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PCR-HRm for Genomic Surveillance of SARS-CoV-2: A Variant Detection Tool in Côte d’Ivoire, West Africa

American Journal of molecular Biology 2024年第3期14卷 166-185页

作者： Aboubacar Sylla Solange Kakou-Ngazoa Tata Gniré Safiatou Coulibaly Yakoura Karidja Ouattara m.reille sylvie kouamé-sina Zeinab Ouattara David Ngolo Coulibaly Brice Kouakou Bla m.reille Dosso molecular Biology Platform Pasteur Institute Cte dIvoire Abidjan Cte dIvoire Laboratory of Biology and Health UFR Biosciences University Flix Houphout Boigny Abidjan Cte dIvoire Genetic and Cancer Laboratory Molecular Genetics Platform Pasteur Institute Cte dIvoire Abidjan Cte dIvoire Epidemic Virus Department Pasteur Institute Cte dIvoire Abidjan Cte dIvoire

The rise of new viruses, like SARS-CoV-2 causing the COVID-19 outbreak, along with the return of antibiotic resistance in harmful bacteria, demands a swift and efficient reaction to safeguard the health and welfare of the global population. It is crucial to have effective measures for prevention, intervention, and monitoring in place to address these evolving and recurring risks, ensuring public health and international security. In countries with limited resources, utilizing recombinant mutation plasmid technology in conjunction with PCR-HRm could help differentiate the existence of novel variants. cDNA synthesis was carried out on 8 nasopharyngeal samples following viral RNA extraction. The P1 segment of the SARS-CoV-2 Spike S protein was amplified via conventional PCR. Subsequently, PCR products were ligated with the pGEm-T Easy vector to generate eight recombinant SARS-CoV-2 plasmids. Clones containing mutations were sequenced using Sanger sequencing and analyzed through PCR-HRm. The P1 segment of the S gene from SARS-CoV-2 was successfully amplified, resulting in 8 recombinant plasmids generated from the 231 bp fragment. PCR-HRm analysis of these recombinant plasmids differentiated three variations within the SARS-CoV-2 plasmid population, each displaying distinct melting temperatures. Sanger sequencing identified mutations A112C, G113T, A114G, G214T, and G216C on the P1 segment, validating the PCR-HRm findings of the variations. These mutations led to the detection of L452R or L452m and F486V protein mutations within the protein sequence of the Omicron variant of SARS-CoV-2. In summary, PCR-HRm is a vital and affordable tool for distinguishing SARS-CoV-2 variants utilizing recombinant plasmids as controls.

关键词： Genomic Surveillance SARS-CoV-2 PCR-HRm Variants Côte d’Ivoire

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Detection of ARV-Resistant mutants in HIV-1-Infected Individuals in a Context of Systematic Switching to an Association Based on Dolutegravir in Abidjan, Côte d’Ivoire

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American Journal of molecular Biology 2024年第3期14卷 138-151页

作者： Odegue Kpadraux Danielle Kakou-Ngazoa Solange Dechi Jean-Jacques Renaud Diallo Zelica sina kouamé m.reille Sylla Aboubacar Tossea Koui Stéphane Kouakou Venance Adagba marius Apia N’Chouo kouamé Basile Touré Offianan André Dosso m.reille molecular Biology Platform Institut Pasteur Abidjan Cte dIvoire Laboratory of the Regional Blood Transfusion Center Yamoussoukro Cte dIvoire Department of Infectious and Tropical Diseases University Hospital Treichville Abidjan Cte dIvoire Laboratory of the Regional Blood Transfusion Center San-Pdro Cte dIvoire Department of Epidemic Virus Institut Pasteur Abidjan Cte dIvoire Department of Parasitology mycology Institut Pasteur Abidjan Cte dIvoire Department of Bacteriology-Virology Institut Pasteur Abidjan Cte dIvoire

