Complete genome characterisation of a novel 26th bluetongue virus serotype from Kuwait

Bluetongue virus is the "type" species of the genus Orbivirus, family Reoviridae. Twenty four distinct bluetongue virus (BTV) serotypes have been recognized for decades, any of which is thought to be capable of causing "bluetongue" (BT), an insect-borne disease of ruminants. However, two further BTV serotypes, BTV-25 (Toggenburg orbivirus, from Switzerland) and BTV-26 (from Kuwait) have recently been identified in goats and sheep, respectively. The BTV genome is composed of ten segments of linear dsRNA, encoding 7 virus-structural proteins (VP1 to VP7) and four distinct non-structural (NS) proteins (NS1 to NS4). We report the entire BTV-26 genome sequence (isolate KUW2010/02) and comparisons to other orbiviruses. Highest identity levels were consistently detected with other BTV strains, identifying KUW2010/02 as BTV. The outer-core protein and major BTV serogroup-specific antigen "VP7" showed 98% aa sequence identity with BTV-25, indicating a common ancestry. However, higher level of variation in the nucleotide sequence of Seg-7 (81.2% identity) suggests strong conservation pressures on the protein of these two strains, and that they diverged a long time ago. Comparisons of Seg-2, encoding major outer-capsid component and cell-attachment protein "VP2" identified KUW2010/02 as 26th BTV, within a 12th Seg-2 nucleotype [nucleotype L]. Comparisons of Seg-6, encoding the smaller outer capsid protein VP5, also showed levels of nt/aa variation consistent with identification of KUW2010/02 as BTV-26 (within a 9th Seg-6 nucleotype - nucleotype I). Sequence data for Seg-2 of KUW2010/02 were used to design four sets of oligonucleotide primers for use in BTV-26, type-specific RT-PCR assays. Analyses of other more conserved genome segments placed KUW2010/02 and BTV-25/SWI2008/01 closer to each other than to other "eastern" or "western" BTV strains, but as representatives of two novel and distinct geographic groups (topotypes). Our analyses indicate that all of the BTV genome segments have evolved under strong purifying selection.     

X-Ray absorption studies of Zn2+ binding sites in bacterial, avian, and bovine cytochrome bc1 complexes

Binding of Zn2+ has been shown previously to inhibit the ubiquinol cytochrome c oxidoreductase (cyt bc1 complex). X-ray diffraction data in Zn-treated crystals of the avian cyt bc1 complex identified two binding sites located close to the catalytic Qo site of the enzyme. One of them (Zn01) might interfere with the egress of protons from the Qo site to the aqueous phase. Using Zn K-edge x-ray absorption fine-structure spectroscopy, we report here on the local structure of Zn2+ bound stoichiometrically to noncrystallized cyt bc1 complexes. We performed a comparative x-ray absorption fine-structure spectroscopy study by examining avian, bovine, and bacterial enzymes. A large number of putative clusters, built by combining information from first-shell analysis and metalloprotein databases, were fitted to the experimental spectra by using ab initio simulations. This procedure led us to identify the binding clusters with high levels of confidence. In both the avian and bovine enzyme, a tetrahedral ligand cluster formed by two His, one Lys, and one carboxylic residue was found, and this ligand attribution fit the crystallographic Zn01 location of the avian enzyme. In the chicken enzyme, the ligands were the His121, His268, Lys270, and Asp253 residues, and in the homologous bovine enzyme they were the His121, His267, Lys269, and Asp254 residues. Zn2+ bound to the bacterial cyt bc1 complex exhibited quite different spectral features, consistent with a coordination number of 6. The best-fit octahedral cluster was formed by one His, two carboxylic acids, one Gln or Asn residue, and two water molecules. It was interesting that by aligning the crystallographic structures of the bacterial and avian enzymes, this group of residues was found located in the region homologous to that of the Zn01 site. This cluster included the His276, Asp278, Glu295, and Asn279 residues of the cyt b subunit. The conserved location of the Zn2+ binding sites at the entrance of the putative proton release pathways, and the presence of His residues point to a common mechanism of inhibition. As previously shown for the photosynthetic bacterial reaction center, zinc would compete with protons for binding to the His residues, thus impairing their function as proton donors/acceptors.     

Activity of secreted cell wall-modifying enzymes and expression of peroxidase-encoding gene following germination of <Emphasis Type="Italic">Orobanche ramosa</Emphasis>

Radicle growth of germinated seed of the root parasite O. ramosa is shown to be rapidly accompanied by secretion of proteins including pectinolytic enzymes, polygalacturonase and rhamnogalacturonase. These secretions peaked between 4 to 8 d after induction of germination and remained constant for some further days in the case of polygalacturonases. After 6 d, germinated seeds secreted proteins which exhibit peroxidase activity. The latter may be correlated with expression of OrPOX1, a putative gene encoding for secreted peroxidase. The involvement of these enzymes in host root attack and haustorium formation by the parasite is discussed.     

