Knowledge sharing and discovery across heterogeneous research infrastructures.

Research infrastructures play an increasingly essential role in scientific research. They provide rich data sources for scientists, such as services and software packages, via catalog and virtual research environments. However, such research infrastructures are typically domain-specific and often not connected. Accordingly, researchers and practitioners face fundamental challenges introduced by fragmented knowledge from heterogeneous, autonomous sources with complicated and uncertain relations in particular research domains. Additionally, the exponential growth rate of knowledge in a specific domain surpasses human experts' ability to formalize and capture tacit and explicit knowledge efficiently. Thus, a knowledge management system is required to discover knowledge effectively, automate the knowledge acquisition based on artificial intelligence approaches, integrate the captured knowledge, and deliver consistent knowledge to agents, research communities, and end-users. In this study, we present the development process of a knowledge management system for ENVironmental Research Infrastructures, which are crucial pillars for environmental scientists in their quest for understanding and interpreting the complex Earth System. Furthermore, we report the challenges we have faced and discuss the lessons learned during the development process.

Cypress Pollinosis: from Tree to Clinic.

Cypress (Cupressus sp.pl) is a genus within the Cupressaceae family. This family covers all of the Earth's continents except for Antarctica, and it includes about 160 species. The most important taxa for allergic diseases belong to five different genera: Cupressus, Hesperocyparis, Juniperus, Cryptomeria, and Chamaecyparis. Cupressaceae species share a common pollen type that can even include the genus Taxus (Taxaceae) when this plant is also present. As Juniperus oxycedrus pollinates in October, Cupressus sempervirens in January and February, Hesperocyparis arizonica (prev. Cupressus arizonica) in February and March, and Juniperus communis in April, the symptomatic period is long-lasting. Due to global warming, the pollination period tends to last longer, and there is a trend for Cupressaceae bioclimate niches to migrate north. In Mediterranean areas, C. sempervirens (Italian cypress or Mediterranean cypress) is by far the most common pollinating species. It accounts for half of the total pollination level. The group 1 major allergens belong to the pectate-lyase family, and members share 70 to 97% sequence homology within the different Cupressaceae. Group 2 allergens correspond to the polygalacturonase protein family, while group 3, a minor allergen, belongs to the family of "thaumatin-like proteins," a pathogenesis-related protein 5. Group 4 allergens are Ca++-binding protein (4 EF-hands). Aside from these four groups, about 15 other allergens have been reported. Prominent among these is a basic low-molecular mass cross-reactive allergen that was identified recently, and which is suspected to be involved in pollen food syndromes which are common with peach and citrus. The prevalence of cypress allergy in the general population ranges from 0.6 to 3%, depending on the degree of exposure to the pollen. Depending on the geographic area and the studied population, 9 to 65% of outpatients consulting an allergist may have sensitization to cypress pollen. Repeated cross-sectional studies performed at different time intervals have demonstrated a threefold increase in the percentage of cypress allergy around the Mediterranean area. Risk factors include a genetic predisposition and/or a strong exposure to pollen, and the natural history of cypress allergy allows identification of a subgroup of patients as allergic rather than atopic. Concerning the clinical expression, rhinitis is the most prevalent symptom, while conjunctivitis is the most disabling. Pharmacological treatment of cypress allergies is not different from that of other seasonal allergies. Immunotherapy has been used, initially by subcutaneous injections, but currently mostly through the sublingual route. Although clinical trials have included only a limited number of patients, it has proven effective and safe. Avoidance can be implemented at the individual level, as well as at the community level, through the use of alternative plants, low-pollinating cypresses, or by trimming hedges before pollination.

A coordinated set of ecosystem research platforms open to international research in ecotoxicology, AnaEE-France.

