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1.
Nat Genet ; 2024 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-38977855

RESUMO

The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.

2.
Transl Oncol ; 44: 101940, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38537326

RESUMO

Precision Medicine is being increasingly used in the developed world to improve health care. While several Precision Medicine (PM) initiatives have been launched worldwide, their implementations have proven to be more challenging particularly in low- and middle-income countries. To address this issue, the "Personalized Medicine in North Africa" initiative (PerMediNA) was launched in three North African countries namely Tunisia, Algeria and Morocco. PerMediNA is coordinated by Institut Pasteur de Tunis together with the French Ministry for Europe and Foreign Affairs, with the support of Institut Pasteur in France. The project is carried out along with Institut Pasteur d'Algérie and Institut Pasteur du Maroc in collaboration with national and international leading institutions in the field of PM including Institut Gustave Roussy in Paris. PerMediNA aims to assess the readiness level of PM implementation in North Africa, to strengthen PM infrastructure, to provide workforce training, to generate genomic data on North African populations, to implement cost effective, affordable and sustainable genetic testing for cancer patients and to inform policy makers on how to translate research knowledge into health products and services. Gender equity and involvement of young scientists in this implementation process are other key goals of the PerMediNA project. In this paper, we are describing PerMediNA as the first PM implementation initiative in North Africa. Such initiatives contribute significantly in shortening existing health disparities and inequities between developed and developing countries and accelerate access to innovative treatments for global health.

3.
Glob Health Epidemiol Genom ; 2023: 6693323, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37766808

RESUMO

Modern biomedical research is characterised by its high-throughput and interdisciplinary nature. Multiproject and consortium-based collaborations requiring meaningful analysis of multiple heterogeneous phenotypic datasets have become the norm; however, such analysis remains a challenge in many regions across the world. An increasing number of data harmonisation efforts are being undertaken by multistudy collaborations through either prospective standardised phenotype data collection or retrospective phenotype harmonisation. In this regard, the Phenotype Harmonisation Working Group (PHWG) of the Human Heredity and Health in Africa (H3Africa) consortium aimed to facilitate phenotype standardisation by both promoting the use of existing data collection standards (hosted by PhenX), adapting existing data collection standards for appropriate use in low- and middle-income regions such as Africa, and developing novel data collection standards where relevant gaps were identified. Ultimately, the PHWG produced 11 data collection kits, consisting of 82 protocols, 38 of which were existing protocols, 17 were adapted, and 27 were novel protocols. The data collection kits will facilitate phenotype standardisation and harmonisation not only in Africa but also across the larger research community. In addition, the PHWG aims to feed back adapted and novel protocols to existing reference platforms such as PhenX.


Assuntos
Estudos Prospectivos , Humanos , Estudos Retrospectivos , África , Coleta de Dados , Fenótipo
4.
Asian Pac J Cancer Prev ; 24(2): 659-665, 2023 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-36853317

RESUMO

BACKGROUND: Chlamydia pneumoniae (C. pneumoniae) is a respiratory pathogen associated with chronic inflammatory and its detection in human lung cancer suggests its involvement in cancerogenesis. Our study aimed to evaluate the association between C. pneumoniae  infection and Lung Cancer disease in Moroccans patients and control cohorts, through a molecular investigation. METHODS: The study comprised 42 lung cancer patients and 43 healthy controls. All participants provided demographics, Clinical, and Toxic behaviors datas, and a peripheral blood sample for testing, a Nested Polymerase Chain Reaction (PCR) was performed for C. pneumoniae Deoxyribonucleic acid (DNA) detection. Statistical analysis was performed using IBM®SPSS®software. RESULTS: Positive Nested PCR results for cases and controls were respectively 33.3% and 4.7%, there by  significant difference between cases and controls   infection was identified (p <0.05). Data analysis also showed that tobacco could act synergically with C. pneumoniae infection as a risk factor of lung cancer. In fact a significant difference between patients and controls was shown for tobacco and alcohol use (p < 0.05). CONCLUSION: C. pneumoniae infection is potentially associated with primary Lung cancer in the Moroccan population and has combined effects with Tabaco consumption.


