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Incidental and secondary findings in trio exome sequencing

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Genes & Diseases 2024年第4期11卷 152-154页

作者： Camille Cohen emeline Bellanger Jeremie Mortreux Laure Raymond Francois Vialard Rodolphe Dard Department of Genetics Centre Hospitalier Intercommunal de Poissy-Saint-Germain-en-LayePoissy 78300France RHuMA UMR-BREEDINRA-ENVA-UVSQMontigny le Bretonneux 78180France Service de Genetique Laboratoire Eurofins BiomnisLyon 69007France

Exome sequencing(ES)generates secondary findings(SFs)in 2%of tested individuals if one follows the American College of Medical Genetics and Genomics(ACMG)guide-lines.i,z2 However,the rate of incidental and secondary findings(ISFs)is higher in routine clinical practice because of(i)the use of trio ES instead of solo sequencing and(i)the exclusion of the incidental findings(IFs)of medical value concerning genes in the ACMG ***,it is not clear how sufficient is a restricted list of genes to detect every ISF of major clinical value;and what is the amount of additional workload for the laboratory.

关键词： routine clinical finding

Application of High-Throughput Sequencing: Discovery of Informative SNPs to Subtype Bacillus anthracis

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Advances in Bioscience and Biotechnology 2014年第7期5卷 669-677页

作者： Guillaume Girault Simon Thierry emeline Cherchame Sylviane Derzelle University Paris-Est ANSES Animal Health Laboratory Bacterial Zoonoses Unit Maisons-Alfort France

Single Nucleotide Polymorphisms (SNPs) are the most common and abundant genetic variation found in the genome of any living species, from bacteria to humans. In bacterial genotyping, these evolutionarily stable point mutations represent important DNA markers that can be used to elucidate deep phylogenetic relationships among worldwide strains, but also to discriminate closely related strains. With the advent of next generation sequencing (NGS) technologies, affordable solutions are now available to get access to the complete genome sequence of an organism. Sequencing efforts of an increasing number of strains provide an unprecedented opportunity to create comprehensive species phylogenies. In this study, a comparative analysis of 161 genomes of Bacillus anthracis has being conducted to discover new informative SNPs that further resolves B. anthracis SNP-based phylogenetic tree. Nine previously unpublished SNPs that define major groups or sub-groups within the B. anthracis species were selected and developed into SNP discriminative assays. We report here a cost-effective high-resolution melting-based genotyping method for the screening of 27 canonical SNPs that includes these new diagnostic markers. The present assays are useful to rapidly assign an isolate to one sub-lineages or sub-groups and determine its phylogenetic placement on the B. anthracis substructure population.

关键词： SNPs Bacillus anthracis Genotyping HRM Phylogeny

Proficiency Testing Scheme for Pesticides in Honey

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Journal of Agricultural Science and Technology(B) 2016年第4期6卷 281-287页

作者： Elvire Messineo emeline Diore Nicolas Le Baron Abdelkader Boubetra Interprofessional Bureau of Analytical Studies (BIPEA) 189 Rue d'Aubervilliers Paris 75018 France

Agricultural contamination with pesticides is a challenging problem for both human and bee health. Consequently, a number of laboratories performing pesticides residues analyse in honey and honey products has gradually increased in recent years. In the framework of their accreditations according to ISO 17025 standard, these laboratories must control their performances through interlaboratory comparison. Interprofessional Bureau of Analytical Studies (BIPEA) organizes regular proficiency testing schemes (PTS) in many analytical domains, including the analysis of pesticides in honey, to compare the performances of the laboratories. As an example, one test was conducted in October 2015 using an organic honey spiked with 21 pesticides, at levels between 15 ^g/kg and 200 ^g/kg, with 27 participating laboratories. This test was intended for the identification and quantification of 21 molecules of pesticides residues. The techniques used by the laboratories were GC-MS-MS, LC-MS-MS, GC-MS and GC-ECD, according to the molecules. Participating laboratories were required to return their results on a dedicated website after a period of one month, and a statistical treatment of the data was performed according to ISO 13528 standard. Assigned (consensus) values were calculated from the participants’ results and the performances of the laboratories could then be evaluated individually and collectively according to ISO 17043 standard. The results of this test were satisfactory for detection and quantification, whatever the analytical technique. The molecules were correctly identified by the laboratories and the recovery rates ranged from 56% up to 88%. The dispersions of the results, studied through the coefficients of variation, were also satisfactory ranging from 7% to 30%. This test showed that the laboratories participating routinely in this kind of tests are very competent in the analysis of pesticides residues in honey. It also allowed the participating laboratories to draw u

