Conservation and multivariate analysis utility in characterization of ecogegraphical relationships of Trifolium and Lotus species

The maintenance of species in an environment and the durability of rangeland and fallow improvement depend on the choice of populations used. The study of abundance and the relationship between the natural distribution of spontaneous legumes species of forage and/or pastoral interest and environmental factors is an important step for an adequate utilization of local genetic resources. Collection of annual Trifolium species and the genus of Lotus were conducted at 45 sites in Morocco in May/June 2004. Ecogeographical information was recorded at each site. Twelve species of annual Trifolium and two species of Lotus were identified. Most prolific were T. tomentosum and L. corniculatus. A principal components analysis and canonical variate analysis were conducted to group the sites, using the ecogeographical variables collected at each site. The variables that were found to be most important in grouping the sites were mean coldest month temperature, mean hottest month temperature, mean annual rainfall, latitude, longitude and soil pH. None of the species identified were limited to only one ecogeographical group.     

A Deep Sequencing Approach to Uncover the miRNOME in the Human Heart

MicroRNAs (miRNAs) are a class of non-coding RNAs of ∼22 nucleotides in length, and constitute a novel class of gene regulators by imperfect base-pairing to the 3′UTR of protein encoding messenger RNAs. Growing evidence indicates that miRNAs are implicated in several pathological processes in myocardial disease. The past years, we have witnessed several profiling attempts using high-density oligonucleotide array-based approaches to identify the complete miRNA content (miRNOME) in the healthy and diseased mammalian heart. These efforts have demonstrated that the failing heart displays differential expression of several dozens of miRNAs. While the total number of experimentally validated human miRNAs is roughly two thousand, the number of expressed miRNAs in the human myocardium remains elusive. Our objective was to perform an unbiased assay to identify the miRNOME of the human heart, both under physiological and pathophysiological conditions. We used deep sequencing and bioinformatics to annotate and quantify microRNA expression in healthy and diseased human heart (heart failure secondary to hypertrophic or dilated cardiomyopathy). Our results indicate that the human heart expresses >800 miRNAs, the majority of which not being annotated nor described so far and some of which being unique to primate species. Furthermore, >250 miRNAs show differential and etiology-dependent expression in human dilated cardiomyopathy (DCM) or hypertrophic cardiomyopathy (HCM). The human cardiac miRNOME still possesses a large number of miRNAs that remain virtually unexplored. The current study provides a starting point for a more comprehensive understanding of the role of miRNAs in regulating human heart disease.     

Inventory of the cichlid olfactory receptor gene repertoires: identification of olfactory genes with more than one coding exon

Background

To help understand the molecular mechanisms underlying the remarkable phenotypic diversity displayed by cichlids, the genome sequences of O. niloticus, P. nyererei, H. burtoni, N. brichardi and M. zebra were recently determined. Here, we present the contents of the olfactory receptor (OR) repertoires in the genomes of these five fishes.

Results

We performed an exhaustive TBLASTN search of the five cichlid genomes to identify their OR repertoires as completely as possible. We used as bait a set of ORs described in the literature. The cichlid repertoires thereby extracted contained large numbers of complete genes (O. niloticus 158; H. burtoni 90; M. zebra 102; N. brichardi 69; P. nyererei 88), a small numbers of pseudogenes and many “edge genes” corresponding to incomplete genes located at the ends of contigs. A phylogenetic tree was constructed and showed these repertoires include a large number of families and subfamilies. It also allowed the identification of a large number of OR analogues between cichlids with very high amino-acid identity (≥99%). Nearly 9% of the full-length cichlid OR genes are composed of several coding exons. This is very unusual for vertebrate OR genes. Nevertheless, the evidence is strong, and includes the donor and acceptor splice junction sequences; also, the positions of these genes in the phylogenetic tree indicate that they constitute subfamilies well apart from non-OR G protein-coupled receptor families.

Conclusions

Cichlid OR repertoires are made up of a larger number of genes and fewer pseudogenes than those in other teleosts except zebrafish. These ORs share all identified properties common to all fish ORs; however, the large number of families and subfamilies, each containing few ORs implies that they have evolved more rapidly. This high level of OR diversity is consistent with the substantial phenotypic diversity that characterizes cichlids.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-586) contains supplementary material, which is available to authorized users.     

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa

With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependencies, and versions of bioinformatics tools along with a lack of local computational infrastructure and expertise. To address this, H3ABioNet developed a 16S rRNA Microbiome Intermediate Bioinformatics Training course, extending its remote classroom model. The course was developed alongside experienced microbiome researchers, bioinformaticians, and systems administrators, who identified key topics to address. Development of containerised workflows has previously been undertaken by H3ABioNet, and Singularity containers were used here to enable the deployment of a standard replicable software stack across different hosting sites. The pilot ran successfully in 2019 across 23 sites registered in 11 African countries, with more than 200 participants formally enrolled and 106 volunteer staff for onsite support. The pulling, running, and testing of the containers, software, and analyses on various clusters were performed prior to the start of the course by hosting classrooms. The containers allowed the replication of analyses and results across all participating classrooms running a cluster and remained available posttraining ensuring analyses could be repeated on real data. Participants thus received the opportunity to analyse their own data, while local staff were trained and supported by experienced experts, increasing local capacity for ongoing research support. This provides a model for delivering topic-specific bioinformatics courses across Africa and other remote/low-resourced regions which overcomes barriers such as inadequate infrastructures, geographical distance, and access to expertise and educational materials.     

