Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance

Fungal plant pathogens secrete effector proteins and metabolites to cause disease. Additionally, some species transfer small RNAs (sRNAs) into plant cells to silence host mRNAs through complementary base pairing and suppress plant immunity. The fungus Sclerotinia sclerotiorum infects over 600 plant species, but little is known about the molecular processes that govern interactions with its many hosts. In particular, evidence for the production of sRNAs by S. sclerotiorum during infection is lacking. We sequenced sRNAs produced by S. sclerotiorum in vitro and during infection of two host species, Arabidopsis thaliana and Phaseolus vulgaris. We found that S. sclerotiorum produces at least 374 distinct highly abundant sRNAs during infection, mostly originating from repeat-rich plastic genomic regions. We predicted the targets of these sRNAs in A. thaliana and found that these genes were significantly more down-regulated during infection than the rest of the genome. Predicted targets of S. sclerotiorum sRNAs in A. thaliana were enriched for functional domains associated with plant immunity and were more strongly associated with quantitative disease resistance in a genome-wide association study (GWAS) than the rest of the genome. Mutants in A. thaliana predicted sRNA target genes SERK2 and SNAK2 were more susceptible to S. sclerotiorum than wild-type, suggesting that S. sclerotiorum sRNAs may contribute to the silencing of immune components in plants. The prediction of fungal sRNA targets in plant genomes can be combined with other global approaches, such as GWAS, to assist in the identification of plant genes involved in quantitative disease resistance.     

HIERARCHICAL SPATIAL STRUCTURE AND DISCRIMINANT ANALYSIS OF GENETIC DIVERSITY IN THE RED ALGA MAZZAELLA LAMINARIOIDES (GIGARTINALES, RHODOPHYTA)

Our study of the genetic structure of Mazzaella laminarioides (Bory) Fredericq (Gigartinales) in the central Chilean region documented a high level of genetic diversity based on random amplified polymorphic DNA (RAPD) markers and indicated the occurrence of significant genetic structure at different spatial scales. A total of 288 haploid gametophytes was analyzed with 17 polymorphic RAPD bands, which produced 202 distinct multilocus genotypes. Within stands, mean gene diversity ranged from 0.210 to 0.249 and no significant linkage disequilibrium could be detected among pairs of alleles, revealing that recombination (sexual reproduction) regularly shuffles the genes at that scale. Analysis of molecular variance within stands (less than 30 m) showed that the structure was very low, only marginally significant, and did not increase with increasing hierarchical levels at this lowest spatial scale. In contrast, at a larger spatial scale (among stands, from 5 to 60 km), increasing geographical distance seemed to account for increasing isolation between populations even if natural barriers, such as sandy beaches or river estuaries, may play a role in such isolation. Moreover, the strong genetic differentiation occurring between locations separated by 60 km allowed the assignment of individuals to their original population through a canonical discriminant analysis. This approach further allowed the identification of potential recent migrants from one population to the other. Thus, in species like M. laminarioides for which the dominance of RAPD markers can be avoided by selecting haploid individuals, RAPD analysis appeared to be specially appropriate for the study of genetic differentiation.     

Seed dispersal distance classes and dispersal modes for the European flora

Motivation

Although dispersal ability is one of the key features determining the spatial dynamics of plant populations and the structure of plant communities, it is also one of the traits for which we still lack data for most species. We compiled a comprehensive dataset of seed dispersal distance classes and predominant dispersal modes for most European vascular plants. Our seed dispersal dataset can be used in functional biogeography, dynamic vegetation modelling and ecological studies at local to continental scales.

Main Types of Variables Contained

Species were classified into seven ordered classes with similar dispersal distances estimated based on the predominant dispersal mode, the morphology of dispersal units (diaspores or propagules), life form, plant height, seed mass, habitat and known dispersal by humans. We evaluated our results by comparing them with dispersal distances calculated using the ‘dispeRsal’ function in R.

Spatial Location

Europe.

Time Period

Present.

Major Taxa and Level of Measurement

The seed dispersal dataset contains information on dispersal distance classes and the predominant dispersal mode for 10,327 most frequent and locally dominant European vascular plant species.

Software Format

Data are available in .csv format.     

Apoptosis-resistant NS/0 E1B-19K myelomas exhibit increased viability and chimeric antibody productivity under cell cycle modulating conditions

Lymphoid cells expressing sufficient levels of Bcl-2 or E1B-19K are known to resist to induction of apoptosis in glutamine-free or nutrient-limited batch cultures. However, despite the increased viability and prolonged stationary phase achieved in batch culture, product yields are not necessarily improved. Here we have found that expression of E1B-19K in NS/0 myeloma cells cultivated in the presence of certain cell cycle modulators could result in a significant increase in MAb productivity as compared to untransfected control cells. The use of E1B-19K significantly enhanced cell survival in the presence of osmolytes (sorbitol, NaCl), DNA synthesis inhibitors (hydroxyurea, excess thymidine), and the cell culture additive OptiMAb™. E1B-19K myelomas cultivated in the presence of NaCl or OptiMAb™ accumulated in the G1 phase, while those arrested with excess thymidine were blocked in all phases. Interestingly, control NS/0 cells treated with these agents were found to die in a cell-cycle specific manner. Thus, while all G1 and most S phase cells quickly underwent apoptosis, G2/M cells remained alive and maintained MAb secretion for more than 10 days if supplied with adequate nutrients. For both control and E1B-19K cells, incubation with sorbitol or hydroxyurea was detrimental for MAb secretion, while addition of NaCl, excess thymidine and OptiMAb™ resulted in an increased specific MAb productivity as compared to the batch culture. However, this increase resulted in an improvement of final MAb yields only in the case of OptiMAb™. The extension of viability conferred by E1B-19K allowed to further improve the final MAb yield obtained using OptiMAb™ with a 3.3-fold increase for E1B-19K cells as compared to 1.8-fold for control NS/0 cells. This revised version was published online in August 2006 with corrections to the Cover Date.     

Study of differences between vertical root maps observed in a maize crop and simulated maps obtained using a model for the three-dimensional architecture of the root system

Differences between observed and simulated vertical root maps were studied in an attempt to evaluate the predictive ability of a simulation model of root system architecture under field conditions on mature plants, and to identify avenues for improvement. Some methodological problems associated with root mapping in the field are considered with a sensitivity analysis.Comparisons were made on a maize crop (early maturing hybrid F1 cultivar Dea) 15 days after silking. Four vertical root maps, perpendicular to the row and midway between two successive plants, were observed. Simulated root maps for different locations along the row showed essentially the same pattern, attesting of an approximately two-dimensional distribution of the roots in such a crop. Simulation of the intesection of roots with thin layers (thickness from 0 to 20 mm) instead of a perfect plane allowed us to assess effects due to the roughness of actual trench walls, and possible artefacts in the observation of root intersections. The simulated root profiles were very sensitive to this thickness, especially in the 0–5 mm range, in both average values, and overall shape. Actual data were close to the 3 mm thick simulations. This value seems plausible under our field conditions.Differences between simulated and actual root maps were shown to be mostly accounted for by the variations in soil bulk density. Thus, this environmental parameter appears as the most important one to include into the model for improving its predictions.     

Ycf1p-dependent Hg(II) detoxification in Saccharomyces cerevisiae.

In Saccharomyces cerevisiae, disruption of the YCF1 gene increases the sensitivity of cell growth to mercury. Transformation of the resulting ycf1 null mutant with a plasmid harbouring YCF1 under the control of the GAL promoter largely restores the wild-type resistance to the metal ion. The protective effect of Ycf1p against the toxicity of mercury is especially pronounced when yeast cells are grown in rich medium or in minimal medium supplemented with glutathione. Secretory vesicles from S. cerevisiae cells overproducing Ycf1p are shown to exhibit ATP-dependent transport of bis(glutathionato)mercury. Moreover, using beta-galactosidase as a reporter protein, a relationship between mercury addition and the activity of the YCF1 promoter can be shown. Altogether, these observations indicate a defence mechanism involving an induction of the expression of Ycf1p and transport by this protein of mercury-glutathione adducts into the vacuole. Finally, possible coparticipation in mercury tolerance of other ABC proteins sharing close homology with Ycf1p was investigated. Gene disruption experiments enable us to conclude that neither Bpt1p, Yor1p, Ybt1p nor YHL035p plays a major role in the detoxification of mercury.     

