PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level.

Plasmid prediction may be of great interest when studying bacteria of medical importance such as Enterobacteriaceae as well as Staphylococcus aureus or Enterococcus. Indeed, many resistance and virulence genes are located on such replicons with major impact in terms of pathogenicity and spreading capacities. Beyond strain outbreak, plasmid outbreaks have been reported in particular for some extended-spectrum beta-lactamase- or carbapenemase-producing Enterobacteriaceae. Several tools are now available to explore the 'plasmidome' from whole-genome sequences with various approaches, but none of them are able to combine high sensitivity and specificity. With this in mind, we developed PlaScope, a targeted approach to recover plasmidic sequences in genome assemblies at the species or genus level. Based on Centrifuge, a metagenomic classifier, and a custom database containing complete sequences of chromosomes and plasmids from various curated databases, PlaScope classifies contigs from an assembly according to their predicted location. Compared to other plasmid classifiers, PlasFlow and cBar, it achieves better recall (0.87), specificity (0.99), precision (0.96) and accuracy (0.98) on a dataset of 70 genomes of Escherichia coli containing plasmids. In a second part, we identified 20 of the 21 chromosomal integrations of the extended-spectrum beta-lactamase coding gene in a clinical dataset of E. coli strains. In addition, we predicted virulence gene and operon locations in agreement with the literature. We also built a database for Klebsiella and correctly assigned the location for the majority of resistance genes from a collection of 12 Klebsiella pneumoniae strains. Similar approaches could also be developed for other well-characterized bacteria.

The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification.

More than a century ago, Theodor Escherich isolated the bacterium that was to become Escherichia coli, one of the most studied organisms. Not long after, the strain began an odyssey and landed in many laboratories across the world. As laboratory culture conditions could be responsible for major changes in bacterial strains, we conducted a genome analysis of isolates of this emblematic strain from different culture collections (England, France, the United States, Germany). Strikingly, many discrepancies between the isolates were observed, as revealed by multilocus sequence typing (MLST), the presence of virulence-associated genes, core genome MLST, and single nucleotide polymorphism/indel analyses. These differences are correlated with the phylogeographic history of the strain and were due to an unprecedented number of mutations in coding DNA repair functions such as mismatch repair (MutL) and oxidized guanine nucleotide pool cleaning (MutT), conferring a specific mutational spectrum and leading to a mutator phenotype. The mutator phenotype was probably acquired during subculturing and corresponded to second-order selection. Furthermore, all of the isolates exhibited hypersusceptibility to antibiotics due to mutations in efflux pump- and porin-encoding genes, as well as a specific mutation in the sigma factor-encoding gene rpoS. These defects reflect a self-preservation and nutritional competence tradeoff allowing survival under the starvation conditions imposed by storage. From a clinical point of view, dealing with such mutator strains can lead microbiologists to draw false conclusions about isolate relatedness and may impact therapeutic effectiveness. IMPORTANCE Mutator phenotypes have been described in laboratory-evolved bacteria, as well as in natural isolates. Several genes can be impacted, each of them being associated with a typical mutational spectrum. By studying one of the oldest strains available, the ancestral Escherich strain, we were able to identify its mutator status leading to tremendous genetic diversity among the isolates from various collections and allowing us to reconstruct the phylogeographic history of the strain. This mutator phenotype was probably acquired during the storage of the strain, promoting adaptation to a specific environment. Other mutations in rpoS and efflux pump- and porin-encoding genes highlight the acclimatization of the strain through self-preservation and nutritional competence regulation. This strain history can be viewed as unintentional experimental evolution in culture collections all over the word since 1885, mimicking the long-term experimental evolution of E. coli of Lenski et al. (O. Tenaillon, J. E. Barrick, N. Ribeck, D. E. Deatherage, J. L. Blanchard, A. Dasgupta, G. C. Wu, S. Wielgoss, S. Cruveiller, C. Médigue, D. Schneider, and R. E. Lenski, Nature 536:165-170, 2016, https://doi.org/10.1038/nature18959) that shares numerous molecular features.

