on probing and bone loss. Microbial findings of each cluster exhibited distinct patterns with some clusters having a high prevalence (83% to 100%) of specific target bacterial species while other clusters had an absence of these species.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed2006

Analysing the effect of candidate genes on complex traits: an application in multiple sclerosis.

The conventional approach of candidate gene studies in complex diseases is to look at the effect of one gene at a time. However, as the outcome of chronic diseases is influenced by a large number of alleles, simultaneous analysis is needed. We demonstrate the application of multivariate regression and cluster analysis to a multiple sclerosis (MS) dataset with genotypes for 489 patients at 11 candidate genes selected on their involvement in the immune response. Using multivariate regression, we observed that different sets of genes were associated with different disease characteristics that reflect different aspects of disease. Out of 15 polymorphisms, we identified one that contributed to the severity of disease. In addition, the set of 15 polymorphisms was predictive for yearly increase in lesion volume as seen on T1-weighted MRI (p=0.044). From this set, no individual polymorphisms could be identified after adjustment for multiple hypotheses testing. By means of a cluster analysis, we aimed to identify subgroups of patients with different pathogenic subtypes of MS on the basis of their genetic profile. We constructed genetic profiles from the genotypes at the 11 candidate genes. The approach proved to be feasible. We observed three clusters in the sample of patients. In this study, we observed no significant differences in the usual clinical and MRI outcome measures between the different clusters. However, a number of consistent trends indicated that this clustering might be related to the course of disease. With a larger number of genes regulating the course of disease, we may be able to identify clinically relevant clusters. The analyses are easily implemented and will be applicable to candidate gene studies of complex traits in general.

Adult↗
PubMed2002

Gene expression profiles in tadpole larvae of Ciona intestinalis.

A set of 12,779 expressed sequence tags (ESTs), both the 5'-most and 3'-most ends, derived from Ciona intestinalis tadpole larvae was categorized into 3521 independent clusters, from which 1013 clusters corresponding to 9424 clones were randomly selected to analyze genetic information and gene expression profiles. When compared with sequences in databases, 545 of the clusters showed significant matches (P < E-15) with reported proteins, while 153 showed matches with putative proteins for which there is not enough information to categorize their function, and 315 had no significant sequence similarities to known proteins. Sequence-similarity analyses of the 545 clusters in relation to the biological functions demonstrated that 407 of them have functions that many kinds of cells use, 104 are associated with cell-cell communication, and 34 are transcription factors or other gene-regulatory proteins. Sequence prevalence distribution analysis demonstrated that more than one-half of the mRNAs are rare mRNAs. All of the 1013 clusters were subjected to whole-mount in situ hybridization to analyze the gene expression profile in the tadpole larva. A total of 361 clusters showed expression specific to a certain tissue or organ: 96 showed epidermis-specific expression, 60 were specific to the nervous system, 108 to endoderm, 34 to mesenchyme, 5 to trunk lateral cells, 4 to trunk ventral cells, 23 to notochord, 28 to muscle, and 3 to siphon rudiments. In addition, 190 clusters showed expression in multiple tissues. Moreover, nervous system-specific genes showed intriguing expression patterns dependent on the cluster. The present study highlights a broad spectrum of genes that are used in the formation of one of the most primitive chordate body plans as well as for the function of various types of tissue and organ and also provides molecular markers for individual tissues and organs constituting the Ciona larva.

Amphibians↗
PubMed1995

Defining the breakpoint of a multigene deletion in the immunoglobulin heavy chain gene cluster.

The constant region of the human immunoglobulin heavy chain (IGHC) is encoded by a cluster of genes near the telomere of chromosome 14q. Deletions and duplications of single or multiple genes in the cluster have been identified, but little information about the breakpoint junctions has been available, in part due to the high degree of sequence similarity between the genes in this region. We report an intensive study of a homozygous deletion, using Southern hybridization and polymerase chain reaction techniques. We found that the deleted DNA includes the functional epsilon gene, and that the breakpoints are located within a 2 kilobase Bam HI/Sac I region of both the IGHEP1 and IGHE genes. These results revise a previous conclusion regarding the deleted region. Definition of breakpoints occurring within this cluster may shed light on recombination mechanisms.