The infrastructure for Analysis and Experimentation on Ecosystems (AnaEE-France) is an integrated network of the major French experimental, analytical, and modeling platforms dedicated to the biological study of continental ecosystems (aquatic and terrestrial). This infrastructure aims at understanding and predicting ecosystem dynamics under global change. AnaEE-France comprises complementary nodes offering access to the best experimental facilities and associated biological resources and data: Ecotrons, seminatural experimental platforms to manipulate terrestrial and aquatic ecosystems, in natura sites equipped for large-scale and long-term experiments. AnaEE-France also provides shared instruments and analytical platforms dedicated to environmental (micro) biology. Finally, AnaEE-France provides users with data bases and modeling tools designed to represent ecosystem dynamics and to go further in coupling ecological, agronomical, and evolutionary approaches. In particular, AnaEE-France offers adequate services to tackle the new challenges of research in ecotoxicology, positioning its various types of platforms in an ecologically advanced ecotoxicology approach. AnaEE-France is a leading international infrastructure, and it is pioneering the construction of AnaEE (Europe) infrastructure in the field of ecosystem research. AnaEE-France infrastructure is already open to the international community of scientists in the field of continental ecotoxicology.

Cypress surrogate mother produces haploid progeny from alien pollen.

Although most living organisms reproduce sexually, some have developed a uniparental reproduction where the embryo usually derives from the female parent. A unique case of paternal apomixis in plants has been recently reported in Cupressus dupreziana, an endangered Mediterranean conifer. This species produces unreduced pollen that develop into all-paternal embryos within the seed tissues. We analyzed seedlings produced by open-pollinated C. dupreziana seed trees using morphological descriptors, ploidy levels assessed through flow cytometry, and AFLP genetic diversity. In situ C. dupreziana seed trees (from Algeria) produced only diploid C. dupreziana progeny. In contrast, only one-third of the progeny produced by ex situ C. dupreziana seed trees planted in French collections were similar to C. dupreziana seedlings; the other progeny were haploid or diploid C. sempervirens seedlings. These results demonstrate that C. dupreziana ovules allow for the development of all-paternal embryos from pollen produced by another species, C. sempervirens. Thus, the in planta androgenesis is achieved through the combination of the embryogenic behavior of pollen grains and the ability of seed tree ovules to act as a surrogate mother. This phenomenon offers a unique opportunity to produce, by natural means, highly valuable material for genetic studies and selection of sterile cultivars.

Block copolymer-oligonucleotide conjugates for genotyping on microarrays.

Polymer-oligonucleotide conjugates were synthesized from the amphiphilic block copolymer poly(tert-butylacrylamide-b-(N-acryloylmorpholine-co-N-acryloxysuccinimide)) using an original solid-phase DNA synthesis strategy. This method provided conjugates highly functionalized with oligonucleotides throughout the polymer chain. After purification, block copolymer-oligonucleotide conjugates were spotted on a multidetection microarray system developed by Apibio using a standard nanodroplet piezo inkjet spotting technique to develop the oligosorbent assay (OLISA). Two genotyping models (HLA-DQB1 and platelet glycoproteins [GPs]), which are particularly difficult to study with standard systems, were evaluated. For both models, block copolymer-oligonucleotide conjugates used as capture probes amplified the responses of in vitro diagnostic assays. The detection limit reached by using conjugates was estimated at 15 pM for a 219-bp DNA target (HLA-DQB1 model). Moreover, single nucleotide polymorphism was detected in the platelet GPs genotyping model. The use of polymer conjugates led to a significant improvement in both sensitivity and specificity of standard hybridization assays even when applied to complex biological models.

Elaboration of silica colloid/polymer hybrid support for oligonucleotide synthesis.

One way to increase the sensitivity of DNA diagnostic assays developed on microarrays is to improve the solid phase that allows the extraction of the target from a biological sample, before detection. Two parameters are influencing the performances of this capture step: (i) the specific surface area being offered for the capture and (ii) the number and the accessibility of oligonucleotide probes immobilized on the surface. In this context, we have developed an attractive approach which fulfills these two points. Our strategy was to elaborate a new material of high specific surface area, suitable to serve as support for both solid-phase oligonucleotide synthesis and in vitro diagnostic assay. This material has consisted of aggregates of colloidal amino-silica nanoparticles covalently linked by poly(ethylene oxide) (PEO) arms. The aggregation of amino-silica particles in the presence of reactive bis-isocyanate PEO was achieved in a controlled manner. The aggregate size and structure were examined by microscopy. The specific surface area of this material was measured by nitrogen adsorption technique. The composition of aggregate was studied by thermogravimetry and X-ray photoelectron spectroscopy. Then, this material has been successfully used as support for oligonucleotide synthesis of high yield and purity. The resulting system will be further evaluated in a diagnostic assay on a microarray.