Assuntos
Chlamydia , Neoplasias Pulmonares , Humanos , Neoplasias Pulmonares/epidemiologia , Neoplasias Pulmonares/etiologia , Consumo de Bebidas Alcoólicas , Análise de Dados , Inflamação , Nicotiana
5.
J Genet Eng Biotechnol ; 20(1): 146, 2022 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-36282371

RESUMO

BACKGROUND: Chlamydia trachomatis is an obligate intracellular gram-negative pathogen, responsible for diverse affections, mainly trachoma and sexually transmitted diseases. Antibiotics are the commonly used drugs to tackle chlamydiae infections. However, when overused or wrongly used this may lead to strains' resistance to antibiotics, this phenomenon represents a real health problem worldwide. Numerous studies showed the association of Chlamydia trachomatis resistance with mutations in different genes; these mutations could have a deleterious or neutral impacts on the encoded proteins. The aim of this study is to perform an in silico analysis of C. trachomatis rpoB-encoded proteins using numerous bioinformatics tools and to identify the functional and structural-related effects of the mutations and consequently their impact on the bacteria sensitivity to antibiotics. RESULTS: The analysis revealed that the prediction of the damaging impact related to the mutations in rpoB-encoded proteins showed eight mutations: V136F, Q458K, V466A, A467T, H471N, H471Y, H471L, and I517M with big deleterious effects. Among them, six mutations, V136F, Q458K, V466A, A467T, H471N, and I517M, are located in a highly conserved regions decreasing the protein's stability. Furthermore, the structures analysis showed that the mutations A467T, H471N, I517M, and V136F models had a high deviation compared to the wild type. Moreover, the prediction of protein-protein network indicated that rpoB wild type interacts strongly with 10 proteins of C. trachomatis, which are playing different roles at different levels. CONCLUSION: As conclusion, the present study revealed that the changes observed in the encoded proteins can affect their functions and structures, in addition to their interactions with other proteins which impact the bacteria sensitivity to antibiotics. Consequently, the information revealed through this in silico analysis would be useful for deeper exploration to understand the mechanisms of C. trachomatis resistance and enable managing the infection to avoid its complications. We recommend further investigations and perform deeper experimental analysis with collaboration between bioinformaticians, physicians, biologists, pharmacists, and chemistry and biochemistry scientists.

6.
Front Genet ; 13: 769919, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35571023

RESUMO

Genomics policy development involves assessing a wide range of issues extending from specimen collection and data sharing to whether and how to utilize advanced technologies in clinical practice and public health initiatives. A survey was conducted among African scientists and stakeholders with an interest in genomic medicine, seeking to evaluate: 1) Their knowledge and understanding of the field. 2) The institutional environment and infrastructure available to them. 3) The state and awareness of the field in their country. 4) Their perception of potential barriers to implementation of precision medicine. We discuss how the information gathered in the survey could instruct the policies of African institutions seeking to implement precision, and more specifically, genomic medicine approaches in their health care systems in the following areas: 1) Prioritization of infrastructures. 2) Need for translational research. 3) Information dissemination to potential users. 4) Training programs for specialized personnel. 5) Engaging political stakeholders and the public. A checklist with key requirements to assess readiness for implementation of genomic medicine programs is provided to guide the process from scientific discovery to clinical application.

7.
J Pers Med ; 12(2)2022 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-35207753

RESUMO

Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available.

9.
Ann Clin Microbiol Antimicrob ; 20(1): 59, 2021 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-34479551

RESUMO

BACKGROUND: Chlamydiae are intracellular bacteria that cause various severe diseases in humans and animals. The common treatment for chlamydia infections are antibiotics. However, when antibiotics are misused (overuse or self-medication), this may lead to resistance of a number of chlamydia species, causing a real public health problem worldwide. MATERIALS AND METHODS: In the present work, a comprehensive literature search was conducted in the following databases: PubMed, Google Scholar, Cochrane Library, Science direct and Web of Science. The primary purpose is to analyse a set of data describing the genes and mutations involved in Chlamydiae resistance to antibiotic mechanisms. In addition, we proceeded to a filtration process among 704 retrieved articles, then finished by focusing on 24 studies to extract data that met our requirements. RESULTS: The present study revealed that Chlamydia trachomatis may develop resistance to macrolides via mutations in the 23S rRNA, rplD, rplV genes, to rifamycins via mutations in the rpoB gene, to fluoroquinolones via mutations in the gyrA, parC and ygeD genes, to tetracyclines via mutations in the rpoB gene, to fosfomycin via mutations in the murA gene, to MDQA via mutations in the secY gene. Whereas, Chlamydia pneumoniae may develop resistance to rifamycins via mutations in the rpoB gene, to fluoroquinolones via mutations in the gyrA gene. Furthermore, the extracted data revealed that Chlamydia psittaci may develop resistance to aminoglycosides via mutations in the 16S rRNA and rpoB genes, to macrolides via mutations in the 23S rRNA gene. Moreover, Chlamydia suis can become resistance to tetracyclines via mutations in the tet(C) gene. In addition, Chlamydia caviae may develop resistance to macrolides via variations in the 23S rRNA gene. The associated mechanisms of resistance are generally: the inhibition of bacteria's protein synthesis, the inhibition of bacterial enzymes' action and the inhibition of bacterial transcription process. CONCLUSION: This literature review revealed the existence of diverse mutations associated with resistance to antibiotics using molecular tools and targeting chlamydia species' genes. Furthermore, these mutations were shown to be associated with different mechanisms that led to resistance. In that regards, more mutations and information can be shown by a deep investigation using the whole genome sequencing. Certainly, this can help improving to handle chlamydia infections and healthcare improvement by decreasing diseases complications and medical costs.


