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Motivation: Among challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available, each having its advantages and drawbacks, without clear guidelines as to how to choose among them. Second, these solutions produce draft assemblies that often require a resource intensive finishing phase., Methods: In this paper we address these two aspects by developing Mix , a tool that mixes two or more draft assemblies, without relying on a reference genome and having the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a set of paths in the extension graph that maximizes the cumulative contig length., Results: We evaluate the performance of Mix on bacterial NGS data from the GAGE-B study and apply it to newly sequenced Mycoplasma genomes. Resulting final assemblies demonstrate a significant improvement in the overall assembly quality. In particular, Mix is consistent by providing better overall quality results even when the choice is guided solely by standard assembly statistics, as is the case for de novo projects., Availability: Mix is implemented in Python and is available at https://github.com/cbib/MIX, novel data for our Mycoplasma study is available at http://services.cbib.u-bordeaux2.fr/mix/.

Background: Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on gene teams and homology teams., Results: Our primary contribution is a local sliding-window SYNS (SYNtenic teamS) algorithm that refines an existing family structure into orthologous sub-families by analyzing the neighborhoods around the members of a given family with a locally sliding window. The neighborhood analysis is done by computing conserved gene clusters. We evaluate our algorithm on the existing homologous families from the Genolevures database over five genomes of the Hemyascomycete phylum., Conclusions: The result is an efficient algorithm that works on multiple genomes, considers paralogous copies of genes and is able to uncover orthologous clusters even in distant genomes. Resulting orthologous clusters are comparable to those obtained by manual curation.

Background: Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments., Description: MeRy-B, the first platform for plant (1)H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues., Conclusion: MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php.

In search of blood-based biomarkers that would enhance the ability to diagnose head and neck/oral squamous cell carcinoma (HNOSCC) in early stages or predict its prognosis, we analyzed the HNOSCC secretome (ensemble of proteins secreted and/or shed from the tumor cells) for potential biomarkers using proteomic technologies. LC-MS/MS was used to identify proteins in the conditioned media of four HNOSCC cell lines (SCC4, HSC2, SCC38, and AMOSIII); 140 unique proteins were identified on the basis of 5% global false discovery rate, 122 of which were secretory proteins, with 29 being previously reported to be overexpressed in HNOSCC in comparison to normal head and neck tissues. Of these, five proteins including α-enolase, peptidyl prolyl isomerase A/cyclophilin A, 14-3-3 ζ, heterogeneous ribonucleoprotein K, and 14-3-3 σ were detected in the sera of HNOSCC patients by Western blot analysis. Our study provides the evidence that analysis of head and neck cancer cells' secretome is a viable strategy for identifying candidate serological biomarkers for HNOSCC. In future, these biomarkers may be useful in predicting the likelihood of transformation of oral pre-malignant lesions, prognosis of HNOSCC patients and evaluate response to therapy using minimally invasive tests., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Current methods for detecting synteny work well for genomes with high degrees of inter- and intra-species chromosomal homology, such as mammals. This paper presents a new algorithm for synteny computation that is well suited to genomes covering a large evolutionary span. It is based on a three-step process: identification of initial microsyntenic homologous regions, extension of homologous boundaries and reconstruction of syntenic blocks by identification of groups of homologous genomic segments that are conserved in every subject genome. Our method performs as well as GRIMM-Synteny on mammalian genomes, and outperforms it for clades with much greater evolutionary distances such as the Hemiascomycetous yeasts.

Objective: To compare long-term survival and incidence of ESRD between patients with and without preoperative renal dysfunction following heart transplantation., Design: Fifty consecutive patients with preoperative estimated GFR < or = than 50 ml/min were compared with 50 age-matched patients with estimated GFR > or = than 80 ml/min who underwent heart transplantation between 1994 and 1998. We investigated two primary outcomes: death and development of ESRD. We also analyzed risk factors., Results: Eight patients (16%) developed ESRD and 19 (38%) died in the control group whereas 10 patients (20%) developed ESRD and 26 (52%) died in the renal failure group during a mean follow-up period of 6.74 +/- 3.31 years. Survival and time to ESRD were not significantly different. In univariate and multivariate analysis, waiting time was the only risk factor found to predict mortality but not ESRD. High cyclosporine levels were only found to be associated with lower estimated GFR (p < 0.009). Among the control group, mortality was significantly higher in the subgroup of patients that developed > or = 50% reduction of estimated GFR at the end of the first post transplant year (p < 0.05)., Conclusions: This study suggests that low pre-transplant estimated GFR may not accurately predict long-term development of ESRD.

Objective: Severe head trauma and/or severe hypothermia (< or =32 degrees C) can cause cardiac arrhythmias. Effect of moderate hypothermia (32-33 degrees C) on cardiac arrhythmias in children after severe traumatic brain injury is not well characterized. The objective is to determine the effect of moderate and short-term (24 hrs) hypothermia therapy on the incidence and severity of cardiac arrhythmias in children with severe traumatic brain injury compared with normothermic control subject using a 24-hr Holter recording., Design: Prospective ancillary study of a multicenter randomized, controlled clinical trial., Setting: A Canadian university-affiliated pediatric intensive care unit in a level III trauma center. PATIENTS Patients <18 yrs with severe traumatic brain injury., Interventions: Holter recording during moderate hypothermia (HYPO group; esophageal temperature 32-33 degrees C) or normothermia (NORMO group; 36.5-37.5 degrees C) induced for 24 hrs started within 8 hrs after a severe traumatic brain injury., Measurements and Main Results: Sixteen patients who had a median age of 12.7 yrs (range, 7.2-17.0 yrs) were enrolled. The time from the injury to the start of the cooling process was 7.3 hrs (range, 6.6-7.8 hrs). The temperature when Holter recording began was 32.9 degrees C (range, 31.6-34.4 degrees C) in the HYPO group. Overall, 44% of all patients (seven of 16 patients) had arrhythmias (two of nine in the NORMO group and five of seven in the HYPO group, p = .13). The most frequent arrhythmias were isolated premature atrial contractions. Hypothermic patients had lower heart rates than normothermic patients (p = .01), but none had a severe bradycardia. In the NORMO group, one patient had accelerated junctional rhythm associated with hypotension. In the HYPO group, one patient had nonsustained monomorphic ventricular tachycardia., Conclusions: Arrhythmias are frequent in severe pediatric traumatic brain injury. Further studies are needed to characterize the epidemiology and clinical impact of arrhythmias associated with severe pediatric head trauma and moderate hypothermia.