Base Sequence↗
PubMed2005

Microswitch clusters to enhance adaptive responses and head control: a programme extension for three children with multiple disabilities.

PURPOSE: We assessed the possibility of extending adaptive responding and head control in three children with multiple disabilities through the use of microswitch clusters. METHOD: The children had previously learned to perform an adaptive hand response and to control head position during that response. They were now taught one or two new adaptive responses (foot lifting, leg touching, or vocalization) and to combine such responses with appropriate head position. Microswitch clusters served to ensure that an adaptive response was followed by positive stimulation only if it was combined with appropriate head position. RESULTS: The results were positive with the children learning the new adaptive responses and combining them with appropriate head position. This performance was maintained during two- or three-month post-intervention checks. During these checks, the children were also successful in using the old adaptive hand response with appropriate head position. CONCLUSIONS: The use of microswitch clusters was effective to extend the level of adaptive responding and enhance appropriate head position during this responding. This outcome, which indicates a successful technical replication and procedural extension of previous work in the area, has positive practical implications for educational and occupational programmes for children with multiple disabilities.

Child↗
PubMed2004

Cluster computing for digital microscopy.

Microscopy is becoming increasingly digital and dependent on computation. Some of the computational tasks in microscopy are computationally intense, such as image restoration (deconvolution), some optical calculations, image segmentation, and image analysis. Several modern microscope technologies enable the acquisition of very large data sets. 3D imaging of live cells over time, multispectral imaging, very large tiled 3D images of thick samples, or images from high throughput biology all can produce extremely large images. These large data sets place a very large burden on laboratory computer resources. This combination of computationally intensive tasks and larger data sizes can easily exceed the capability of single personal computers. The large multiprocessor computers that are the traditional technology for larger tasks are too expensive for most laboratories. An alternative approach is to use a number of inexpensive personal computers as a cluster; that is, use multiple networked computers programmed to run the problem in parallel on all the computers in the cluster. By the use of relatively inexpensive over-the-counter hardware and open source software, this approach can be much more cost effective for many tasks. We discuss the different computer architectures available, and their advantages and disadvantages.

Cells↗
PubMed2006

Symptom clustering in advanced cancer.

A major goal of palliative medicine is to control symptoms that interfere with quality of life. Identification of symptoms that occur together (cluster) may aid in symptom management, resulting in greater therapeutic benefit to the patient. An analysis of 25 symptoms from 922 patients with advanced cancer was undertaken to determine if symptom clusters could be identified. Cluster analysis was done using an agglomerative hierarchical method with average linkage; the absolute value of the correlation between pairs of symptoms was used as the measure of similarity. A correlation of >or=0.68 was used to define the final clusters. Seven clusters were identified: (1) fatigue: anorexia-cachexia; (2) neuropsychological; (3) upper gastrointestinal; (4) nausea and vomiting; (5) aerodigestive; (6) debility; (7) pain. Recognition of symptom clusters should help understand symptom pathophysiology and target therapies that perhaps can be used to relieve multiple symptoms in that cluster. This could result in improved quality of life for patients with advanced cancer and perhaps reduce polypharmacy, lessen drug side effects, and have pharmacoeconomic benefits.

Adolescent↗
PubMed1997

BCL-6 is phosphorylated at multiple sites in its serine- and proline-clustered region by mitogen-activated protein kinase (MAPK) in vivo.

