RIME: Repeat Identification

We present an algorithm for detecting long similar fragments occurring at least twice in a set of biological sequences. The problem becomes computationally challenging when the frequency of a repeat is allowed to increase and when a non-negligible number of insertions, deletions and substitutions are allowed. We introduce in this paper an algorithm, Rime1 1 Rime is also a reference to Coleridge's poem "The Rime of an Ancient Mariner" which contains many repetitions as a poetic device. (for Repeat Identification: long, Multiple, and with Edits) that performs this task, and manages instances whose size and combination of parameters cannot be handled by other currently existing methods. This is achieved by using a filter as a preprocessing step, and by then exploiting the information gathered by the filter in the following actual repeat inference step. To the best of our knowledge, Rime is the first algorithm that can accurately deal with very long repeats (up to a few thousands), occurring possibly several times, and with a rate of differences (substitutions and indels) allowed among copies of a same repeat of 10-15% or even more

Cophylogeny reconstruction via an approximate bayesian computation

Despite an increasingly vast literature on cophylogenetic reconstructions for studying host-parasite associations, understanding the common evolutionary history of such systems remains a problem that is far from being solved. Most algorithms for host-parasite reconciliation use an event-based model, where the events include in general (a subset of) cospeciation, duplication, loss, and host switch. All known parsimonious event-based methods then assign a cost to each type of event in order to find a reconstruction of minimum cost. The main problem with this approach is that the cost of the events strongly influences the reconciliation obtained. Some earlier approaches attempt to avoid this problem by finding a Pareto set of solutions and hence by considering event costs under some minimization constraints. To deal with this problem, we developed an algorithm, called Coala, for estimating the frequency of the events based on an approximate Bayesian computation approach. The benefits of this method are 2-fold: (i) it provides more confidence in the set of costs to be used in a reconciliation, and (ii) it allows estimation of the frequency of the events in cases where the data set consists of trees with a large number of taxa. We evaluate our method on simulated and on biological data sets. We show that in both cases, for the same pair of host and parasite trees, different sets of frequencies for the events lead to equally probable solutions. Moreover, often these solutions differ greatly in terms of the number of inferred events. It appears crucial to take this into account before attempting any further biological interpretation of such reconciliations. More generally, we also show that the set of frequencies can vary widely depending on the input host and parasite trees. Indiscriminately applying a standard vector of costs may thus not be a good strategy

MOMO - multi-objective metabolic mixed integer optimization : application to yeast strain engineering

BACKGROUND: In this paper, we explore the concept of multi-objective optimization in the field of metabolic engineering when both continuous and integer decision variables are involved in the model. In particular, we propose a multi-objective model that may be used to suggest reaction deletions that maximize and/or minimize several functions simultaneously. The applications may include, among others, the concurrent maximization of a bioproduct and of biomass, or maximization of a bioproduct while minimizing the formation of a given by-product, two common requirements in microbial metabolic engineering. RESULTS: Production of ethanol by the widely used cell factory Saccharomyces cerevisiae was adopted as a case study to demonstrate the usefulness of the proposed approach in identifying genetic manipulations that improve productivity and yield of this economically highly relevant bioproduct. We did an in vivo validation and we could show that some of the predicted deletions exhibit increased ethanol levels in comparison with the wild-type strain. CONCLUSIONS: The multi-objective programming framework we developed, called MOMO, is open-source and uses POLYSCIP (Available at http://polyscip.zib.de/). as underlying multi-objective solver. MOMO is available at http://momo-sysbio.gforge.inria.fr

NTRFinder: a software tool to find nested tandem repeats

We introduce the software tool NTRFinder to search for a complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that NTRs can be used as phylogenetic and population markers. We have tested our algorithm on both real and simulated data, and present some real NTRs of interest. NTRFinder can be downloaded from http://www.maths.otago.ac.nz/~aamatroud/