Assuntos
Antibacterianos/farmacologia , Infecções por Chlamydia/tratamento farmacológico , Chlamydia trachomatis/efeitos dos fármacos , Chlamydia trachomatis/genética , Macrolídeos/farmacologia , RNA Ribossômico 16S/genética , Tetraciclinas/farmacologia , Infecções por Chlamydia/diagnóstico , Chlamydia trachomatis/isolamento & purificação , Fluoroquinolonas/farmacologia , Humanos , Mutação , RNA Ribossômico 23S/genética , Rifamicinas/farmacologia
10.
Database (Oxford) ; 20212021 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-33864455

RESUMO

African genomic medicine and microbiome datasets are usually not well characterized in terms of their origin, making it difficult to find and extract data for specific African ethnic groups or even countries. The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for developing data portals for African genomic medicine and African microbiomes to address this and ran a hackathon to initiate their development. The two portals were designed and significant progress was made in their development during the hackathon. All the participants worked in a very synergistic and collaborative atmosphere in order to achieve the hackathon's goals. The participants were divided into content and technical teams and worked over a period of 6 days. In response to one of the survey questions of what the participants liked the most during the hackathon, 55% of the hackathon participants highlighted the familial and friendly atmosphere, the team work and the diversity of team members and their expertise. This paper describes the preparations for the portals hackathon and the interaction between the participants and reflects upon the lessons learned about its impact on successfully developing the two data portals as well as building scientific expertise of younger African researchers. Database URL: The code for developing the two portals was made publicly available in GitHub repositories: [https://github.com/codemeleon/Database; https://github.com/codemeleon/AfricanMicrobiomePortal].


Assuntos
Biologia Computacional , Microbiota , Bases de Dados Factuais , Genoma , Genômica , Humanos , Microbiota/genética
11.
OMICS ; 25(4): 213-233, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33794662

RESUMO

Following the publication of the first human genome, OMICs research, including genomics, transcriptomics, proteomics, and metagenomics, has been on the rise. OMICs studies revealed the complex genetic diversity among human populations and challenged our understandings of genotype-phenotype correlations. Africa, being the cradle of the first modern humans, is distinguished by a large genetic diversity within its populations and rich ethnolinguistic history. However, the available human OMICs tools and databases are not representative of this diversity, therefore creating significant gaps in biomedical research. African scientists, students, and publics are among the key contributors to OMICs systems science. This expert review examines the pressing issues in human OMICs research, education, and development in Africa, as seen through a lens of computational biology, public health relevant technology innovation, critically-informed science governance, and how best to harness OMICs data to benefit health and societies in Africa and beyond. We underscore the disparities between North and Sub-Saharan Africa at different levels. A harmonized African ethnolinguistic classification would help address annotation challenges associated with population diversity. Finally, building on the existing strategic research initiatives, such as the H3Africa and H3ABioNet Consortia, we highly recommend addressing large-scale multidisciplinary research challenges, strengthening research collaborations and knowledge transfer, and enhancing the ability of African researchers to influence and shape national and international research, policy, and funding agendas. This article and analysis contribute to a deeper understanding of past and current challenges in the African OMICs innovation ecosystem, while also offering foresight on future innovation trajectories.


