Use of correspondence discriminant analysis to predict the subcellular location of bacterial proteins

Correspondence discriminant analysis (CDA) is a multivariate statistical method derived from discriminant analysis which can be used on contingency tables. We have used CDA to separate Gram negative bacteria proteins according to their subcellular location. The high resolution of the discrimination obtained makes this method a good tool to predict subcellular location when this information is not known. The main advantage of this technique is its simplicity. Indeed, by computing two linear formulae on amino acid composition, it is possible to classify a protein into one of the three classes of subcellular location we have defined. The CDA itself can be computed with the ADE-4 software package that can be downloaded, as well as the data set used in this study, from the P?le Bio-Informatique Lyonnais (PBIL) server at http://pbil.univ-lyon1.fr.     

Statistical analysis and graphical display of multivariate data on the Macintosh

Two Macintosh programs written for multivariate data analysis and multivariate data graphical display are presented. MacMul includes principal component analysis (PCA), correspondence analysis (CA) and multiple correspondence analysis (MCA), with a complete, original and unified set of numerical aids to interpretation. GraphMu is designed for drawing collections of elementary graphics (curves, maps, graphical models) thus allowing comparisons between variables, individuals, and principal axes planes of multivariate methods. Both programs are self-documented applications and make full use of the user-oriented graphical interface of the Macintosh to simplify the process of analysing data sets. An example is described to show the results obtained on a small ecological data set.     

Multivariate analysis of the spatial patterns of 8 trace elements using the French soil monitoring network data

Geostatistical and spatially constrained multivariate analysis methods (MULTISPATI-PCA) have been applied at the scale of France to differentiate the influence of natural background from the pollution due to human activities on the content of 8 trace elements in the topsoil. The results of MULTISPATI-PCA evidence strong spatial structures attributed to different natural and artificial processes. The first axis can be interpreted as an axis of global richness in trace elements. Axis 2 reflects geochemical anomalies in Tl and Pb. Axis 3 exhibits on one hand natural pedogeogenic anomalies and on the other hand, it shows high values attributable to anthropogenic contamination. Finally, axis 4 is driven by anthropogenic copper contamination. At the French territory scale, we show that the main factors controlling trace elements distribution in the topsoil are soil texture, variations in parent material geology and weathering, and various anthropogenic sources.     

Ecology of larval mosquitoes, with special reference to Anopheles arabiensis (Diptera: Culcidae) in market-garden wells in urban Dakar, Senegal

The urban area of Dakar, Senegal, contains > 5,000 market-garden wells that provide permanent sites for mosquito larvae, in particular Anopheles arabiensis Patton, the major vector of malaria. A study of the bioecology of mosquito larvae was conducted over 1 yr with a monthly visit to 48 of these wells. Overall, 9,589 larvae were collected of which 80.1% were Culicinae and 11.9% Anophelinae. Larvae from stages III and IV (n = 853) were identified to 10 species. An. arabiensis represented 86% of the anophelines collected and An. ziemanni Grunberg 14%. The most common Culicinae species included Aedeomyia africana Neveu-Lemaire, Culex quinquefasciatus Say, and Mimomyia splendens Theobald. Maximum anopheline abundance was observed at the end of the dry season in June, whereas maximum Culicinae abundance was observed at the end of the rainy season in September. Most wells (67%) did not harbor any An. arabiensis larvae and in the remaining 33% the larval abundance was low, averaging 0.54 larvae in stages III-IV per tray sample. To identify factors that determine the abundance of larvae in these wells, a co-inertia (multivariate) analysis was carried out to account for physicochemical variables (depth, turbidity, temperature, pH, conductivity, Na+, Cl-, HCO3-, CO3--, and NO3- concentrations) and biological variables (abundance of mosquito species, predators [e.g., fish, Dytiscidae, Notonectidae, odonates], molluscs [Bulinus and Biomphalaria], and surface plants [water lettuce, Lemna, and filamentous algae]). The co-inertia analysis indicated that the abundance of An. arabiensis was associated with Cx. quinquefasciatus and Cx. decens for the physiochemical data but was not associated with other mosquito species for floro-faunistic data. The conditions associated with abundant An. arabiensis were warm temperature (28-30 degrees C), clear and not too deep water (< 0.5 m), elevated concentrations of HCO3- and CO3--, low concentrations of NO3- and NaCl, low populations of larvivorous fish and invertebrate predators (notably odonates), the presence of water lettuce, and an absence of Lemna. These results indicate that many contributing factors influence the ecology of the immature stages of An. arabiensis.     

