A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization

BACKGROUND: Numerous DNA microarray hybridization experiments have been performed in yeast over the last years using either synthetic oligonucleotides or PCR-amplified coding sequences as probes. The design and quality of the microarray probes are of critical importance for hybridization experiments as well as subsequent analysis of the data. RESULTS: We present here a novel design of Saccharomyces cerevisiae microarrays based on a refined annotation of the genome and with the aim of reducing cross-hybridization between related sequences. An effort was made to design probes of similar lengths, preferably located in the 3'-end of reading frames. The sequence of each gene was compared against the entire yeast genome and optimal sub-segments giving no predicted cross-hybridization were selected. A total of 5660 novel probes (more than 97% of the yeast genes) were designed. For the remaining 143 genes, cross-hybridization was unavoidable. Using a set of 18 deletant strains, we have experimentally validated our cross-hybridization procedure. Sensitivity, reproducibility and dynamic range of these new microarrays have been measured. Based on this experience, we have written a novel program to design long oligonucleotides for microarray hybridizations of complete genome sequences. CONCLUSIONS: A validated procedure to predict cross-hybridization in microarray probe design was defined in this work. Subsequently, a novel Saccharomyces cerevisiae microarray (which minimizes cross-hybridization) was designed and constructed. Arrays are available at Eurogentec S. A. Finally, we propose a novel design program, OliD, which allows automatic oligonucleotide design for microarrays. The OliD program is available from authors

Antimicrobial, Antioxidant and Protective Effect of Methanol Extract of Trichilia emetica (Meliaceae) Stem and Root Bark against Free Radical-induced Oxidative Haemolysis

Background: The objectives of this study are to investigate the antimicrobial, antioxidant and antiradical properties of methanol extract of the stem and root bark of Trichilia emetica on a model of free radical-induced membrane damage. Methodology: p-Iodonitrotetrazolium chloride colorometric assay was used to determined bacterial and yeast susceptibility to plant samples. The antioxidant activity was evaluated using DPPH radical, hydroxyl radical, nitric oxide scavenging and reducing power assays. The cellular oxidative stress was evaluated through haematolysis and haematoprotective assays. Results: The stem bark extract revealed a great antibacterial activity against 62.5% of bacteria strains tested with minimal inhibitory concentrations ranging from 32 to 64 µg/ml. The IC50 value the stem and root bark extracts were 9.68 ± 0.75 and 10.05 ± 0.86 μg/ml, 9.98 ± 0.52 and 200.49 ± 3.40 μg/ml, 45.92 ± 2.45 and 4081 ± 212 μg/ml, respectively for DPPH radical, hydroxyl radical and reducing ability assays. Both extracts exhibited concentration dependent haemolysis of sheep red blood cells (RBCs). Stem and root bark extracts (25 µg/ml) diminish respectively by 95.9 and 85.68% hydrogen peroxide-mediated cytotoxicity. Conclusion: Our data reveals that antibacterial and antioxidant activities of the methanol extract of Trichilia emetica stem bark were better than that of root bark

Iron-Sulfur (Fe/S) Protein Biogenesis: Phylogenomic and Genetic Studies of A-Type Carriers