关键词： Proficiency testing schemes pesticides honey quality control laboratory performance

Analysis of Contributions to NO2Ambient Air Quality Levels in Madrid City (Spain) through Modeling. Implications for the Development of Policies and Air Quality Monitoring

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Journal of Geoscience and Environment Protection 2014年第1期2卷 6-11页

作者： Rafael Borge David de la Paz Julio Lumbreras Javier Pérez Michel vedrenne Laboratory of Environmental Modelling Technical University of Madrid (UPM) Spain

As environmental standards become more stringent (e.g. European Directive 2008/50/EC), more reliable and sophisticated modeling tools are needed to simulate measures and plans that may effectively tackle air quality exceedances, common in large cities across Europe, particularly for NO2. Modeling air quality in urban areas is rather complex since observed concentration values are a consequence of the interaction of multiple sources and processes that involve a wide range of spatial and temporal scales. Besides a consistent and robust multi-scale modeling system, comprehensive and flexible emission inventories are needed. This paper discusses the application of the WRF-SMOKE-CMAQ system to the Madrid city (Spain) to assess the contribution of the main emitting sectors in the region. A detailed emission inventory was compiled for this purpose. This inventory relies on bottom-up methods for the most important sources. It is coupled with the regional traffic model and it makes use of an extensive database of industrial, commercial and residential combustion plants. Less relevant sources are downscaled from national or regional inventories. This paper reports the methodology and main results of the source apportionment study performed to understand the origin of pollution (main sectors and geographical areas) and define clear targets for the abatement strategy. Finally the structure of the air quality monitoring is analyzed and discussed to identify options to improve the monitoring strategy not only in the Madrid city but the whole metropolitan area.

关键词： Air Quality Modeling Source Apportionment NO2 CMAQ Urban Air Quality Madrid

Unveiling the Threat: Case Reports of Extra-Pulmonary Tuberculosis among Sanctuary Chimpanzees

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Advances in Infectious Diseases 2024年第1期14卷 105-132页

作者： emeline Chanove Yedra Feltrer Antoine Collomb-Clerc Angela Ceballos-Caro Marina Spinu Department of Infectious Diseases University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca Romania International Primate Health and Welfare Group (IPHWG) Madrid Spain NeuroX Institute and Brain Mind Institute School of Life Sciences Swiss Federal Institute of Technology (EPFL) Lausanne Switzerland Malaria and Emerging Parasitic Diseases Laboratory National Centre for Microbiology Instituto de Salud Carlos III Madrid Spain

Primate sanctuaries across Africa play a pivotal role in the rescue and rehabilitation of confiscated and rescued wild primates, many of whom have had extensive contact with humans prior to their arrival and throughout the rehabilitation process, heightening the risk of disease transmission. While tuberculosis is not naturally occurring in free-living chimpanzees, it has been extensively observed in captive primates that have been in close proximity to humans or other captive primates infected with Mycobacterium tuberculosis. This case report delves into an outbreak of extra-pulmonary tuberculosis among juvenile chimpanzees within a sanctuary, detailing the associated diagnostic challenges and treatment approaches. The five cases had close contact with a caregiver infected with tuberculosis, subsequently transmitting the infection to other in-contact chimpanzees. Prolonged treatment, employing the human protocol of quadri-therapy (rifampicin, isoniazid, pyrazinamide, and ethambutol), followed by bi-therapy (rifampicin and isoniazid), resulted in complete resolution for all five cases. These cases underscore the critical importance of maintaining high levels of biosecurity, implementing effective quarantine measures, and adhering to strict hygiene practices when working with non-human primates.

关键词： Extrapulmonary Tuberculosis Tuberculosis Chimpanzees Zoonotic Risk Biosecurity Diagnosis Challenges

MiR-3031通过靶基因POU2F3调控奶山羊乳腺发育的研究

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MiR-3031通过靶基因POU2F3调控奶山羊乳腺发育的研究