Genius loci reloaded, The creative renaissance of Nantes and Saint Etienne

Since the middle of the 1990s, the creative city concept has gradually interfered with debates related to the governance and development of urban areas in France. This interference has occurred through a discourse which seeks to praise the territorial virtues of culture. This concept emerged in Anglo-Saxon countries and has since seduced numerous local decision-makers in France. Culture is thus central to city strategies, and is seen as a resource which is mobilised and used in political, economic or touristic projects. This new trend has benefit from the increasing power of cities in terms of public policy implementation, but also from the « post industrialisation » of urban economies, in which culture is part of territorial showcasing. Undoubtedly, Paris has always been considered to be one of the most creative cities in the world, in cultural as in touristic terms. The city, number one tourist spot in Europe, and equipped with one of the best museums of the world is considered to be a creative city par excellence. However, other cities in France, such as Lyon, Lille, Nantes, St Etienne, Nice or Marseille are worthwhile to explore when it comes to illustrate the French attitudes towards the creative city paradigm. Two of these cities, St Etienne and Nantes are taken as examples in this paper because of their earlier strategies to promote their creative soul as an urban development tool

Polarized Growth in the Absence of F-Actin in Saccharomyces cerevisiae Exiting Quiescence

Polarity establishment and maintenance are crucial for morphogenesis and development. In budding yeast, these two intricate processes involve the superposition of regulatory loops between polarity landmarks, RHO GTPases, actin-mediated vesicles transport and endocytosis. Deciphering the chronology and the significance of each molecular step of polarized growth is therefore very challenging.We have taken advantage of the fact that yeast quiescent cells display actin bodies, a non polarized actin structure, to evaluate the role of F-actin in bud emergence. Here we show that upon exit from quiescence, actin cables are not required for the first steps of polarized growth. We further show that polarized growth can occur in the absence of actin patch-mediated endocytosis. We finally establish, using latrunculin-A, that the first steps of polarized growth do not require any F-actin containing structures. Yet, these structures are required for the formation of a bona fide daughter cell and cell cycle completion. We propose that upon exit from quiescence in the absence of F-actin, secretory vesicles randomly reach the plasma membrane but preferentially dock and fuse where polarity cues are localized, this being sufficient to trigger polarized growth

Episiotomy practices in France: epidemiology and risk factors in non-operative vaginal deliveries

Episiotomy use has decreased due to the lack of evidence on its protective effects from maternal obstetric anal sphincter injuries. Indications for episiotomy vary considerably and there are a great variety of factors associated with its use. The aim of this article is to describe the episiotomy rate in France between 2013 and 2017 and the factors associated with its use in non-operative vaginal deliveries. In this retrospective population-based cohort study, we included vaginal deliveries performed in French hospitals (N= 584) and for which parity was coded. The variable of interest was the rate of episiotomy, particularly for non-operative vaginal deliveries. Trends in the episiotomy rates were studied using the Cochran-Armitage test. Hierarchical logistic regression was used to identify variables associated with episiotomy according to maternal age and parity. Between 2013 and 2017, French episiotomy rates fell from 21.6 to 14.3% for all vaginal deliveries (p< 0.01), and from 15.5 to 9.3% (p< 0.01) for all non-operative vaginal deliveries. Among non-operative vaginal deliveries, epidural analgesia, non-reassuring fetal heart rate, meconium in the amniotic fluid, shoulder dystocia, and newborn weight (≥4,000 g) were risk factors for episiotomy, both for nulliparous and multiparous women. On the contrary, prematurity reduced the risk of its use. For nulliparous women, breech presentation was also a risk factor for episiotomy, and for multiparous women, scarred uterus and multiple pregnancies were risk factors. In France, despite a reduction in episiotomy use over the last few years, the factors associated with episiotomy have not changed and are similar to the literature. This suggests that the decrease in episiotomies in France is an overall tendency which is probably related to improved care strategies that have been relayed by hospital teams and perinatal networks

MOMO - multi-objective metabolic mixed integer optimization : application to yeast strain engineering

In this paper, we explore the concept of multi-objective optimization in the field of metabolic engineering when both continuous and integer decision variables are involved in the model. In particular, we propose a multi-objective model that may be used to suggest reaction deletions that maximize and/or minimize several functions simultaneously. The applications may include, among others, the concurrent maximization of a bioproduct and of biomass, or maximization of a bioproduct while minimizing the formation of a given by-product, two common requirements in microbial metabolic engineering. Production of ethanol by the widely used cell factory Saccharomyces cerevisiae was adopted as a case study to demonstrate the usefulness of the proposed approach in identifying genetic manipulations that improve productivity and yield of this economically highly relevant bioproduct. We did an in vivo validation and we could show that some of the predicted deletions exhibit increased ethanol levels in comparison with the wild-type strain. The multi-objective programming framework we developed, called Momo, is open-source and uses PolySCIP‡ as underlying multi-objective solver. Momo is available at http://momo-sysbio.gforge.inria.f