Forecasting Physicochemical Variables by a Classification Tree Method. Application to the Berre Lagoon (South France)

The dynamics of the "Etang de Berre", a brackish lagoon situated close to the French Mediterranean sea coast, is strongly disturbed by freshwater inputs coming from an hydroelectric power station. The system dynamics has been described as a sequence of daily typical states from a set of physicochemical variables such as temperature, salinity and dissolved oxygen rates collected over three years by an automatic sampling station. Each daily pattern summarizes the evolution, hour by hour of the physicochemical variables. This article presents results of forecasts of the states of the system subjected to the simultaneous effects of meteorological conditions and freshwater releases. We recall the main step of the classification tree method used to build up the predictive model (Classification and Regression Trees, Breiman et al., 1984) and we propose a transfer procedure in order to test the stability of the model. Results obtained on the Etang de Berre data set allow us to describe and predict the effects of the environmental variables on the system dynamics with a margin of error. The transfer procedure applied after the tree building process gives a maximum gain in prediction accuracy of about 15%.     

Intergeneric Transfer of Conjugative and Mobilizable Plasmids Harbored by Escherichia coli in the Gut of the Soil Microarthropod Folsomia candida (Collembola)

The gut of the soil microarthropod Folsomia candida provides a habitat for a high density of bacterial cells (T. Thimm, A. Hoffmann, H. Borkott, J. C. Munch, and C. C. Tebbe, Appl. Environ. Microbiol. 64:2660–2669, 1998). We investigated whether these gut bacteria act as recipients for plasmids from Escherichia coli. Filter mating with E. coli donor cells and collected feces of F. candida revealed that the broad-host-range conjugative plasmid pRP4-luc (pRP4 with a luciferase marker gene) transferred to fecal bacteria at estimated frequencies of 5.4 × 10⁻¹ transconjugants per donor. The mobilizable plasmid pSUP104-luc was transferred from the IncQ mobilizing strain E. coli S17-1 and less efficiently from the IncF1 mobilizing strain NM522 but not from the nonmobilizing strain HB101. When S17-1 donor strains were fed to F. candida, transconjugants of pRP4-luc and pSUP104-luc were isolated from feces. Additionally, the narrow-host-range plasmid pSUP202-luc was transferred to indigenous bacteria, which, however, could not maintain this plasmid. Inhibition experiments with nalidixic acid indicated that pRP4-luc plasmid transfer took place in the gut rather than in the feces. A remarkable diversity of transconjugants was isolated in this study: from a total of 264 transconjugants, 15 strains belonging to the alpha, beta, or gamma subclass of the class Proteobacteria were identified by DNA sequencing of the PCR-amplified 16S rRNA genes and substrate utilization assays (Biolog). Except for Alcaligenes faecalis, which was identified by the Biolog assay, none of the isolates was identical to reference strains from data banks. This study indicates the importance of the microarthropod gut for enhanced conjugative gene transfer in soil microbial communities.Gene transfer is a process by which bacterial populations substantially increase their rates of evolution and adaptation (12, 59). Particularly, plasmid-located genes, which are transferred by conjugation from donor to recipient cells, can disseminate rapidly between even phylogenetically different bacterial groups (17, 36, 41) and microbial communities in different spatial habitats (34, 71). Such microbial genetic networks should be considered in risk assessments of releases of genetically engineered microorganisms into the environment (22, 37, 43). The probability and rate of plasmid transfer from a donor to indigenous microorganisms in a given habitat are influenced by plasmid-borne genes which determine the type of transfer mechanism (self-transmissible or mobilizable) and the host range of autonomous plasmid replication. Additionally, specific physicochemical conditions, such as temperature, water potential, and the availability of energy (substrates) for donor and recipient cells, are important factors influencing gene transfer rates in terrestrial and aquatic environments (23, 53, 64).The spread of plasmid-borne genes is still extremely difficult to predict for terrestrial habitats, since a large variety of microhabitat conditions which are not well characterized exists. In bulk soil under laboratory conditions, conjugative gene transfer from recombinant bacterial donor strains to indigenous soil bacteria has been found only under specific selective conditions or on rare occasions (11, 20, 24, 27, 50, 61). Several studies failed to detect such transfer events, and it was concluded that heterogeneity and low densities of recipient cells, as well as a lack of substrates for microbial metabolism, prevented efficient plasmid transfer in bulk soil (19, 49, 54, 75). Plant exudates increased rates of gene transfer in soil (33, 48), and higher rates of gene transfer were found in rhizospheres than in bulk soil (50, 61). It was assumed that other microsites which favor gene transfer in terrestrial habitats are associated with soil invertebrates (74). However, to date little experimental evidence to prove this assumption is available.Intraspecies transconjugants of added Enterobacter cloacae donor and recipient cells could be isolated from microcosm experiments with the variegated cutworm, Peridroma saucia, and plant material (2). The investigators in that study concluded that gene transfer events happened, most likely, in the digestive tracts or in the feces of the insects. Another recent report demonstrated that a conjugative plasmid was transferred between fed Escherichia coli strains in the guts of Rhabditis nematodes (1). Earthworms mediated transport and enhanced plasmid transfer from added donor cells to added recipients and to indigenous bacteria in soil (14, 15). High rates of intraspecies plasmid transfer, comparable to those obtained in pure broth cultures, were detected with Bacillus thuringiensis in infected lepidopterous larvae (31).Microarthropods (collembolans and mites) are the most abundant invertebrate group in the majority of soils (5) but have not been recognized, so far, for their impact on microbial gene transfer. There are some indications that microarthropods harbor a large variety of microorganisms in their guts and thereby contribute to microbial biodiversity in terrestrial environments (7, 9, 57). In the accompanying paper, we have described the gut of Folsomia candida (Collembola) as a habitat and species-specific vector for microorganisms (67). The gut of this soil-dwelling insect, which has a volume of only several nanoliters, was found to be densely colonized, predominantly by rod-shaped bacterial cells. We were interested to know whether such bacterial cells act as recipients for plasmids and thereby promote gene transfer in microbial communities. F. candida feeds, under natural conditions, on bacteria (3), fungal mycelia (6, 66), and nematodes (35). Here, we report on the results of experiments in which plasmid-bearing E. coli strains were fed to F. candida in microcosms. Self-transferable plasmids, as well as mobilizable plasmids with different host ranges, and a nonmobilizable plasmid were included in this study in order to determine the specific capacities of these different classes of plasmids to spread into indigenous bacterial populations. For detection purposes, all plasmids were engineered by the insertion of the luciferase-encoding marker gene luc or lux (30, 47).     

