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Biomedical subjects

Paul Cullen

Publications and source records attributed to Paul Cullen.

At least 19 recordsLinked to original sources
PubMed2006

IsoSVM--distinguishing isoforms and paralogs on the protein level.

BACKGROUND: Recent progress in cDNA and EST sequencing is yielding a deluge of sequence data. Like database search results and proteome databases, this data gives rise to inferred protein sequences without ready access to the underlying genomic data. Analysis of this information (e.g. for EST clustering or phylogenetic reconstruction from proteome data) is hampered because it is not known if two protein sequences are isoforms (splice variants) or not (i.e. paralogs/orthologs). However, even without knowing the intron/exon structure, visual analysis of the pattern of similarity across the alignment of the two protein sequences is usually helpful since paralogs and orthologs feature substitutions with respect to each other, as opposed to isoforms, which do not. RESULTS: The IsoSVM tool introduces an automated approach to identifying isoforms on the protein level using a support vector machine (SVM) classifier. Based on three specific features used as input of the SVM classifier, it is possible to automatically identify isoforms with little effort and with an accuracy of more than 97%. We show that the SVM is superior to a radial basis function network and to a linear classifier. As an example application we use IsoSVM to estimate that a set of Xenopus laevis EST clusters consists of approximately 81% cases where sequences are each other's paralogs and 19% cases where sequences are each other's isoforms. The number of isoforms and paralogs in this allotetraploid species is of interest in the study of evolution. CONCLUSION: We developed an SVM classifier that can be used to distinguish isoforms from paralogs with high accuracy and without access to the genomic data. It can be used to analyze, for example, EST data and database search results. Our software is freely available on the Web, under the name IsoSVM.

Algorithms↗
PubMed2006

Gap between guidelines and practice: attainment of treatment targets in patients with primary hypercholesterolemia starting statin therapy. Results of the 4E-Registry (Efficacy Calculation and Measurement of Cardiovascular and Cerebrovascular Events Including Physicians' Experience and Evaluation).

BACKGROUND: The aim of this study was to determine the achievement of National Cholesterol Education Program Adult Treatment Panel III goals in patients with primary hypercholesterolemia starting statin therapy in clinical practice. METHODS AND RESULTS: Data were collected by 4401 physicians in private practice on 52 848 patients aged 35-65 years (46.3% women, 53.7% men). 56.1% of patients had no manifested atherosclerosis (primary prevention) among whom 34.9% of men and 0.5% of women had a 10-year coronary heart disease risk over 20% (high-risk) as calculated using the Prospective Cardiovascular Münster study (PROCAM) algorithm. After 6 weeks of statins, only 6.9% of these high-risk men and 4.6% of these high-risk women reached their low-density lipoprotein (LDL) cholesterol target of 2.6 mmol/l or below (100 mg/dl). Even after 9 months, only 8.0% of these men and 6.2% of these women achieved their LDL target. No fewer than 57.3% of treated women had a coronary risk below 10%, and 18.8% of women were already at target before statins were prescribed. Of patients 43.9% had manifest atherosclerosis (secondary prevention). After 6 weeks of therapy, only 12.9% of the women and 16.3% of the men in this secondary prevention group reached LDL target levels of 2.6 mmol/l or below. Even after 9 months, only 21.3% of men and 17.3% of women with manifest atherosclerosis reached target LDL. CONCLUSIONS: Most high-risk patients do not achieve LDL targets. Overtreatment of low-risk groups is also very common.

Cardiovascular Diseases↗
PubMed2005

Correspondence of function and phylogeny of ABC proteins based on an automated analysis of 20 model protein data sets.

Using our BLAST-based procedure RiPE (Retrieval-induced Phylogeny Environment), which automates the evolutionary analysis of a protein family, we assembled a set of 1138 ABC protein components [adenosine triphosphate (ATP)-binding cassette and transmembrane domain] from the protein data sets of 20 model organisms and subjected them to phylogenetic and functional analysis. For maximum speed, we based the alignment directly on a homology search with a profile of all known human ABC proteins and used neighbor-joining tree estimation. All but 11 sequences from Homo sapiens, Arabidopsis thaliana, Drosophila melanogaster, and Saccharomyces cerevisiae were placed into the correct subtree/subfamily, reproducing published classifications of the individual organisms. By following a simple "function transfer rule", our comparative phylogenetic analysis successfully predicted the known function of human ABC proteins in 19 of 22 cases. Three functional predictions did not correspond, and 10 were novel. Predictions based on BLAST alone were inferior in five cases and superior in two. Bacterial sequences were placed close to the root of most subtrees. This placement coincides with domain architecture, suggesting an early diversification of the ABC family before the kingdoms split apart. Our approach can, in principle, be used to annotate any protein family of any organism included in the study.