Assuntos
Pesquisa Biomédica , Biologia Computacional , África , Ecossistema , Genômica , Humanos
12.
Per Med ; 17(2): 155-170, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32125935

RESUMO

Effective interventions and treatments for complex diseases have been implemented globally, however, coverage in Africa has been comparatively lower due to lack of capacity, clinical applicability and knowledge on the genetic contribution to disease and treatment. Currently, there is a scarcity of genetic data on African populations, which have enormous genetic diversity. Pharmacogenomics studies have the potential to revolutionise treatment of diseases, therefore, African populations are likely to benefit from these approaches to identify likely responders, reduce adverse side effects and optimise drug dosing. This review discusses clinical pharmacogenetics studies conducted in African populations, focusing on studies that examined drug response in complex diseases relevant to healthcare. Several pharmacogenetics associations have emerged from African studies, as have gaps in knowledge.


Assuntos
População Negra/genética , Variantes Farmacogenômicos , Ensaios Clínicos como Assunto , Estudos de Associação Genética , Humanos
13.
Microb Pathog ; 139: 103860, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31707079

RESUMO

BACKGROUND: Chlamydia pneumoniae is an obligate intracellular bacterium that activates cell mediated immune responses; several investigations have demonstrated its strong implication in atherosclerosis. OBJECTIVES: The main objective of our study was to explore the cell-mediated immune response to C. pneumoniae infection in patients with atherosclerosis by evaluating CD14, CD8 and CD4 expression. METHODS: This investigation involved a total of 27 patients with atherosclerosis and 32 controls, among patients recruited to evaluate the association of C. pneumoniae with atherosclerosis. C. pneumoniae DNA was detected in PBMCs by nested PCR as described in our previous studies. CD4, CD8 and CD14 expression was measured by flow cytometry and data analysis was performed using FlowJo software. RESULTS: The results revealed an increase in MFI expression of CD4, CD8 and CD14 in Cpn DNA+ subjects among both patients and healthy subject controls (CD4 Cpn DNA+ = 829.11 vs. CD4 Cpn DNA- = 571.14; CD8 Cpn DNA+ = 1562 vs. CD8 Cpn DNA- = 699; CD14 Cpn DNA+ = 1513.83 vs. CD14 Cpn DNA- = 1170.70), with a statistically significant difference (p < 0.05). Furthermore, the comparison of CD4, CD8 and CD14 expression between Cpn DNA+ patients and Cpn DNA+ healthy subject controls showed a statistically significant increase in expression in the former group (p < 0.05). CONCLUSION: These data provide incentive to further explore the role of C. pneumoniae in stimulating and changing mechanisms of the cell-mediated immune response induced by C. pneumoniae antigens. This may alter immune cell-mediated responses via increased expression of CD4, CD8 and CD14 during inflammation and the development of thrombosis, leading to fatal atherosclerosis.


Assuntos
Aterosclerose/etiologia , Aterosclerose/imunologia , Infecções por Chlamydophila/complicações , Infecções por Chlamydophila/imunologia , Imunidade Celular/imunologia , Antígenos CD4/metabolismo , Antígenos CD8/metabolismo , Chlamydophila pneumoniae , Citometria de Fluxo , Genótipo , Humanos , Inflamação , Leucócitos Mononucleares/imunologia , Receptores de Lipopolissacarídeos/metabolismo , Trombose
14.
Infect Dis Health ; 24(2): 67-74, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30541691

RESUMO

BACKGROUND: Chlamydia pneumoniae is a pathogen associated with human respiratory tract infection, its viable presence in atherosclerotic plaques is also assumed to play significant function in cardiac diseases. Our study's main objective is to evaluate Chlamydia pneumoniae sero-prevalence in Moroccan patients with cardiovascular diseases using and comparing two serological methods. METHODS: Two hundred eighteen patients were enrolled; serums were tested by microimmunofluorescence to explore the sero-prevalence. Simultaneously 74 serums were analyzed by both immunoblot and micro-immunofluorescence to evaluate recombinant proteins diagnosis value. RESULTS: MIF results revealed 81% male and 84.5% female positive cases. The comparative study among 74 patients showed 78% men and 89% women positive cases by immunoblot, whereas MIF showed respectively 80% and 72%, a significant concordance between these methods was revealed. However, this comparison showed also two types of discrepancies, which may be related to difficulties in antigens detection by micro-immunofluorescence resulting from their structure complexity, or the antibodies reactivity with species' common antigens. CONCLUSIONS: The study revealed a high sero-prevalence of Chlamydia pneumoniae in the studied population, a big interest of recombinant protein was also revealed in the diagnosis accuracy. We suggest therefore using immunoblot for diagnosis confirmation because it provides additional useful information.