Draft genome sequence of the purple photosynthetic bacterium Phaeospirillum molischianum DSM120, a particularly versatile bacterium.

Here we present the draft genome sequence of the versatile and adaptable purple photosynthetic bacterium Phaeospirillum molischianum DSM120. This study advances the understanding of the adaptability of this bacterium, as well as the differences between the Phaeospirillum and Rhodospirillum genera.

[Anti-Müllerian hormone, an endocrine predictor of the response to ovarian stimulation in the bovine species]. / L'hormone antimüllérienne, prédicteur endocrinien de la réponse à une stimulation ovarienne chez les bovins.

The strong between-animal variability in the number of ovulations and embryos produced after ovarian stimulation by gonadotropins is a major limit to the development of embryo biotechnologies in cattle. In reproductive medicine, anti-mullerian hormone (AMH) is now widely used as an endocrine marker of the ovarian follicular reserve. In the cow, as in the woman, AMH is secreted by the granulosa cells of growing follicles. We have shown recently that in the cow, AMH is a very good endocrine marker of the population of small antral follicles that constitute the direct target of ovarian stimulatory treatments. AMH concentration measured in plasma before treatment varies between animals and is positively correlated to the number of ovulations and transferable embryos produced after an ovarian stimulatory treatment. Interestingly, AMH concentrations can remain stable over several months for each animal. Moreover, the number of embryos produced after ovarian stimulation is highly repeatable and has a relatively good heritability. From these observations, we propose the determination of AMH concentration in the plasma of a potential donor cow as a simple predictive method to evaluate both its level of ovarian activity and its capacity to produce high or low numbers of embryos. Optimal conditions for implementing this diagnostic test in cattle remain to be defined considering the age, the breed, the physiological status and the environmental factors related to breeding conditions for each animal.

MicroScope: a platform for microbial genome annotation and comparative genomics.

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of microbial genome annotation, especially for genomes initially analyzed by automatic procedures alone.Database URLs: http://www.genoscope.cns.fr/agc/mage and http://www.genoscope.cns.fr/agc/microcyc.

Ventilatory thresholds assessment from heart rate variability during an incremental exhaustive running test.

The present study examined whether the ventilatory thresholds during an incremental exhaustive running test could be determined using heart rate variability (HRV) analysis. Beat-to-beat RR interval, V(.-)O (2), V(.-)CO (2) and V(.-) (E) of twelve professional soccer players were collected during an incremental test performed on a track until exhaustion. The "smoothed pseudo Wigner-Ville distribution" (SPWVD) time-frequency analysis method was applied to the RR time series to compute the usual HRV components vs. running speed stages. The ventilatory equivalent method was used to assess the ventilatory thresholds (VT1 and VT2) from respiratory components. In addition, ventilatory thresholds were assessed from the instantaneous components of respiratory sinus arrhythmia (RSA) by two different methods: 1) from the high frequency peak of HRV ( FHF), and 2) from the product of the spectral power contained within the high frequency band (0.15 Hz to fmax) by FHF (HF x FHF) giving two thresholds: HFT1 and HFT2. Since the relationship between FHF and running speed was linear for all subjects, the VTs could not be determined from FHF. No significant differences were found between respective running speeds at VT1 vs. HFT1 (9.83 +/- 1.12 vs. 10.08 +/- 1.29 km x h (-1), n.s.) nor between the respective running speeds at VT2 vs. HFT2 (12.55 +/- 1.31 vs. 12.58 +/- 1.33 km x h (-1), n.s.). Linear regression analysis showed a strong correlation between VT1 vs. HFT1 (R (2) = 0.94, p < 0.001) and VT2 vs. HFT2 (R (2) = 0.96, p < 0.001). The Bland-Altman plot analysis reveals that the assessment from RSA gives an accurate estimation of the VTs, with HF x FHF providing a reliable index for the ventilatory thresholds detection. This study has shown that VTs could be assessed during an incremental running test performed on a track using a simple beat-to-beat heart rate monitor, which is less expensive and complex than the classical respiratory measurement devices.