ATP-Binding Cassette Transporters↗
PubMed2005

Importance of arterial pulse pressure as a predictor of coronary heart disease risk in PROCAM.

AIMS: To investigate pulse pressure (PP) as an independent predictor of coronary heart disease (CHD) risk. METHODS AND RESULTS: On the basis of a 10-year follow-up of 5389 men aged 35-65 at recruitment into PROCAM, we used a proportional hazards model to calculate the effect of systolic blood pressure (SBP), diastolic blood pressure (DBP), and PP on CHD risk after correcting for age, high-density lipoprotein cholesterol, LDL cholesterol, triglycerides, smoking, diabetes, and family history of premature CHD. Increases of 10 mmHg in DBP, SBP, and PP were associated with an increased CHD hazard ratio (HR) of approximately 10%. When the group was divided into the age groups <50, 50-59, and >59 years, this relationship was seen in the age group 50-59 years for DBP, SBP, and PP and in men aged > or =60 for PP only (25% increase in HR). Overall, CHD risk in men with PP > or =70 mmHg was more three times that of men with PP <50 mmHg. This increased risk was not apparent at age <50 years, was greatest at age >60 years, and was also present in men who were normotensive at recruitment (SBP < or =160 mmHg, DBP < or =95 mmHg). CONCLUSION: In older European men, increased PP is an important independent determinant of coronary risk, even among those initially considered normotensive.

Adult↗
PubMed2005

Plasma sitosterol elevations are associated with an increased incidence of coronary events in men: results of a nested case-control analysis of the Prospective Cardiovascular Münster (PROCAM) study.

BACKGROUND AND AIM: Sitosterolemia, a rare genetic disorder characterized by profoundly elevated plasma sitosterol concentrations, is associated with premature atherosclerosis in some individuals. This study was conducted to evaluate if the modest sitosterol elevations seen in the general population are also associated with the occurrence of coronary events. METHODS AND RESULTS: A nested case-control study using stored samples from male participants in the Prospective Cardiovascular Münster (PROCAM) study was performed. Each of 159 men who suffered a myocardial infarction or sudden coronary death (major coronary event) within 10 years of follow-up in PROCAM was matched with 2 controls (N = 318) by age, smoking status, and date of investigation. Analysis was performed using conditional logistic regression. Plasma sitosterol concentrations were elevated in cases compared with controls (4.94 +/- 3.44 micromol/L versus 4.27 +/- 2.38 micromol/L; P = 0.028). The upper quartile of sitosterol (>5.25 micromol/L) was associated with a 1.8-fold increase in risk (P < 0.05) compared with the lower three quartiles. Among men with an absolute coronary risk > or = 20% in 10 years as calculated using the PROCAM algorithm, high sitosterol concentrations were associated with an additional 3-fold increase in the incidence of coronary events (P = 0.032); a similar, significant relationship was observed between a high sitosterol/cholesterol ratio and coronary risk (P = 0.030). CONCLUSIONS: Elevations in sitosterol concentrations and the sitosterol/cholesterol ratio appear to be associated with an increased occurrence of major coronary events in men at high global risk of coronary heart disease. Further evaluations are warranted to confirm these preliminary findings.

Adolescent↗
PubMed2005

Cloning, cellular localization, genomic organization, and tissue-specific expression of the TGFbeta1-inducible SMAP-5 gene.

SMAP-5 is a member of the five-pass transmembrane protein family localizing in the Golgi apparatus and the endoplasmic reticulum. These proteins have been implicated in intracellular trafficking, in secretion and in vesicular transport. Phylogenetic analyses revealed that SMAP-5 is a member of a small Rab GTPase interacting factor protein family. The human SMAP-5 gene spans about 12.5 kb and comprises 6 exons on chromosomal locus 5q32. The proximal 5'-flanking region of the gene lacks a TATA box and is highly GC rich. Consistent with this, the SMAP-5 gene is expressed in all tissues. The highest level of expression was found in coronary smooth muscle cells, in which expression of the SMAP-5 gene was induced by transforming growth factor beta1, thus indicating that this protein may play an important role in inflammation.

Alternative Splicing↗
PubMed2005

Pharmacological regulation of cholesterol efflux in human monocyte-derived macrophages in the absence of exogenous cholesterol acceptors.