SERCA2a gene transfer ameliorates heart failure pathologic processes in left ventricular myocardium. We sought to assess the simultaneous molecular changes that occur in the right ventricle. Sprague-Dawley rats underwent aortic banding and were followed by echocardiography for development of heart failure. After a decrease in fractional shortening of 25 % from baseline, intracoronary injection of adenoviral-SERCA2a or adenoviral-beta-galactosidase was performed. Successful gene transfer was confirmed by immunoblotting. Rats were randomly euthanized on post-operative day 7 or 21. Protein analysis including right ventricular levels of SERCA2a, betaARK1, inflammatory mediators (IL-1, IL-6 and TNF-alpha), apoptotic markers (Bax, Bak and Bcl-2) and MAPK (Jnk, p38 and Erk) was performed. Adenoviral-SERCA2a-treated animals showed increased right ventricular expression of SERCA2a compared with controls. Decreased levels of inflammatory markers were also demonstrated in this group. Expression of pro-apoptotic markers was similarly improved. Levels of MAPK were increased compared with the control group. These differences were most significant 7 days after gene transfer, but the majority of these changes persisted at 21 days. These results suggest that attenuation of pathologic mechanisms of calcium cycling, inflammation and apoptosis also occur in the right ventricular myocardium after SERCA2a gene transfer during heart failure. These findings support a therapeutic role for genetic manipulation of this pathway in patients with right ventricular or biventricular failure.

In a rat model of left ventricular pressure overload hypertrophy with biventricular failure, we studied the effects of intracoronary delivery of mesenchymal stem cells (MCS) upon right ventricular hemodynamic performance, profiles of local inflammation and apoptosis, and determinants of extracellular matrix remodeling. Sprague-Dawley rats underwent aortic banding and were followed by echocardiography. After a decrease in left ventricular fractional shortening of 25% from the baseline (relative 50% reduction), animals were randomized to an intracoronary injection of MSC (n=28) or PBS (n=20). Right ventricular hemodynamic assessment and measurement of local inflammatory markers, proapoptotic factors, and determinants of extracellular matrix remodeling were performed on post-transplantation day 7, 14, 21 or 28. MSC injection improved right ventricular systolic function in the MSC group compared to the control group (mean+/-SD, max dP/dt 772+/-272 mm Hg/s vs. 392+/-132 at 28 days, P<0.01). Diastolic function was similarly improved (mean+/-SD, max -dP/dt -558+/-171 mm Hg/s vs. -327+/-131 at 28 days, P<0.05). Right ventricular levels of IL-1, IL-6, TNF-alpha, bax, bak and p38 were significantly decreased in the MSC treated animals. Expression of MMP-3, MMP-6, MMP-9, TIMP-1 and TIMP-3 declined in the MSC group compared with controls after 28 days. In this model of left ventricular pressure overload hypertrophy and biventricular failure, intracoronary delivery of MSC was associated with an improvement in the right ventricular hemodynamic performance, profiles of local inflammation and apoptosis, and determinants of extracellular matrix remodeling.

Purpose: Gastroesophageal reflux disease (GERD) is associated with allograft dysfunction after lung transplantation (LTX). We attempted to identify outcomes in LTX recipients with clinical evidence of GERD., Methods: Retrospective review of 162 LTX recipients at our institution between January 1994 and June 2006 was performed. GERD was confirmed in symptomatic patients by esophagogastroduodenoscopy (EGD) and/or esophagography. Occurrence of biopsy-proven obliterative bronchiolitis (OB) and bronchiolitis obliterans syndrome (BOS) were analyzed. Kaplan-Meier analysis of survival and Cox proportional hazard analysis of risk factors were performed., Results: GERD was diagnosed in 21 (13%) of patients, usually following LTX (71%). There was no difference in mean survival (1603 +/- 300 vs. 1422 +/- 131 days; log rank P > 0.05), or development of OB (5% vs. 6%, respectively; P > 0.05) in patients with GERD compared with patients without GERD. However, there was correlation between GERD and BOS (P = 0.01)., Conclusions: Symptomatic GERD is increased following LTX. Patients with symptomatic GERD demonstrated an increased incidence of BOS, but survival was not affected in this study. More sensitive and specific diagnostic tools should be implemented in all LTX recipients to investigate the impact of symptomatic and silent GERD and thus improve outcomes after LTX.

Background: Loss of p16 expression by promoter hypermethylation has been reported as an early event in the development of oral cancer. The aim of our study was to explore the prognostic implications of presence of promoter hypermethylation of p16 gene in surgical margins in carcinoma tongue., Methods: A prospective analysis of 38 patients with resectable carcinoma tongue was carried out. DNA from tumor and the surgical margins was assessed by methylation-specific polymerase chain reaction. Follow-up duration was 17 to 37 months., Results: About 86.8% of tumors showed promoter hypermethylation of p16 gene. Out of 30 patients with histologically free margins, 43.3% showed positivity on molecular assessment. Patients with positive molecular margins had a 6.3-fold increased risk of having local recurrence as compared to patients with negative margins., Conclusion: Promoter hypermethylation of p16 gene may serve as a useful molecular marker for predicting local recurrence in carcinoma tongue., ((c) 2009 Wiley Periodicals, Inc. Head Neck, 2009.)

Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.