A new Hyphoderma from Europe

The new species Hyphoderma tibia (Aphyllophorales, Basidiomycotina) is described and illustrated using drawings and scanning electron microscope.     

The Putative “Switch 2” Domain of the Ras-related GTPase, Rab1B, Plays an Essential Role in the Interaction with Rab Escort Protein

Posttranslational modification of Rab proteins by geranylgeranyltransferase type II requires that they first bind to Rab escort protein (REP). Following prenylation, REP is postulated to accompany the modified GTPase to its specific target membrane. REP binds preferentially to Rab proteins that are in the GDP state, but the specific structural domains involved in this interaction have not been defined. In p21 Ras, the α2 helix of the Switch 2 domain undergoes a major conformational change upon GTP hydrolysis. Therefore, we hypothesized that the corresponding region in Rab1B might play a key role in the interaction with REP. Introduction of amino acid substitutions (I73N, Y78D, and A81D) into the putative α2 helix of Myc-tagged Rab1B prevented prenylation of the recombinant protein in cell-free assays, whereas mutations in the α3 and α4 helices did not. Additionally, upon transient expression in transfected HEK-293 cells, the Myc-Rab1B α2 helix mutants were not efficiently prenylated as determined by incorporation of [³H]mevalonate. Metabolic labeling studies using [³²P]orthophosphate indicated that the poor prenylation of the Rab1B α2 helix mutants was not directly correlated with major disruptions in guanine nucleotide binding or intrinsic GTPase activity. Finally, gel filtration analysis of cytosolic fractions from 293 cells that were coexpressing T7 epitope-tagged REP with various Myc-Rab1B constructs revealed that mutations in the α2 helix of Rab1B prevented the association of nascent (i.e., nonprenylated) Rab1B with REP. These data indicate that the Switch 2 domain of Rab1B is a key structural determinant for REP interaction and that nucleotide-dependent conformational changes in this region are largely responsible for the selective interaction of REP with the GDP-bound form of the Rab substrate.     

