Root cone angle is enlarged in docs1 LRR-RLK mutants in rice.

BACKGROUND: The DEFECTIVE IN OUTER CELL LAYER SPECIFICATION 1 (DOCS1) gene belongs to the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) subfamily. It has been discovered few years ago in Oryza sativa (rice) in a screen to isolate mutants with defects in sensitivity to aluminum. The c68 (docs1-1) mutant possessed a nonsense mutation in the C-terminal part of the DOCS1 kinase domain. FINDINGS: We have generated a new loss-of-function mutation in the DOCS1 gene (docs1-2) using the CRISPR-Cas9 technology. This new loss-of-function mutant and docs1-1 present similar phenotypes suggesting the original docs1-1 was a null allele. Besides the aluminum sensitivity phenotype, both docs1 mutants shared also several root phenotypes described previously: less root hairs and mixed identities of the outer cell layers. Moreover, our new results suggest that DOCS1 could also play a role in root cap development. We hypothesized these docs1 root phenotypes may affect gravity responses. As expected, in seedlings, the early gravitropic response was delayed. Furthermore, at adult stage, the root gravitropic set angle of docs1 mutants was also affected since docs1 mutant plants displayed larger root cone angles. CONCLUSIONS: All these observations add new insights into the DOCS1 gene function in gravitropic responses at several stages of plant development.

Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping.

Early vigour of rice, defined as seedling capacity to accumulate shoot dry weight (SDW) rapidly, is a complex trait. It depends on a genotype propensity to assimilate, store, and/or use non-structural carbohydrates (NSC) for producing large and/or numerous leaves, involving physiological trade-offs in the expression of component traits and, possibly, physiological and genetic linkages. This study explores a plant-model-assisted phenotyping approach to dissect the genetic architecture of rice early vigour, applying the Genome Wide Association Study (GWAS) to morphological and NSC measurements, as well as fitted parameters for the functional-structural plant model, Ecomeristem. Leaf size, number, SDW, and source-leaf NSC concentration were measured on a panel of 123 japonica accessions. The data were used to estimate Ecomeristem genotypic parameters driving organ appearance rate, size, and carbon dynamics. GWAS was performed based on 12 221 single-nucleotide polymorphisms (SNP). Twenty-three associations were detected at P <1×10(-4) and 64 at P <5×10(-4). Associations for NSC and model parameters revealed new regions related to early vigour that had greater significance than morphological traits, providing additional information on the genetic control of early vigour. Plant model parameters were used to characterize physiological and genetic trade-offs among component traits. Twelve associations were related to loci for cloned genes, with nine related to organogenesis, plant height, cell size or cell number. The potential use of these associations as markers for breeding is discussed.

Genetic architecture of sensory exploitation: QTL mapping of female and male receiver traits in an acoustic moth.

The evolution of extravagant sexual traits by sensory exploitation occurs if males incidentally evolve features that stimulate females owing to a pre-existing environmental response that arose in the context of natural selection. The sensory exploitation process is thus expected to leave a specific genetic imprint, a pleiotropic control of the original environmental response and the novel sexual response in females. However, females may be subsequently selected to improve their discrimination of environmental and sexual stimuli. Accordingly, responses may have diverged and the original genetic architecture may have been modified. These possibilities may be considered by studying the genetic architecture of responses to male signals and to the environmental stimuli that were purportedly 'exploited' by those signals. However, no previous study has addressed the genetic control of sensory exploitation. We investigated this question in an acoustic pyralid moth, Achroia grisella, in which a male ultrasonic song attracts females and perception of ultrasound likely arose in the context of detecting predatory bats. We examined the genetic architecture of female response to bat echolocation signals and to male song via a cartographic study of quantitative trait loci (QTL) influencing these receiver traits. We found several QTL for both traits, but none of them were colocalized on the same chromosomes. These results indicate that - to the extent to which male A. grisella song originated by the process of sensory exploitation - some modification of the female responses occurred since the origin of the male signal.

Investigation of a planar optical waveguide in 2D PPLN using helium implantation technique.

In this work, we report the investigation of a planar waveguide in a 2D periodically-poled lithium niobate (PPLN). The waveguide is fabricated by helium (He(+)) implantation at 2 MeV and a fluence of 1.5 x 10(16) ions/cm(2). Second harmonic generation (SHG) at 532 nm using a Q-switched laser and a CW laser diode at 1064 nm, was measured as a function of angular distribution and temperature. The experimental results show higher gain in SHG conversion efficiency in the waveguide than in the bulk 2D PPLN. In particular, SHGs from 2D reciprocal lattice vectors (RLV) are observed and studied.