The emergence of antiretroviral resistance mutations represents a major threat to the achievement of national and global goals for the elimination of HIV-1 infection. The global strategy in 2019 in Cte d'Ivoire is a new national policy for the management of people living with HIV with the administration of dolutegravir (DTG)-based fixed-dose combination. The aim of our study was to evaluate HIV-1 resistance to antiretrovirals (ARVs) in infected adult subjects in Cte d’Ivoire in the context of a systematic switch to a DTG-based combination. Between February 2022 and October 2023, a cross-sectional survey with random sampling was conducted in 06 services caring for people living with HIV. A total of 139 participants were included in the study. Adults with a viral load ≥ 1000 copies/mL were tested for HIV-1 ARV resistance mutations. molecular analyses were performed using protocol of ANRS-mIE (National Agency for Research on AIDS and emerging infectious diseases). The interpretation is performed by HIVGRAD (https://***/cms/grade/). The frequencies of HIV-1 resistance to non-nucleotide reverse transcriptase inhibitors (NNRTIs), nucleotide reverse transcriptase inhibitors (NRTIs), integrase inhibitors (IINTs) and protease inhibitors (PIs) were 82%, 73%, 19% and 11% respectively. The main mutations observed in the different classes were K103N (45%), m184V (64%), E157Q (19%) and L10V/m46I/A71V/I54V (6%) respectively. This study reveals the emergence of resistance to DTG-based fixed-dose combinations, favored by high rates of resistance to NRTIs and NNRTIs. This finding underlines the need for enhanced viral load monitoring and HIV-1 genotyping tests to guide the choice of NRTIs for combination therapy. In addition, monitoring for mutations to second-generation NRTIs is essential, given the scale-up of DTG-based regimens currently underway in Cte d’Ivoire.

关键词： Resistant mutants Dolutegravir HIV-1 Antiretrovirals Côte d’Ivoire

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A physics informed bayesian optimization approach for material design: application to NiTi shape memory alloys

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npj Computational materials 2023年第1期9卷 85-95页

作者： Danial Khatamsaz Raymond Neuberger Arunabha m.Roy sina Hossein Zadeh Richard Otis Raymundo Arróyave materials Science and Engineering Department Texas A&M UniversityCollege StationTX 77843USA Engineering and Science Directorate Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCA 91109USA mechanical Engineering Department Texas A&M UniversityCollege StationTX 77843USA Department of Industrial&Systems Engineering Texas A&M UniversityCollege StationTX 77843USA

The design of materials and identification of optimal processing parameters constitute a complex and challenging task,necessitating efficient utilization of available *** Optimization(BO)has gained popularity in materials design due to its ability to work with minimal ***,many BO-based frameworks predominantly rely on statistical information,in the form of input-output data,and assume black-box objective *** practice,designers often possess knowledge of the underlying physical laws governing a material system,rendering the objective function not entirely black-box,as some information is partially *** this study,we propose a physics-informed BO approach that integrates physics-infused kernels to effectively leverage both statistical and physical information in the decision-making *** demonstrate that this method significantly improves decision-making efficiency and enables more data-efficient *** applicability of this approach is showcased through the design of NiTi shape memory alloys,where the optimal processing parameters are identified to maximize the transformation temperature.

关键词： alloys shape approach

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Third-Order Optical Nonlinearity in Two-Dimensional Transition metal Dichalcogenides

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Communications in Theoretical Physics 2018年第9期69卷 344-360页

作者： sina Khorasani School of Electrical Engineering Sharif University of TechnologyTehranIran Ecole Polytechnique Federale de Lausanne CH-1015LausanneSwitzerland