作者： SELEH-ZO emeline Diane Mariam（李若兰）西北农林科技大学

学位级别：硕士

microRNAs是一类短的,高度保守的非编码RNA,可调节基因的表达。MiR-3031作为一个功能性miRNA,参与调节奶山羊乳腺发育和泌乳等多种重要的生物学过程。本试验旨在研究POU2F3和miR-3031在奶山羊乳腺上皮细胞中的靶向关系及其功能,为奶山... 详细信息

microRNAs是一类短的,高度保守的非编码RNA,可调节基因的表达。MiR-3031作为一个功能性miRNA,参与调节奶山羊乳腺发育和泌乳等多种重要的生物学过程。本试验旨在研究POU2F3和miR-3031在奶山羊乳腺上皮细胞中的靶向关系及其功能,为奶山羊乳腺发育和泌乳提供理论依据。通过RT-qPCR,Western blot和构建双荧光素酶报告载体验证miR-3031与POU2F3的靶向调节作用。生物信息学分析表明,POU2F3的3’UTR区包含miR-3031的结合位点。同时,miR-3031降低了PsiCHECKTM2-POU2F3 3’UTR-wt的双荧光素酶活性。RT-qPCR和Western blot结果显示,与对照组NC相比,miR-3031 mimics显著降低POU2F3的mRNA和蛋白水平的表达;结果表明POU2F3是miR-3031的靶基因。转染miR-3031 24h、48h后CCK8检测miR-3031对奶山羊乳腺上皮细胞活力的影响。结果显示,miR-3031 mimic显著提高奶山羊乳腺上皮细胞的活力。转染siPOU2F3 24h后EDU检测奶山羊乳腺上皮细胞增殖的情况,结果显示,干扰POU2F3显著促进奶山羊乳腺上皮细胞的增殖。将siPOU2F3和si-NC转染到乳腺上皮细胞中,进一步研究POU2F3对奶山羊乳腺上皮细胞凋亡的作用机理。流式结果表明,siPOU2F3显著抑制奶山羊乳腺上皮细胞凋亡。同时,siPOU2F3显著抑制Bcl-2和Bax蛋白的表达,上调Bcl-2/Bax的比率;同时,检测AKT和mTOR的磷酸化水平。结果表明,siPOU2F3显著上调了AKT、mTOR的磷酸化水平和PTEN的蛋白水平以及显著下调PI3K蛋白的表达。综上所述,miR-3031靶向POU2F3通过AKT/mTOR信号通路促进奶山羊乳腺上皮细胞增殖,抑制凋亡。

关键词：奶山羊 miRNAs 基因表达上皮细胞调节

Modeling vulnerability of protected areas to invasion by Chromolaena odorata under current and future climates

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Ecosystem Health and Sustainability 2015年第6期1卷 28-39页

作者： A.Belarmain Fandohan Ayub M.O.Oduor A.Idelphonse Sode Liang Wu Aida Cuni-Sanchez emeline Assede Gerard N.Gouwakinnou Forestry Agroforestry and Biogeography Unit University of Agriculture of KetouBP43KetouRepublic of Benin Biometry and Environmental System Analysis Faculty of Forest and Environmental SciencesAlbert-Ludwigs-University of FreiburgTennebacher Strasse 4Freiburg79085 Germany UNEP-International Ecosystem Management Partnership c/o Institute of Geographic Sciences and Natural Resources ResearchChinese Academy of SciencesNo.11A Datun RoadBeijing 100101 China Ecology Department of BiologyUniversity of Konstanz.Universitatsstrasse 10D-78457 KonstanzGermany Laboratoire d’Ecologie Appliquee FacultedesSciencesAgronomiquesUniversited’Abomey-Calavi01BP526CotonouBenin Environment Department University of YorkHeslingtonYO105DDYorkUnited Kingdom Ecole Nationale Superieur d’Amenagement et de Gestion des Aires Protegees Universite de ParakouBP287KandiBenin

Invasive plant species and climate change are among the biggest threats to the ecological integrity of many ecosystems,including those of protected *** management of invasive plants requires information regarding their spatialdistributions Using maximum entropy,wemodeled habitat suitability for an invasive plant species Chromolaena odorata under current and future climatic conditions(HadGEM2-ESand MIROC5)in protected areas of four West African countries(Benin,Cote d'voire,Ghana,and Togo).Under current climatic conditions,approximately 73%of total land area within the protected areas was suitable for colonization by *** future climate projections,the total area of suitable habitats for this invasive plant was projected to decrease by 7-9%(HadGEM2-ES)and 12-14%(MIROC5).Country-specific patterns suggest that major protected areas in Cote d'Ivoire and Ghana will be more vulnerable to invasion by *** than those in Benin and Togo under both current and future dimatic *** maintain normal ecosystem functioning and provisioning of ecosystem services within the protected areas studied here,locations that have been identified as most vulnerable to invasion by *** should be accorded proportionately higher priority when formulating appropriate management strategies.