Isolation and characterization of Photosystem I from two strains of the marine oxychlorobacterium Prochlorococcus

Photosystem I (PS I) complexes from two strains of the marine photosynthetic prokaryote Prochlorococcus, MED4 (= clone CCMP1378) and SS120 (= clone CCMP1375), were isolated by centrifugation on sucrose gradients after detergent treatment. The PS I-enriched fractions of both strains contained about 100 chlorophyll molecules per P700. Electron microscopy showed that the PS I complexes were in a trimeric form. The characteristic long wavelength fluorescence emission of PS I at 77 K, currently observed in chloroplasts and most cyanobacteria was absent both in intact cells and in PS I preparations of both strains. The major proteins of the PS I-enriched fractions were identified immunologically as PsaA and PsaB. Two proteins with apparent molecular masses of about 21 and 25 kDa were present in PS I preparations of Prochlorococcus, whereas the small PS I subunits in cyanobacteria all have molecular masses below 18 kDa. The 25 kDa protein showed a strong cross-reaction with a heterologous antibody against PsaL. Relatedness of the 21 kDa protein to PsaF was demonstrated by internal protein sequencing. Although only trace amounts of the major divinyl-Chl a/b-binding antenna complexes were present in the PS I preparations, significant amounts of divinyl-Chl b were observed in this fraction. The putative organization of this Chl b in PS I is discussed.     

From Panspermia to Bioastronomy,the Evolution of the Hypothesis of Universal Life

During the 19th and early 20th centuries, ideas related to the possible origin in space of bioorganic molecules, or seeds, or even germs and organisms (and how they reached the Earth) included the Panspermia theory. Based on the idea of the eternity of life proposed by eminent physicists – such as Arrhenius and Kelvin – Panspermia is mainly divided into two branches: lithopanspermia (transport of germs inside stones traveling in space) and radiopanspermia (transport of spores by radiative pressure of stellar light). We point out some arguments to help to understand whether Panspermia could exist nowadays as the same theory defined one century ago. And we wonder about the kind of evolution Panspermia could have undergone during only a few decades. This possible evolution of the Panspermia concept takes place in the framework of the emergence of a new field, Bioastronomy. We present how this discipline has emerged during a few decades and how it has evolved. We consider its relationship with the progression of other scientific fields, and finally we examine how it is now included in different projects of space agencies. Bioastronomy researches having become more and more robust during the last few years, we emphasize several questions about new ideas and their consequences for the current hypothesis of Panspermia and of universal life.     

Équilibres conformationnels de glucides au niveau de liaisons σ SP-SP: Partie V. Dérivés 2,3,-O-isopropylidène de pyranosides hybrides sp en C-4. Comparaison avec leurs analogues saturés

The conformation in solution of derivatives of methyl hexopyranosides has been studied by n.m.r. The esters of methyl 2,3-O-isopropylidene-α-D-manno- and -talopyranosides as well as their 4-deoxy-4-C-methyl analog having a manno configuration exist mainly in a flattened (^4,0F) chair conformation (⁴C₁). The presence in the talo epimer of the 4-deoxy-4-C-methyl analog of the bulky methyl group on the endo side of the bicyclic system results in a skew form (³S₁). The methyl 4-deoxy-2,3-O-isopropylidene-4-C-methylene-α-D-lyxo-hexopyranosides monosubstituted at C-4′ adopt, in solution, a conformation close to ³S₁, whichever their configuration (cis or trans) at the double bond, as indicated by their allylic coupling constants.     

All the colors of the world: biotic homogenization-differentiation dynamics of freshwater fish communities on demand of the Brazilian aquarium trade

Hydrobiologia - Non-native freshwater fish introduced via the aquarium trade can cause major changes at the community level over time and space, resulting in dynamics context dependencies within...