Assessment of ventilatory thresholds from heart rate variability in well-trained subjects during cycling.

The purpose of this study was to implement a new method for assessing the ventilatory thresholds from heart rate variability (HRV) analysis. ECG, VO2, VCO2, and VE were collected from eleven well-trained subjects during an incremental exhaustive test performed on a cycle ergometer. The "Short-Term Fourier Transform" analysis was applied to RR time series to compute the high frequency HRV energy (HF, frequency range: 0.15 - 2 Hz) and HF frequency peak (fHF) vs. power stages. For all subjects, visual examination of ventilatory equivalents, fHF, and instantaneous HF energy multiplied by fHF (HF.fHF) showed two nonlinear increases. The first nonlinear increase corresponded to the first ventilatory threshold (VT1) and was associated with the first HF threshold (T(RSA1) from fHF and HFT1 from HF.fHF detection). The second nonlinear increase represented the second ventilatory threshold (VT2) and was associated with the second HF threshold (T(RSA2) from fHF and HFT2 from HF.fHF detection). HFT1 , T(RSA1), HFT2, and T(RSA2) were, respectively, not significantly different from VT1 (VT1 = 219 +/- 45 vs. HFT1 = 220 +/- 48 W, p = 0.975; VT1 vs. T(RSA1) = 213 +/- 56 W, p = 0.662) and VT2 (VT2 = 293 +/- 45 vs. HFT2 = 294 +/- - 48 W, p = 0.956; vs. T(RSA2) = 300 +/- 58 W, p = 0.445). In addition, when expressed as a function of power, HFT1, T(RSA1), HFT2, and T(RSA2) were respectively correlated with VT1 (with HFT1 r2 = 0.94, p < 0.001; with T(RSA1) r2 = 0.48, p < 0.05) and VT2 (with HFT2 r2 = 0.97, p < 0.001; with T(RSA2 )r2 = 0.79, p < 0.001). This study confirms that ventilatory thresholds can be determined from RR time series using HRV time-frequency analysis in healthy well-trained subjects. In addition it shows that HF.fHF provides a more reliable and accurate index than fHF alone for this assessment.

Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp.

The spirochetes of the Leptospira genus contain saprophytic and pathogenic members, the latter being responsible for leptospirosis. Despite the recent sequencing of the genome of the pathogen L. interrogans, the slow growth of these bacteria, their virulence in humans, and a lack of genetic tools make it difficult to work with these pathogens. In contrast, the development of numerous genetic tools for the saprophyte L. biflexa enables its use as a model bacterium. Leptospira spp. require iron for growth. In this work, we show that Leptospira spp. can acquire iron from different sources, including siderophores. A comparative genome analysis of iron uptake systems and their regulation in the saprophyte L. biflexa and the pathogen L. interrogans is presented in this study. Our data indicated that, for instance, L. biflexa and L. interrogans contain 8 and 12 genes, respectively, whose products share homology with proteins that have been shown to be TonB-dependent receptors. We show that some genes involved in iron uptake were differentially expressed in response to iron. In addition, we were able to disrupt several putative genes involved in iron acquisition systems or iron regulation in L. biflexa. Comparative genomics, in combination with gene inactivation, gives us significant functional information on iron homeostasis in Leptospira spp.

Effect of exercise intensity and repetition on heart rate variability during training in elite trotting horse.