The study of evolutionary mechanisms is made more and more accurate by the increase in the number of fully sequenced genomes. One of the main problems is to reconstruct plausible ancestral genome architectures based on the comparison of contemporary genomes. Current methods have largely focused on finding complete architectures for ancestral genomes, and, due to the computational difficulty of the problem, stop after a small number of equivalent minimal solutions have been found. Recent results suggest, however, that the set of minimum complete architectures is very large and heterogeneous. In fact these solutions are collections of conserved blocks, freely rearranged. In this paper, we identify these conserved super-blocks, using a new method of analysis of ancestral architectures that reconciles both breakpoint and rearrangement analyses, as well as respects biological constraints. The resulting algorithms permit the first reliable reconstruction of plausible ancestral architectures for several non-WGD yeasts simultaneously, a problem hitherto intractable due to the extensive map reshuffling of these species. See online Supplementary Material at www.liebertonline.com.

Objectives: Several paradoxical adverse events (PAEs), e.g. IBDs, acute anterior uveitis (AAU) and psoriasis, have been described in patients taking anti-TNF drugs. This retrospective study aimed to describe the different PAEs that have occurred in a population of SpA patients treated with anti-TNF drugs, and to determine whether they are drug specific., Methods: Since 2000, we have followed 296 patients with SpA [198 AS, 21 SpA associated with IBD (9 ulcerative colitis, 12 Crohn's disease) and 77 psoriatic arthritis] treated with at least one anti-TNF drug (infliximab, etanercept or adalimumab), and 112 SpA patients treated only with conventional DMARDs who served as controls. Considering the cumulative time of exposure to each anti-TNF agent, the frequencies of new-onset PAEs in exposed patients were calculated., Results: Respective cumulative exposure times were 287, 290 and 62 patient-years for infliximab, etanercept and adalimumab. We observed the following PAEs: five psoriasis (three under infliximab and one with etanercept or adalimumab), three AAU (1/100 patient-years, all under etanercept) and four IBD (three under etanercept and one under infliximab). There was no significant association among any of these PAEs and a specific anti-TNF agent; nor significant difference in the overall PAEs among patients receiving anti-TNF drugs or controls (P = 0.303), the latter experiencing two psoriasis and three AAU., Conclusions: Undesirable side effects--IBD, AAU and psoriasis--may appear with anti-TNF drugs. Even if they are, a priori, paradoxical, no evidence supports any PAEs to be anti-TNF agent-specific in SpA.

Heart failure is associated with abnormalities in betaAR cascade regulation, calcium cycling, expression of inflammatory mediators and apoptosis. Adenoviral mediated gene transfer of betaARKct has beneficial indirect effects on these pathologic processes upon the left ventricular myocardium. The concomitant biochemical changes that occur in the right ventricle have not been well characterized. Sprague-Dawley rats underwent aortic banding and were followed by echocardiography. After a decrease in fractional shortening of 25% from baseline, intracoronary injection of adenoviral-betaARKct (n=14) or adenoviral-beta-galactosidase (control, n=13) was performed. Rats were randomly euthanized on post-operative day 7, 14 or 21. Protein analysis including RV myocardial levels of betaARKct, betaARK1, SERCA(2a), inflammatory tissue mediators (IL-1, IL-6 and TNF-alpha), apoptotic markers (bax and bak), and MAP kinases (jnk, p38 and erk) was performed. ANOVA was employed for group comparison. Adenoviral-betaARKct treated animals showed increased expression of betaARKct and decreased levels of betaARK1 compared with controls. This treatment group also demonstrated normalization of SERCA(2a) expression and decreased levels of the inflammatory markers IL-1, IL-6 and TNF-alpha. The pro-apoptotic markers bax and bak were similarly improved. Ventricular levels of the MAP kinase jnk were increased. Differences were most significant 7 days after gene transfer, but the majority of these changes persisted at 21 days. These results suggest that attenuation of the pathologic mechanisms of beta adrenergic receptor desensitization, SERCA(2a) expression, inflammation and apoptosis, not only occur in the left ventricle but also in the right ventricular myocardium after intracoronary gene transfer of betaARKct during heart failure.

Background: We studied a novel animal model of pressure overload hypertrophy in transition to heart failure following ascending aortic constriction. We sought to assess chronologic changes in hemodynamic parameters, echocardiographic signs of left ventricular (LV) remodeling, exercise tolerance, and profiles of systemic and local inflammation., Materials and Methods: A cohort of Sprague Dawley rats underwent aortic constriction proximal to the innominate artery and were followed by echocardiography. A group of animals were euthanized 20 wk after aortic constriction, before any detectable decline in fractional shortening (normal fractional shortening (FS) or control group; n = 6). When additional animals reached an absolute 25% decline in fractional shortening, they were randomized to be euthanized on d 0 (25% downward arrow FS group; n = 5), or d 21 (>25% downward arrow FS group; n = 6). Hemodynamic and echocardiographic assessment, swim testing to exhaustion, and measurement of systemic and local inflammatory markers was performed at each time interval., Results: An absolute decline of 25% in FS after aortic constriction was observed between 24 and 28 wk for most animals. The transition from compensated to decompensated hypertrophy was associated with markedly decreased dP/dt(max) and dP/dt(min), increased LV end-systolic diameter and LV end-diastolic diameter, stabilization of LV free wall diameter, decreased exercise performance and up-regulation in expression of interleukin-1, interleukin-6, tumor necrosis factor-alpha, and atrial natriuretic peptide. All animals developed heart failure., Conclusions: This study demonstrates that proximal aortic constriction in young rats represents an excellent experimental model of pressure overload hypertrophy that may be useful for testing the efficacy of novel therapies for the treatment of heart failure.