Targeted association analysis identified japonica rice varieties achieving Na(+)/K (+) homeostasis without the allelic make-up of the salt tolerant indica variety Nona Bokra.

During the last decade, a large number of QTLs and candidate genes for rice tolerance to salinity have been reported. Using 124 SNP and 52 SSR markers, we targeted 14 QTLs and 65 candidate genes for association mapping within the European Rice Core collection (ERCC) comprising 180 japonica accessions. Significant differences in phenotypic response to salinity were observed. Nineteen distinct loci significantly associated with one or more phenotypic response traits were detected. Linkage disequilibrium between these loci was extremely low, indicating a random distribution of favourable alleles in the ERCC. Analysis of the function of these loci indicated that all major tolerance mechanisms were present in the ERCC although the useful level of expression of the different mechanisms was scattered among different accessions. Under moderate salinity stress some accessions achieved the same level of control of Na(+) concentration and Na(+)/K(+) equilibrium as the indica reference variety for salinity tolerance Nona Bokra, although without sharing the same alleles at several loci associated with Na(+) concentration. This suggests (a) differences between indica and japonica subspecies in the effect of QTLs and genes involved in salinity tolerance and (b) further potential for the improvement of tolerance to salinity above the tolerance level of Nona Bokra, provided the underlying mechanisms are complementary at the whole plant level. No accession carried all favourable alleles, or showed the best phenotypic responses for all traits measured. At least nine accessions were needed to assemble the favourable alleles and all the best phenotypic responses. An effective strategy for the accumulation of the favourable alleles would be marker-assisted population improvement.

Variability of grain quality in sorghum: association with polymorphism in Sh2, Bt2, SssI, Ae1, Wx and O2.

To ensure food security in Africa and Asia, developing sorghum varieties with grain quality that matches consumer demand is a major breeding objective that requires a better understanding of the genetic control of grain quality traits. The objective of this targeted association study was to assess whether the polymorphism detected in six genes involved in synthesis pathways of starch (Sh2, Bt2, SssI, Ae1, and Wx) or grain storage proteins (O2) could explain the phenotypic variability of six grain quality traits [amylose content (AM), protein content (PR), lipid content (LI), hardness (HD), endosperm texture (ET), peak gelatinization temperature (PGT)], two yield component traits [thousand grain weight (TGW) and number of grains per panicle (NBG)], and yield itself (YLD). We used a core collection of 195 accessions which had been previously phenotyped and for which polymorphic sites had been identified in sequenced segments of the six genes. The associations between gene polymorphism and phenotypic traits were analyzed with Tassel. The percentages of admixture of each accession, estimated using 60 RFLP probes, were used as cofactors in the analyses, decreasing the proportion of false-positive tests (70%) due to population structure. The significant associations observed matched generally well the role of the enzymes encoded by the genes known to determine starch amount or type. Sh2, Bt2, Ae1, and Wx were associated with TGW. SssI and Ae1 were associated with PGT, a trait influenced by amylopectin amount. Sh2 was associated with AM while Wx was not, possibly because of the absence of waxy accessions in our collection. O2 and Wx were associated with HD and ET. No association was found between O2 and PR. These results were consistent with QTL or association data in sorghum and in orthologous zones of maize. This study represents the first targeted association mapping study for grain quality in sorghum and paves the way for marker-aided selection.

Structural investigation of an exopolysaccharide substituted with a lactyl ether group produced by Raoultella terrigena Ez-555-6 isolated in the Chernobyl exclusion zone.

Raoultella terrigena strain Ez-555-6, isolated from a root nodule of Medicago sativa harvested in the Chernobyl exclusion zone, produces a non-referenced high-molecular-mass exopolysaccharide (EPS). The structure of this EPS was determined using a combination approach including monosaccharide composition (GLC-FID, HPAEC-PAD), determination of glycosylation sites (GLC-EIMS) and 1D/2D NMR ((1)H, (13)C) and ESIMS (HR, MS/MS) studies of oligosaccharides obtained from mild acid hydrolysis. The EPS was found to be a charged pentasaccharide with a repeating unit composed of D-galactose, D-glucose, D-mannose and D-glucuronic acid (1:2:1:1). Lactic acid and O-acetyl substituents were localized on galactose and glucose residues, respectively, as presented in the following structure:

QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.).