Assuntos
Anticorpos Antibacterianos/sangue , Antígenos de Bactérias/sangue , Doenças Cardiovasculares/microbiologia , Infecções por Chlamydia/diagnóstico , Infecções por Chlamydia/epidemiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Doenças Cardiovasculares/complicações , Infecções por Chlamydia/complicações , Chlamydophila pneumoniae , Feminino , Imunofluorescência , Humanos , Immunoblotting , Imunoglobulina G/sangue , Masculino , Pessoa de Meia-Idade , Prevalência , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/microbiologia , Estudos Soroepidemiológicos , Testes Sorológicos/normas
15.
J Infect Public Health ; 11(2): 246-249, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-28869155

RESUMO

Chlamydia pneumoniae is an intracellular bacterium responsible for respiratory diseases and is highly involved in cardiovascular disease development, mainly atherosclerosis. The main objective of our study was to evaluate C. pneumoniae prevalence in Moroccan patients suffering from cardiovascular diseases. A total of 115 patients with cardiovascular diseases were enrolled, and their clinical and behavioral information was recorded. Blood was sampled from all patients as well as the atheroma plaques from 36 patients undergoing surgery. Nested PCR was performed for C. pneumoniae DNA detection in both peripheral blood mononuclear cells (PBMCs) and atheroma plaques. Statistical analysis was performed using EpiInfo software. Data analysis showed cardiovascular disease dominance in men, with a sex ratio M/F of 3.4, a majority of tobacco users (52.2%), and many diabetics (44.3%). A significant difference between genders was shown for tobacco use (p<0.05). Positive cases for PBMCs and atheroma plaques were 61% and 86%, respectively, and a significant difference between PBMCs and atheroma plaque infection was identified (p=0.02). Data analysis also showed that 12% of patients presented only C. pneumoniae infection as a risk factor. Therefore, the high prevalence of C. pneumoniae suggests its involvement in atherosclerosis, and further investigation is recommended for confirmation.


Assuntos
Doenças Cardiovasculares/epidemiologia , Infecções por Chlamydophila/epidemiologia , Chlamydophila pneumoniae/genética , Anticorpos Antibacterianos/sangue , Aterosclerose/epidemiologia , Aterosclerose/microbiologia , Doenças Cardiovasculares/diagnóstico , Doenças Cardiovasculares/microbiologia , Infecções por Chlamydophila/sangue , Infecções por Chlamydophila/diagnóstico , Chlamydophila pneumoniae/imunologia , Chlamydophila pneumoniae/isolamento & purificação , DNA Bacteriano/genética , Feminino , Humanos , Leucócitos Mononucleares/microbiologia , Masculino , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular , Reação em Cadeia da Polimerase , Prevalência , Fatores de Risco
16.
IEEE Trans Nanobioscience ; 16(8): 682-686, 2017 12.
Artigo em Inglês | MEDLINE | ID: mdl-28945599

RESUMO

Automated DNA sequencers produce chromatogram files in ABI format. When viewing chromatograms, some ambiguities are shown at various sites along the DNA sequences, because the program implemented in the sequencing machine and used to call bases cannot always precisely determine the right nucleotide, especially when it is represented by either a broad peak or a set of overlaying peaks. In such cases, a letter other than A, C, G, or T is recorded, most commonly N. Thus, DNA sequencing chromatograms need manual examination: checking for mis-calls and truncating the sequence when errors become too frequent. The purpose of this paper is to develop a program allowing the automatic correction of these ambiguities. This application is a Web-based program powered by Shiny and runs under R platform for an easy exploitation. As a part of the interface, we added the automatic ends clipping option, alignment against reference sequences, and BLAST. To develop and test our tool, we collected several bacterial DNA sequences from different laboratories within Institut Pasteur du Maroc and performed both manual and automatic correction. The comparison between the two methods was carried out. As a result, we note that our program, ABI base recall, accomplishes good correction with a high accuracy. Indeed, it increases the rate of identity and coverage and minimizes the number of mismatches and gaps, hence it provides solution to sequencing ambiguities and saves biologists' time and labor.