Changes in ventricular extracellular matrix (ECM) composition of pressure overload hypertrophy determine clinical outcomes. The effects of mesenchymal stem cell (MSC) transplantation upon determinants of ECM composition in pressure overload hypertrophy have not been studied. Sprague-Dawley rats underwent aortic banding and were followed by echocardiography. After an absolute decrease in fractional shortening of 25% from baseline, 1 x 10(6) MSC (n = 28) or PBS (n = 20) was randomly injected intracoronarily. LV protein analysis, including matrix metalloproteinases (MMP-2, MMP-3, MMP-6, MMP-9) and tissue inhibitors of metalloproteinases (TIMP-1, TIMP-2, TIMP-3), was performed after sacrifice on postoperative day 7, 14, 21 or 28. Left ventricular levels of MMP-3, MMP-6, MMP-9, TIMP-1 and TIMP-3 were demonstrated to be decreased in the MSC group compared with controls after 28 days. Expression of MMP-2 and TIMP-2 remained relatively stable in both groups. Successful MSCs delivery was confirmed by histological analysis and visualization of labelled MSCs. In this model of pressure overload hypertrophy, intracoronary delivery of MSCs during heart failure was associated with specific changes in determinants of ECM composition. LV reverse remodeling was associated with decreased ventricular levels of MMP-3, MMP-6, MMP-9, TIMP-1 and TIMP-3, which were upregulated in the control group as heart failure progressed. These effects were most significant at 28 days following injection., ((c) 2008 John Wiley & Sons, Ltd.)

The Génolevures online database (http://cbi.labri.fr/Genolevures/ and http://genolevures.org/) provides exploratory tools and curated data sets relative to nine complete and seven partial genome sequences determined and manually annotated by the Génolevures Consortium, to facilitate comparative genomic studies of Hemiascomycete yeasts. The 2008 update to the Génolevures database provides four new genomes in complete (subtelomere to subtelomere) chromosome sequences, 50,000 protein-coding and tRNA genes, and in silico analyses for each gene element. A key element is a novel classification of conserved multi-species protein families and their use in detecting synteny, gene fusions and other aspects of genome remodeling in evolution. Our purpose is to release high-quality curated data from complete genomes, with a focus on the relations between genes, genomes and proteins.

Objective: Morbid obesity is increasingly observed in patients being evaluated for heart transplantation and represents a relative contraindication. We sought to evaluate the influence of pre-transplant obesity on morbidity and mortality after heart transplantation., Design: We retrospectively reviewed 90 consecutive patients with preoperative obesity (BMI > or = 30) and 90 age matched patients with normal weight (BMI 19 - 26) who underwent heart transplantation at our institution between January 1997 and December 2005., Results: Morbidly obese patients experienced higher rates of pre-transplant diabetes (29% vs 15%, p < 0.05) and prolonged waiting time before transplantation (191.4+/-136.1 vs 117.4+/-143.2 days, p < 0.001). There were no significant differences in post-operative complications including rejection and major and minor infections. There was no difference in actuarial survival between the obese and control groups after a mean follow-up of 4.26+/-2.95 years (p = 0.513, log-rank statistic 0.452). Causes of death did not differ. Cox proportional hazard analysis revealed increased association of peripheral vascular disease (HR 31.718, p = 0.001), and pre operative inotropic support (HR 33.725, p = 0.013) with increased mortality in the obese group., Conclusions: This study suggests morbid obesity does not affect survival or rates of infection and rejection after heart transplantation.

Objective: We hypothesized that intracoronary adenoviral-mediated delivery of betaARKct would improve heart failure associated pathophysiologic abnormalities related to exercise capacity, cardiac contractility, systemic inflammation and volume overload., Methods: After aortic banding, a cohort of Sprague-Dawley rats was followed by echocardiography. When an absolute decline of 25% in fractional shortening was detected, animals were randomized to intracoronary delivery of Ad.ssARKct (n=14), Ad.beta-Gal (n=13), or followed without any other further intervention (n=18). Assessment of exercise tolerance and hemodynamic profile and measurement of markers of systemic inflammation and volume overload was performed at 7, 14, and 21 days after gene delivery. Data were analyzed using ANOVA., Results: Animals receiving Ad.ssARKct showed improved exercise tolerance compared to Ad.Gal-treated animals at 14 days (507+/-26 s vs. 408+/-19 s, P=0.01) and 21 days (526+/-55 s vs. 323+/-19 s, P<0.001) following injection. Animals receiving Ad.ssARKct demonstrated improved +dP/dtmax (mean+/-SD, 5,581+/-960 mmHg/s vs. 3,134+/-438 mmHg/s, P<0.01) and -dP/dtmax (mean+/-SD, -3,494+/-1,269 mmHg/s vs. -1,925+/-638 mmHg/s, P<0.01) compared to Ad.Gal-treated animals at 7 days. These differences were observed up to 21 days following injection. Serum levels of IL-1, IL-6, and TNF-alpha, as well as ANP were also decreased in animals receiving Ad.betaARKct., Conclusions: Genetic modulation of heart failure using the betaARKct gene was associated with improved exercise capacity and cardiac function as well as amelioration in heart failure-associated profiles of systemic inflammation and volume overload.

Gene fusion and fission events are key mechanisms in the evolution of gene architecture, whose effects are visible in protein architecture when they occur in coding sequences. Until now, the detection of fusion and fission events has been performed at the level of protein sequences with a post facto removal of supernumerary links due to paralogy, and often did not include looking for events defined only in single genomes. We propose a method for the detection of these events, defined on groups of paralogs to compensate for the gene redundancy of eukaryotic genomes, and apply it to the proteomes of 12 fungal species. We collected an inventory of 1,680 elementary fusion and fission events. In half the cases, both composite and element genes are found in the same species. Per-species counts of events correlate with the species genome size, suggesting a random mechanism of occurrence. Some biological functions of the genes involved in fusion and fission events are slightly over- or under-represented. As already noted in previous studies, the genes involved in an event tend to belong to the same functional category. We inferred the position of each event in the evolution tree of the 12 fungal species. The event localization counts for all the segments of the tree provide a metric that depicts the "recombinational" phylogeny among fungi. A possible interpretation of this metric as distance in adaptation space is proposed.