A quantitative trait locus (QTL) analysis designed for a multi-parent population was carried out and tested in oil palm (Elaeis guineensis Jacq.), which is a diploid cross-fertilising perennial species. A new extension of the MCQTL package was especially designed for crosses between heterozygous parents. The algorithm, which is now available for any allogamous species, was used to perform and compare two types of QTL search for small size families, within-family analysis and across-family analysis, using data from a 2 x 2 complete factorial mating experiment involving four parents from three selected gene pools. A consensus genetic map of the factorial design was produced using 251 microsatellite loci, the locus of the Sh major gene controlling fruit shell presence, and an AFLP marker of that gene. A set of 76 QTLs involved in 24 quantitative phenotypic traits was identified. A comparison of the QTL detection results showed that the across-family analysis proved to be efficient due to the interconnected families, but the family size issue is just partially solved. The identification of QTL markers for small progeny numbers and for marker-assisted selection strategies is discussed.

Hybrid performance in taro (Colocasia esculenta) in relation to genetic dissimilarity of parents.

Taro (Colocasia esculenta) breeding, as other root crop breeding, is based on the production and evaluation of large numbers of hybrids. The selection of parents is based on their phenotypic value in the absence of information concerning general combining ability (GCA), specific combining ability (SCA), or genetic distances between varieties. By combining data from heritability trials and from genetic diversity studies conducted with AFLP and SSR markers, we aimed at studying the relationship between hybrid vigour and genetic dissimilarity between parents. The traits studied included number of suckers, corm weight, corm dimensions, and dry matter content. Correlation coefficients between hybrid gain and dissimilarity values were calculated. The prediction of hybrid performance based on the mid-parent value was compared to the prediction based on a modified expression that takes into account the genetic relationships between parents. Correlations were all but one positive but not statistically significant for all traits, with the exception of the number of suckers, when using SSR markers for dissimilarity calculations. Accordingly, the genetic dissimilarities in the prediction of hybrid performances did not increase the correlation between predicted and observed hybrid vigour values. However, large differences were observed among the residual means from the regression between predicted and observed values when using AFLP or SSR markers, mainly due to the much higher polymorphism revealed by the latter. Models need to be further adapted to the type of molecular marker used, since their ability to reveal different rates of polymorphism will have a direct incidence on the calculation of genetic dissimilarities between genotypes. Nevertheless, since SSR markers are more polymorphic and more informative than AFLP markers, they should be preferentially used for these studies. Low genetic dissimilarity of parents yielded weak heterosis effects and future studies need to be conducted by using a broader genetic base. This is the first study assessing the relationship of hybrid vigour with the genetic distances between parents, conducted on a tropical root crop.

Oligogalacturonans production by free radical depolymerization of polygalacturonan.

The large production of acidic oligosaccharides was investigated by non-enzymatic depolymerization of polygalacturonic acid (PGA) using free hydroxyl radical hydrolysis process from H2O2/copper (II) system. A large amount of oligogalacturonides (OGAs) with degrees of polymerization up to 6 were fractionated, and characterized by ESI-Q/TOF-MASS spectrometry and 1H NMR spectroscopy. This efficient production of uronic oligosaccharides from PGA constitutes an original process to produce bioactive compounds in large scale up.

Production of oligoglucuronans using a monolithic enzymatic microreactor.

A glucuronan lyase (EC 4.2.2.14) was immobilized on a monolithic Convective Interaction Media (CIM) disk. The immobilization yield was equal to 29% of the initial activity and 35% of the initial protein amount. Degradations of three glucuronans with various O-acetylation degrees were investigated and compared with degradations using free enzyme. The immobilized glucuronan lyase was inhibited by the O-acetylation degree like the free enzyme. (1)H NMR analyses were used to study the O-acetylation degree of oligoglucuronans and demonstrated that the average degrees of polymerization were inclusive between 4 and 13 after 24h of degradation. This first immobilization of a glucuronan lyase constitutes a new tool to produce oligoglucuronans.

[Prevention of occupational respiratory diseases]. / Prévention des maladies professionnelles respiratoires.