RR intervals of ten elite trotting horses were recorded during an interval training session performed on track. This study examined two hypotheses. Firstly, like in humans, the hyperpnea combined with a decrease in cardiac autonomic control on heart rate during heavy exercise could result in a prevalence of high frequency heart rate variability. Secondly, this prevalence could increase with the heavy exercise repetition. Two exercise intensities were compared: moderate (ME) and heavy (HE). Furthermore, heavy exercise repetitions were compared between the beginning and the end of the interval training session. When comparing ME and HE periods: heart rate was significantly lower (155 +/- 12 vs. 210 +/- 9 ms, p < 0.001), LF spectral energy (0.04 - 0.2 Hz) was significantly higher (ME: 6.94 +/- 4.80 and HE: 0.24 +/- 0.14 ms(2) . Hz (-1), p < 0.001) whereas HF (0.2 - 2 Hz) was significantly lower (ME: 7.09 +/- 2.24 and HE: 10.60 +/- 3.64 ms(2) . Hz (-1), p < 0.05). In relative terms, ME showed similar results in both LFn (LF/LF+HF) and HFn (HF/LF+HF) whereas HE showed a large prevalence of HFn energy compared to LFn (p < 0.001). The difference in LF/HF ratio between the two exercise conditions was significant (1.14 +/- 0.92 vs. 0.09 +/- 0.12, p < 0.001). Exercise repetition induced a significant increase in heart rate between the beginning and the end of the interval training session (207 +/- 10 beats . min (-1) vs. 212 +/- 9 beats . min (-1), p < 0.001) whereas LF energy decreases (1.54 +/- 1.65 vs. 0.32 +/- 0.24 ms(2) . Hz (-1), p < 0.01) and HF energy remained constant (10.79 +/- 4.10 vs. 10.40 +/- 3.35 ms(2) . Hz (-1), NS). This study confirmed the results observed in humans during heavy exercise conditions with a large prevalence of HF in contrast to LF, this prevalence increasing with exercise repetitions. The observed decrease in LF/HF ratio could provide an index of hyperpnea in horses during interval training.

Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis.

Yersinia pestis, the causative agent of plague, is a highly uniform clone that diverged recently from the enteric pathogen Yersinia pseudotuberculosis. Despite their close genetic relationship, they differ radically in their pathogenicity and transmission. Here, we report the complete genomic sequence of Y. pseudotuberculosis IP32953 and its use for detailed genome comparisons with available Y. pestis sequences. Analyses of identified differences across a panel of Yersinia isolates from around the world reveal 32 Y. pestis chromosomal genes that, together with the two Y. pestis-specific plasmids, to our knowledge, represent the only new genetic material in Y. pestis acquired since the the divergence from Y. pseudotuberculosis. In contrast, 149 other pseudogenes (doubling the previous estimate) and 317 genes absent from Y. pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer function in Y. pestis. Extensive insertion sequence-mediated genome rearrangements and reductive evolution through massive gene loss, resulting in elimination and modification of preexisting gene expression pathways, appear to be more important than acquisition of genes in the evolution of Y. pestis. These results provide a sobering example of how a highly virulent epidemic clone can suddenly emerge from a less virulent, closely related progenitor.

Cardiorespiratory system dynamics in chronic heart failure.

AIMS: With the complex demodulation (CDM) method, we assessed the instantaneous amplitude and frequency of cardiovascular (CV) and respiratory oscillations, and the instant phase (IP) between the CV and respiratory signals using respiration as a periodic forced stimulation. We hypothesised a possible lack of synchronisation between CV and respiratory signals under regular breathing at different frequencies. METHODS: RR interval (ECG), blood pressure (SBP/DBP, Finapress), respiration (Respitrace) were monitored during two random-order periods of voluntary paced-breathing (0.15 Hz/0.25 Hz) in 10 moderate CHF patients and 10 age-matched controls. The CDM method provides the amplitude and frequency of a particular spectral component as a function of time in both LF and HF bands. IP between CV and respiratory oscillations was assessed using the real modulating breathing rate. RESULTS: (i) Continuous phase variations between CV oscillations and the respiratory signal were evidenced in CHF patients, the slower the breathing rate, the greater the phase variation (RR/Resp; 0.25 Hz, 23+/-17 degrees; 0.15 Hz, 46+/-57 degrees, P<0.01; RR/Resp at 0.15 Hz 6+/-3 vs. 46+/-57 P<0.01 controls vs. CHF). Phase was constant in controls. (ii) In patients, the instant amplitude of the cardiovascular oscillations in the high frequency domain is more markedly altered when the breathing rate was slowed down as compared to controls. CONCLUSION: The lack of synchronisation between physiological signals during voluntary breathing in CHF patients highlights a central uncoupling between CV and respiratory neuronal activities.

