Estimating the fitness effect of an insertion sequence

Since its discovery, mobile DNA has fascinated researchers. In particular, many researchers have debated why insertion sequences persist in prokaryote genomes and populations. While some authors think that insertion sequences persist only because of occasional beneficial effects they have on their hosts, others argue that horizontal gene transfer is strong enough to overcome their generally detrimental effects. In this study, we model the long-term fate of a prokaryote cell population, of which a small proportion of cells has been infected with one insertion sequence per cell. Based on our model and the distribution of IS5, an insertion sequence for which sufficient data is available in 525 fully sequenced proteobacterial genomes, we show that the fitness cost of insertion sequences is so small that they are effectively neutral or only slightly detrimental. We also show that an insertion sequence infection can persist and reach the empirically observed distribution if the rate of horizontal gene transfer is at least as large as the fitness cost, and that this rate is well within the rates of horizontal gene transfer observed in nature. In addition, we show that the time needed to reach the observed prevalence of IS5 is unrealistically long for the fitness cost and horizontal gene transfer rate that we computed. Occasional beneficial effects may thus have played an important role in the fast spreading of insertion sequences like IS

A survey of bacterial insertion sequences using IScan

Bacterial insertion sequences (ISs) are the simplest kinds of bacterial mobile DNA. Evolutionary studies need consistent IS annotation across many different genomes. We have developed an open-source software package, IScan, to identify bacterial ISs and their sequence elements—inverted and target direct repeats—in multiple genomes using multiple flexible search parameters. We applied IScan to 438 completely sequenced bacterial genomes and 20 IS families. The resulting data show that ISs within a genome are extremely similar, with a mean synonymous divergence of Ks = 0.033. Our analysis substantially extends previously available information, and suggests that most ISs have entered bacterial genomes recently. By implication, their population persistence may depend on horizontal transfer. We also used IScan's ability to analyze the statistical significance of sequence similarity among many IS inverted repeats. Although the inverted repeats of insertion sequences are evolutionarily highly flexible parts of ISs, we show that this ability can be used to enrich a dataset for ISs that are likely to be functional. Applied to the thousands of genomes that will soon be available, IScan could be used for many purposes, such as mapping the evolutionary history and horizontal transfer patterns of different IS

A survey of bacterial insertion sequences using IScan

Bacterial insertion sequences (ISs) are the simplest kinds of bacterial mobile DNA. Evolutionary studies need consistent IS annotation across many different genomes. We have developed an open-source software package, IScan, to identify bacterial ISs and their sequence elements—inverted and target direct repeats—in multiple genomes using multiple flexible search parameters. We applied IScan to 438 completely sequenced bacterial genomes and 20 IS families. The resulting data show that ISs within a genome are extremely similar, with a mean synonymous divergence of Ks = 0.033. Our analysis substantially extends previously available information, and suggests that most ISs have entered bacterial genomes recently. By implication, their population persistence may depend on horizontal transfer. We also used IScan's ability to analyze the statistical significance of sequence similarity among many IS inverted repeats. Although the inverted repeats of insertion sequences are evolutionarily highly flexible parts of ISs, we show that this ability can be used to enrich a dataset for ISs that are likely to be functional. Applied to the thousands of genomes that will soon be available, IScan could be used for many purposes, such as mapping the evolutionary history and horizontal transfer patterns of different ISs

Emotional and physical demands on caregivers in home care to the elderly in Switzerland and their relationship to nursing home admission

Background: Planning the home care of growing numbers of old, dependent people must include the caregivers' burden. Methods: A convenience sample of 129 caregivers of elderly patients with multiple diagnoses was interviewed about the caregiving context, burden, caregivers' tolerance of patients' troublesome behaviours and physical symptoms, mutuality and feelings of closeness between caregiver and patient. Continued maintenance of home care was assessed by a follow-up telephone call. Results: Caregivers were mainly spouses (67%) and female (73%), and the mean duration of care was 5.5 years. In five activities of daily living (ADL) 50-69% of the patients needed full help. Caregivers reported predominantly negative effects of caregiving on their physical and mental health, rest and sleep, leisure time and social life, problems with patients' symptoms and behaviours and little or no conversing (51%) or exchanging feelings with patients (71%). Predictive models: Contributors to variance were for burden (35%), impact of care on caregivers' mental health, social relations and leisure time, patients' gender, accumulation of patients' symptoms and behaviours; for caregivers' tolerance toward patients' symptoms and behaviours (17%) caregivers' physical health, patients' level of confusion, feelings of mutuality; for mutuality (22%) and for closeness (19%) caregivers' mental health, patients' accumulation of symptoms and behaviours. Within 23 months 19% of the patients had been institutionalized. Factors giving a higher likelihood of institutionalization were: being male, caregiver was not a partner, and less closeness between caregiver and patient. Conclusion: Caregiving of older persons has bio-psychosocial ramifications for caregivers. Closeness between caregiver and patient seems to be a key factor in determination of the long-term outcom