BCL-6 gene alterations have been observed in 27-45% of diffuse large B-cell lymphomas (DLBs) with chromosomal translocations at 3q27. The deregulated expression of normal BCL-6 protein caused by this chromosomal translocation is believed to be responsible for lymphomagenesis. Recently, we demonstrated that BCL-6 is expressed at high levels in germinal center B-cells as a 92-98 kDa nuclear protein in a constitutively phosphorylated form. In this study, we show that BCL-6 is phosphorylated by mitogen-activated protein kinase (MAPK) in vitro at the sites phosphorylated in vivo. These numerous phosphorylation sites were found to be located in its serine- and proline-clustered (SPC) region (amino acids-250-483). BCL-6 phosphorylation significantly increased in Ramos cells following stimulation with 12-o-tetradecanoylphorbol-13-acetate (TPA) or BCL-6- and erk1-transfected COS-7 cells stimulated with epidermal growth factor (EGF), and the increase of phosphorylation was inhibited by MEK1 inhibitor, PD98059. Furthermore, we observed that BCL-6 was associated with MAPK in vivo and its SPC region was important for this association. These results suggest that the functions of BCL-6 are regulated by phosphorylation mediated by the MAPK signaling pathway.

Calcium-Calmodulin-Dependent Protein Kinases↗
PubMed2000

Binary data with two, non-nested sources of clustering: an analysis of physician recommendations for early prostate cancer treatment.

A prospective cohort study of men with newly diagnosed early prostate cancer was undertaken Talcott et al. (1998) in order to evaluate both the patient-level and the physician-level determinants of physician recommendations for radical prostatectomy (surgery) versus radiation therapy. Each patient sought recommendations from as many as six physicians, and each physician provided recommendations for as many as 113 patients. Thus, the recommendations are clustered within physician and within patient. While methods have been developed for binary data with multiple-nested sources of clustering, they have not been fully explored for binary data with non-nested sources of clustering, such as the treatment recommendations. Here we propose reclustering the data to form binary data with one source of clustering. Because the reclustered data result in one very large cluster and several clusters of size one and two, marginal logistic regression models for the probability of a recommendation of surgery fit using a generalized estimating equation approach would produce unreliable estimates of uncertainty for the parameters. Thus, in addition to the mean model, we attempt to model the associations in as much detail as possible. We compare this model to a mixed-effects model that implicitly adjusts for both sources of clustering and to models based on the assumption of conditional independence with regard to one source of clustering.

Journal Article↗
PubMedDate not supplied

A cluster of nosocomial cross-infection due to multiple antibiotic-resistant Acinetobacter baumannii: Characterization of the strain and antibiotic susceptibility studies.

A multiple antibiotic-resistant (MAR) strain of Acinetobacter baumannii caused nosocomial cross-infection among 3 patients of a surgical intensive care unit. The isolates were of identical biochemical profile (77776 S-U-) and serotype (serovar 36) and identical in terms of pulsed-field gel electrophoresis macrorestriction (SmaI, ApaI) analysis. This MAR strain was susceptible only to netilmicin, tobramycin, imipenem, meropenem, polymyxin B, and trovafloxacin. The minimal bactericidal concentrations of imipenem and meropenem were markedly higher than the corresponding minimal inhibitory concentrations against this strain. Combined fresh defibrinated human blood (65 vol%) and antimicrobial drug assays yielded the following results: polymyxin was the most rapidly bactericidally effective antibiotic in the presence of blood and in broth. Tobramycin and netilmicin were efficacious in 65 vol% blood. Imipenem was slightly more effective than meropenem in broth, whereas both carbapenems sterilized blood-containing assay tube contents. Trovafloxacin failed to achieve bactericidal activity (to 99.9% kill) in the presence of blood, presumably because this strain was resistant to ciprofloxacin and borderline susceptible to ofloxacin. Trovafloxacin combined with either imipenem or meropenem yielded an indifferent effect. However, the combination of trovafloxacin (2 microg/ml) plus tobramycin (1 microg/ml) achieved sterilization of tube contents in the presence of blood within 4 h after exposure and in broth following extended (overnight) incubation. This MAR strain of A. baumannii was high-level resistant to rifampin; thus the combination of polymyxin B plus rifampin proved indifferent.

Acinetobacter↗