Background: We hypothesized that sarcoplasmic reticulum Ca2+ ATPase pump (SERCA-2a) gene delivery would have beneficial effects upon exercise capacity and markers of inflammation in the setting of heart failure., Materials and Methods: A pressure-overload model of experimental heart failure was used in rats. Following a decrease in fractional shortening of >or=25%, animals underwent intracoronary adenoviral-mediated gene transfection using SERCA-2a. Heart failure animals were randomized to receive the SERCA-2a gene, the beta galactosidase (control) gene, or followed without any further intervention. Exercise and hemodynamic testing were performed, and myocardial and systemic markers of inflammation were assayed after 7 and 21 d., Results: Animals receiving Ad.SERCA-2a showed an increase in exercise tolerance (499.0 +/- 14.9 versus 312.8 +/- 10.5 s, P < 0.0001) relative to Ad.Gal group. Groups treated with Ad.SERCA-2a had significantly decreased serum levels of the inflammatory markers interleukin-1, interleukin-6, and tumor necrosis factor-alpha compared with Ad.Gal-treated animals. Serum levels of atrial natriuretic peptide were decreased in animals receiving Ad.SERCA-2a compared with animals receiving Ad.Gal at day 7 (0.35 +/- 0.03 versus 0.52 +/- 0.11 pg/mL, P = 0.001). Myocardial levels of the proapoptotic protein bax were reduced in Ad.SERCA-2a -treated animals compared with those receiving Ad.Gal at day 7 (protein level/actin: 0.24 +/- 0.05 versus 0.33 +/- 0.04, P = 0.04) and day 21 (protein level/actin: 0.61 +/- 0.04 versus 0.69 +/- 0.01, P = 0.001)., Conclusions: Genetic modulation of heart failure using the SERCA-2a gene was associated with improvement in cardiac function and exercise capacity as well as improvements in heart-failure associated inflammatory markers.

Mathematical models of biological processes for the model yeast Saccharomyces cerevisiae are the subject of intensive effort and are available in increasing numbers. An open question is whether such models are informative for related yeasts of biotechnological and medical interest that will not themselves benefit from an equivalent effort. In this study, we assess a method for extrapolating reference models to other completely sequenced yeasts, using a combination of graph-theoretic analysis and reliable identification of homologous genes using Génolevures protein families. In this first assessment, we focus on subtractive modeling, identified through the correlated loss of input and output ports in metabolic pathways. We confirm that the major, highly connected, pathways of central metabolism are conserved and might be universal. In 60-80% of our results, further analysis is not required to determine whether the pathway is lost or conserved, so that our method can be systematically applied as a first step in developing species-specific models.

Objectives: In a rat model of pressure overload hypertrophy, we studied the effects of intracoronary delivery of mesenchymal stem cells on hemodynamic performance, exercise capacity, systemic inflammation, and left ventricular reverse remodeling., Methods: Sprague-Dawley rats underwent aortic banding and were followed up by echocardiographic scanning. After a decrease in fractional shortening of 25% from baseline, animals were randomized to intracoronary injection of mesenchymal stem cells (MSC group; n = 28) or phosphate-buffered saline solution (control group; n = 20). Hemodynamic and echocardiographic assessment, swim testing to exhaustion, and measurement of inflammatory markers were performed before the rats were humanely killed on postoperative day 7, 14, 21, or 28., Results: Injection of mesenchymal stem cells improved systolic function in the MSC group compared with the control group (mean +/- standard deviation: maximum dP/dt 3048 +/- 230 mm Hg/s vs 2169 +/- 97 mm Hg/s at 21 days and 3573 +/- 741 mm Hg/s vs 1363 +/- 322 mm Hg/s at 28 days: P < .001). Time to exhaustion was similarly increased in the MSC group compared with controls (487 +/- 35 seconds vs 306 +/- 27 seconds at 28 days; P < .01). Serum levels of interleukins 1 and 6, tumor necrosis factor-alpha, and brain natriuretic peptide-32 were significantly decreased in animals treated with mesenchymal stem cells. Stem cell transplantation improved left ventricular fractional shortening at 21 and 28 days. Left ventricular end-systolic and end-diastolic diameters were also improved at 28 days., Conclusions: In this model of pressure overload hypertrophy, intracoronary delivery of mesenchymal stem cells during heart failure was associated with an improvement in hemodynamic performance, maximal exercise tolerance, systemic inflammation, and left ventricular reverse remodeling. This study suggests a potential role of this treatment strategy for the management of hypertrophic heart failure resulting from pressure overload.

Thorough knowledge of the model organism S. cerevisiae has fueled efforts in developing theories of cell ageing since the 1950s. Models of these theories aim to provide insight into the general biological processes of ageing, as well as to have predictive power for guiding experimental studies such as cell rejuvenation. Current efforts in in silico modeling are frustrated by the lack of efficient simulation tools that admit precise mathematical models at both cell and population levels simultaneously. We developed a novel hierarchical simulation tool that allows dynamic creation of entities while rigorously preserving the mathematical semantics of the model. We used it to expand a single-cell model of protein damage segregation to a cell population model that explicitly tracks mother-daughter relations. Large-scale exploration of the resulting tree of simulations established that daughters of older mothers show a rejuvenation effect, consistent with experimental results. The combination of a single-cell model and a simulation platform permitting parallel composition and dynamic node creation has proved to be an efficient tool for in silico exploration of cell behavior.

