Inhibitory effect of Teucrium ramosissimum extracts on aflatoxin B1, benzo[a]pyrene, 4-nitro-o-phenylenediamine and sodium azide induced mutagenicity: Correlation with antioxidant activity

AbstractThe mutagenic potential of total oligomers flavonoids (TOF), ethyl acetate (EA) and petroleum ether (PE) extracts from aerial parts of Teucrium ramosissimum was assessed using Ames Salmonella tester strains TA98, TA100 and TA1535 with and without metabolic activation (S9). None of the different extracts produced a mutagenic effect. Likewise, the antimutagenicity of the same extracts was tested using the “Ames test”. Our results showed that T. ramosissimum extracts possess antimutagenic activity against all the tested genotoxicants (aflatoxin B1, benzo[a]pyrene, 4-nitro-o-phenylenediamine and sodium azide) in the Salmonella assay systems used in this study. In addition, all extracts showed important free radical scavenging activity toward the radicals DPPH and ABTS except the PE extract

Pressure dependence of the spin gap in BaVS_3

We carried out magnetotransport experiments under hydrostatic pressure in order to study the nature of the metal-insulator transition in BaVS$_3$. Scaling relations for $\rho(T,H,p)$ are established and the pressure dependence of the spin gap is determined. Our new results, in conjunction with a re-analysis of earlier specific heat and susceptibility data, demonstrate that the transition is weakly second order. The nature of the phase diagram in the $T$--$p$--$H$ space is discussed.Comment: 5 pages, 5 figures, submitted to PRB Rap. Co

Quasielastic 12C(e,e'p) Reaction at High Momentum Transfer

We measured the 12C(e,e'p) cross section as a function of missing energy in parallel kinematics for (q,w) = (970 MeV/c, 330 MeV) and (990 MeV/c, 475 MeV). At w=475 MeV, at the maximum of the quasielastic peak, there is a large continuum (E_m > 50 MeV) cross section extending out to the deepest missing energy measured, amounting to almost 50% of the measured cross section. The ratio of data to DWIA calculation is 0.4 for both the p- and s-shells. At w=330 MeV, well below the maximum of the quasielastic peak, the continuum cross section is much smaller and the ratio of data to DWIA calculation is 0.85 for the p-shell and 1.0 for the s-shell. We infer that one or more mechanisms that increase with $\omega$ transform some of the single-nucleon-knockout into multinucleon knockout, decreasing the valence knockout cross section and increasing the continuum cross section.Comment: 14 pages, 7 figures, Revtex (multicol, prc and aps styles), to appear in Phys Rev

Molecular epidemiology and genotype distribution of Human Papillomavirus (HPV) among Arab women in the state of Qatar

Background: Human Papilloma Virus (HPV) infection is the major cause of cervical cancer worldwide. With limited data available on HPV prevalence in the Arab countries, this study aimed to identify the prevalence and genotypic distribution of HPV in the State of Qatar. Methods: 3008 cervical samples, exclusively of women with Arabic origin residing in Qatar were collected from the Women’s Hospital and Primary Health Care Corporation in Doha, State of Qatar. HPV DNA detection was done using GP5+/6+ primers based real time-polymerase chain reaction (RT-PCR) assay followed by the usage of HPV type specific primers based RT- PCR reactions and Sanger sequencing for genotype identification. Results: Similar prevalence rates of HPV infection was identified in both Qatari and non-Qatari women at 6.2% and 5.9% respectively. HPV prevalence rate of 5.8% and 18.4% was identified in women with normal cytology and in women with abnormal cytology respectively. HPV 81, 11 and 16, in decreasing order were the most commonly identified genotypes. HPV 81 was the most frequent low-risk genotype among women with both normal (74.0%) and abnormal (33.3%) cytology. HPV 16 (4.6%) was identified as the predominant high-risk HPV genotype among women with normal cytology and HPV 16, HPV 18, and HPV 56 (22.2% each) were the most common identified high-risk genotypes in women with abnormal cytology Conclusions: The overall HPV prevalence in Arab women in Qatar was identified as 6.1% with an increased HPV prevalence seen in women with abnormal cytology results and no significant trends seen with age. In contrast to Western countries, we report a varied genotypic profile of HPV with a high prevalence of low-risk HPV genotype 81 among the Arab women residing in Qatar.Weill Cornell Medical College in Qatar; and by a grant from the Qatar National Research Fund (NPRP- 09-344-3-082)

Polar extracts from (Tunisian) Acacia salicina Lindl. Study of the antimicrobial and antigenotoxic activities