We present a detailed calculation of the linear and nonlinear optical response of four types of monolayer twodimensional (2D) transition-metal dichalcogenides (TmDCs), having the formula mX2 with m=mo, W and X=S, *** calculations are based on 6-band tight-binding model of TmDCs, and then performing a semi-classical perturbation analysis of response functions. We numerically calculate the linearχ(1)μν(-ω;ω) and nonlinear surface susceptibility tensorsχ(3)μνζη(-ωΣ;ωr,ωs,ωt) withωΣ=ωr+ωs+ωt. Both non-degenerate and degenerate cases are studied for thirdharmonic generation and nonlinear refractive index, respectively. Computational results obtained with no external fitting parameters are discussed regarding two recent reported experiments on mo S2, and thus we can confirm the extraordinarily strong optical nonlinearity of TmDCs. As a possible application, we demonstrate generation of aπ/4-rotated squeezed state by means of nonlinear response of TmDCs, in a silica micro-disk resonator covered with the 2D material. Our proposed method will enable accurate calculations of nonlinear optical response, such as four-wave mixing and highharmonic generation in 2D materials and their heterostructures, thus enabling study of novel functionalities of 2D photonic integrated circuits.

关键词：非线性金属计算结果二维光反应集成电路非退化 2D

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Conventional *** pseudo-dynamic seismic analyses in the shallow strip footing bearing capacity problem

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Earthquake Engineering and Engineering Vibration 2021年第4期20卷 993-1006页

作者： Ghazal Rezaie Soufi Reza Jamshidi Chenari sina Javankhoshdel Department of Civil Engineering Faculty of EngineeringUniversity of GuilanP.O.3756RashtGuilanIran Rocscience Inc. 54 Saint Patrick St.Toronto M5T 1V1OntarioCanada

The conventional pseudo-dynamic(CPD)and modified pseudo-dynamic(mPD)methods are invoked to obtain the seismic bearing capacity of strip foundations using the limit equilibrium method,with a two-wedge failure mechanism.A spectral version of the conventional pseudo-dynamic method(SPD)is also invoked by considering the ground motion amplification factor,to be a function of the non-dimensional frequencyλ/B and soil *** analyses show that bearing capacity results obtained by the mPD and SPD methods are generally *** experience the same general reduction in bearing capacity with the increase ofλ/B,with successive ups and downs corresponding to soil′s natural *** 5mPD results fluctuated between falling above and below CPD ***λ/BmPD results were consistent with attenuation of the shear wave,while for 10mplification was *** obtained by the CPD method monotonically decrease,due to the fact that CPD fails to inherently consider site effects and damping,and instead and relies on a single factor to consider the ground motion amplification.

关键词： bearing capacity modified pseudo-dynamic method conventional pseudo-dynamic method spectral analysis

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The spatial dynamics of Ukraine air quality impacted by the war and pandemic

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International Journal of Digital Earth 2023年第1期16卷 3680-3705页

作者： vizhi Qian Liu Theodore S.Trefonidesc sina Hasheminassab Jennifer Smith Thomas Huang Kevin m.marlis Joe T.Roberts Zifu Wang Dexuan Sha Ana Beatriz moura Pereira Heramb Podar Jacob Cain Chaowei Yang Department of Geography and GeoInformation Science George Mason UniversityFairfaxVAUSA Jet Propulsion Laboratory California Institute of TechnologyPasaden1CAUSA Dartmouth College HanoverNHUSA Bayer WashingtonDCUSA Northern Virginia Community College AnnandaleVAUSA Indian Institute of Technology RoorkeeIndia

In recent years,our world has experienced significant disruptions due to the COviD-19 pandemic,and Russia's 2022 invasion of Ukraine,impacting human activities and the global *** paper explored air quality changes in Ukraine due to COVID-19,and Russia's invasion of Ukraine using on-demand with a what-you-see-is-what-you-get *** the cOVID-19 pandemic,strict quarantine policies in Ukraine led to a 2%reduction in tropospheric NO_(2) concentration before the lockdown and 4%during the lockdown *** like Kyiv,Donetsk,and Dnipro exhibited reductions of 5%,11%,and 16%,*** SO_(2) column concentration decreased by 6%before the lockdown and 2.5%during the lockdown period,except in high population density *** showed the highest reduction of 17%in SO_(2) concentration,while Donetsk and Dnipro exhibited an 11%***,during the Russian invasion,there was a significant increase in tropospheric NO_(2) concentration in heavily destroyed Kharkiv while most eastern regions experienced a *** total SO_(2) column was 48%higher before the war but reduced throughout the country after the war,except for in Kyiv and a few central *** findings can contribute to analyzing air pollution and building digital twin simulations for future reconstruction scenarios.

