Legumes of the Sardinia Island: Knowledge on Symbiotic and Endophytic Bacteria and Interactive Software Tool for Plant Species Determination.

A meta-analysis was carried out on published literature covering the topic of interactive plant microbiology for botanical species of legumes occurring within the boundary of the Italian island Sardinia, lying between the Tyrrhenian and the western Mediterranean seas. Reports were screened for the description of three types of bacterial occurrences; namely, (a) the nitrogen-fixing symbionts dwelling in root nodules; (b) other bacteria co-hosted in nodules but having the ancillary nature of endophytes; (c) other endophytes isolated from different non-nodular portions of the legume plants. For 105 plant species or subspecies, over a total of 290 valid taxonomical descriptions of bacteria belonging to either one or more of these three categories were found, yielding 85 taxa of symbionts, 142 taxa of endophytes in nodules, and 33 in other plant parts.

Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity.

Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N into ammonia (nitrogen-fixation).

The Role of the Endophytic Microbiome in the Grapevine Response to Environmental Triggers.

Endophytism within represents a topic of critical relevance due to the multiple standpoints from which it can be approached and considered. From the biological and botanical perspectives, the interaction between microorganisms and perennial woody plants falls within the category of stable relationships from which the plants can benefit in multiple ways. The life cycle of the host ensures persistence in all seasons, repeated chances of contact, and consequent microbiota accumulation over time, leading to potentially high diversity compared with that of herbaceous short-lived plants.

Nodule-associated microbiome diversity in wild populations of Sulla coronaria reveals clues on the relative importance of culturable rhizobial symbionts and co-infecting endophytes.

The culturable bacteria from root nodules of Sulla coronaria growing in spontaneous conditions in Sardinia were characterized. This plant's peculiarity is to represent a legume still found in both wild and cropped statuses. We tested whether culturable bacteria would differ from those commonly isolated from its field-cropped varieties, to date exclusively represented by Rhizobium sullae.

Draft Genome Sequence of the Nitrogen-Fixing Type Strain IS123 Focusing on the Key Genes for Symbiosis with its Host L.

The prominent feature of rhizobia is their molecular dialogue with plant hosts. Such interaction is enabled by the presence of a series of symbiotic genes encoding for the synthesis and export of signals triggering organogenetic and physiological responses in the plant. The genome of the type strain IS123 nodulating the legume , was sequenced and resulted in 317 scaffolds for a total assembled size of 7,889,576 bp.

Microbial immigration across the Mediterranean via airborne dust.

Dust particles lifting and discharge from Africa to Europe is a recurring phenomenon linked to air circulation conditions. The possibility that microorganisms are conveyed across distances entails important consequences in terms of biosafety and pathogens spread. Using culture independent DNA-based analyses via next generation sequencing of the 16 S genes from the airborne metagenome, the atmospheric microbial community was characterized and the hypothesis was tested that shifts in species diversity could be recorded in relation to dust discharge.

Antioxidant treatments counteract the non-culturability of bacterial endophytes isolated from legume nodules.

In many wild legumes, attempts to cultivate nodule bacteria fail. We hypothesized that the limited culturability could be related to injury from oxidative stress caused by disruption of plant tissues during isolation. To test that, we isolated bacteria from nodules of Hedysarum spinosissimum and Tetragonolobus purpureus using buffers supplemented with scavenging systems to prevent damage from reactive oxygen species (ROS).

Colutea arborescens is nodulated by diverse rhizobia in Eastern Morocco.

Eighteen isolates of rhizobia isolated from root nodules of Colutea arborescens (Bladder senna) grown in different soils of the eastern area of Morocco were characterized by phenotypic and genomic analyses. All the isolates characterized were fast growers. This is may be due to the isolation procedures used.

Bacteria colonizing root nodules of wild legumes exhibit virulence-associated properties of mammalian pathogens.

Bacteria not proficient in nitrogen fixing symbiosis were proven able to invade root nodules of three wild legumes of the genus Hedysarum in Algeria and to be multiplying in these in place of the natural rhizobium symbionts. The involved species featured taxa known as human pathogens including: Enterobacter cloacae, Enterobacter kobei, Escherichia vulneris, Pantoea agglomerans and Leclercia adecarboxylata. A direct screening of the phenotypic determinants of virulence using human cultured cells tested positive for the traits of cytotoxicity, vital stain exclusion and adhesion to epithelia.

Diversity of bacteria that nodulate Prosopis juliflora in the eastern area of Morocco.