Effect of thiol-containing monomer on the preparation of temperature-sensitive hydrogel microspheres.

The main objective of this study is to prepare, thermally, sensitive microgel particles bearing thiol groups via precipitation polymerization of N-isopropylacrylamide (NIPAM), methylenebisacrylamide (MBA) and vinylbenzylisothiouronium chloride (VBIC) using 2-2'-azobis(2-amidinopropane)-dihydrochloride (V50) as initiator. The influence of various parameters has been investigated as a systematic study to point out the role of each reactant on polymerization conversion, and consequently, on particles and water-soluble polymer formation. The final microgel particles were characterized with respect to particle size and swelling ability. The aim of this paper is to complete our first short communication; Macromolecular symposia, 2000. 150: p. 283-290.

New insights into self-organization of a model lipid mixture and quantification of its adsorption on spherical polymer particles.

The adsorption of lipids onto spherical polymer colloids led to original assemblies presenting structural characteristics adjustable with the lipid formulation. The model system selected for this work involved sulfate-charged poly(styrene) submicrometer particles and zwitterionic/cationic lipid mixtures composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dipalmitoyl-3-trimethylammonium-propane (DPTAP). According to the theoretical packing parameter calculations and whatever the DPPC/DPTAP ratio, the two lipids self-assembled in aqueous media to spontaneously form vesicles. A phase transition investigation of these DPPC/DPTAP vesicles using differential scanning calorimetry revealed particular thermotropic behaviors, especially for the equimolar formulation where very strong interactions occurred between DPPC and DPTAP. Furthermore, the coating of the lipids around particles was monitored versus DPPC/DPTAP ratio by means of numerous appropriate techniques. First, a thermogravimetric analysis, providing decomposition profiles of lipid/polymer particle assemblies with temperature, was atypically carried out for such nanostructures. Then, 1H NMR spectroscopy enabled the exact DPPC/DPTAP molar ratios adsorbed on particles to be determined by differentiating both lipids. Subsequently, it also pointed out the major role of electrostatic interactions as driving forces in the assembly elaboration process. In addition to these findings, quantitative information has been collected and correlated with chemical lipid assays and permitted the statement of a lipid bilayer coverage for the assemblies prepared in water, in agreement with quasi-elastic light scattering data.

Formation of polyelectrolyte complex particles from self-complexation of N-sulfated chitosan.

This work investigated the elaboration of biocompatible nanoparticles from the pH-induced self-complexation of the amphoteric polysaccharide N-sulfated chitosan. The acidification of aqueous solutions of chitosan having a degree of acetylation of 24% and a degree of sulfation of 34% or 56% was followed stepwise by turbidimetry, dynamic light scattering, and electrophoresis. With the highest sulfated chitosan, no turbidity was recorded between pH = 7.8 and 2.0, traducing a high apparent solubility of the polymer chains in this domain of pH. With the lowest sulfated chitosan, a steady increase in turbidity was monitored from pH = 6.90 to 6.15 followed by the flocculation of the polymer at pH approximately 6.0. In this range of pH, the polymer phase separated to yield particles having hydrodynamic diameters decreasing from 350 to 260 nm and an almost constant negative charge. These particles were assembled by electrostatic interactions between the protonated amino residues and the sulfate functions and stabilized by an excess of surface sulfate groups. The particles could be separated from the reaction medium and concentrated by centrifugation-redispersion cycles without alteration of their structure.

Polymer-oligonucleotide conjugate synthesis from an amphiphilic block copolymer. Applications to DNA detection on microarray.