关键词： Chromolaena odorata climate change HadGEM2-ES maximum entropy MIROC5 representative concentration pathways risk assessment Siam weed West Africa

In Vitroand in VivoAnti-Inflammatory Effect of a Biotechnologically Modified Borage Seed Extract: Evidence for Lipid Pro-Resolving Mediators’ Implication in the Enhancement of Psoriatic and Atopic Dermatitis Lesions

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Journal of Cosmetics, Dermatological Sciences and Applications 2015年第2期5卷 151-160页

作者： Gérald Chene Vincent Baillif emeline Van Goethem Jean-Eric Branka Toni Ionescu Géraldine Robert Luc Lefeuvre Ambiotis SAS Cana Biotech 2 Toulouse France EPHYSCIENCE Nantes France Laboratoires Dermatologiques d’Uriage Siège Social Courbevoie France

Aim: Resolvins, maresins and lipoxins are lipid mediators issued from essential polyunsaturated fatty acids which are the first anti-inflammatory and pro-resolving signals identified during the resolution phase of inflammation. As borage oil and/or borage seed extracts have shown beneficial action in treatment of atopic dermatitis or eczema in human and canine, we have modified a borage oil component by using biotechnology in order to get a compound structurally related to a polyunsaturated fatty acid, and we have studied its ability to reduce inflammation mediators production through the generation of resolvins, maresins and/or lipoxins. Additionally, we have demonstrated the potent anti-inflammatory effect of this new compound which consists in borage seed oil aminopropanediol amides, through an in vivo study concerning subjects suffering from psoriasis or atopic dermatitis. Study Design/Methods: For the in vitro study, inflammation was induced in co-cultures of human dendritic cells and normal keratinocytes by the addition of PMA and the calcium ionophore A23187. Ability of our borage seed oil aminopropanediol amides to increase resolvin D2, maresin 1 and lipoxins A4 and B4 synthesis was then measured. Pro-inflammatory cytokines (IL-1β, IL-6, IL-8) and PGE2 productions were also quantified. For the in vivo study, 36 subjects suffering from psoriasis or atopic dermatitis have used twice a day during 30 days, a formulation containing borage seed oil aminopropanediol amides. Before the beginning of the study and after 30 days’ treatment, the severity of psoriasis and of atopic dermatitis was evaluated by using the PGA and the SCORAD scoring scales, respectively. Results: Borage seed oil aminopropanediol amides were able to significantly increase the resolvin D2, maresin 1 and lipoxins A4 and B4 synthesis. Concomitantly, they were also able to significantly inhibit the production of IL-1β, IL-6, IL-8 and PGE2 induced by the PMA and the calcium ionophore A23187 in the

关键词： Human Skin Biotechnologically Modified Borage Extract Interleukins Inflammation Psoriasis Atopic Dermatitis Resolvins Maresins Lipoxins

BIERMER’s Disease: About 4 Cases Diagnosed at Regional University Hospital of Ouahigouya (Chur/Ohg) and Literature Review

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Open Journal of Gastroenterology 2024年第9期14卷 322-329页

作者： Zanga Damien Ouattara Stève Léonce Zoungrana Saïdou Santi emeline Agathe Carama Fabien Dembele Bafima Désiré Diarra Alain Bougouma Department of Gastroenteroly Ouahigouya Regional University Hospital Ouahigouya Burkina Faso Department of Neurology Bogodogo University Hospital Ouagadougou Burkina Faso Department of Gastroenterology Yalgado Oudraogo University Hospital Center Ouagadougou Burkina Faso

Megaloblastic pernicious anemia is an autoimmune disorder, considered rare in African context. The objective of this study was to report four clinical cases collected at the CHUR/OHG, and to review the literature. The study population consisted of two men and two women. The clinical manifestations were mainly neurological and hematological. The neurological signs were mainly paresthesia. One patient presented memory problems. On the biological level, macrocytic anemia and vitamin B12 deficiency were reported in two cases prior to treatment while the other two without serological assay of vitamin B12 were put on trial treatment. Anti-intrinsic factor antibodies were positive in three patients. The Schilling test was not used. Upper gastrointestinal endoscopy revealed atrophic fundic gastritis in all four patients who received treatment through intramuscular injection of hydroxocobalamin (vitamin B12). The evolution was favorable after one month of treatment in all cases. The literature review is dominated by clinical case reports, the largest cohorts of which are from the Maghreb.

关键词： Anemia Pernicious Megaloblastic Vitamin B12