Assuntos
Automação Laboratorial/métodos , Alinhamento de Sequência/métodos , Análise de Sequência de DNA/métodos , Software , Biologia Computacional , DNA/análise , DNA/genética , Internet
17.
Pathog Dis ; 75(4)2017 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-28387800

RESUMO

Chlamydia pneumoniae is a respiratory pathogen associated with chronic inflammatory diseases such as asthma and atherosclerosis, and its detection in human carotid and coronary atheroma suggests some support for its involvement in atherogenesis. The main objective of our study was to evaluate the association between Chlamydia pneumoniae and atherosclerosis in Moroccan patients through a case-control approach and detected strain genotyping. A total of 137 cases and 124 controls were enrolled, nested PCR was performed for Chlamydia pneumoniae screening of the peripheral blood mononuclear cells (PBMCs) of both cases and controls as well as atheroma plaques from 37 cases, and positive samples were subjected to sequencing for genotyping and phylogenetic analysis. The results showed 54% and 18%, respectively, for positivity in cases and control PBMCs and 86.5% in atheroma plaques, the difference being significant between the two groups (P < 0.001, ORa = 8.580, CI, 95% [3.273-22.491]). Strain sequence analyses showed more than 98% similarity with human reference strains, and revealed various genotypes. This study supports the involvement of Chlamydia pneumoniae in atherosclerosis in the studied population and genotyping revealed that detected strains were identical to human strains circulating worldwide.


Assuntos
Aterosclerose/microbiologia , Infecções por Chlamydophila/microbiologia , Chlamydophila pneumoniae/genética , DNA Bacteriano/genética , Filogenia , Placa Aterosclerótica/microbiologia , Adulto , Idoso , Aterosclerose/patologia , Técnicas de Tipagem Bacteriana , Sequência de Bases , Estudos de Casos e Controles , Infecções por Chlamydophila/patologia , Chlamydophila pneumoniae/classificação , Chlamydophila pneumoniae/isolamento & purificação , Feminino , Humanos , Leucócitos Mononucleares/metabolismo , Leucócitos Mononucleares/microbiologia , Masculino , Pessoa de Meia-Idade , Marrocos , Placa Aterosclerótica/patologia , Alinhamento de Sequência , Análise de Sequência de DNA , Homologia de Sequência do Ácido Nucleico
18.
Glob Heart ; 12(2): 91-98, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-28302555

RESUMO

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.


Assuntos
Pesquisa Biomédica/métodos , Biologia Computacional/tendências , Genômica/métodos , África , Humanos
19.
Genome Res ; 26(2): 271-7, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26627985

RESUMO

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.


Assuntos
População Negra/genética , Promoção da Saúde , África , Biologia Computacional , Sistemas Computacionais , Variação Genética , Genética Médica , Genômica , Humanos
20.
Can J Microbiol ; 53(12): 1360-8, 2007 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-18059568

RESUMO

A new chlamydial test system, the Chlamycheck assay, which uses 4 purified recombinant antigens of Chlamydia trachomatis and Chlamydophila pneumoniae and one antigen of Chlamydophila psittaci, has been developed and commercialized. We investigated the reactivities of the recombinant antigens with sera from a group of 30 patients with acute Chlamydia trachomatis infection, 88 patients consulting for sexually transmitted infections, and 46 patients with serological evidence of Chlamydophila pneumoniae infection. The results obtained from human and infected mouse sera suggest that Chlamycheck serology against multiple proteins may provide additional useful information that is not available by conventional whole elementary body microimmunofluorescence or single-antigen enzyme-linked immunosorbent assay serology. Specific serological profiles were associated with acute versus past Chlamydia trachomatis infection or with Chlamydia trachomatis primo-infection versus infection in a Chlamydophila pneumoniae history context.


Assuntos
Antígenos de Bactérias/sangue , Western Blotting/métodos , Infecções por Chlamydia/diagnóstico , Chlamydia/isolamento & purificação , Imunoensaio/métodos , Proteínas Recombinantes/sangue , Adolescente , Adulto , Idoso , Animais , Especificidade de Anticorpos , Criança , Chlamydia/imunologia , Infecções por Chlamydia/sangue , Infecções por Chlamydia/imunologia , Clonagem Molecular , Feminino , Humanos , Masculino , Camundongos , Camundongos Endogâmicos BALB C/sangue , Camundongos Endogâmicos BALB C/imunologia , Camundongos Endogâmicos BALB C/microbiologia , Pessoa de Meia-Idade , Proteínas Recombinantes/imunologia , Sensibilidade e Especificidade
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