Motivation: Reliable identification of protein families is key to phylogenetic analysis, functional annotation and the exploration of protein function diversity in a given phylogenetic branch. As more and more complete genomes are sequenced, there is a need for powerful and reliable algorithms facilitating protein families construction., Results: We have formulated the problem of protein families construction as an instance of consensus clustering, for which we designed a novel algorithm that is computationally efficient in practice and produces high quality results. Our algorithm uses an election method to construct consensus families from competing clustering computations. Our consensus clustering algorithm is tailored to serve the specific needs of comparative genomics projects. First, it provides a robust means to incorporate results from different and complementary clustering methods, thus avoiding the need for an a priori choice that may introduce computational bias in the results. Second, it is suited to large-scale projects due to the practical efficiency. And third, it produces high quality results where families tend to represent groupings by biological function., Availability: This method has been used for Génolevures project to compute protein families of Hemiascomycetous yeasts. The data are available online at http://cbi.labri.fr/Genolevures/fam/

A 65-year-old man presented to the emergency room following an episode of syncope. His vital signs and physical examination were unremarkable. A chest X-ray and an ECG were also normal. He was admitted to the hospital for further work-up. A computed tomography scan of his brain did not reveal any evidence of stroke, hemorrhage, or mass effect. A transesophageal echocardiogram, however, revealed tricuspid regurgitation and a right atrial mass with finger-like projections, which appeared to originate from the tricuspid valve. Left heart catheterization was performed, showing a 99% proximal right coronary artery stenosis. The patient was scheduled to undergo atrial mass resection, tricuspid valve annuloplasty, and coronary bypass. During the procedure, a large myxoma was found to be adherent to the right side of the atrial septum, adjacent to the fossa ovalis. The mass was friable and was attached to the endocardium by a pedicle. Following resection of the atrial mass and tricuspid valve annuloplasty, a single saphenous vein graft bypass to the right coronary artery was performed. The patient's postoperative course was unremarkable and he was discharged home on postoperative day 6.

The Génolevures online database (http://cbi.labri.fr/Genolevures/) provides tools and data relative to 4 complete and 10 partial genome sequences determined and manually annotated by the Génolevures Consortium, to facilitate comparative genomic studies of hemiascomycetous yeasts. With their relatively small and compact genomes, yeasts offer a unique opportunity for exploring eukaryotic genome evolution. The new version of the Génolevures database provides truly complete (subtelomere to subtelomere) chromosome sequences, 25 000 protein-coding and tRNA genes, and in silico analyses for each gene element. A new feature of the database is a novel collection of conserved multi-species protein families and their mapping to metabolic pathways, coupled with an advanced search feature. Data are presented with a focus on relations between genes and genomes: conservation of genes and gene families, speciation, chromosomal reorganization and synteny. The Génolevures site includes an area for specific studies by members of its international community.

As part of an interdisciplinary research project, we studied the performance response of sows and their litters to the probiotic strain Bacillus cereus var. toyoi as well as feces consistency of piglets. Gestating sows (n=26) were randomly allotted into two groups. The probiotic B. cereus var. toyoi was administered by dietary supplementation to one group of sows and their respective litters (probiotic group) whereas the second group (control group) received no probiotic supplementation. The duration of the application was nearly 17 weeks for sows (day 90 ante partum until day 28 post partum) and six weeks for piglets (day 15-56). Piglets were weaned after 28 days. Body weight and feed consumption were recorded weekly and fecal consistency of weaned piglets was studied daily. B. cereus var. toyoi was recovered from feces of sows and piglets as well as from digesta of piglets in the probiotic group, while being absent from all samples of control animals. In addition, the probiotic was detected in piglet feces and digesta before pre-starter feed was offered, indicating a second route of uptake besides diet. Sows of the probiotic group nursed numerically more piglets and supported a higher sum of total nursing days of all piglets within each litter than control sows (p = 0.04). In turn, body weight (BW) up to day 35 was greater for control piglets (p < 0.01), while average daily gain and gain to feed ratio (G:F) in weeks six and eight postweaning was higher in the probiotic group (p < 0.05). The overall G:F of the total postweaning period was 680 g/kg and 628 g/kg in the probiotic group and control group, respectively (p = 0.009). During the trial a high prevalence of liquid feces with its maximum in the second week after weaning was observed. Probiotic supplementation led to a reduction in the incidence of liquid feces and postweaning diarrhea by 38% and 59%, respectively (p < 0.001).

Limit-dilution procedures were used to isolate seven, helically coiled bacterial strains from faeces of swine that constituted two unidentified taxa. Comparative 16S rRNA gene sequence analysis showed highest similarity values with species of the genus Treponema indicating that the isolates are members of this genus. Strain 7CPL208(T), as well as five further isolates, and 14V28(T) displayed the highest 16S rRNA gene sequence similarities with Treponema pectinovorum ATCC 33768(T) (92.3%) and Treponema parvum OMZ 833(T) (89.9%), respectively. Polar lipid profiles distinguished 7CPL208(T) and 14V28(T) from each other as well as from related species. Based on their phenotypic and genotypic distinctiveness, strains 7CPL208(T) and 14V28(T) are suggested to represent two novel species of the genus Treponema, for which the names Treponema berlinense sp. nov. and Treponema porcinum sp. nov. are proposed. The type strain for Treponema berlinense is 7CPL208(T) (=ATCC BAA-909(T)=CIP 108244(T)=JCM 12341(T)) and for Treponema porcinum 14V28(T) (=ATCC BAA-908(T)=CIP 108245(T)=JCM 12342(T)).

Myocardial bridging, the overlying of myocardial tissue onto epicardial coronary arteries, is an anatomic variant that is widely present in the general population. This condition can be associated with reduced forward coronary flow. Once these hearts are identified in potential donors by either visual inspection or coronary catheterization, they may no longer be considered suitable for transplantation. We present a case study that successfully utilized such a heart explanted from an older donor with "bench" myotomy repair before implantation.