<p>Abstract</p> <p>Background</p> <p>Methanolic, aqueous and Total Oligomer Flavonoids (TOF)-enriched extracts obtained from the leaves of <it>Acacia salicina </it>'Lindl.' were investigated for antibacterial, antimutagenic and antioxidant activities.</p> <p>Methods</p> <p>The antimicrobial activity was tested on the Gram positive and Gram negative reference bacterial strains. The Mutagenic and antimutagenic activities against direct acting mutagens, methylmethane sulfonate (MMS) and 4-nitro-o-phenylenediamine (NOPD), and indirect acting mutagens, 2-aminoanthracene (2-AA) and benzo[a]pyrene (B(a)P) were performed with <it>S. typhimurium </it>TA102 and TA98 assay systems. In addition, the enzymatic and nonenzymatic methods were employed to evaluate the anti-oxidative effects of the tested extracts.</p> <p>Results</p> <p>A significant effect against the Gram positive and Gram negative reference bacterial strains was observed with all the extracts. The mutagenic and antimutagenic studies revealed that all the extracts decreased the mutagenicity induced by B(a)P (7.5 μg/plate), 2-AA (5 μg/plate), MMS (1.3 mg/plate) and NOPD (10 μg/plate). Likewise, all the extracts showed an important free radical scavenging activity towards the superoxide anion generated by the xanthine/xanthine oxidase assay system, as well as high Trolox Equivalent Antioxidant Capacity (TEAC), against the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS)⁺• radical. TOF-enriched extract exhibited the highest protective effect against free radicals, direct acting-mutagen and metabolically activated S9-dependent mutagens.</p> <p>Conclusions</p> <p>The present study indicates that the extracts from <it>A. salicina </it>leaves are a significant source of compounds with the antimutagenic and antioxidant activities, and this may be useful for developing potential chemopreventive substances.</p

Bioinformatics education—perspectives and challenges out of Africa

The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s.The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of virtually every field in the life sciences. This has placed a scientific premium on the availability of skilled bioinformaticians, a qualification that is extremely scarce on the African continent. The reasons for this are numerous, although the absence of a skilled bioinformatician at academic institutions to initiate a training process and build sustained capacity seems to be a common African shortcoming.This dearth of bioinformatics expertise has had a knock-on effect on the establishment of many modern high-throughput projects at African institutes, including the comprehensive and systematic analysis of genomes from African populations, which are among the most genetically diverse anywhere on the planet. Recent funding initiatives from the National Institutes of Health and theWellcomeTrust are aimed at ameliorating this shortcoming. In this paper, we discuss the problems that have limited the establishment of the bioinformatics field in Africa, as well as propose specific actions that will help with the education and training of bioinformaticians on the continent. This is an absolute requirement in anticipation of a boom in high-throughput approaches to human health issues unique to data from African populations

Development of Bioinformatics Infrastructure for Genomics Research in H3Africa

Background: Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet’s role has evolved in response to changing needs from the consortium and the African bioinformatics community. Objectives: H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. Methods and Results: Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training. Conclusions: For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa

Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for Sickle Cell Disease

Sickle cell disease (SCD) is a debilitating single gene disorder caused by a single point mutation that results in physical deformation (i.e. sickling) of erythrocytes at reduced oxygen tensions. Up to 75% of SCD in newborns world-wide occurs in sub-Saharan Africa, where neonatal and childhood mortality from sickle cell related complications is high. While SCD research across the globe is tackling the disease on multiple fronts, advances have yet to significantly impact on the health and quality of life of SCD patients, due to lack of coordination of these disparate efforts. Ensuring data across studies is directly comparable through standardization is a necessary step towards realizing this goal. Such a standardization requires the development and implementation of a disease-specific ontology for SCD that is applicable globally. Ontology development is best achieved by bringing together experts in the domain to contribute their knowledge. The SCD community and H3ABioNet members joined forces at a recent SCD Ontology workshop to develop an ontology covering aspects of SCD under the classes: phenotype, diagnostics, therapeutics, quality of life, disease modifiers and disease stage. The aim of the workshop was for participants to contribute their expertise to development of the structure and contents of the SCD ontology. Here we describe the proceedings of the Sickle Cell Disease Ontology Workshop held in Cape Town South Africa in February 2016 and its outcomes. The objective of the workshop was to bring together experts in SCD from around the world to contribute their expertise to the development of various aspects of the SCD ontology

Many Body approach to the inclusive (e,e′)(e,e') reaction from the quasielastic to the Δ\Delta excitation region

We have performed a many body calculation of the inclusive (e,e') cross section which runs over the three traditional regions at intermediate energies: the quasielastic peak, the dip region and the delta region. The longitudinal and transverse response functions in the quasielastic peak have also been evaluated. Traditional effects like polarization, meson exchange currents, final state interaction and delta renormalization in the nuclear medium have been included. Meson exchange currents are generated from a model of pion electroproduction on the nucleon which reproduces accurately the experimental data. The inclusive cross section accounts for 1N,2N,3N mechanisms of virtual photon absorption and one pion production. Meson exchange currents associated to the (\gamma^*,2\pi) reaction are also accounted for. We obtain good results for the (e,e') cross sections in the whole energy range and for different nuclei. The response functions are also in good agreement with the latest experimental analysis. On the other hand, the method provides the separation of the contribution to the inclusive cross section from different physical channels which is a necessary input to evaluate cross sections like (e,e' N), (e,e' NN), (e,e' \pi) etc.Comment: 65 pages (LaTeX + ps-figure files