Iron sulfur (Fe/S) proteins are ubiquitous and participate in multiple biological processes, from photosynthesis to DNA repair. Iron and sulfur are highly reactive chemical species, and the mechanisms allowing the multiprotein systems ISC and SUF to assist Fe/S cluster formation in vivo have attracted considerable attention. Here, A-Type components of these systems (ATCs for A-Type Carriers) are studied by phylogenomic and genetic analyses. ATCs that have emerged in the last common ancestor of bacteria were conserved in most bacteria and were acquired by eukaryotes and few archaea via horizontal gene transfers. Many bacteria contain multiple ATCs, as a result of gene duplication and/or horizontal gene transfer events. Based on evolutionary considerations, we could define three subfamilies: ATC-I, -II and -III. Escherichia coli, which has one ATC-I (ErpA) and two ATC-IIs (IscA and SufA), was used as a model to investigate functional redundancy between ATCs in vivo. Genetic analyses revealed that, under aerobiosis, E. coli IscA and SufA are functionally redundant carriers, as both are potentially able to receive an Fe/S cluster from IscU or the SufBCD complex and transfer it to ErpA. In contrast, under anaerobiosis, redundancy occurs between ErpA and IscA, which are both potentially able to receive Fe/S clusters from IscU and transfer them to an apotarget. Our combined phylogenomic and genetic study indicates that ATCs play a crucial role in conveying ready-made Fe/S clusters from components of the biogenesis systems to apotargets. We propose a model wherein the conserved biochemical function of ATCs provides multiple paths for supplying Fe/S clusters to apotargets. This model predicts the occurrence of a dynamic network, the structure and composition of which vary with the growth conditions. As an illustration, we depict three ways for a given protein to be matured, which appears to be dependent on the demand for Fe/S biogenesis

Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes

The iron-oxidizing species Acidithiobacillus ferrivorans is one of few acidophiles able to oxidize ferrous iron and reduced inorganic sulfur compounds at low temperatures (<10°C). To complete the genome of At. ferrivorans strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. The At. ferrivorans CF27 genome comprises a 3,409,655 bp chromosome and a 46,453 bp plasmid. At. ferrivorans CF27 possesses genes allowing its adaptation to cold, metal(loid)-rich environments, as well as others that enable it to sense environmental changes, allowing At. ferrivorans CF27 to escape hostile conditions and to move toward favorable locations. Interestingly, the genome of At. ferrivorans CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. Furthermore, several genes specific to At. ferrivorans CF27 have been identified that could be responsible for the phenotypic differences of this strain compared to other Acidithiobacillus species. Most genes located inside At. ferrivorans CF27-specific gene clusters which have been analyzed were expressed by both ferrous iron-grown and sulfur-attached cells, indicating that they are not pseudogenes and may play a role in both situations. Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups

ANTIDEPRESSANT PROPERTIES OF AQUEOUS MACERATE FROM GLADIOLUS DALENII CORMS

Background: Gladiolus dalenii Van Geel (Iridaceae) has been used for the treatment of depression and psychotic disorders in African traditional medicine. The aim of this study was to assess the effect of the aqueous extract from the corm of Gladiolus dalenii and its possible mechanisms of action. Materials and Methods: We assessed the antidepressant properties of G. dalenii corm aqueous extract in mice, using the open field, forced swimming, and tail suspension tests. Spontaneous locomotor activity of mice given various doses of G. dalenii extract (per os) was determined in the open field, whereas immobility was evaluated in the other two tests. Results: Extract maximal effect was observed at 15 mg/kg, as mice displayed a marked reduction in immobility time in both the forced swimming test (80%) and the tail suspension test (66%). In further studies aimed at investigating the mechanism of action of G. dalenii extract, the latter significantly antagonized the effect of N-methyl-D- aspartate (NMDA, 75 mg/kg) at both the doses 15 mg/kg (

Elaboration d’un SVA d’aide à l’éducation sous forme d’application mobile sur un réseau d’opérateur de télécommunications: recherche d'assistants pédagogiques à domicile

La présente recherche a pour objectif de proposer un Service à Valeur Ajouté (SVA) axé sur l’élaboration d’une plateforme collaborative en ligne entre les assistants pédagogiques et les apprenants. Il sera question dans cet article de répondre aux questions de recherche. Comment les technologies peuvent-ils contribuer à reconfigurer l’environnement de formation pris en otage par les diverses crises sociopolitiques ? Comment l’usage des technologies peut-il contribuer à favoriser l’émergence des nouveaux métiers comme le conseiller ou l’assistant pédagogique à domicile? En vue de répondre aux deux questions de recherche, nous avons par une démarche méthodologie rigoureuse, analysé et conçu l’application en passant par une étude détaillée des fonctionnalités à offrir, la modélisation du système et le choix de l’architecture du système. Par la suite, nous avons étudié le déploiement d’un SVA dans un réseau de télécommunications plus particulièrement celui de Viettel Cameroun. Un ensemble d’applications "NextSchool" et "NextScool Admin" testées par des utilisateurs sur le réseau d’opérateur Viettel Cameroun S.A ont vu le jour

Complete Genome Sequence of the Piezophilic, Mesophilic, Sulfate-Reducing Bacterium Desulfovibrio hydrothermalis AM13(T.).

International audienceDesulfovibrio hydrothermalis AM13(T) is a piezophilic, mesophilic, hydrogenotrophic sulfate-reducing bacterium collected from a deep-sea hydrothermal chimney on the East Pacific Rise (2,600 m depth, 13°N). We report the genome sequence of this bacterium, which includes a 3,702,934-bp chromosome and a circular plasmid of 5,328 bp

Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium

Background The colonial cyanobacterium Microcystis proliferates in a wide range of freshwater ecosystems and is exposed to changing environmental factors during its life cycle. Microcystis blooms are often toxic, potentially fatal to animals and humans, and may cause environmental problems. There has been little investigation of the genomics of these cyanobacteria. Results Deciphering the 5,172,804 bp sequence of Microcystis aeruginosa PCC 7806 has revealed the high plasticity of its genome: 11.7% DNA repeats containing more than 1,000 bases, 6.8% putative transposases and 21 putative restriction enzymes. Compared to the genomes of other cyanobacterial lineages, strain PCC 7806 contains a large number of atypical genes that may have been acquired by lateral transfers. Metabolic pathways, such as fermentation and a methionine salvage pathway, have been identified, Conclusion Microcystis aeruginosa PCC 7806 appears to have adopted an evolutionary strategy relying on unusual genome plasticity to adapt to eutrophic freshwater ecosystems, a property shared by another strain of M. aeruginosa (NIES-843). Comparisons of the genomes of PCC 7806 and other cyanobacterial strains indicate that a similar strategy may have also been used by the marine strain Crocosphaera watsonii WH8501 to adapt to other ecological niches, such as oligotrophic open oceans.

EVALUATION OF THE SEDATIVE AND ANTICONVULSANT PROPERTIES OF THREE CAMEROONIAN PLANTS

Millettia thonningii, Ocinum sanctum and Securitaca longepedunculaca are used in traditional medicine in Cameroon to treat epilepsy, insomnia and headaches. Animal models of epilepsy (maximal electroshock (MES), n-methyl-d-aspartate (NMDA), pentylenetetrazol (PTZ), isonicotinic hydrazide acid (INH), picrotoxine (PIC) and strychnine (STR)-induced convulsions or turning behavior were used to evaluate anticonvulsant activity while diazepam-induced sleep test was used to evaluate sedative activity of the plants. Four doses of extracts were used for each plant (100, 200, 500 and 1000 mg/kg). At a dose of 1000 mg/kg, Millettia thonningii protected 60 and 90% of mice against MES and PTZ-induced convulsions, respectively. At the same dose, Millettia thonningii also protected 80% of mice against NMDA-induced turning behavior. At a dose of 1000 mg/kg, Ocinum sanctum provided complete protection against MES, PIC and STR- induced convulsions and 83.3% of protection in PTZ test. Securitaca longepedunculata completely protected (100%) mice in PIC test at a dose of 200 mg/kg, in MES test at a dose of 500 mg/kg and in PTZ test at a dose of 1000 mg/kg. 66.7% of mice were protected against STR-induced convulsions. All the three plants showed also sedative properties for they increased significantly and in a dose dependent manner the total sleep time induced by diazepam. The total sleep time of the control groups was multiplied by a factor of 3 at least by each extract. The presence of sedative and anticonvulsant activity in the three plants could explain their use in traditional medicine in the treatment of epilepsy and insomnia in Cameroon