INTRODUCTION: The purpose of this paper is to describe the prevention of occupational respiratory diseases and to make lung specialists aware of their role in preventing these conditions. BACKGROUND: We present briefly the basic points concerning the technical methods for prevention of occupational respiratory diseases. Occurrence of such diseases can be avoided only by effective prevention techniques. Some of the tools described can provide physicians with valuable information for the management of their patients. The physician's role in this preventative approach is discussed in relation to the different stages of the socio-occupational life of the patients. The actions to be taken vary, depending on whether the patient is under vocational guidance, working or retired. We introduce a number of prevention professionals able to assist the lung specialist in his advisory role, along with several document- and regulation- based tools suited to implementing the prevention of occupational respiratory diseases. CONCLUSION: Greater knowledge of the different professionals involved and promotion of more active working cooperation between all specialists should ensure more effective screening and care of people suffering from the harmful effects of these diseases.

Phylogeographic evidence of crop neodiversity in sorghum.

Sorghum has shown the adaptability necessary to sustain its improvement during time and geographical extension despite a genetic foundation constricted by domestication bottlenecks. Initially domesticated in the northeastern part of sub-Saharan Africa several millenia ago, sorghum quickly spread throughout Africa, and to Asia. We performed phylogeographic analysis of sequence diversity for six candidate genes for grain quality (Shrunken2, Brittle2, Soluble starch synthaseI, Waxy, Amylose extender1, and Opaque2) in a representative sample of sorghum cultivars. Haplotypes along 1-kb segments appeared little affected by recombination. Sequence similarity enabled clustering of closely related alleles and discrimination of two or three distantly related groups depending on the gene. This scheme indicated that sorghum domestication involved structured founder populations, while confirming a specific status for the guinea margaritiferum subrace. Allele rooted genealogy revealed derivation relationships by mutation or, less frequently, by recombination. Comparison of germplasm compartments revealed contrasts between genes. Sh2, Bt2, and SssI displayed a loss of diversity outside the area of origin of sorghum, whereas O2 and, to some extent, Wx and Ae1 displayed novel variation, derived from postdomestication mutations. These are likely to have been conserved under the effect of human selection, thus releasing valuable neodiversity whose extent will influence germplasm management strategies.

[Three-dimensional imaging of root axes in patients from X-ray computed tomography slices]. / Visualisation tridimensionnelle des axes radiculaires des dents chez les patients explorés en coupes TDM.

The authors propose to materialize the corono-radicular axes of the teeth starting from their centre of gravity. This last is calculated with the data of the matrix of inertia resulting from the segmentation from tomodensitometric cuts (TDM). The sample is composed of 37 subjects (16 women and 21 men) old from 15 to 65 years, pertaining to a orthomorphic population. The helicoid acquisition of the data is carried out by an apparatus CT Twin Flash (Elscint Haïfa, Israel) on the subjects in decubitus dorsal under 120 kV with 100 mAs. The software C2000 allows the building of the maxillo-facial frame 8 points which becomes the absolute reference mark of the study. The same software allows by thresholding the selection of the teeth on the native cuts. The calculation of their axis of inertia makes it possible to materialize their barycentre. It becomes thus possible to visualize the position and the orientation of each tooth inside the maxillo-facial frame and the intra-reports/ratios and inter-arcades. The observations which result from this introduce interrogations as for the relevance of certain dogmas occlusodontic.

Development of NIRS equations for food grain quality traits through exploitation of a core collection of cultivated sorghum.

A sorghum core collection representing a wide range of genetic diversity and used in the framework of a sorghum breeding and genetics program was evaluated by near-infrared reflectance spectroscopy (NIRS) to predict food grain quality traits: amylose content (AM), protein content (PR), lipid content (LI), endosperm texture (ET), and hardness (HD). A total of 278 sorghum samples were scanned as whole and ground grain to develop calibration equations. Laboratory analyses were performed on NIRS sample subsets that preserved the core collection racial distribution. Principal component analysis performed on NIRS spectra evidenced a level of structure following known sorghum races, which underlined the importance of using a wide range of genetic diversity. Performances of calibration equations were evaluated by the coefficient of determination, bias, standard error of laboratory (SEL), and ratio of performance deviation (RPD). Ground grain spectra gave better calibration equations than whole grain. PR equation (RPD of 5.7) can be used for quality control. ET, LI, and HD equations (RPD of 2.9, 2.6, and 2.6, respectively) can be used for screening steps. Even with a small SEL in whole sample analysis, a RPD of 1.8 for AM confirmed that this variable is not easy to predict with NIRS.

Purification and characterization of a novel glucuronan lyase from Trichoderma sp. GL2.