A total of 274 bacterial strains were isolated from the root nodules of Prosopis juliflora, growing in two arid soils of the eastern area of Morocco. A physiological plate screening allowed the selection of 15 strains that could tolerate NaCl concentrations between 175 and 500 mM. These were compared with 15 strains chosen from among the ones which did not tolerate high salinity.

Coexistence of predominantly nonculturable rhizobia with diverse, endophytic bacterial taxa within nodules of wild legumes.

A previous analysis showed that Gammaproteobacteria could be the sole recoverable bacteria from surface-sterilized nodules of three wild species of Hedysarum. In this study we extended the analysis to eight Mediterranean native, uninoculated legumes never previously investigated regarding their root-nodule microsymbionts. The structural organization of the nodules was studied by light and electron microscopy, and their bacterial occupants were assessed by combined cultural and molecular approaches.

PCR primers based on different portions of insertion elements can assist genetic relatedness studies, strain fingerprinting and species identification in rhizobia.

Using the sequence of an insertion element originally found in Rhizobium sullae, the nitrogen-fixing bacterial symbiont of the legume Hedysarum coronarium, we devised three primer pairs (inbound, outbound and internal primers) for the following applications: (a) tracing genetic relatedness within rhizobia using a method independent of ribosomal inheritance, based on the presence and conservation of IS elements; (b) achieve sensitive and reproducible bacterial fingerprinting; (c) enable a fast and unambiguous detection of rhizobia at the species level. In terms of taxonomy, while in line with part of the 16S rRNA gene- and glutamine synthetase I-based clustering, the tools appeared nonetheless more coherent with the actual geographical ranges of origin of rhizobial species, strengthening the European-Mediterranean connections and discerning them from the asian and american taxa. The fingerprinting performance of the outward-pointing primers, designed upon the inverted repeats, was shown to be at least as sensitive as BOX PCR, and to be functional on a universal basis with all 13 bacterial species tested.

Gamma proteobacteria can nodulate legumes of the genus Hedysarum.

The bacteria hosted in the root nodules of the three Mediterranean wild legume species Hedysarum carnosum, Hedysarum spinosissimum subsp. capitatum, and Hedysarum pallidum, growing in native stands in different habitats in Algeria were isolated. Bacteria were recovered on yeast-mannitol-agar or on minimal media from a total of 52 nodules.

A 9.1-kb gap in the genome reference map is shown to be a stable deletion/insertion polymorphism of ancestral origin.

We show a mute 9.1-kb gap in the human genome reference map, unraveled by RDA studies, to be a worldwide deletion/insertion polymorphism of stable type. The molecular and population data presented suggest its origin from a unique ancestral transposition event in chromosomal region 22q11.

Chromosomal abnormalities and microsatellite instability in sporadic endometrial cancer.

Defective DNA mismatch repair and nonfunctional mechanisms controlling the proper progression of the cell cycle have been proposed as being responsible for the genomic instability and accumulation of karyotypic alterations in endometrial cancer (EC). To assess whether numerical chromosomal anomalies (aneuploidy) and microsatellite instability (MSI) might be representative of distinctive tumour behaviour, paraffin-embedded tissue samples from 86 patients with sporadic EC were evaluated by both fluorescence in situ hybridisation (FISH) and microsatellite analysis, using free nuclei and genomic DNAs (respectively). Approximately one-third of the tumours analysed (24/74; 32%) exhibited MSI, whereas 38/86 (44%) of the EC samples displayed aneuploidy.

Numerical abnormalities of chromosomes 1 and 10 in endometrial adenocarcinoma: fluorescence in situ hybridization analysis of 23 archival paraffin-embedded samples.

Retrospective analysis of chromosomal changes in endometrial carcinoma was performed by fluorescence in situ hybridization on free nuclei isolated from formalin-fixed paraffin-embedded tissue. We examined 23 archival samples for numerical aberrations of chromosomes 1 and 10 with the use of specific DNA probes for the pericentromeric and centromeric regions of these two chromosomes. Numerical aberrations of chromosomes 1 and 10 were detected in 39% of the case analyzed, and the frequency of trisomy 10 tended to increase as the histological grade worsened.

Detailed physical analysis of a 1.5-megabase YAC contig containing the MXI1 and ADRA2A genes.

