Dataset Information

Short and long-term genome stability analysis of prokaryotic genomes.

ABSTRACT:

Background

Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on the other, insertions and deletions leave the backbone gene order unchanged but they alter the gene neighborhoods by breaking the syntenic regions. A complete picture about genome organization evolution therefore requires to account for both kinds of events.

Results

We developed an approach where we model chromosomes as graphs on which we compute different stability estimators; we consider genome rearrangements as well as the effect of gene insertions and deletions. In a first part of the paper, we fit a measure of backbone gene order conservation (hereinafter called backbone stability) against phylogenetic distance for over 3000 genome comparisons, improving existing models for the divergence in time of backbone stability. Intra- and inter-specific comparisons were treated separately to focus on different time-scales. The use of multiple genomes of a same species allowed to identify genomes with diverging gene order with respect to their conspecific. The inter-species analysis indicates that pathogens are more often unstable with respect to non-pathogens. In a second part of the text, we show that in pathogens, gene content dynamics (insertions and deletions) have a much more dramatic effect on genome organization stability than backbone rearrangements.

Conclusion

In this work, we studied genome organization divergence taking into account the contribution of both genome order rearrangements and genome content dynamics. By studying species with multiple sequenced genomes available, we were able to explore genome organization stability at different time-scales and to find significant differences for pathogen and non-pathogen species. The output of our framework also allows to identify the conserved gene clusters and/or partial occurrences thereof, making possible to explore how gene clusters assembled during evolution.

SUBMITTER: Brilli M

PROVIDER: S-EPMC3683328 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Short and long-term genome stability analysis of prokaryotic genomes.

Brilli Matteo M Liò Pietro P Lacroix Vincent V Sagot Marie-France MF

BMC genomics 20130508

<h4>Background</h4>Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbo ...[more]

PMID: 23651581

Similar Datasets

Project description:Study objectivesAssess the short- and long-term stability of sleep duration in patients with insomnia and normal-sleeping controls.DesignObservational short-term and prospective studies.SettingSleep laboratory.ParticipantsPatients with insomnia (n = 150) and controls (n = 151) were recruited from the local community or sleep disorders clinic. A subsample of 95 men from the Penn State Adult Cohort (PSAC) were followed up 2.6 y after their initial visit.MeasurementsParticipants underwent a physical examination and 8-h polysomnography (PSG) recording for 3 consecutive nights (controls and insomniacs), or 2 single nights separated by several years (PSAC). Intraclass correlation coefficients (ICCs) assessed the stability of the variables total sleep time (TST), sleep onset latency (SOL), and wake after sleep onset (WASO). We also examined persistence of the first-night classification of "short" versus "normal" sleep duration on subsequent nights.ResultsStability of TST, SOL, and WASO based on 1 night were slight to moderate in both patients with insomnia (ICC = 0.37-0.57) and controls (ICC = 0.39-0.59), and became substantial to almost perfect when based on the average of 3 nights (ICC = 0.64-0.81). We observed similar degrees of stability for TST and WASO in the longitudinal sample, with moderate stability based on a single night and substantial stability based on both nights. In examining the persistence of "short" and "normal" sleep duration, 71.4% (controls), 74.7% (patients with insomnia), and 72.6% (longitudinal sample) of participants retained their first-night classifications over subsequent nights.ConclusionsSleep duration variables, particularly total sleep time based on 3 consecutive nights in both patients with insomnia and controls or two single-night recordings separated by several years, are stable and reflect a person's habitual sleep. Furthermore, a single night in the laboratory may be useful for reliably classifying one's sleep duration.

Project description:The aim of this study was to assess the short- and long-term effects of resistance training (RT) with different stability requirements. Fifty-nine men underwent a 3-week familiarization period followed by a 7-week training period. During familiarization, all participants trained four sessions of squats with a Smith machine, free weights and free weights standing on a wobble board. After week-3, participants were randomized into a low (Smith machine), medium (Free-weight) or high (Wobble board) stability RT program, and Control group. All participants were tested pre-, after week-3 and post-intervention. Ten repetition maximum (10RM), rate of force development (RFD), electromyography (EMG) and maximum voluntary isometric contraction (MVIC) were tested in all three squat conditions in addition to countermovement jump (CMJ) on stable and unstable surfaces, and muscle thickness. After familiarization, greater 10RM loads (21.8-27.3%), MVIC (7.4-13.5%), RFD (29.7-43.8%) and CMJ (4.9-8.5%) were observed in all conditions. Between week 3 and 10, the Free-weight and Wobble board groups similarly improved 10RM in all conditions. Smith machine group demonstrated greater improvement in the trained exercise than the medium and high stability exercises. All training groups showed similar improvement in muscle thickness, RFD and MVIC. There was no CMJ improvement on the stable surface, but the Wobble board group demonstrated significantly greater improvement on the unstable surface. In conclusion, low, medium or high stability RT resulted in similar improvements in trained and non-trained testing conditions except for greater CMJ on the unstable surface in the Wobble group. Greater 10RM strength in trained than non-trained exercise was only observed in low stability group. Familiarization was associated with substantial improvements in 10RM and CMJ, with greater improvement associated with higher stability requirements. These findings suggest that high stability can increase strength, muscle thickness and explosive measurements similar to training with lower stability.

Dataset Information

Short and long-term genome stability analysis of prokaryotic genomes.

Background

Results

Conclusion

Publications

Short and long-term genome stability analysis of prokaryotic genomes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets