The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes

Background  

The legume Medicago truncatula has emerged as a model plant for the molecular and genetic dissection of various plant processes involved in rhizobial, mycorrhizal and pathogenic plant-microbe interactions. Aiming to develop essential tools for such genetic approaches, we have established the first genetic map of this species. Two parental homozygous lines were selected from the cultivar Jemalong and from the Algerian natural population (DZA315) on the basis of their molecular and phenotypic polymorphism.     

Mimicking the plant cell interior under water stress by macromolecular crowding: disordered dehydrin proteins are highly resistant to structural collapse

The dehydrins are a class of drought-induced proteins in plants that lack a fixed three-dimensional structure. Their specific molecular action, as well as the reason for their disordered character, is as yet poorly understood. It has been speculated, however, that the dehydrins are tuned to acquire a biologically active structure only under the conditions in which they normally function (i.e. upon dehydration). To test this hypothesis, we here investigate the effect of reduced water content and macromolecular crowding on three dehydrins from Arabidopsis (Arabidopsis thaliana). As a simplistic model for mimicking cellular dehydration, we used polyethylene glycol, glycerol, and sugars that plants naturally employ as compatible solutes (i.e. sucrose and glucose). Macromolecular crowding was induced by the large polysaccharides Ficoll and dextran. The results show that the dehydrins are remarkably stable in their disordered state and are only modestly affected by the solvent alterations. A notable exception is the dehydrin Cor47, which shows a small, intrinsic increase in helical structure at high concentrations of osmolytes. We also examined the effect of phosphorylation but found no evidence that such posttranslational modifications of the dehydrin sequences modulate their structural response to osmolytes and crowding agents. These results suggest that the dehydrins are highly specialized proteins that have evolved to maintain their disordered character under conditions in which unfolded states of several globular proteins would tend to collapse.     

Effects of endocrine disruptors on genes associated with 17beta-estradiol metabolism and excretion

In order to provide a global analysis of the effects of endocrine disruptors on the hormone cellular bioavailability, we combined 17beta-estradiol (E2) cellular flow studies with real-time PCR and Western blot expression measurements of genes involved in the hormone metabolism and excretion. Three endocrine disruptors commonly found in food were chosen for this study, which was conducted in the estrogen receptor (ER) negative hepatoblastoma HepG2 cell line: bisphenol A (BPA), genistein (GEN) and resveratrol (RES). We showed that 24h after a single dose treatment with genistein, resveratrol or bisphenol A, the expression of ATP-binding cassette transporters (the multidrug resistance or MDR, and the multidrug resistance associated proteins or MRP) uridine diphosphate-glucuronosyltransferases (UGT) and/or sulfotransferases (ST) involved in 17beta-estradiol elimination process were significantly modulated and that 17beta-estradiol cellular flow was modified. Resveratrol induced MDR1 and MRP3 expressions, bisphenol A induced MRP2 and MRP3 expressions, and both enhanced 17beta-estradiol efflux. Genistein, on the other hand, inhibited ST1E1 and UGT1A1 expressions, and led to 17beta-estradiol cellular retention. Thus, we demonstrate that bisphenol A, genistein and resveratrol modulate 17beta-estradiol cellular bioavailability in HepG2 and that these modulations most probably involve regulations of 17beta-estradiol phase II and III metabolism proteins. Up to now, the estrogenicity of environmental estrogenic pollutants has been based on the property of these compounds to bind to ERs. Our results obtained with ER negative cells provide strong evidence for the existence of ER-independent pathways leading to endocrine disruption.     

Developmentally programmed DNA splicing in Paramecium reveals short-distance crosstalk between DNA cleavage sites

Somatic genome assembly in the ciliate Paramecium involves the precise excision of thousands of short internal eliminated sequences (IESs) that are scattered throughout the germline genome and often interrupt open reading frames. Excision is initiated by double-strand breaks centered on the TA dinucleotides that are conserved at each IES boundary, but the factors that drive cleavage site recognition remain unknown. A degenerate consensus was identified previously at IES ends and genetic analyses confirmed the participation of their nucleotide sequence in efficient excision. Even for wild-type IESs, however, variant excision patterns (excised or nonexcised) may be inherited maternally through sexual events, in a homology-dependent manner. We show here that this maternal epigenetic control interferes with the targeting of DNA breaks at IES ends. Furthermore, we demonstrate that a mutation in the TA at one end of an IES impairs DNA cleavage not only at the mutant end but also at the wild-type end. We conclude that crosstalk between both ends takes place prior to their cleavage and propose that the ability of an IES to adopt an excision-prone conformation depends on the combination of its nucleotide sequence and of additional determinants.     

