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.     

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.     

Molecular analysis of a reciprocal translocation t(5;11)(q11;p13) in a WAGR patient

Summary Most patients with the complex association aniridia — predisposition to Wilms' tumor (WAGR syndrome) present with a de novo constitutional deletion of band 11p13. We report a patient with WAGR syndrome and a reciprocal translocation between chromosomes 5 and 11 t(5;11)(q11;p13). High resolution banding cytogenetic analysis and molecular characterization using 11p13 DNA markers showed a tiny deletion encompassing the gene for CAT but sparing the gene for FSHB. This suggests that syndromes associated with apparently balanced translocations may be due to undetectable loss of material at the breakpoint(s) rather than to breakage in the gene itself.     

Stereochemistry of the hydrolysis of α,α-trehalose by trehalase,determined by using a labelled substrate

(1,1′-¹³C)α,α-Trehalose was obtained in 37% yield from the Pavia condensation of 2,3,4,6-tetra-O-benzyl-d-(1-¹³C)glucopyranose, in dichloromethane in the presence of trifluoromethanesulfonic anhydride, followed by the usual deprotection techniques. The hydrolysis of this substrate by cockchafer trehalase was monitored at 37° by using ¹³C-n.m.r. spectroscopy with short recording times. Equimolecular amounts of α- and β-d-glucopyranose are released simultaneously by the action of the enzyme. This result is consistent with a bimolecular substitution mechanism, taking into account previous results involving C-2 asymmetric participation in the catalytic step of hydrolysis of α,α-trehalose. For comparative evaluation of its accuracy, the usual polarimetric technique was also used for the determination of the anomeric configuration of the d-glucose released by the action of the enzyme on α,α-trehalose.     

Lysosomes of root tip cells in corn seedlings

Summary Nine acid hydrolases are present in lysosomes which are found in the mitochondrial fraction of a cell-free extract prepared from root tips of corn seedlings.Light and heavy lysosomes can be distinguished. The latter are sedimentable in a sucrose-medium, the former only in sorbitol-medium. The fraction of heavy lysosomes is in turn composed of at least three populations of lysosomes differing in density and enzyme content.Light lysosomes are membrane-bound particles with diameters from 0.3 to 1.5 . Electron micrographs of frozen-etched tissue and isolated particles provide evidence that light lysosomes are identical with small vacuoles. This type of lysosome is characterized by presence of transaminases in addition to that of hydrolases. Heavy lysosomes are small spheres (diameters from 0.1–0.3 ) with membranes resembling those of vacuoles and of the endoplasmic reticulum. These lysosomes are characterized by high specific activities of two oxydoreductases known to occur also in the membranes of the reticulum.The different types of particles are thought to represent stages of the development of the lysosomal apparatus; according to this hypothesis the large vacuole of parenchymatous cells represents the end product of this process.     

Vacuolation: Origin and development of the lysosomal apparatus in root-tip cells

Summary The morphology of vacuolation has been investigated in root tip cells of corn using the freeze-etching technique. The genesis of vacuoles involves the following processes: a) Formation of small, endoplasmic-reticulum (ER)-derived vesicles (provacuoles); b) fusion of provacuoles resulting in the formation of small vacuoles, and followed by fusion and expansion of vacuoles; c) incorporation of large, dictyosome-derived vesicles into vacuoles by invagination of the tonoplast; d) invagination of the tonoplast resulting in the incorporation of cytoplasmic material into vacuoles. The morphological findings are correlated with biochemical data obtained from isolated vacuoles (lysosomes). Provacuoles (ER-derived vesicles) are shown to be primary lysosomes; their hydrolases arise from the ER. Vacuoles represent secondary lysosomes (digestive vacuoles) of the higher-plant cell. The metabolic role of lytic processes proceeding in the lysosomal apparatus is discussed.     