An amphiphilic block copolymer poly(tert-butylacrylamide-b-(N-acryloylmorpholine-N-acryloxysuccinimide)) (poly(TBAm-b-(NAM/NAS)) and a random copolymer poly(NAM/NAS), synthesized by the reversible addition-fragmentation chain transfer (RAFT) polymerization process, have been used as support for oligonucleotide (ODN) synthesis, to elaborate polymer-oligonucleotide conjugates. In a first step, starters of ODN solid-phase synthesis were coupled to activated ester functions of polymers, and second, resulting functionalized polymers were covalently grafted onto hydroxylated controlled pore glass (CPG) support to further accomplish ODN synthesis. An efficient capping of residual hydroxyl functions of CPG was performed before synthesis, with both acetic anhydride and diethoxy-N,N-diisopropyl-phosphoramidite reagents, to suppress parasite-free ODN population present in conjugate crude material and resulting from syntheses directly initiated on silica beads. After purification, conjugates were evaluated in a DNA hybridization assay on a microarray, as macromolecules being able to favor capture of the target. Conjugate coating conditions were studied on the dT25/dA25 model. The role of the hydrophobic part (poly(TBAm)) of the conjugate synthesized with the block copolymer in the orientation of the conjugate after coating was revealed by spotting experiments achieved in a mixed solvent (DMF/H(2)O). The use of block copolymer-dT25 conjugate afforded a significant sensitivity improvement of the hybridization assay.

Physicochemical and interfacial investigation of lipid/polymer particle assemblies.

A model study was investigated to develop colloidal supramolecular assemblies consisting of particles coated with lipid layers. The interactions between monodisperse sulfate-charged poly(styrene) submicrometer particles and zwitterionic/cationic lipid vesicles composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and 1,2-dipalmitoyl-3-trimethylammonium propane were considered. The influence of relevant experimental parameters on the final associations was examined by quasi-elastic light scattering to point out some new phenomena occurring in these colloidal systems. The major role of electrostatic interactions as driving forces to control the organization between cationic lipids and oppositely charged poly(styrene) particles was clearly evident, whereas this influence was less pronounced when considering the zwitterionic lipids. The characterization of these original complex assemblies was completed by a thorough study of the surface modification. The combination of zeta potential measurements, X-ray photoelectron spectroscopy analyses, and microscopy observations proved that the envisioned model can really correspond to polymer particles surrounded by lipids.

New hydrolyzable pH-responsive cationic polymers for gene delivery: a preliminary study.

Here we want to report the synthesis and the characterization of 2-methylacrylic acid 2-(3-imidazol-1-yl-propionyloxy)ethyl ester (IPEMA), a new methacrylate derivative monomer bearing an hydrolyzable side chain terminated by an imidazole group. The kp/kt(1/2) value for its homopolymerization in N,N-dimethylformamide at 60 degrees C was found to be 0.120 mol(-1/2) x L(1/2) x s(-1/2). The free radical copolymerization of N,N-dimethylaminoethyl methacrylate and this monomer was studied in N,N-dimethylformamide at 60 degrees C, the reactivity ratios of this couple of monomers were determined to be r(DMAEMA) = 1.13 +/- 0.09 and r(IPEMA) = 0.82 +/- 0.09 (using distinct calculation methods). Molecular weights analysis, parallely with refractive index increments measurements, were performed to characterize the obtained polymers. Potentiometric titrations showed the ability of these copolymers to act as a 'proton sponge'. Preliminary study of the copolymers hydrolysis proved that imidazole units could be slowly cleaved from the polymer backbone at 37 degrees C in neutral aqueous buffer. Agarose gel electrophoresis of plasmid DNA/polymer complexes demonstrated the DNA complexing properties of these imidazole-based copolymers.

Versatile and efficient formation of colloids of biopolymer-based polyelectrolyte complexes.

The formation of colloids based on polyelectrolyte complexes (PECs) of biopolymers was investigated through the complexation between two charged polysaccharides, chitosan as polycation, and dextran sulfate as polyanion. The slow dropwise addition of components, generally used for the formation of PECs, allowed to elaborate both cationic or anionic particles with an excess of chitosan or dextran sulfate, respectively. The PEC particles featured a core/shell structure, the hydrophobic core resulting from the segregation of complexed segments whereas excess component in the outer shell ensured the colloidal stabilization against further coagulation. Considering the host/guest concept for the formation of PECs, the influence of the molecular weight of components on particles sizes could be well explained by the chain length ratios of the two polymers. As an irreversible flocculation occurred with a dropwise approach for both cationic and anionic PEC particles when the mixing ratio was close to unity, a more versatile, and simpler to setup, method was designed: the one-shot addition of one solution to the other. Because process of addition is faster than the flocculation, cationic or anionic particles could be elaborated irrespective of the order of addition of the reactant. Characterization of these particles by quasielastic light scattering, electrophoresis, and scanning electron microscopy revealed very similar properties to those obtained by a slow dropwise approach. Critical coagulation concentrations of 0.12 and 0.09 M (with sodium chloride) for cationic and anionic particles evidenced a mostly electrostatic stabilization.