Crystal structure of Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase complexed with an analogue of 1,3-bisphospho-d-glyceric acid.

We report here the first crystal structure of a stable isosteric analogue of 1,3-bisphospho-d-glyceric acid (1,3-BPGA) bound to the catalytic domain of Trypanosoma cruzi glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) in which the two phosphoryl moieties interact with Arg249. This complex possibly illustrates a step of the catalytic process by which Arg249 may induce compression of the product formed, allowing its expulsion from the active site. Structural modifications were introduced into this isosteric analogue and the respective inhibitory effects of the resulting diphosphorylated compounds on T. cruzi and Trypanosoma brucei gGAPDHs were investigated by enzymatic inhibition studies, fluorescence spectroscopy, site-directed mutagenesis, and molecular modelling. Despite the high homology between the two trypanomastid gGAPDHs (> 95%), we have identified specific interactions that could be used to design selective irreversible inhibitors against T. cruzi gGAPDH.     

Control of 5′,5′-Dinucleoside Triphosphate Catabolism by APH1, a Saccharomyces cerevisiae Analog of Human FHIT

The putative human tumor suppressor gene FHIT (fragile histidine triad) (M. Ohta et al., Cell 84:587–597, 1996) encodes a protein behaving in vitro as a dinucleoside 5′,5′′′-P¹,P³-triphosphate (Ap₃A) hydrolase. In this report, we show that the Saccharomyces cerevisiae APH1 gene product, which resembles human Fhit protein, also hydrolyzes dinucleoside 5′,5′-polyphosphates, with Ap₃A being the preferred substrate. Accordingly, disruption of the APH1 gene produced viable S. cerevisiae cells containing reduced Ap₃A-hydrolyzing activity and a 30-fold-elevated Ap₃N concentration.     

MCQTL: multi-allelic QTL mapping in multi-cross design

The aim of the MCQTL software package is to perform QTL mapping in multi-cross designs. It allows the analysis of the usual populations derived from inbred lines and can link the families by assuming that the QTL locations are the same in all of them. Moreover, a diallel modelling of the QTL genotypic effects is allowed in multiple related families. The implemented model is a linear regression model. A composite interval mapping and an iterative QTL mapping are implemented to deal with multiple QTL models. Marker cofactor selections by forward or backward stepwise methods are implemented as well as computation of threshold test value by permutation. AVAILABILITY: The program is available on request after signing a licence agreement; free of charge for academic and non-profit organizations at http://www.genoplante.org (Bioinformatics products).     

Auditory hair cell-afferent fiber synapses are specialized to operate at their best frequencies

Auditory afferent fiber activity is driven by high-fidelity information transfer from the sensory hair cell. Presynaptic specializations, posited to maintain fidelity, are investigated at synapses with characteristic frequencies of 120 Hz and 320 Hz. Morphological data indicate that high-frequency cells have more synapses and higher vesicle density near dense bodies (DBs). Tracking vesicular release via capacitance changes identified three overlapping kinetic components of release corresponding to morphologically identified vesicle pools. High-frequency cells released faster; however, when normalized to release site number, low-frequency cells released faster, likely due to a greater Ca2+ load per synapse. The Ca(2+)-dependence of release was nonsaturating and independent of frequency, suggesting that release, not refilling, was rate limiting. A model of release derived from vesicle equilibration between morphologically defined pools reproduced the capacitance data, supporting a critical role in vesicle trafficking for DBs. The model suggests that presynaptic specializations enable synapses to operate most efficiently at their characteristic frequencies.