The filamentous fungus Trichoderma sp. GL2 produces an extracellular glucuronan lyase (GL) when grown on glucuronan as the sole carbon source. In this paper, we report the purification to electrophoretical homogeneity of this polysaccharide lyase by size exclusion chromatography and anion exchange chromatography. The purified GL, classified as an endopolyglucuronate lyase, is a monomer with an apparent molecular weight of 27 kDa and an isoelectric point of 6.95. Despite an inhibition of the activity when polysaccharide substrates were substituted by acetates, the enzyme was active toward glucuronans (acetylated or not) and ulvan, leading to various (4,5)-unsaturated products as oligoglucuronans (acetylated or deacetylated), highly acetylated low-molecular-weight (LMW) glucuronans, and LMW ulvans.

OryGenesDB: a database for rice reverse genetics.

Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics. We have developed OryGenesDB (http://orygenesdb.cirad.fr/), a database dedicated to rice reverse genetics. Insertion mutants of rice genes are catalogued by Flanking Sequence Tag (FST) information that can be readily accessed by this database. Our database presently contains 44166 FSTs generated by most of the rice insertional mutagenesis projects. The OryGenesDB genome browser is based on the powerful Generic Genome Browser (GGB) developed in the framework of the Generic Model Organism Project (GMOD). The main interface of our web site displays search and analysis interfaces to look for insertions in any candidate gene of interest. Several starting points can be used to exhaustively retrieve the insertions positions and associated genomic information using blast, keywords or gene name search. The toolbox integrated in our database also includes an 'anchoring' option that allows immediate mapping and visualization of up to 50 nucleic acid sequences in the rice Genome Browser of OryGenesDB. As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors.

Purification of oligouronides using hollow-fiber membrane functionalised with L-histidine.

The pseudobioaffinity chromatography with L-histidines immobilized onto poly(ethylene-vinyl alcohol) hollow-fiber membranes was studied for a selective purification of anionic oligosaccharides. Oligoglucuronans with different degrees of polymerization and acetylation, prepared by an enzymatic degradation of bacterial polyglucuronic acid, were used as models. The adsorption and elution parameters were studied to optimise the selective adsorption. A better understanding of the physico-chemical phenomena governing this selectivity was attempted and a few hypotheses on the mechanism of selectivity are proposed.

Contributions of intermolecular interactions between constitutive arabinoxylans to the flaxseeds mucilage properties.

The main fraction (about 75%) of the mucilage extracted from seeds of Linum usitatissimum which consists of arabino-xylans (AX) has been studied in dilute and semidilute regimes by SEC/MALLS analysis and rheology, respectively. It has been found that AX contains 3 populations of about 5 000 000 g mol(-1) (less than 10%), 1 000 000 g mol(-1) (about 40%), and 200 000 g mol(-1) (about 50%). We have also observed a great retention of polymer during the filtration procedure, which is much pronounced as the AX concentration increases. This evidences the presence of large aggregates in the solution. The retention can be greatly diminished if the filtration is conducted under higher temperature. Aggregation could result from the establishment of intermolecular associations via hydrogen bonds. This hypothesis seems to be confirmed by the two higher populations in molar masses which present a random coil conformation consistent with a low degree of branching. Rheological measurements, conducted at 20 g L(-1), have confirmed the association tendency leading to pseudo gels behavior. Viscoelastic properties have been evidenced by time-temperature master curves of dynamic spectra. Such master curves have also been established with addition of chaotropic (i.e., KSCN) and lyotropic (i.e., NaCl) salts. It has been shown that intermolecular associations are greatly diminished under chaotropic salts influence. This has been also confirmed by SEC/MALLS analysis. These results point out the role of hydrogen bonds in the organization of the AX system.

Production of glucuronan oligosaccharides using a new glucuronan lyase activity from a Trichoderma sp. strain.

Sinorhizobium meliloti M5N1CS synthesizes a homopolymer of glucuronic acids beta-(1,4) linked and variably C2 and/or C3O-acetylated. To obtain beta-Delta-(4,5)-unsaturated oligoglucuronans, various acetylated forms of this bacterial polymer were cleaved by a Trichoderma sp. GL2 glucuronan lyase. Oligomers with polymerization degrees up to 8 were then produced, purified by liquid chromatography (size exclusion and anions exchange) and characterized using 1H NMR and ESI-Q/TOF-MS. Finally, the production (in gram quantity) of pure unsaturated oligoglucuronans non-acetylated (di- and trisaccharide) was investigated thanks to the complete depolymerization of deacetylated glucuronan.