Formation and properties of positively charged colloids based on polyelectrolyte complexes of biopolymers.

Formation of colloids based on polyelectrolyte complexes (PECs) was mainly studied with synthetic polyelectrolytes. In this study, we describe the elaboration of positively charged PEC particles at a submicrometer level obtained by the complexation between two charged polysaccharides, chitosan as polycation and dextran sulfate (DS) as polyanion. The complexes were elaborated by dropwise addition of default amounts of DS to excess chitosan. Quasi-elastic light scattering was used to investigate in detail the influence of the characteristics of components (chain length, degree of acetylation) and parameters linked to the reaction of complexation (molar mixing ratio, ionic strength, concentration in polymer) on the sizes and polydispersity of colloids. Chain length of chitosan is the major parameter affecting the dimensions of the complexes, high molar mass chitosans leading to the largest particles. Variations of hydrodynamic diameters of PECs with the molar mass of chitosan are consistent with a mechanism of particle formation through the segregation of the neutral and then hydrophobic blocks of the polyelectrolyte complexed segments. Resulting particles display probably a structure constituted by a neutral core surrounded by a chitosan shell ensuring the colloidal stabilization. Such a structure was evidenced by measurements of electrophoretic mobilities revealing that the positive charge of particles was decreasing with pH, in relation with the neutralization of excess glucosamine hydrochloride moieties.

Typical physicochemical behaviors of chitosan in aqueous solution.

Physicochemical properties of a homogeneous series of chitosans with different degrees of acetylation and almost the same degree of polymerization were investigated in an ammonium acetate buffer. Techniques such as interferometry, static light scattering (in batch or coupled on line with a chromatographic system), and viscometry were processed. All of the results agree with a unique law of behavior only depending on the degree of acetylation of the polymer. Indeed, values of the refractive index increment, radius of gyration, second viral coefficient, and intrinsic viscosity are decreasing in the same way as DA is increasing. Three distinct domains of DA were defined and correlated to the different behaviors of chitosans: (i) a polyeletrolyte domain for DA below 20%; (ii) a transition domain between DA = 20% and 50% where chitosan loses its hydrophilicity; (iii) a hydrophobic domain for DAs over 50% where polymer associations can arise. Conformations of chitosan chains were studied by the calculations of the persistence lengths (L(p)). The average value was found to be close to 5 nm, in agreement with the wormlike chain model, but no significant variation of L(p) with the degree of acetylation was noticed.

Polymer functionalized submicrometric emulsions as potential synthetic DNA vectors.

Triglyceride-based emulsions were first prepared by a solvent displacement procedure which was modified to achieve their functionalization by surface deposition of various amphiphilic comb-like copolymers. These emulsions have been characterized as regards to hydrodynamic particle size and surface charges using dynamic light scattering and electrophoretic mobility measurements. The adsorption isotherms of a polydT15 oligonucleotide and a model plasmid showed that the process was dependent on the nature of the interfaces, the affinity for the nucleic acid increasing with more cationic charges, together with improved accessibility. The binding process was found to proceed according to two regimes: one at low nucleic acid coverage, independent of the initial plasmid concentration, and the second one at high coverage, which was nucleic-acid-concentration dependent. This behavior was considered to occur because of the development of repulsive interactions upon increasing the amount of immobilized nucleic acid. The complexation of plasmid complexed at the interface was finally investigated using the ethidium bromide displacement technique. The level of compaction of plasmid complexed onto the functionalized emulsions was lower than that obtained with the parent free polymer.