The emergence of complexity and restricted pleiotropy in adapting networks.

International audienceABSTRACT: BACKGROUND: The emergence of organismal complexity has been a difficult subject for researchers because it is not readily amenable to investigation by experimental approaches. Complexity has a myriad of untested definitions and our understanding of its evolution comes primarily from static snapshots gleaned from organisms ranked on an intuitive scale. Fisher's geometric model of adaptation, which defines complexity as the number of phenotypes an organism exposes to natural selection, provides a theoretical framework to study complexity. Yet investigations of this model reveal phenotypic complexity as costly and therefore unlikely to emerge. RESULTS: We have developed a computational approach to study the emergence of complexity by subjecting neural networks to adaptive evolution in environments exacting different levels of demands. We monitored complexity by a variety of metrics. Top down metrics derived from Fisher's geometric model correlated better with the environmental demands than bottom up ones such as network size. Phenotypic complexity was found to increase towards an environment-dependent level through the emergence of restricted pleiotropy. Such pleiotropy, which confined the action of mutations to only a subset of traits, better tuned phenotypes in challenging environments. However, restricted pleiotropy also came at a cost in the form of a higher genetic load, as it required the maintenance by natural selection of more independent traits. Consequently, networks of different sizes converged in complexity when facing similar environment. CONCLUSIONS: Phenotypic complexity evolved as a function of the demands of the selective pressures, rather than the physical properties of the network architecture, such as functional size. Our results show that complexity may be more predictable, and understandable, if analyzed from the perspective of the integrated task the organism performs, rather than the physical architecture used to accomplish such tasks. Thus, top down metrics emphasizing selection may be better for describing biological complexity than bottom up ones representing size and other physical attributes

Motile bacteria, active biohybrids and cellular physiology

This thesis investigates bacterial motility from active matter and physiological perspectives using experiments and theoretical modelling. In the first part, I design and characterize a system made of motile Escherichia coli encapsulated in giant lipid vesicles. For slightly deflated vesicles, the bacteria extrude active membrane tubes that can propel the vesicles. I show that the propulsion arises from a physical coupling between the lipid membrane tubes and the flagella of the encapsulated bacteria and develop a simple theoretical model to estimate the propulsive force. In a second part, I present two studies using motility as a tool to gain insight into bacterial physiology. First, I study the motility of dense suspensions of Escherichia coli fermenting glucose. Using new experimental data gathered by others, I develop a semi-empirical model that quantitatively links the swimming speed of the bacteria to the concentration of protonated organic acids in anaerobic conditions. Secondly, I focus on bacterial motility during complete starvation. Combining single-cell and population-level experiments, I show that Escherichia coli maintains a motile phenotype in the early stages of starvation, but that the swimming speed and motile fraction decay over a few tens of hours. I show that the complete decay of motility in these conditions happens on a much faster timescale than cell death. Interestingly, while swimming speed and flagellar motor measurements both show that the motility fully decays in about 24 h in these conditions, they seem to return different temporal dynamics

First description of Campylobacter lanienae from feces of organic and conventional pigs, in France

In the frame of the CORE Organic II funded European project SafeOrganic, fecal samples of 58 conventional pigs and 56 organic pigs, originated from 31 organic herds and 31 conventional herds, were collected in a slaughterhouse in order to isolate Campylobacter coli. Direct streaking from feces and incubation at 37°C of the Karmali plates allowed the isolation of another Campylobacter species: Campylobacter lanienae. Indeed, among the 381 typical Campylobacter colonies isolated, it was not possible to identify the species for 118 isolates with the Wang’s multiplex-PCR. However, 85 of these isolates were confirmed C. lanienae by Maldi-Tof and by 16S rRNA PCR. With the two species, coli and lanienae, the occurrence of Campylobacter in pig was estimated to 87.9% (51/58) for conventional pigs and 96.5% (52/56) for organic pigs. A total of 55 isolates of C. lanienae were tested for their resistance to 7 antibiotics. Only one was pansusceptible. Natural resistance of this species to Nalidixic acid was confirmed. Resistance to Tetracycline was significantly different between the two productions (p to 0.98). No link between PFGE profile and isolate origin or antibiotic resistance pattern was evidenced. This study allowed us to demonstrate for the first time in France that pigs may also carry in their feces a species rarely highlighted: C. lanienae. The lower level of antibiotic resistance and multiresistance of C. lanienae strains for organic pigs may be related to the restricted use of antibiotics in this production

No Clear Differences between Organic or Conventional Pig Farms in the Genetic Diversity or Virulence of Campylobacter coli Isolates

To evaluate the impact of pig farm management on the genetic diversity and on the virulence of Campylobacter coli, we characterized isolates from 19 organic pig farms (62 isolates) and from 24 conventional pig farms (58 isolates). The 120 C. coli isolates were typed using pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) and the presence of nine virulence genes was screened using real-time PCR. The capacity of adhesion and invasion of 61 isolates (32 from organic and 29 from conventional farms)were then tested on human intestinal Caco-2 cells. A total of 59 PFGE types and of 50 sequence types (STs) were identified. Twelve PFGE types and nine STs, accounting for 34 and 41.6%of the isolates, respectively, were common between the two production systems with ST854 dominating (18.3% of the isolates). Twenty-nine PFGE types and 25 STs were only found in isolates from organic farms, and 18 PFGE types and 16 STs from conventional farms. No significant differences were found in diversity despite the differences in rearing systems, except at the locus level for the glnA, gltA, and uncA genes. All isolates, regardless of their origin, carried the ceuE, iam, ciaB, and flaA genes and more than 95% of the isolates carried the cadF and cdtABC genes. No significant differences were found in pathogenicity between the two farming systems. The pathogenicity of the C. coli isolates was low compared to C. jejuni control strains tested. The plasmid gene virb11 was detected in only 13 isolates from organic farms; these isolates showed greater invasion capacity than those without this gene. Our study indicates that pig farm management does not significantly affect the diversity and the virulence of Campylobacter coli isolated from pigs. The common genotypes between conventional and organic farms may indicate that some genotypes are adapted to pigs