Isolation and properties of the plasmalemma in yeast

Summary A method is described for the isolation of fragments of the plasmalemma based on differential and density gradient centrifugation using cell free extracts from anaerobically grown Saccharomyces cerevisiae. Electron microscopically investigated frozen-etched specimens of isolated plasmalemma revealed the presence of globular particles attached to the outer surface of the membrane; these particles correspond to those observed in situ.In isolated plasmalemma a high specific activity of Mg⁺⁺-dependent ATPase, which is not sensitive to Oligomycin, is present. Yeast plasmalemma contains protein, lipids (including phospholipids) and an appreciable amount of polysaccharide. Hydrolysis of this polysacharide yields only mannose.The treatment of the isolated plasmalemma with detergents liberates the globular particles which can be isolated by density gradient centrifugation. Protein and polysaccharide occur in the respective fraction; therefore the globular particle represents a mannan-protein. It is concluded that the particles, which cover the plasma-membrane of plant cells, represent glycoproteins, that is, building stones to be incorporated into the fibrillar network of the cell walls.     

Prevalence of fungi in carpeted floor environment: Analysis of dust samples from living-rooms,bedrooms, offices and school classrooms

The results of 100 carpet dust analyses from atopic individuals' environment were compared according to the sampling period or the location. Dust samples were collected with a standard domestic vacuum cleaner, in locations with carpeted floor: in residences (living-room and/or bedroom), in school classrooms and in offices. The quantities of fungi vary from 5000 CFU/g to 66 000 000 CFU/g of dust. More than 100 species were isolated by dilution plating. The main species found in carpet dust wereEurotium repens, Penicillium chrysogenum, Alternaria alternata, Aureobasidium pullulans andPhoma herbarum. Strict xerophilic species were rather rare and detected in small quantities. Differences in the distribution of the CFU concentrations were examined for the four different sampling locations and were statistically significant (P=0.0174). In this study, schools were open spaces, and offices, mostly with air conditioning systems, were locations in which air is not confined. This, added to frequent professional carpet cleaning, probably explains the lowest levels of fungal concentration found in these locations. The majority of the homes had the largest fungal concentration in the living-room (median: 2×10⁵ CFU/g) while some bedrooms (median: 7×10⁴ CFU/g) had the highest concentrations. It is suggested that, when fungi are suspected to be the origin of respiratory allergy or irritating symptoms, the mycoflora of the bedroom, principally, should be investigated first.     

Identification of Catabolites of Chlorophyll-Porphyrin in Senescent Rape Cotyledons

Developing shoots of rape seedlings (Brassica napus L.) were excised and fed with 4-[14C]5-aminolevulinic acid to label the pyrroles in chlorophyll (Chl) synthesized during the final phase of expansion and greening of the cotyledons. About 80% of 14C taken up into the cotyledons was incorporated into Chl. The subsequent incubation of labeled shoots in permanent darkness caused the rapid loss of labeled Chl while increasing proportions of 14C appeared in the fraction of water-soluble compounds. Reversed-phase high performance liquid chromatography resolved three nonfluorescent polar catabolites of Chl-porphyrin that were progressively accumulated as senescence advanced. At intermediate stages of senescence, the cotyledons contained a fluorescent radio-active derivative of Chl that was also detectable, together with traces of other putative fluorescent catabolites, in isolated senescent chloroplasts. The nonfluorescent catabolites, identified by means of radiolabeling, were also found to accumulate in attached cotyledons senescing under photoperiod; under these conditions, one of the compounds, NCC-1, was particularly abundant. The catabolites of rape exhibited the same ultraviolet spectra, characterized by a maximum at 320 nm, as a previously reported secoporphinoid catabolite from barley (B. Krautler, B. Jaun, W. Amrein, K. Bortlik, M. Schellenberg, P. Matile [1992] Plant Physiol Biochem 30: 333-346). Different polarities suggest, however, that the structures may be different. A terminology for Chl catabolites is proposed because present knowledge suggests that a large number of different structures results from species-specific processing of breakdown products and may require a suitable nomenclature.