Harbor porpoise thyroids: histologic investigations and potential interactions with environmental factors

The thyroid plays an important role in development and is of primary importance in metabolism and heat loss for cetaceans, including the harbor porpoise (Phocoena phocoena). Several studies have demonstrated that environmental contaminants can alter various aspects of thyroid function in mammals and may contribute to various histologic changes. The present study completes the data set of a 2006 study by Das et al., by performing histological and immunohistologic investigations on thyroids of 36 harbor porpoises from Belgian and United Kingdom waters. The number and mean diameter of follicles (mum) and the relative proportion of follicular, connective, and vascular tissue (%) were quantified in the thyroid gland of each individual. Interfollicular fibrosis has been observed in these thyroid glands, and the collective findings support the hypothesis of an endocrine disruption of thyroid function through organochlorinated compounds. Our study aimed also to reveal potential relationships between thyroid morphometric data and metal levels (Cd, Fe, Zn, Cu, Se, and Hg) using multivariate statistical analysis. The multiple regressions revealed statistically significant relationships between trace elements (cadmium, selenium, and copper) and thyroid fibrosis. The largely negative relationships are interesting findings but do not support the hypothesis that these elements have an adverse effect on thyroid morphometry. Further research is needed to understand the nature of any relationship between organochlorine and trace element exposure and thyroid gland morphology and function in harbor porpoises.     

Microsatellite markers in soil‐feeding termites (Cubitermes subarquatus,Isoptera, Termitidae,Termitinae)

Seven microsatellite markers were isolated from Cubitermes subarquatus belonging to the soil‐feeding termite trophic group that plays a key role in tropical rain forests. A variability study performed by using a population of C. subarquatus (n = 73) sampled in the La Lopé forest reserve (Gabon) from 42 nests revealed from 4 to 12 alleles per locus and an heterozygosity from 0.28 to 0.84. Tests for cross‐species amplification realized in the sympatric C. intercalatus and in eight other sympatric termite genera indicated a wider application of the primers isolated from Cubitermes in soil‐feeding termites.     

Postglacial vegetation history in Luxembourg: new charcoal data from the cave of la Karelslé (Waldbillig, eastern Gutland)

The archaeological site of La Karelslé (Waldbillig, Luxembourg) provides the first important charcoal sequence in Luxembourg for the development of Holocene plant cover. During the Pre-boreal, the results show open woodland vegetation dominated by Pinus sylvestris type in association with Betula sp. and Rosaceae. After an important gap covering the Boreal and the early Atlantic, the data reveal the dominance of a deciduous Quercus woodland with Tilia sp., Fraxinus excelsior and Corylus avellana. Finally during the sub-Boreal, the assemblages indicate a cooler and wetter climate and Quercus woods with Fagus sylvatica and Taxus baccata. There is no clear evidence for human impact. Received June 5, 2001 / Accepted December 3, 2001     

A new mechanism of antibiotic resistance in Enterobacteriaceae induced by a structural modification of the major porin

In Enterobacter aerogenes, multidrug resistance involves a decrease in outer membrane permeability associated with changes in an as yet uncharacterized porin. We purified the major porin from the wild-type strain and a resistant strain. We characterized this porin, which was found to be an OmpC/OmpF-like protein and analysed its pore-forming properties in lipid bilayers. The porin from the resistant strain was compared with the wild-type protein and we observed (i) that its single-channel conductance was 70% lower than that of the wild type; (ii) that it was three times more selective for cations; (iii) a lack of voltage sensitivity. These results indicate that the clinical strain is able to synthesize a modified porin that decreases the permeability of the outer membrane. Mass spectrometry experiments identified a G to D mutation in the putative loop 3 of the porin. Given the known importance of this loop in determining the pore properties of porins, we suggest that this mutation is responsible for the novel resistance mechanism developed by this clinical strain, with changes in porin channel function acting as a new bacterial strategy for controlling beta-lactam diffusion via porins.     

FOUNTAIN: A JAVA open-source package to assist large sequencing projects

Background  

Better automation, lower cost per reaction and a heightened interest in comparative genomics has led to a dramatic increase in DNA sequencing activities. Although the large sequencing projects of specialized centers are supported by in-house bioinformatics groups, many smaller laboratories face difficulties managing the appropriate processing and storage of their sequencing output. The challenges include documentation of clones, templates and sequencing reactions, and the storage, annotation and analysis of the large number of generated sequences.