Autonomic control of the cardiovascular system during sleep in normal subjects.

The autonomic control of heart rate and blood pressure during sleep is controversial: although it has been reported that vagal activity is more often lower in rapid eye movement sleep (REM) than in other stages of sleep (non-REM, NREM), the opposite has also been described. Initially, it was reported that baroreflex sensitivity (BRS) increases during sleep (REM and NREM), but in later studies, this was only partially confirmed. We therefore studied autonomic control of the cardiovascular (CV) system during sleep in 12 normal adults. The spectral components of the heart rate R-R interval, blood pressure (BP), and BRS were computed at low (LF) and actual breathing frequency (high frequency, HF). Analysis of sleep stage and a cycle-by-cycle stage II analysis were performed. CV variability is affected largely by sleep-stage and sleep-cycle organisation: NREM and the last cycle exhibit the greatest vagal activity and the lowest sympathetic activity. BRS estimation for both the LF and HF bands confirmed previous results obtained by pharmacological and spontaneous slope methods: BRS is greater during sleep than during nocturnal wake periods, and further increased in REM. BRS is frequency dependent: in NREM, the higher value of HF BRS compared to LF BRS favours the HF control of BP variability, whereas higher BRS HF and LF components contribute to the strongest control in REM. BRS variability exhibits no significant pattern during the night. Our results suggest that both sleep-cycle organisation and BRS estimation in the LF and HF bands should be considered in sleep studies of autonomic CV control.

Relationship between pulse interval and respiratory sinus arrhythmia: a time- and frequency-domain analysis of the effects of atropine.

Respiratory sinus arrhythmia (RSA) estimation is commonly used as a non-invasive index of cardiac vagal tone. To test this relationship, vagal tone was augmented or blocked using atropine. The study was carried out using 14 healthy volunteers, following beta-adrenoceptor blockade (10 mg bisoprolol per os) and during controlled respiration (0.25 Hz) in order to limit the confounding effects of cardiac sympathetic tone and respiration pattern changes. Atropine was slowly infused intravenously over a 30-min period up to a vagolytic cumulative dose of 0.04 mg/kg. The instant vagal tone was compared to the instant RSA value obtained from a time-/frequency-domain analysis of pulse interval (PI). RSA and PI varied in the same direction with an initial increase corresponding to the early vagomimetic effect of atropine followed by a decrease during the vagolytic phase. The comparative percentage fluctuations of RSA and PI over this large vagal tone range indicate that RSA is more sensitive (about twofold) than PI in reflecting fluctuations around the set point. This dissociated behaviour of PI and heart rate variability could be important to our understanding of the circulatory changes that result from fluctuations in vagal inputs to the sinus node.

Altered baroreflex gain during voluntary breathing in chronic heart failure.

BACKGROUND: We assessed the behavior of the baroreflex (BR) gain in chronic heart failure (CHF) patients using the spectral analysis method during application of a forcing stimulus, i.e. respiration. METHODS: Simultaneous RR interval and arterial pressure fluctuation recordings were obtained during two random-order periods of voluntary paced-breathing (0.15 Hz and 0.25 Hz) in seven patients with moderate CHF (NYHA class II/III; EF, 30+/-9%; peak VO(2), 18+/-5 ml kg(-1) min(-1)) and six age-matched controls. BR gain was assessed in the time (sequential method) and frequency (cross-spectral gain in the low and high frequency) domains. RESULTS: Slower breathing was associated with a BR gain decrease in CHF patients whereas a BR gain increase was evidenced in controls (BR gain: 6+/-5 ms mmHg(-1) at 0.25 Hz vs. 4+/-3 ms mmHg(-1) at 0.15 Hz, P<0.05 in CHF; BR gain: 12+/-7 ms mmHg(-1) at 0.25 Hz vs. 15+/-7 ms mmHg(-1) at 0.15 Hz, P<0.05 in controls). CONCLUSIONS: Voluntary breathing, which involves cortical centers in the brain, had major effects on cardiovascular system controller gain in CHF patients, indicating an impairment of the central neural regulation of the autonomic outflow.

