Software Replica of Minimal Living Processes

There is a long tradition of software simulations in theoretical biology to complement pure analytical mathematics which are often limited to reproduce and understand the self-organization phenomena resulting from the non-linear and spatially grounded interactions of the huge number of diverse biological objects. Since John Von Neumann and Alan Turing pioneering works on self-replication and morphogenesis, proponents of artificial life have chosen to resolutely neglecting a lot of materialistic and quantitative information deemed not indispensable and have focused on the rule-based mechanisms making life possible, supposedly neutral with respect to their underlying material embodiment. Minimal life begins at the intersection of a series of processes which need to be isolated, differentiated and duplicated as such in computers. Only software developments and running make possible to understand the way these processes are intimately interconnected in order for life to appear at the crossroad. In this paper, I will attempt to set out the history of life as the disciples of artificial life understand it, by placing these different lessons on a temporal and causal axis, showing which one is indispensable to the appearance of the next and how does it connect to the next. I will discuss the task of artificial life as setting up experimental software platforms where these different lessons, whether taken in isolation or together, are tested, simulated, and, more systematically, analyzed. I will sketch some of these existing software platforms: chemical reaction networks, Varela’s autopoietic cellular automata, Ganti’s chemoton model, whose running delivers interesting take home messages to open-minded biologists.     

Plasma FA composition in familial LCAT deficiency indicates SOAT2-derived cholesteryl ester formation in humans

Mutations in the LCAT gene cause familial LCAT deficiency (Online Mendelian Inheritance in Man ID: #245900), a very rare metabolic disorder. LCAT is the only enzyme able to esterify cholesterol in plasma, whereas sterol O-acyltransferases 1 and 2 are the enzymes esterifying cellular cholesterol in cells. Despite the complete lack of LCAT activity, patients with familial LCAT deficiency exhibit circulating cholesteryl esters (CEs) in apoB-containing lipoproteins. To analyze the origin of these CEs, we investigated 24 carriers of LCAT deficiency in this observational study. We found that CE plasma levels were significantly reduced and highly variable among carriers of two mutant LCAT alleles (22.5 [4.0–37.8] mg/dl) and slightly reduced in heterozygotes (218 [153–234] mg/dl). FA distribution in CE (CEFA) was evaluated in whole plasma and VLDL in a subgroup of the enrolled subjects. We found enrichment of C16:0, C18:0, and C18:1 species and a depletion in C18:2 and C20:4 species in the plasma of carriers of two mutant LCAT alleles. No changes were observed in heterozygotes. Furthermore, plasma triglyceride-FA distribution was remarkably similar between carriers of LCAT deficiency and controls. CEFA distribution in VLDL essentially recapitulated that of plasma, being mainly enriched in C16:0 and C18:1, while depleted in C18:2 and C20:4. Finally, after fat loading, chylomicrons of carriers of two mutant LCAT alleles showed CEs containing mainly saturated FAs. This study of CEFA composition in a large cohort of carriers of LCAT deficiency shows that in the absence of LCAT-derived CEs, CEs present in apoB-containing lipoproteins are derived from hepatic and intestinal sterol O-acyltransferase 2.     

c-Myc Regulates Proliferation and Fgf10 Expression in Airway Smooth Muscle after Airway Epithelial Injury in Mouse

During lung development, Fibroblast growth factor 10 (Fgf10), which is expressed in the distal mesenchyme and regulated by Wnt signaling, acts on the distal epithelial progenitors to maintain them and prevent them from differentiating into proximal (airway) epithelial cells. Fgf10-expressing cells in the distal mesenchyme are progenitors for parabronchial smooth muscle cells (PSMCs). After naphthalene, ozone or bleomycin-induced airway epithelial injury, surviving epithelial cells secrete Wnt7b which then activates the PSMC niche to induce Fgf10 expression. This Fgf10 secreted by the niche then acts on a subset of Clara stem cells to break quiescence, induce proliferation and initiate epithelial repair. Here we show that conditional deletion of the Wnt target gene c-Myc from the lung mesenchyme during development does not affect proper epithelial or mesenchymal differentiation. However, in the adult lung we show that after naphthalene-mediated airway epithelial injury c-Myc is important for the activation of the PSMC niche and as such induces proliferation and Fgf10 expression in PSMCs. Our data indicate that conditional deletion of c-Myc from PSMCs inhibits airway epithelial repair, whereas c-Myc ablation from Clara cells has no effect on airway epithelial regeneration. These findings may have important implications for understanding the misregulation of lung repair in asthma and COPD.     