The early phase of a bacterial insertion sequence infection

Bacterial insertion sequences are the simplest form of autonomous mobile DNA. It is unknown whether they need to have beneficial effects to infect and persist in bacterial populations, or whether horizontal gene transfer suffices for their persistence. We address this question by using branching process models to investigate the critical, early phase of an insertion sequence infection. We find that the probability of a successful infection is low and depends linearly on the difference between the rate of horizontal gene transfer and the fitness cost of the insertion sequences. Our models show that the median time to extinction of an insertion sequence that dies out is very short, while the median time for a successful infection to reach a modest population size is very long. We conclude that horizontal gene transfer is strong enough to allow the persistence of insertion sequences, although infection is an erratic and slow process

Pion interferometry in Au+Au collisions at sqrt[sNN]=200GeV

We present a systematic analysis of two-pion interferometry in Au+Au collisions at sqrt[sNN]=200GeV using the STAR detector at Relativistic Heavy Ion Collider. We extract the Hanbury-Brown and Twiss radii and study their multiplicity, transverse momentum, and azimuthal angle dependence. The Gaussianness of the correlation function is studied. Estimates of the geometrical and dynamical structure of the freeze-out source are extracted by fits with blast-wave parametrizations. The expansion of the source and its relation with the initial energy density distribution is studied

Dynamics of an insertion sequence infection in a spatially structured environment

Bacterial insertion sequences (ISs), the simplest form of autonomous mobile DNA, depend on their prokaryote hosts to spread in a spatially structured environment. We use a spatially explicit metapopulation model to simulate the spread of an IS that can have both detrimental and beneficial effects on its host cell. We find that, on the one hand, the spatial structure of the metapopulation and cell dispersal between subpopulations have no strong effect on the time to full infection of the metapopulation. On the other hand, factors that influence the IS infection dynamics within a subpopulation have a strong effect on that time. These factors are mainly the fitness benefit of an IS and the rate of horizontal gene transfer. We also find that the infection process of a metapopulation is very erratic in its early phase. Finally, we show that the infection’s success depends critically on the initially infected subpopulation

Emotional and physical demands on caregivers in home care to the elderly in Switzerland and their relationship to nursing home admission

Background: Planning the home care of growing numbers of old, dependent people must include the caregivers' burden. Methods: A convenience sample of 129 caregivers of elderly patients with multiple diagnoses was interviewed about the caregiving context, burden, caregivers' tolerance of patients' troublesome behaviours and physical symptoms, mutuality and feelings of closeness between caregiver and patient. Continued maintenance of home care was assessed by a follow-up telephone call. Results: Caregivers were mainly spouses (67%) and female (73%), and the mean duration of care was 5.5 years. In five activities of daily living (ADL) 50–69% of the patients needed full help. Caregivers reported predominantly negative effects of caregiving on their physical and mental health, rest and sleep, leisure time and social life, problems with patients' symptoms and behaviours and little or no conversing (51%) or exchanging feelings with patients (71%). Predictive models: Contributors to variance were for burden (35%), impact of care on caregivers' mental health, social relations and leisure time, patients' gender, accumulation of patients' symptoms and behaviours; for caregivers' tolerance toward patients' symptoms and behaviours (17%) caregivers' physical health, patients' level of confusion, feelings of mutuality; for mutuality (22%) and for closeness (19%) caregivers' mental health, patients' accumulation of symptoms and behaviours. Within 23 months 19% of the patients had been institutionalized. Factors giving a higher likelihood of institutionalization were: being male, caregiver was not a partner, and less closeness between caregiver and patient. Conclusion: Caregiving of older persons has bio-psychosocial ramifications for caregivers. Closeness between caregiver and patient seems to be a key factor in determination of the long-term outcome