[Obstructive sleep apnea syndrome and heart failure]. / Syndrome d'apnées obstructives du sommeil et insuffisance cardiaque.

Heart failure has an increasing prevalence in middle age adults. The prognosis is very poor even with improved medical therapy and heart transplants. The outcome is related to the neurohumoral disease resulting from heart failure which leads to sympathetic activation that in turns worsens the prognosis. About half of the patients have sleep breathing disorders with variable proportions of central and obstructive apneas. Obstructive apneas are acutely deleterious to ventricular function. On the long run, they may be responsible for a worsening of the disease due to the permanent sympathetic activation seen in obstructive sleep apnea. It is therefore important to detect sleep apnea in patients and to apply a treatment. The best therapeutic procedure in obstructive events appears to be CPAP, provided hemodynamic status is closely monitored.

Converting enzyme inhibition normalizes QT interval in spontaneously hypertensive rats.

We quantified the repolarization time (so-called QT interval) in a rat, an animal species that does not show a well-characterized T wave on surface ECG. We used spontaneously hypertensive rats (SHR) and converting enzyme inhibition to demonstrate a reversible increase in QT interval in pressure-overloaded hearts in the absence of ischemia. An implanted telemetry system recording ECG data in freely moving rats was used to automatically calculate the RR interval. The QT duration was manually determined by use of a calibrated gauge, and a time-frequency domain analysis was used to evaluate heart rate variability. Left ventricular mass was sequentially assessed by echocardiography. Before treatment, 12-month-old SHR had higher left ventricular mass, QT and RR intervals, and unchanged heart rate variability compared with age-matched Wistar rats. A 2-month converting enzyme inhibition treatment with trandolapril reduces systolic blood pressure, left ventricular mass, and QT interval. The RR interval and heart rate variability remains unchanged. There is a positive correlation between the QT interval and left ventricular mass. The SHR is suitable for longitudinal studies on the QT interval. Thus, the detection of the QT interval reflects the phenotypic changes that occur during mechanical overload and, on the basis of these criteria, allows an in vivo determination of the adaptational process.

Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence.

During the determination of a DNA sequence, the introduction of artifactual frameshifts and/or in-frame stop codons in putative genes can lead to misprediction of gene products. Detection of such errors with a method based on protein similarity matching is only possible when related sequences are available in databases. Here, we present a method to detect frameshift errors in DNA sequences that is based on the intrinsic properties of the coding sequences. It combines the results of two analyses, the search for translational initiation/termination sites and the prediction of coding regions. This method was used to screen the complete Bacillus subtilis genome sequence and the regions flanking putative errors were resequenced for verification. This procedure allowed us to correct the sequence and to analyze in detail the nature of the errors. Interestingly, in several cases in-frame termination codons or frameshifts were not sequencing errors but confirmed to be present in the chromosome, indicating that the genes are either nonfunctional (pseudogenes) or subject to regulatory processes such as programmed translational frameshifts. The method can be used for checking the quality of the sequences produced by any prokaryotic genome sequencing project.

Imagene: an integrated computer environment for sequence annotation and analysis.