Comparing and classifying one-dimensional spatial patterns: an application to laser altimeter profiles

Numerical analyses of remotely sensed data may valuably contribute to an understanding of the vegetation/land surface interface by pointing out at which scales a given variable displays a high level of spatial variability. Thus, there is a need of methods aimed at classifying many one-dimensional signals, such as airborne laser profiles, on the basis of their spatial structure. The present paper proposes a theoretical framework ensuring a consistent combination of a multi-scale pattern characterization, based on the Haar wavelet variance (also called in ecology Two Terms Local Variance, TTLV), with two multivariate techniques such as principal components analysis (PCA) and hierarchical cluster analysis. We illustrate our approach by comparing and classifying 257 laser profiles, with a length of 64 measurements (448 m), that were collected by the BRGM in French Guiana over three main landscape units with distinct geomorphological and ecological characteristics. We calculate for each profile a scalogram that summarized the multi-scale pattern and analyze the structural variability of profiles via a typology and a classification of one-dimensional patterns. More than 80% of the variability between spatial patterns of laser profiles has been summarized by two PCA axes, while four classes of spatial patterns were identified by cluster analysis. Each landscape unit was associated with one or two dominant classes of spatial patterns. These results confirmed the ability of the method to extract landscape scaling properties from complex and large sets of remotely sensed data.     

Validation and study of the transferability of the selected technique by SFBC for the determination of creatinine in plasma

A selected method for the determination of creatinine in plasma, using the reaction with alkaline picrate without prior pretreatment has been proposed by the Commission 'Validation de techniques' in the SFBC (Société Fran?aise de biologie clinique). The transferability step was conducted in seven laboratories, equipped with different automatic analyzers, using analytical procedures derived from the recommended method. Its goal was to test whether the original analytical performances could be maintained and consistent results obtained. The validation step was designed to evaluate the linearity limits of the analytical range, the detection limit, to assess accuracy as compared to a high performance liquid chromatography and to investigate the effect of the main interferents. Linearity limits are 15 and 2000 mumol/L. The detection limit is 3 to 8 mumol/L according to the analytical systems. The selected method can fulfil the set imprecision goals: intralaboratory CV minus than 2% (within-run), minus than 4% (run-to-run), interlaboratory CV minus than 5% (for 100 mumol/L creatinine). Inaccuracy evaluated for the chosen control sera is 1 to 15% as compared to the chromatographic method, according to the sera and to the analytical systems. The results obtained with the selected method are more consistent with the HPLC than are those obtained with an alkaline picrate method without SDS or with an enzymatic method. No interference could be demonstrated for acetoacetate (up to 8 mmol/L), hemoglobin (up to 210 mumol/L), unconjugated bilirubin (up to 250 mumol/L), glucose (up to 30 mmol/L), IgG (up to 45 g/L), albumin (up to 60 g/L). The effect of cephalosporins depends on the molecule. The reagents are stable for at least 6 months when stored in closed vials at +20 degrees C. The alkaline reagent is stable 30 days at +4 degrees C. Reference limits (0.025 and 0.975 fractiles) have been established for healthy adults. They are respectively 73 to 126 mumol/L for men and 59 to 100 mumol/L for females.     

