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Barbier, M.

Publications and source records attributed to Barbier, M..

5 recordsLinked to original sources

Pyramids and cascades: a synthesis of food chain functioning and stability

Food chain theory is one of the cornerstones of ecology, providing many of its basic predictions, such as biomass pyramids, trophic cascades and predator-prey oscillations. Yet, ninety years into this theory, the conditions under which these patterns may occur and persist in nature remain subject to debate. Rather than address each pattern in isolation, we propose that they must be understood together, calling for synthesis in a fragmented landscape of theoretical and empirical results. As a first step, we propose a minimal theory that combines the long-standing energetic and dynamical approaches of food chains. We chart theoretical predictions on a concise map, where two main regimes emerge: across various functioning and stability metrics, one regime is characterized by pyramidal patterns, the other by cascade patterns. The axes of this map combine key physiological and ecological variables, such as metabolic rates and self-regulation. A quantitative comparison with data sheds light on conflicting theoretical predictions and empirical puzzles, from size spectra to causes of trophic cascade strength. We conclude that drawing systematic connections between various existing approaches to food chains, and between their predictions on functioning and stability, is a crucial step in confronting this theory to real ecosystems.

ecology

Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia

Bacterial factors favoring the unprecedented multidrug-resistant tuberculosis (MDR-TB) epidemic in the former Soviet Union remain unclear.\n\nWe utilized whole genome sequencing and Bayesian statistics to analyze the evolutionary history, temporal emergence of resistance and transmission networks of MDR-MTBC strains from Karakalpakstan, Uzbekistan (2001-2006).\n\nOne MTBC-clone (termed Central Asian outbreak, CAO) with resistance mediating mutations to eight anti-TB drugs existed prior the worldwide introduction of standardized WHO-endorsed directly observed treatment, short-course (DOTS). DOTS implementation in Karakalpakstan in 1998 likely selected for these CAO-strains, comprising 75% of sampled MDR-TB strains in 2005/2006. CAO-strains were also identified in a previously published cohort from Samara, Russia (2008-2010). Similarly, transmission success and resistance development was linked to mutations compensating fitness deficits associated with rifampicin resistance.\n\nThe genetic make-up of these outbreak clades threatens the success of both empirical and standardized guideline driven MDR-TB therapies, including the newly WHO-endorsed short MDR-TB regimen in Uzbekistan.

evolutionary biology

The cavity method for community ecology

This article is addressed to researchers and students in theoretical ecology, as an introduction to \"disordered systems\" approaches from statistical physics, and how they can help understand large ecological communities. We discuss the relevance of these approaches, and how they fit within the broader landscape of models in community ecology. We focus on a remarkably simple technique, the cavity method, which allows to derive the equilibrium properties of Lotka-Volterra systems. We present its predictions, the new intuitions it suggests, and its technical underpinnings. We also discuss a number of new results concerning possible extensions, including different functional responses and community structures.

ecology

Generic assembly patterns in large ecological communities

The study of ecological communities often involves detailed simulations of complex networks. But our empirical knowledge of these networks is typically incomplete, and the space of simulation models and parameters is vast, leaving room for uncertainty in theoretical predictions. Here, we show that a large fraction of this space of possibilities exhibits generic behaviors that are robust to modelling choices. We consider a wide array of model features, including interaction types and community structures, known to generate different dynamics for a few species. We combine these features in large simulated communities, and show that equilibrium diversity, functioning and stability can be predicted analytically using a random model parameterized by a few statistical properties of the community. We give an ecological interpretation of this \"disordered\" limit where structure fails to emerge from complexity. We also demonstrate that some well-studied interaction patterns remain relevant in large ecosystems, but their impact can be encapsulated in a minimal number of additional parameters. Our approach provides a powerful framework for predicting the outcomes of ecosystem assembly and quantifying the added value of more detailed models and measurements.

ecology

Development Of RNAseq Methodologies To Profile The In Vivo Transcriptome Of Bordetella pertussis During Murine Lung Infection

Bordetella pertussis is an obligate human respiratory pathogen that causes the disease whooping cough. A whole cell vaccine (DTP) was developed in the 1940s and was subsequently replaced in the 1990s with a protein-based subunit acellular vaccine (DTaP; tdap). Today, we are observing a resurgence of whooping cough due to evolution of the pathogen and waning vaccine immunity. The use of vaccines decreased the need for basic research on this pathogen. As a result, numerous questions on the basic pathogenesis of B. pertussis remain to be answered. Microarrays and more recently, RNA sequencing (RNAseq), have allowed the field to describe the in vitro gene expression profiles of the pathogen growing in both virulent and avirulent phases; however, no published studies have described an in vivo transcriptome of the pathogen. To address this need, we have designed and evaluated workflows to characterize the in vivo transcriptome of B. pertussis during infection of the murine lung. During our initial studies, we observed that only 0.014% of the ~100 million 2x50bp illumina reads corresponded to the pathogen, which is insufficient for analysis. Therefore, we developed a simple protocol to filter the bacteria out of the tissue homogenates and separate bacterial cells from the host tissue. RNA is then prepared, quantified, and the B. pertussis to host RNA ratio is determined. Here, we present the protocol and discuss the uses and next directions for which this RNAseq workflow can be applied. With this strategy we plan to fully characterize the B. pertussis transcriptome when the pathogen is infecting the murine lung in order to identify expressed genes that encode potential new vaccine antigens that will facilitate the development of the next generation of pertussis vaccines.

microbiology