Unlabelled: ProViz is a tool for the visualization of protein-protein interaction networks, developed by the IntAct European project. It provides facilities for navigating in large graphs and exploring biologically relevant features, and adopts emerging standards such as GO and PSI-MI., Availability: ProViz is available under the GPL and may be freely downloaded. Source code and binaries are available at http://cbi.labri.fr/eng/proviz.htm, Contact: david.sherman@labri.fr

Background: Despite the increasingly common use of donor hearts at least 50 years of age, controversy still remains regarding long-term outcome. Our goal was to determine if older donor age is associated with an increased risk of mortality and specifically if the use of donor hearts at least 50 years of age reduces survival., Methods: We retrospectively studied records of all primary heart transplants performed between January 1990 and July 2002. Fifty-six patients who had received donor hearts at least 50 years of age were compared with 611 recipients of donor hearts less than 50 years of age. Clinicopathologic parameters were analyzed for their effect on mortality using the Cox proportional hazard model with calculation of hazard ratios (HR). Cut-point analysis of donor age was used to determine which donor age is associated with the greatest risk of mortality after transplant., Results: Recipients of donor hearts at least 50 years of age were older (58.5 years +/- 7.0 vs 53.2 +/- 11.6; mean +/- standard deviation [SD]; p < 0.0001), suffered more often from ischemic cardiomyopathy (69% vs 50%, p = 0.01), and experienced a longer waiting time (192.2 days +/- 301.0 vs 138.6 +/- 190.8, p < 0.0001). Donor hearts at least 50 years of age (age 54.1 +/- 3.5 years) were more often female (50% vs 34%, p = 0.03), died less often of "head trauma" (9% vs 42%, p < 0.0001), and exhibited fewer cytomegalovirus (CMV) mismatches (29% vs 39%, p = 0.04) than donor hearts less than 50 years of age (age 26.8 +/- 12.3 years). Multivariate predictors of mortality were rejection index (HR 1.90 per unit [rejections/100 survival days], p < 0.0001), donor age (HR 1.16 per 10-year increment, p = 0.002), and recipient age (HR 1.24 per 10-year increment, p = 0.04). Recipients of donor hearts at least 50 years of age had reduced 1-year and 5-year survival ([65.7% vs 81.7%, p < 0.05] and [48.3% vs 68.4%, p < 0.05], respectively), as well as a higher proportion of deaths occurring within 1 month of transplant (41% of total deaths vs 23%, p = 0.06). Cut-point analysis indicated the characteristic of donor age of at least 40 years (categorical variable) to predict mortality with the same degree of fit as age used as a continuous variable., Conclusions: Although we observed a substantial reduction in survival among patients who were allocated donor hearts at least 50 years of age, this difference was not solely attributable to the categorical variable of donor age 50 in this group. Donor age as a continuous variable, however, was determined to be a notable predictor of survival and use of the donor age cut-point of 40 years (categorical variable) allowed risk stratification with similar accuracy. The use of a donor age cut-point of 40 years may be a useful clinical criterion for graft-related risk assessment.

A 55-year-old heart transplant recipient with reflux esophagitis presented for routine endoscopic surveillance of an area of Barrett's metaplasia initially seen 3 years previously. Esophagogastroduodenoscopy revealed adenocarcinoma at 33 cm from the incisors. The preoperative clinical stage was T1N0M0 by endoscopic ultrasound. Transhiatal esophagectomy was performed with R0 resection of the cancer, and the patient recovered uneventfully. Pathologic examination confirmed esophageal adenocarcinoma (T1N0M0) in Barrett's mucosa. The patient is doing well, and has no evidence of disease after 18 months.

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.

A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

The Génolevures online database (http://cbi.labri.fr/Genolevures/) provides data and tools to facilitate comparative genomic studies on hemiascomycetous yeasts. Now, four complete genome sequences recently determined (Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, Yarrowia lipolytica) have been added to the partial sequences of 13 species previously analysed by a random approach. The database also includes the reference genome Saccharomyces cerevisiae. Data are presented with a focus on relations between genes and genomes: conservation of genes and gene families, speciation, chromosomal reorganization and synteny. The Génolevures site includes a community area for specific studies by members of the international community.

Background: Multiple episodes of rejection following cardiac transplantation have been associated with an increased incidence of coronary atherosclerosis. Total lymphoid irradiation (TLI) has been shown to be a successful treatment for persistent allograft rejection, but its effect on coronary arterial disease has yet to be evaluated., Methods: From 1987 to 1999, 40 patients required TLI for persistent or recurrent allograft rejection following heart transplantation. Each patient's (Group 1, n = 31) post-transplant coronary angiograms were examined and compared with those of a control group (Group 2, (n = 32) matched for time of transplantation. Degree of coronary stenosis was assessed on a 6-point scale. All patients received induction therapy (rabbit anti-thymocyte globulin or OKT3) and standard triple immunosuppressive therapy. TLI (80 cGy x 10 fractions) was used for the treatment of recurrent or persistent rejection on the basis of clinical indications. Actuarial survival, number and treatment of rejection episodes, and severity of coronary artery disease were compared in each group., Results: Recipient gender, age, race and cytomegalovirus (CMV) status at time of transplant, along with donor gender, CMV status and graft ischemia time, were similar in both groups. Group 1 donor age was younger than that of Group 2 (22.2 +/- 11.2 vs 31.5 +/- 13.6 years, p = 0.004), and the indication for surgery in Group 1 patients was more likely to be ischemic heart disease (15 of 31 vs 6 of 32, p = 0.02). Mean follow-up was 5.7 +/- 3.5 years in Group 1 vs 6.9 +/- 3.8 in Group 2 (p = NS). Group 1 had more rejection episodes (4.4 +/- 2.2 vs 2.3 +/- 2.0, p = 0.0002) and more steroid treatments (9.78 +/- 4.0 g vs 5.14 +/- 4.7 g, p < 0.0001), but less coronary artery disease compared with Group 2 (p = 0.035)., Conclusions: Despite multiple episodes of rejection, patients treated with TLI after cardiac transplant appear to develop less coronary atherosclerosis than appropriately matched controls.