Quels tests de concept pour le développement de nouveaux produits et services ?

Concept test is a key step in the New Product Development Process. The aim of the paper is to present the different methods of tests and ways of presenting the concept, in order to see how to use these different methodologies according to the context. To achieve this, interviews with experts in market research firms as well as marketing experts in NPD within companies (both in B2C and B2B contexts) have been conducted and compared to what is written in the literature. This allowed us to build a typology of different concept tests and their sources of biases, with some suggestions to reduce them

Transport properties of Layer-Antiferromagnet CuCrS2: A possible thermoelectric material

The electrical, thermal conductivity and Seebeck coefficient of the quenched, annealed and slowly cooled phases of the layer compound CuCrS2 have been reported between 15K to 300K. We also confirm the antiferromagnetic transition at 40K in them by our magnetic measurements between 2K and 300K. The crystal flakes show a minimum around 100K in their in-plane resistance behavior. For the polycrystalline pellets the resistivity depends on their flaky texture and it attains at most 10 to 20 times of the room temperature value at the lowest temperature of measurement. The temperature dependence is complex and no definite activation energy of electronic conduction can be discerned. We find that the Seebeck coefficient is between 200-450 microV/K and is unusually large for the observed resistivity values of between 5-100 mOhm-cm at room temperature. The figure of merit ZT for the thermoelectric application is 2.3 for our quenched phases, which is much larger than 1 for useful materials. The thermal conductivity K is mostly due to lattice conduction and is reduced by the disorder in Cu- occupancy in our quenched phase. A dramatic reduction of electrical and thermal conductivity is found as the antiferromagnetic transition is approached from the paramagnetic region, and K subsequently rises in the ordered phase. We discuss the transport properties as being similar to a doped Kondo-insulator

Ab-initio vibrational properties of transition metal chalcopyrite alloys determined as high-efficiency intermediate-band photovoltaic materials

In this work, we present frozen phonon and linear response ab-initio research into the vibrational properties of the CuGaS2 chalcopyrite and transition metal substituted (CuGaS2)M alloys. These systems are potential candidates for developing a novel solar-cell material with enhanced optoelectronic properties based in the implementation of the intermediate-band concept. We have previously carried out ab-initio calculations of the electronic properties of these kinds of chalcopyrite metal alloys showing a narrow transition metal band isolated in the semiconductor band gap. The substitutes used in the present work are the 3d metal elements, Titanium and Chromium. For the theoretical calculations we use standard density functional theory at local density and generalized gradient approximation levels. We found that the optical phonon branches of the transition metal chalcopyrite, are very sensitive to the specific bonding geometry and small changes in the transition metal environment

Campylobacter coli in Organic and Conventional Pig Production in France and Sweden: Prevalence and Antimicrobial Resistance.

The purpose of the study was to evaluate and compare the prevalence and antimicrobial resistance of Campylobacter coli in conventional and organic pigs from France and Sweden. Fecal or colon samples were collected at farms or at slaughterhouses and cultured for Campylobacter. The minimum inhibitory concentrations of ciprofloxacin, nalidixic acid, streptomycin, tetracycline, erythromycin, and gentamicin were determined by microdilution for a total of 263 French strains from 114 pigs from 50 different farms and 82 Swedish strains from 144 pigs from 54 different farms. Erythromycin resistant isolates were examined for presence of the emerging rRNA methylase erm(B) gene. The study showed that within the colon samples obtained in each country there was no significant difference in prevalence of Campylobacter between pigs in organic and conventional productions [France: conventional: 43/58 (74%); organic: 43/56 (77%) and Sweden: conventional: 24/36 (67%); organic: 20/36 (56%)]. In France, but not in Sweden, significant differences of percentages of resistant isolates were associated with production type (tetracycline, erythromycin) and the number of resistances was significantly higher for isolates from conventional pigs. In Sweden, the number of resistances of fecal isolates was significantly higher compared to colon isolates. The erm(B) gene was not detected in the 87 erythromycin resistant strains tested

Encapsulated bacteria deform lipid vesicles into flagellated swimmers

We study a synthetic system of motile Escherichia coli bacteria encapsulated inside giant lipid vesicles. Forces exerted by the bacteria on the inner side of the membrane are sufficient to extrude membrane tubes filled with one or several bacteria. We show that a physical coupling between the membrane tube and the flagella of the enclosed cells transforms the tube into an effective helical flagellum propelling the vesicle. We develop a simple theoretical model to estimate the propulsive force from the speed of the vesicles and demonstrate the good efficiency of this coupling mechanism. Together, these results point to design principles for conferring motility to synthetic cells