European Flint Landraces Grown In Situ Reveal Adaptive Introgression from Modern Maize

We have investigated the role of selection in the determination of the detected levels of introgression from modern maize hybrid varieties into maize landraces still cultivated in situ in Italy. We exploited the availability of a historical collection of landraces undertaken before the introduction and widespread use of modern maize, to analyse genomic changes that have occurred in these maize landraces over 50 years of co-existence with hybrid varieties. We have combined a previously published SSR dataset (n=21) with an AFLP loci dataset (n=168) to provide higher resolution power and to obtain a more detailed picture. We show that selection pressures for adaptation have favoured new alleles introduced by migration from hybrids. This shows the potential for analysis of historical introgression even over this short period of 50 years, for an understanding of the evolution of the genome and for the identification of its functionally important regions. Moreover, this demonstrates that landraces grown in situ represent almost unique populations for use for such studies when the focus is on the domesticated plant. This is due to their adaptation, which has arisen from their dynamic evolution under a continuously changing agro-ecological environment, and their capture of new alleles from hybridisation. We have also identified loci for which selection has inhibited introgression from modern germplasm and has enhanced the distinction between landraces and modern maize. These loci indicate that selection acted in the past, during the formation of the flint and dent gene pools. In particular, the locus showing the strongest signals of selection is a Misfit transposable element. Finally, molecular characterisation of the same samples with two different molecular markers has allowed us to compare their performances. Although the genetic-diversity and population-structure analyses provide the same global qualitative pattern, which thus provides the same inferences, there are differences related to their natures and characteristics.     

Unreduced gametes in diploid Medicago and their importance in alfalfa breeding

Summary In the genus Medicago, it is known that 2n gametes have been important in the evolution and breeding of cultivated alfalfa, which is a natural polysomic polyploid (2n=4x=32), however little is known on the frequency of male and female 2n gametes in diploid relatives of alfalfa. To obtain data on the frequency of 2n gametes, more than 12,000 2x–4x and 4x–2x crosses were made in 1982 at Madison (USA). Diploid parents in crosses were from four populations of M. coerulea, two of M. falcata and one diploid population of cultivated M. sativa which was derived by haploidy. The tetraploid seed parent in the crosses was a male-sterile M. sativa clone and vigorous tetraploid M. sativa plants were used as pollen parents. Each of 274 diploid plants was utilized both as male and as female. Of the 548 cross combinations, 266 crosses produced variable quantities of seeds which were sown in 1983 in a greenhouse at Perugia (Italy); the plants were subsequently space transplanted in the field in 1984. The identification of ploidy level of these genotypes was made on the basis of morphological characters, plant fertility, pollen stainability and chromosome counts.Of the 515 plants analyzed, the majority behaved as normal tetraploids indicating that many diploid plants produced 2n gametes. Diplogynous and diplandrous gamete production was not correlated with each other, which indicated a different genetic control of 2n sporogenesis in the 2 sexes. Only 4 F₁ triploid plants confirmed the presence of a very effective triploid block in alfalfa. In consequence, bilateral sexual polyploidization is a more likely alternative for the origin of tetraploid alfalfa than triploid bridges. The present study showed that it is possible to efficiently identify genotypes able to produce high frequencies of 2n gametes within natural populations of diploids Medicago that are useful in alfalfa breeding.Part of this study was conducted at the Agronomy Department, University of Wisconsin, Madison, Wis, USA, while one of us (F. Veronesi) was in receipt of financial assistance provided by the National Research Council of Italy; part was conducted at Centro di Studio per il Miglioramento Genetico delie Piante Foraggere, C.N.R., Perugia, Italy. The paper was presented at the Eucarpia Fodder Crops Section Meeting, Svalöv, Sweden, 16–19th September 1985     

Mesenchymal stem cells in maxillary sinus augmentation: A systematic review with meta-analysis

AIM: To investigate the effectiveness of mesenchymal stem cells (MSCs) in maxillary sinus augmentation (MSA), with various scaffold materials.METHODS: MEDLINE, EMBASE and SCOPUS were searched using keywords such as sinus graft, MSA, maxillary sinus lift, sinus floor elevation, MSC and cell-based, in different combinations. The searches included full text articles written in English, published over a 10-year period (2004-2014). Inclusion criteria were clinical/radiographic and histologic/ histomorphometric studies in humans and animals, on the use of MSCs in MSA. Meta-analysis was performed only for experimental studies (randomized controlled trials and controlled trials) involving MSA, with an outcome measurement of histologic evaluation with histomorphometric analysis reported. Mean and standard deviation values of newly formed bone from each study were used, and weighted mean values were assessed to account for the difference in the number of subjects among the different studies. To compare the results between the test and the control groups, the differences of regenerated bone in mean and 95% confidence intervals were calculated.RESULTS: Thirty-nine studies (18 animal studies and 21 human studies) published over a 10-year period (between 2004 and 2014) were considered to be eligible for inclusion in the present literature review. These studies demonstrated considerable variation with respect to study type, study design, follow-up, and results. Meta-analysis was performed on 9 studies (7 animal studies and 2 human studies). The weighted mean difference estimate from a random-effect model was 9.5% (95%CI: 3.6%-15.4%), suggesting a positive effect of stem cells on bone regeneration. Heterogeneity was measured by the I² index. The formal test confirmed the presence of substantial heterogeneity (I² = 83%, P < 0.0001). In attempt to explain the substantial heterogeneity observed, we considered a meta-regression model with publication year, support type (animal vs humans) and follow-up length (8 or 12 wk) as covariates. After adding publication year, support type and follow-up length to the meta-regression model, heterogeneity was no longer significant (I² = 33%, P = 0.25).CONCLUSION: Several studies have demonstrated the potential for cell-based approaches in MSA; further clinical trials are needed to confirm these results.     

Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces

The study of phenotypic and genetic diversity in landrace collections is important for germplasm conservation. In addition, the characterisation of very diversified materials with molecular markers offers a unique opportunity to define significant marker-trait associations of biological and agronomic interest. Here, 50 tomato landraces (mainly collected in central Italy), nine vintage and modern cultivars, and two wild outgroups were grown at two locations in central Italy and characterised for 15 morpho-physiological traits and 29 simple sequence repeat (SSR) loci. The markers were selected to include a group of loci in regions harbouring reported quantitative trait loci (QTLs) that affect fruit size and/or shape (Q-SSRs) and a group of markers that have not been mapped or shown to have a priori known linkage (NQ-SSRs). As revealed by univariate and multivariate analyses of morphological data, the landraces grouped according to vegetative and reproductive traits, with emphasis on fruit size, shape and final destination of the product. Compared to the low molecular polymorphism reported in tomato modern cultivars, our data reveal a high level of molecular diversity in landraces. Such diversity has allowed the inference of the existence of a genetic structure that was factored into the association analysis. As the proportion of significant associations is higher between the Q-SSR subset of markers and the subset of traits related to fruit size and shape than for all of the other combinations, we conclude that this approach is valid for establishing true-positive marker-trait relationships in tomato. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L.

The Sequence-Specific Amplification Polymorphism (S-SAP) method, recently derived from the Amplified Fragment Length Polymorphism (AFLP) technique, produces amplified fragments containing a retrotransposon LTR sequence at one end and a host restriction site at the other. We report the application of this procedure to the LTR of the Tms1 element from Medicago sativa L. Genomic dot-blot analysis indicated that Tms1 LTRs represent about 0.056% of the M. sativa genome, corresponding to 16 x 10(3) copies per haploid genome. An average of 66 markers were amplified for each primer combination. Overall 49 polymorphic fragments were reliably scored and mapped in a F(1) population obtained by crossing diploid M. falcata with M. coerulea. The utility of the LTR S-SAP markers was higher than that of AFLP or SAMPL (Selective Amplification of Microsatellite Polymorphic Loci) markers. The efficiency index of the LTR S-SAP assay was 28.3, whereas the corresponding values for AFLP and SAMPL markers were 21.1 and 16.7, respectively. The marker index for S-SAP was 13.1, compared to 8.8 for AFLP and 9.5 for SAMPL. Application of the Tms1 LTR-based S-SAP to double-stranded cDNA resulted in a complex banding pattern, demonstrating the presence of Tms1 LTRs within exons. As the technique was successfully applied to other species of the genus Medicago, it should prove suitable for studying genetic diversity within, and relatedness between, alfalfa species.     

Hearing loss: frequency and functional studies of the most common connexin26 alleles

Mutations in the GJB2 gene, encoding the gap-junction channel protein connexin 26, account for the majority of recessive forms and some of the dominant cases of deafness. Here, we report the frequency of GJB2 alleles in the Italian population affected by hearing loss and the functional analysis of six missense mutations. Genetic studies indicate that, apart from the common 35delG, only few additional mutations can be detected with a significant frequency in our population. Transfection of communication-incompetent HeLa cells with Cx26 missense mutations revealed three distinct classes of functional deficits in terms of protein expression, subcellular localisation and/or functional activity. Moreover, the M34T mutant acted as a dominant inhibitor of wild-type Cx26 channel activity when the two proteins were co-expressed in a manner mimicking a heterozygous genotype. These data support the hypothesis of a functional role for M34T as a dominant allele and represent a further step towards a complete understanding of the role of GJB2 in causing hearing loss.     

WaterLOGSY as a method for primary NMR screening: Practical aspects and range of applicability

WaterLOGSY represents a powerful method for primary NMR screening in the identification of compounds interacting with macromolecules, including proteins and DNA or RNA fragments. Several relay pathways are used constructively in the experiment for transferring bulk water magnetization to the ligand. The method is particularly useful for the identification of novel scaffolds of micromolar affinity that can be then optimized using directed screening, combinatorial chemistry, medicinal chemistry and structure-based drug design. The practical aspects and range of applicability of the WaterLOGSY experiment are analyzed in detail here. Competition binding and titration WaterLOGSY permit, after proper correction, the evaluation of the dissociation binding constant. The high sensitivity of the technique in combination with the easy deconvolution of the mixtures for the identification of the active components, significantly reduces the amount of material and time needed for the NMR screening process.