We present a case of left ventricular assist device (Thoratec; Thoratec Laboratories Corp, Pleasanton, CA) insertion performed through a left thoracotomy without cardiopulmonary bypass in a patient with severe end-stage congestive heart failure with renal and respiratory dysfunction and a history of multiple cardiac operations.

Transhiatal esophagectomy is gaining increasing use as the preferred technique for esophagectomy. In this article, the indications, diagnostic evaluation, and technical details of the operative procedure for transhiatal esophagectomy are reviewed. Results of large clinical series are discussed and the potential pitfalls and risks of the procedure are reviewed. Current controversies and future trends are also discussed.

A fetus with lobar holoprosencephaly and lumbosacral meningomyelocele associated with duplication of the short arm of chromosome 3 is reported. The anomalies were detected on fetal ultrasound at 20 weeks' gestation and the autopsy findings correlated well with the prenatal findings. The fetal karyotype was 46,XY,der(3)del(3)(p26) dup(3)(p26p21.3). The association of holoprosencephaly with duplication 3p is well known, but to the best of our knowledge this is the first reported association of meningomyelocele with 3p duplication. These findings suggest that a gene or genes with a crucial role in central nervous system development are located on the short arm of chromosome 3., (Copyright 2000 Wiley-Liss, Inc.)

Purpose: Recent revision of the lissencephaly critical region on chromosome 17p13.3 and confirmation of LIS1 as the causative gene for classical lissencephaly has allowed the development and application of fluorescence in situ hybridization (FISH) probes corresponding directly to this gene., Method: We have analyzed patients with isolated lissencephaly sequence (ILS) by FISH with probes at D17S379, an anonymous locus distal to LIS1, and with LIS1 specific probes., Results: In 110 patients with ILS, a deletion at D17S379 was detected in 23.6%. Of those patients without a deletion, 32 were available for further study with LIS1 probes. Deletions were found in eight additional individuals., Conclusion: The overall deletion mutation rate detectable by FISH with LIS1 probes is approximately 40%. This rate is significantly higher than the deletion rate observed at D17S379. This indicates that FISH studies using probes specific to LIS1 should be undertaken as the initial diagnostic assay for the evaluation of patients with ILS, and the high frequency of deletions raises the possibility of "hotspots" for chromosome breakage in this region.

This paper summarizes the authors' in vivo experience in evaluating a miniature centrifugal blood pump designed for pediatric/neonatal ventricular support. Left ventricular bypass was accomplished in two adult sheep and five juvenile lambs (5.5-80.0 kg) via either central (left ventricle to carotid artery) or peripheral (jugular vein to carotid artery) cannulation. Animals were weaned from mechanical ventilation and continuously monitored. Hemodynamic parameters remained within a normal range over the duration of the bypass. Two of five lambs were electively killed at 8, and 76 hours; the remaining three lambs died from respiratory complications at 33, 44, and 156 hours. There were no mechanical complications, and blood seal integrity was confirmed beyond 6 days. The pump speed was maintained at 3,000-4,500 rpm with pump flow rates between 0.4-1.5 L/min. Average plasma free hemoglobin was below 20 mg/dl in the five lamb experiments. Renal, hepatic, and hematologic indices also remained within physiologic ranges. Histopathologic analyses of major organs revealed renal cortical infarctions in two of five lambs. Examination of the pump surfaces after explant indicated small areas of thrombus in the housing adjacent to the outflow ports in two experiments. These encouraging results support further testing and refinement of this miniature centrifugal pump.

This paper summarizes the authors' in vivo experience to date with an implantable axial flow blood pump designed for long-term ventricular support. This small, valveless pump with blood-lubricated bearings has been implanted in six calves (83 +/- 6 kg) as a left ventricular assist device (LVAS). The left ventricle and descending thoracic aorta were cannulated by left thoracotomy, and the pump was placed in a subcutaneous pocket below the costal margin. Animals remained hemodynamically stable throughout the course of support during partial left ventricular bypass. Five animals were killed after 15, 27, 52, 57, and 181 days. The longest survivor (181 days) demonstrated normal pump function at the time death. Pump speed was maintained at 10,100 +/- 100 rpm, with an average pump flow rate of 4.9 +/- 0.5 L/min under resting physiologic conditions. Average plasma free hemoglobin was 17.4 +/- 7.5 mg/dl. Renal, hepatic, and hematologic indices remained within physiologic range in all of these animals, except during the immediate postoperative period. Histopathologic analyses of major organs after death revealed small renal cortical infarcts in five of six animals; the remaining organs were normal. These animal studies support the feasibility of this small implanted axial flow pump for long-term ventricular assistance.

The role of pulsatile flow as a physiologic stimulus for endothelium mediated vasoregulation is poorly understood. Furthermore, non pulsatile flow, which is associated with increased vascular resistance and end-organ failure, has been demonstrated to lead to a decrease in nitric oxide (NO) production in vitro. Anesthetized pigs (23.4 +/- 0.3 kg) were placed on cardiopulmonary bypass using either non pulsatile or pulsatile perfusion for 60 min. In both groups, animals were maintained with a constant mean aortic flow (1.0-1.3 L/min). Serum samples obtained during bypass were assayed for the stable end-products of NO (nitrate [NO3-] and nitrite [NO2-]) by a method based on the Greiss reaction. Systemic vascular resistance was higher after 60 min in the non pulsatile (3712.5 +/- 481.2 dyne sec cm(-5)) vs the pulsatile group (2672.6 +/- 427.0 dyne sec cm(-5)), but not statistically significant (p > .05). However, NO production was decreased in the non pulsatile flow group (27 +/- 6%) vs the pulsatile flow group (14 +/- 5%) at a statistically significant level (p < .005). The results suggest that non pulsatile flow is associated with diminished endothelial shear stress and a reduction in endothelial nitric oxide production. This may contribute to the detrimental physiologic effects observed in prolonged non pulsatile flow states.