MOTIVATION: To be fully and efficiently exploited, data coming from sequencing projects together with specific sequence analysis tools need to be integrated within reliable data management systems. Systems designed to manage genome data and analysis tend to give a greater importance either to the data storage or to the methodological aspect, but lack a complete integration of both components. RESULTS: This paper presents a co-operative computer environment (called Imagenetrade mark) dedicated to genomic sequence analysis and annotation. Imagene has been developed by using an object-based model. Thanks to this representation, the user can directly manipulate familiar data objects through icons or lists. Imagene also incorporates a solving engine in order to manage analysis tasks. A global task is solved by successive divisions into smaller sub-tasks. During program execution, these sub-tasks are graphically displayed to the user and may be further re-started at any point after task completion. In this sense, Imagene is more transparent to the user than a traditional menu-driven package. Imagene also provides a user interface to display, on the same screen, the results produced by several tasks, together with the capability to annotate these results easily. In its current form, Imagene has been designed particularly for use in microbial sequencing projects. AVAILABILITY: Imagene best runs on SGI (Irix 6.3 or higher) workstations. It is distributed free of charge on a CD-ROM, but requires some Ilog licensed software to run. Some modules also require separate license agreements. Please contact the authors for specific academic conditions and other Unix platforms. CONTACT: imagene home page: http://wwwabi.snv.jussieu.fr/imagene

Instant power spectrum analysis of heart rate variability during orthostatic tilt using a time-/frequency-domain method.

BACKGROUND: Spectral analysis of heart rate (HR) variability (HRV) requires, as a rule, some level of stationarity and, as a result, is inadequate to quantify biological transients. A time-/frequency-domain method (TF) was developed to obtain an instant spectral power (SP) of HRV during tilt. METHODS AND RESULTS: HR was recorded by Holter monitoring in volunteers and analyzed with a TF, the smoothed pseudo-Wigner-Ville transformation (SPWVT), with the table inclination randomly set or continuously increased while the table rotated in head-up position. (1) The SPWVT assesses, beat by beat, the instant center frequency (ICF) of the SP. ICF correlates better with instant HR than the ratio of low- (LF) to high-frequency (HF) oscillations. The transient effect of tilt is better characterized as a shift of SP toward lower frequencies than by changes in amplitudes. (2) The method evidences variations of HR from one second to another. During the passage to head-up position, the vagal withdrawal and the sympathetic activation occur nearly simultaneously, as indicated by the instant changes in both LF and HF amplitudes and ICF. (3) The averaged results of the SPWVT give results similar to those previously obtained with autoregressive algorithms. CONCLUSIONS: The SPWVT is a new tool to explore HR transitions such as periods before episodes of arrhythmias on a time scale of one beat and allows quantification of an instant frequency index (ICF) that closely reflects the instantaneous relationship between sympathetic and vagal modulations.

Heart rate and heart rate variability, a pharmacological target.

Heart rate varies with respiration, blood pressure, emotion, etc., and heart rate variability (HRV) is presently one of the best indices to predict fatal issues in cardiac failure and after myocardial infarction. HRV depends on various reflexes. In addition, parallel studies of HRV and the myocardial adrenergic and muscarinic transduction system in experimental models of cardiac hypertrophy (CH) have suggested that the myocardial phenotype at the sinus-node level may also play a role. A transgenic strain of mice with atrial overexpression of the beta 1-adrenergic receptors was generated with attenuated HRV, which demonstrates that the phenotype itself is a determinant of HRV. HRV is explored by noninvasive techniques, including simple determination of the standard error of the mean, time-domain analysis, and Fourier transformation. We recently developed a time and frequency domain method of analysis, the smoothed pseudo-Wigner-Ville transformation, which allows better exploration of nonstationarity. Nonlinear methods have also been applied due to the extreme complexity of the biological determinants, and have provided evidence of a chaotic attractor in certain conditions. It is proposed that in steady state a very simple process, which is not completely deterministic, could better explain intermit interval regulations than chaotic behavior. In contrast, under extreme circumstances the regulation proceeds using chaotic behavior. Arrhythmias and HRV can be quantitated in 16-month-old unanesthetized spontaneously hypertensive rats (SHR). Ventricular premature beats are more frequent in SHR than in age-matched controls; they disappear after converting enzyme inhibition (CEI) relative to the reduction of both cardiac hypertrophy and ventricular fibrosis. HRV is attenuated in SHR, as it is in compensatory CH in humans. When CH is prevented, HRV returns to normal. CEI is therefore antiarrhythmic. Another pharmacological application of this concept concerns the bradycardic agents that may improve HRV.