Fluorescent pseudomonads occurring in Macrotermes subhyalinus mound structures decrease Cd toxicity and improve its accumulation in sorghum plants

Cd-tolerant bacterial strains of fluorescent pseudomonads, mostly belonging to Pseudomonas monteillii, were isolated from termite mound soil (Macrotermes subhyalinus, a litter-forager and fungus-growing termite), in a Sudanese shrubby savanna, Burkina Faso. Such large mounds appeared as sites of great bacterial diversity and could be considered as hot spots of metal-tolerant fluorescent pseudomonads. Microbial isolates were inoculated to Sorghum plants (S. bicolor) in glasshouse experiments with soil amended with CdCl(2) (560 mg Cd kg(-1) soil). Microbial functional diversity was assessed at the end of the experiment by measurement of in situ patterns of catabolic potentials. All the bacteria isolates significantly improved the shoot and total biomass of sorghum plants compared to the control. Results concerning root biomass were not significant with some strains. Arbuscular mycorrhiza (AM) was greatly reduced by CdCl(2) amendment, and fluorescent pseudomonad inoculation significantly increased AM colonisation in the contaminated soil. The bacterial inoculation significantly improved Cd uptake by sorghum plants. Measurement of catabolic potentials on 16 substrates showed that the microbial communities were different according to the soil amendment. Soils samples inoculated with pseudomonad strains presented a higher use of ketoglutaric and hydroxybutiric acids, as opposed to fumaric acid in soil samples not inoculated. It is suggested that fluorescent pseudomonads could act indirectly in such metabolic processes by involving a lower rate of degradation of citric acid, in line with the effect of small organic acid on phytoextraction of heavy metals from soil. This is a first contribution to bioremediation of metal-contaminated sites with soil-to-plant transfer, using termite built structures. Further data are required on the efficiency of the bacterial strains isolated and on the processes involved.     

Une nouvelle analyse multi-temporelle d'images satellitales,les résidus de l'Analyse en Composantes Principales. Un cas d'étude: une série d'images Landsat Thematic Mapper de la Camargue,France

Résumé. Les méthodes d'analyses de séries temporelles d'images satellitales sont nombreuses. Après une brève revue de ces méthodes, une nouvelle approche est proposée. Elle consiste à calculer les résidus de l'ACP (Analyse en Composantes Principales) du tableau des NDVI par la procédure suivante: calculer les variables NDVI à chacune des dates; construire le tableau de données espace × temps, par accolement des variables NDVI; réaliser l'ACP de ce tableau; déterminer le nombre, k, de facteurs de l'ACP explicatifs des structures stables au cours du temps du paysage; et calculer les résidus entre le tableau NDVI et celui reconstruit à partir des k facteurs. Cette méthode appliquée à l'analyse d'une série de trois scènes Landsat TM acquises en 1983, 1984 and 1993 sur la Camargue (France) a permis de séparer les structures permanentes d'occupation du sol de leurs variations annuelles. La spécificité de cette région, appelée ‘île Camargue’, qui est totalement sous le contrôle des systèmes d'irrigation mis en place par l'homme, apparaît ainsi nettement.

Abstract. Numerous methods exist for the analysis of changes applied to time series of satellite images. After a quick review of these methods, a new approach is proposed. This approach is based on residuals computed from PCA (Principal Component Analysis) on a NDVI table. It consists of: computing the NDVI variable for each date; building a space × time table which joins NDVI variables; carrying out a PCA on this table; choosing the number, k, of factors of PCA which explain time invariant landscape structures; and computing residuals between NDVI table and the table computed from the k factors. This method applied to the analysis of a series of three Landsat TM scenes acquired in 1983, 1984 and 1993 on the Camargue region (France) allows separation of the permanent land use structure from its annual variations. The specificity of the so called ‘island Camargue’ is clearly shown; control of water exchanges by man alters the land use every year.     

High-speed modulation of an electrooptic directional coupler

A LiNbO3:Ti directional coupler driven by an RF signal has been tested at 1.06 μm over a large modulation bandwidth. An analytical model has been developed leading to simple usable expressions to describe the theoretical dependence of the frequency spectrum of sinusoidally modulated light. The frequency response has been measured with a scanning Fabry-Perot and also with a high-speed photodiode. Both methods provided results which are in good agreement. The 9 mm long switch exhibited a 2.5 GHz bandwidth; a 16 dB extinction ratio has been achieved with a driving power of approximately 50μW/MHz. The confirmation of practical modulation response expressions shows the advantage of the optical spectrum observation, which is a very simple measurement method without any bandwidth limitation. In addition, this method has the advantage of remaining quite accurate even for large modulation signals.