Cholesterol efflux from human monocyte-derived macrophages in the absence of exogenous acceptors has been described, but is unclear in mechanism. We investigated this process in relation to the expression of relevant genes, intracellular cholesterol storage and apoE secretion using drugs affecting different aspects of cholesterol metabolism. Both natural (22R-hydroxycholesterol/9-cis-retinoic acid) and synthetic (T0901317 and RO264456) LXR/RXR ligands increased ABCA1 and ABCG1 mRNAs in native macrophages and in cells loaded with acetylated LDL (acLDL). The ACAT inhibitor avasimibe increased only ABCG1 mRNA, whereas no treatment affected apoE mRNA. Avasimibe, progesterone, and natural but not synthetic LXR/RXR ligands prevented cholesterol esterification after acLDL-loading. Cholesterol efflux into acceptor-free medium was increased only by synthetic LXR/RXR ligands and avasimibe in acLDL-loaded cells. ApoE secretion was reduced by drugs affecting cholesterol trafficking but enhanced by LXR/RXR ligands. Incubation with an anti-apoE antibody virtually removed immunodetectable apoE from the medium, significantly increasing cholesterol storage and decreasing efflux. These findings indicate that in human macrophages spontaneous cholesterol efflux: (i) is not necessarily promoted by increasing intracellular free cholesterol, (ii) is increased by compounds that activate ABCA1 and, to a greater extent, ABCG1 and (iii) is only partially correlated with secretion of endogenous apoE, which acted as a cholesterol acceptor.

ATP Binding Cassette Transporter 1↗
PubMed2005

Implications of emerging risk factors for therapeutic intervention.

Recently, the National Cholesterol Education Panel (NCEP) of the United States of America commented on the implications of new clinical trials for the Adult Treatment Panel III (ATP III) guidelines. In this commentary, new categories of "moderately high" and "very high" coronary risk were proposed with new "therapeutic options" for low-density lipoprotein (LDL) cholesterol of < or = 100 mg/dL and < or = 70 mg/dL respectively. In ATP III, these "moderately high" risk patients had been classified as moderate risk with an LDL treatment goal of < or = 130 mg/dL, while the "very high" risk patients had been classified as high risk with a treatment goal of < or = 100 mg/dL. Risk classification in the new NCEP publication is based essentially on the combination of the Framingham risk score plus counting of classical risk factors. In the present document, the International Task Force for Prevention of Coronary Heart Disease responds to this NCEP commentary and supports the suggestion of more intensive LDL cholesterol lowering in particular cases. However, the Task Force feels that a classification based on a combination of a risk score plus a count of emerging risk factors is a more logical way to identify such patients requiring lower LDL cholesterol levels than a scheme in which classical risk factors are taken into account twice, once in a count and once in a risk score.

Advisory Committees↗
PubMed2005

Human antibody response to outer membrane protein G1a, a lipoprotein of Moraxella catarrhalis.

Moraxella catarrhalis is an important cause of respiratory infections in adults with chronic obstructive pulmonary disease (COPD) and of otitis media in children. Outer membrane protein (OMP) G1a is an approximately 29-kDa surface lipoprotein and is a potential vaccine candidate. The gene that encodes OMP G1a was expressed and purified using a novel plasmid vector. [(3)H]palmitic acid labeling demonstrated that both native and recombinant OMP G1a contain covalently bound palmitic acid. To assess the expression of OMP G1a during human infection, paired sera and sputum supernatants from adults with COPD followed prospectively were studied by enzyme-linked immunosorbent assays with recombinant lipidated OMP G1a to detect antibodies made specifically during carriage of M. catarrhalis. Overall, 23% of patients developed either a serum immunoglobulin G (IgG) response (9%) or sputum IgA response (21%) to OMP G1a, following 100 episodes of acquisition and clearance of M. catarrhalis. Patients developed antibody responses at similar rates following episodes of clinical exacerbation compared to asymptomatic colonization. Serum IgG antibodies following natural infection were directed predominantly at OMP G1a epitopes that are not exposed on the bacterial surface. These data show that OMP G1a is expressed during infection of the human respiratory tract and is a target of systemic and mucosal antibodies. These observations indicate that OMP G1a, a highly conserved surface protein, should be evaluated further as a vaccine candidate.

Antibodies, Bacterial↗
PubMed2005

The Leptospira interrogans lexA gene is not autoregulated.

Footprinting and mutagenesis experiments demonstrated that Leptospira interrogans LexA binds the palindrome TTTGN(5)CAAA found in the recA promoter but not in the lexA promoter. In silico analysis revealed that none of the other canonical SOS genes is under direct control of LexA, making the leptospiral lexA gene the first described which is not autoregulated.

Bacterial Proteins↗
PubMed2004

Characterization of the synthetic compatible solute homoectoine as a potent PCR enhancer.