IFNL4 rs12979860 polymorphism influences HBV DNA viral loads but not the outcome of HBV infection in Moroccan patients

ObjectivesThe interferon (IFN) is known to bridge innate and adaptive immune responses, and to play a critical role particularly against hepatitis B virus (HBV) infection. Defects in IFN signals may result, therefore, in attenuated responses against HBV. Accordingly, polymorphisms in genes coding for immune response effectors may affect the clinical outcome of HBV infection. We analyzed the putative association between IFNL4 rs12979860 polymorphism and the outcome of HBV infection in Moroccan patients.MethodsIn this study, 237 chronic HBV (CHB) patients and 129 spontaneously resolved HBV (SRB) individuals were enrolled and genotyped using a predesigned Taqman allelic discrimination assay.ResultsOur data show a significant increase of HBV DNA loads in patients with IFNL4 rs12979860 CC genotype compared to patients with CT and TT genotypes (p = 0.0008). However, there was no consistent association between IFNL4 rs12979860 polymorphism and the outcome of HBV infection.ConclusionsAlthough IFNL4 rs12979860 polymorphism seems to modulate circulating HBV DNA levels, it is disconnected from chronic disease progression. This observation suggests that the role of rs12979860 in liver disease is restricted to viral control and inactive in the deleterious immune pathology that affects liver tissue. Taken together, our data suggest that rs12979860 CC genotypes could be useful as a predictor of success or failure of IFN-based therapy in chronic HBV-infected patients.     

Molecular basis of beta-thalassemia in Morocco: possible origins of the molecular heterogeneity

We present the molecular spectrum of beta-thalassemia in the Moroccan population obtained by the identification of molecular defects responsible for this disease, and herewith we show that the Moroccan population is genetically heterogeneous; 18 different mutations have been found in the 158 beta-globin chromosomes studied. Eight mutations [codon 39 (C --> T), FSC-8 (-AA), IVS-II-745 (C --> G), -29 (A --> G), FSC-6 (-A), IVS-I-110 (G --> A), IVS-I-2 (T --> C), and IVS-I-1 (G --> A)] out of 18 beta-thalassemia mutations identified accounted for 76% of the Moroccan beta-thalassemia chromosomes. Restriction fragment length polymorphism (RFLP) haplotype analysis showed that the observed genetic diversity originated from both new mutational events and gene flow due to migration.     

Preferential vulnerability of mesencephalic dopamine neurons to glutamate transporter dysfunction

Nigral depletion of the main brain antioxidant GSH is the earliest biochemical event involved in Parkinson's disease pathogenesis. Its causes are completely unknown but increasing number of evidence suggests that glutamate transporters [excitatory amino acid transporters (EAATs)] are the main route by which GSH precursors may enter the cell. In this study, we report that dopamine (DA) neurons, which express the excitatory amino acid carrier 1, are preferentially affected by EAAT dysfunction when compared with non-DA neurons. In rat embryonic mesencephalic cultures, l -trans-pyrrolidine-2,4-dicarboxylate, a substrate inhibitor of EAATs, is directly and preferentially toxic for DA neurons by decreasing the availability of GSH precursors and lowering their resistance threshold to glutamate excitotoxicity through NMDA-receptors. In adult rat, acute intranigral injection of l -trans-pyrrolidine-2,4-dicarboxylate induces a large regionally selective and dose-dependent loss of DA neurons and α-synuclein aggregate formation. These data highlight for the first time the importance of excitatory amino acid carrier 1 function for the maintenance of antioxidant defense in DA neurons and suggest its dysfunction as a candidate mechanism for the selective death of DA neurons such as occurring in Parkinson's disease.     

Rhizobium laguerreae is the main nitrogen-fixing symbiont of cultivated lentil (Lens culinaris) in Morocco

Genetic diversity and population structure of 268 Lens culinaris symbiotic rhizobia collected from 40 cultivated fields in the main lentil production regions in Morocco were estimated. Three chromosomal housekeeping genes (recA, glnII and atpD) and one common symbiotic gene (nodC) were sequenced and analyzed in order to identify the local symbionts of lentil. The molecular phylogeny of the concatenated housekeeping genes clustered more than 95% of the isolates in one main clade together with Rhizobium laguerreae species. R. laguerreae represents the main symbiont of cultivated lentil in Morocco and, for the first time, a large sample of individuals is obtained for this species. There is a significant and high genetic differentiation of bacterial populations among the four regions for their symbiotic gene, and much lower for their housekeeping genes. The reasons why R. laguerreae is so frequently recovered in our study is discussed.     

Solitary fibrous tumor of the kidney: a case report and review of the literature

A solitary fibrous tumor (SFT) is an unusual spindle cell neoplasm that usually occurs in the pleura but has recently been described in diverse extrapleural sites. Urogenital localization is rare, and only 19 cases of SFT of the kidney have been described. We report a case of a large SFT clinically thought to be renal cell carcinoma arising in the kidney of a 70-year-old man. The tumor was well circumscribed and composed of a mixture of spindle cells and dense collagenous bands, with areas of necrosis or cystic changes noted macroscopically and microscopically. Immunohistochemical studies revealed reactivity for CD34, CD99, and Bcl-2 protein, with no staining for keratin, S-100 protein, or muscle markers, confirming the diagnosis of SFT. This tumor is benign in up to 90% of cases. The immunohistochemical study is the key to diagnosis.     

A concise synthesis of 5-amino-5-deoxyaldonic acids as monomers for the preparation of nylon 5

Saponification of 5-azido-5-deoxy-D-pentonolactones (ribo-, arabino-, xylo-) with NaOH gave the corresponding 5-azido-5-deoxyaldonic acids sodium salts which, after regeneration of the acid form followed by catalytic reduction, led to the target compounds in 98% overall yields.