Review of the New Caledonian species of Acritoptila Wells, 1982 (Trichoptera,Insecta), with descriptions of 3 new species

We review the New Caledonian representatives of the Australasian endemic hydroptiline genus Acritoptila, based on examination of a considerable collection of material in the Swedish Museum of Natural History and of types of previously established species. A key for identification of males is given and includes 3 species newly described here: A. parallela sp. n., A. forficata sp. n. and A. macrospina sp. n. For all New Caledonian species, male genitalia are illustrated, and for 5 associated females, distinctive features are illustrated and described.     

Space use and genetic structure do not maintain color polymorphism in a species with alternative behavioral strategies

Space use including territoriality and spatial arrangement within a population can reveal important information on the nature, dynamics, and evolutionary maintenance of alternative strategies in color polymorphic species. Despite the prevalence of color polymorphic species as model systems in evolutionary biology, the interaction between space use and genetic structuring of morphs within populations has rarely been examined. Here, we assess the spatial and genetic structure of male throat color morphs within a population of the tawny dragon lizard, Ctenophorus decresii. Male color morphs do not differ in morphology but differ in aggressive and antipredator behaviors as well as androgen levels. Despite these behavioral and endocrine differences, we find that color morphs do not differ in territory size, with their spatial arrangement being essentially random with respect to each other. There were no differences in genetic diversity or relatedness between morphs; however, there was significant, albeit weak, genetic differentiation between morphs, which was unrelated to geographic distance between individuals. Our results indicate potential weak barriers to gene flow between some morphs, potentially due to nonrandom pre‐ or postcopulatory mate choice or postzygotic genetic incompatibilities. However, space use, spatial structure, and nonrandom mating do not appear to be primary mechanisms maintaining color polymorphism in this system, highlighting the complexity and variation in alternative strategies associated with color polymorphism.     

PROXIMATE AND ULTIMATE SOURCES OF WITHIN-INDIVIDUAL VARIATION IN SEED MASS IN PRUNELLA VULGARIS (LAMIACEAE)

Substantial variation in seed mass within individual seed parents is at odds with predictions of models for the evolution of optimum offspring size and with empirical observations of directional selection on seed mass. To elucidate the ultimate causes of this variation, I examined several proximal sources of within-individual variation in seed mass in the perennial herb Prunella vulgaris. Position of inflorescence, position of flower within an inflorescence, date of anthesis, and number of seeds produced per flower all explained some within-individual variation in seed mass. Hand pollination in the field failed to reveal any effect of pollen source (self pollen or outcross pollen) on seed mass. My results, in conjunction with those from studies of selection on seed mass in P. vulgaris, do not support hypotheses that within-individual variation in seed mass is favored by the pattern of natural selection on seed mass. Rather, the results suggest that seed parents are not capable of producing a uniform seed crop in the face of changes in resource availability in the course of a season. The inability to produce a uniform seed crop may persist because of selection for variability in traits correlated with seed mass or because of a true constraint on the evolution of uniform offspring size.     

Viral and bacterial contamination of mussels (Mytilus edulis) exposed in an unpolluted marine environment

Bacteria indicating faecal contamination, cell-culturable enteroviruses and hepatitis A virus (HAV) were investigated in sea-water and in mussels exposed in an unpolluted marine environment, over a 7-month period with two samplings per month. Of the 16 mussel samples examined, none contained cell-culturable enteroviruses, four showed a low-level contamination by HAV and two did not conform to the current bacteriological norms. No connection was observed between the viral and bacterial contamination. No viral contamination was detected in the sea-water samples, but two gave bacterial counts above current norms.