The distal long arm of chromosome 10 harbors genes of biomedical interest such as MXI1, a putative tumor suppressor gene, and those encoding the adrenergic receptors alpha2A (ADRA2A) and beta1 (ADRB1). As part of a physical and genetic study of this genomic region, we constructed a 1.5-Mb YAC contig mapping to 10q25 that contains MXI1 and ADRA2A as well as a number of STSs.

Search for neuroblastoma loci: characterization of tumor cell lines that could facilitate their positional cloning.

Specific chromosomal aberrations might indicate the position of genes responsible for a particular disease. Neuroblastoma is characterized by frequent deletions and/or rearrangements of the subtelomeric 1p region which, accordingly, is believed to host one or more oncosuppressor gene(s) directly or indirectly involved in the development of this and other tumors. Identification of these genes could be facilitated if cell lines with well characterized interstitial deletions or reciprocal translocations could be available for application of positional cloning strategies.

Molecular and genetic studies on the region of translocation and duplication in the neuroblastoma cell line NGP at the 1p36.13-p36.32 chromosomal site.

Cytogenetic and molecular studies suggest that chromosome 1p might contain oncosuppressor genes involved in the pathogenesis of neuroblastoma and other adult tumors. The isolation of these genes by the 'positional cloning' approach will be facilitated by the characterization of cell lines with well defined chromosomal aberrations. In the present report we provide molecular data on the NGP neuroblastoma cell line which contains a reciprocal t(1;15) translocation.

A 2.4-megabase physical map spanning the CYP2C gene cluster on chromosome 10q24.

The CYP2C gene cluster on chromosome 10q24 encodes the P450IIC enzymes, members of the cytochrome P450 monooxygenase superfamily. The P450-IIC enzymes are required for the metabolism of a number of foreign compounds, including the drugs mephenytoin and tolbutamide, and are also thought to be involved in the metabolism of endogenous steroid hormones. Several different CYP2C cDNA clones have been isolated; however, the exact number of genes and the genomic arrangement of the CYP2C cluster have remained unknown.

Cytogenetic and molecular studies on the neuroblastoma cell line NGP: identification of a reciprocal t(1;15) involving the "consensus region" 1p36.1.

A reciprocal t(1;15)(p36.1-36.3;q25-26) has been identified in an established neuroblastoma cell line (NGP) that earlier studies had shown to carry, among others, a rearrangement at the 1p subtelomeric region.

A new method for identification of Trichomonas vaginalis by fluorescent DNA in situ hybridization.

The protozoan flagellate Trichomonas vaginalis is responsible for human trichomoniasis, one of the most widespread sexually transmitted diseases in the world. Several methods are currently used for laboratory diagnosis, including direct microscopic observation, cell culture, immunological techniques, and more recently, DNA probing and gene amplification. This report describes an in situ hybridization technique with specific DNA probes labeled with either biotin, rhodamine, or fluorescein for detection of T.

Mapping of the gene coding for a paraneoplastic encephalomyelitis antigen (HuD) to human chromosome site 1p34.

A cDNA clone coding for a human brain protein (HuD), which is highly homologous to the Drosophila neuronal determination protein Elav and elicits antibody formation in a high proportion of patients with paraneoplastic encephalomyelitis, was used to isolate a lambda phage recombinant clone, including a large fragment of the relevant human genomic region. The fragment proved to be an efficient probe for the precise subregional mapping of the gene by molecular in situ hybridization onto extended human prometaphase chromosomes. Analysis of banded metaphases with clear hybridization signals pointed unequivocally to the localization of the HuD gene to human chromosome band 1p34.

Concurrent mapping of an adenovirus 5/SV40 integration site and the U1 snRNA cluster (RNU1) within 400 kb of the chromosome region 1p36.1.

Previous reports from our group suggested the preferential integration of the viral construct Ad5/SV40 at the short arm subtelomeric region of human chromosome 1. The present study narrows the region of viral integration to site 1p36.1 in a close cytogenetic overlap with the U1 snRNA gene cluster (RNU1) within a distance necessarily smaller than 400 kb as suggested by the size of the YAC in which the two markers were found to coexist.

Mapping on human and mouse chromosomes of the gene for the beta-galactoside-binding protein, an autocrine-negative growth factor.

The structural gene for beta-galactoside-binding protein (Lgals-1), a cell growth regulatory molecule and cystostatic factor, is assigned to the E-region of mouse chromosome 15 and to the region q12-q13.1 of human chromosome 22. The evolutionary conservation of these two regions has been previously suggested from comparative mapping of several loci.