Different substances such as dimethyl sulfoxide, tetramethylene sulfoxide, 2-pyrollidone, and the naturally occurring compatible solute betaine enhance PCR amplification of GC-rich DNA templates with high melting temperatures. In particular, cyclic compatible solutes outperform traditional PCR enhancers. We therefore investigated the effects that cyclic naturally occurring ectoine-type compatible solutes and their synthetic derivatives have on melting temperature of double-stranded DNA (dsDNA) and on PCR amplification of different templates. L-ectoine, betaine, and derivatives of L-ectoine decreased, whereas beta-hydroxyectoine increased, the melting temperature of dsDNA. The ability to decrease the melting temperature was greatest for homoectoine, a new synthetic derivative of l-ectoine. Furthermore, compatible solutes, especially homoectoine, enhanced PCR amplification of GC-rich DNA (72.6% GC content; effective range: 0.1-0.5M).

Amino Acids, Diamino↗
PubMed2004

ADP-ribosylation factor (ARF)-like 7 (ARL7) is induced by cholesterol loading and participates in apolipoprotein AI-dependent cholesterol export.

Here, we identify ADP-ribosylation factor (ARF)-like 7 (ARL7) as the only ARF- and ARL-family member whose mRNA-expression is induced by liver X-receptor/retinoid X-receptor agonists or cholesterol loading in human macrophages. Moreover, subcellular distribution of mutant and wild type ARL7-enhanced green fluorescent protein (EGFP) supports that ARL7 may be involved in a vesicular transport step between a perinuclear compartment and the plasma membrane. Therefore, we investigated the effect of ARL7 over-expression on the cholesterol secretory pathway. We found that expression of wild type and dominant active ARL7-EGFP stimulated the rate of apolipoprotein AI-specific cholesterol efflux 1.7- and 2.8-fold. In contrast, expression of the dominant negative form of ARL7-EGFP led to approximately 50% inhibition of cholesterol efflux. This data is consistent with a model in which ARL7 is involved in transport between a perinuclear compartment and the plasma membrane apparently linked to the ABCA1-mediated cholesterol secretion pathway.

ADP-Ribosylation Factors↗
PubMed2004

VisCoSe: visualization and comparison of consensus sequences.

We introduce visualization and comparison of consensus sequences (VisCoSe) as a WWW service and a stand-alone command line Perl script for visualizing and comparing consensus sequences of protein and nucleotide sequences. VisCoSe is the only interface available that simultaneously calculates consensus sequences of multiple data sets and automatically compares these consensus sequences. Furthermore, VisCoSe allows visualization of chemical properties of amino acids.

Algorithms↗
PubMed2004

Laser microdissection-based analysis of mRNA expression in human coronary arteries with intimal thickening.

Intimal thickening is an early phase of atherosclerosis characterized by differentiation of plaque smooth muscle cells (SMCs) from a contractile to a synthetic phenotype. We used laser microdissection (LMD) plus real-time RT-PCR to quantify mRNAs for calponin-1 and smoothelin, markers of the contractile phenotype, and for serum response factor (SRF), a regulator of SMC differentiation, in intimal and medial SMCs of human coronary arteries with intimal thickening. RNA expression was also analyzed by ISH and protein expression was detected by IHC. LMD plus RT-PCR found similar levels of SRF mRNA in intimal and medial SMCs, while medial mRNA levels for calponin-1 and smoothelin were higher. ISH confirmed that smoothelin mRNA levels in media exceeded those in intima, whereas SRF mRNA levels were similar at both sites. For calponin-1 and smoothelin, protein levels mirrored respective mRNA levels. By contrast, more medial than intimal SRF protein was present. Our results indicate that intimal SMCs exhibit a largely synthetic phenotype, perhaps reflecting lower intimal levels of SRF protein; ISH and LMD plus real-time RT-PCR provide comparable results; as a valuable alternative to ISH, LMD plus RT-PCR allows parallel measurement of several transcripts; and tissue gene expression studies must measure both protein and mRNA levels.

Biomarkers↗
PubMed2004

Cell aggregation: a mechanism of pathogenic Leptospira to survive in fresh water.

Transmission of leptospirosis is facilitated by the survival of pathogenic leptospires in moist environments outside their mammalian host. In the present study, the survival mechanisms of Leptospira interrogans serovar Canicola in aqueous conditions and lack of nutrients were investigated. In distilled water, leptospires were able to remain motile for 110 days (pH 7.2). However, when incubated in a semi-solid medium composed of distilled water and 0.5% purified agarose (pH 7.2), they survived 347 days. In this viscous environment, aggregates of live spirochetes were observed. Neither antibiotics (e.g. tetracycline and ampicillin) nor nutrients inhibited leptospiral aggregation. Immunoblot analysis suggested that cells incubated in water down-regulate the expression of LipL31, an inner-membrane protein, but retain expression of other membrane proteins. These studies provide insights into the mechanisms by which pathogenic Leptospira survives for prolonged periods of time in natural aqueous environments, a key stage in the leptospiral lifecycle.

Animals↗