关键词： ukraine war air pollution pandemic climate change environment spatiotemporal computing digital twins

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Real-world outcomes of anti-vascular endothelial growth factor therapy for retinal vascular vein occlusion in Tibet,China

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International Journal of Ophthalmology(English edition) 2022年第11期15卷 1814-1820页

作者： Xue-mei Zhu Ying-Ying Yu sina Zhuoga Xiao Dawa Yong-Kang Zhou Ouzhu Wangmu Deji Yangzong Fang An Heng miao ming-Wei Zhao Department of Ophthalmology&Clinical Centre of Optometry Peking University People's HospitalEye Diseases and Optometry InstituteBeijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid DiseasesCollege of OptometryPeking University Health Science CenterBeijing 100044China Department of Ophthalmology Tibet Autonomous Region People's HospitalLhasa 850010Tibet Autonomous RegionChina

AIm: To evaluate the outcomes of intravitreal antivascular endothelial growth factor(anti-VEGF) agents for patients with retinal vein occlusion(RVO) related-macular edema(mE) in ***: A retrospective, observational, single-center study. The demographic and clinical data of 90 RVO Tibetan patients(93 eyes) treated with either ranibizumab or conbercept in Tibet Autonomous Region People’s Hospital from Jan 2018 to December 2019 were ***: The mean patient age was 56.8±10.6y, 45(50%) of them were female. The mean living altitude was 3867.8±567.9 m. At the last visit, the best-corrected visual acuity(BCVA) significantly increased(52.2±21.8 letters) in comparison with the baseline(38.2±24.1 letters, Pm) in comparison with the baseline(504.1±165.2 μm, Pmore than 10 letters during follow-up period. The mean number of injections was 2.4±1.8. No severe ocular or systemic adverse events related to either the drug or injection were ***: Anti-VEGF therapy is effective and safe in Tibetan patients for the treatment of RVO related mE.

关键词： anti-vascular endothelial growth factor therapy macular edema retinal venous occlusive disease intravitreal visual acuity Tibet

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Anti-Anaemic Activity and Potential Toxicity of Extracts of Four Tinctorial Plants Used in the Treatment of Anemia in Benin: Gossypium barbadense, Sorghum bicolor, Hibiscus sabdariffa and Justicia secunda

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American Journal of Plant Sciences 2022年第12期13卷 1460-1477页

作者： Louis Fagbohoun Gbènagnon C. Nonvidé Aziz sina Orou Alban Houngbèmè Amoussatou Sakirigui Felix Gunin Joachim Djimon Gbénou Kaba Research Laboratory in Chemistry and Applications (LaKReCA) National University of Sciences Technologies Engineering and Mathematics Abomey Benin Laboratory of Biologie and molecular Typing in microbiology Department of Biochemistry and Cell Biology Univessity of Abomey-Calavi Abomey-Calavi Benin Laboratory of Pharmacognosy and Essential Oils Department of Chemistry University of Abomey-Calavi Abomey-Calavi Benin

Justicia secunda, Sorghum bicolor, Gossypiun barbadense and Hibiscus sabdariffa are dye plants traditionally used in Benin for the treatment of anemia. This work is part of the therapeutic valorization of dyes from these plants. Its objective is to characterize their composition in chemical groups and evaluate their harmlessness and their anti-anaemic property in laboratory rats. Anemia was induced in Wistar rats by phenylhydrazine hydrochloride followed by treatment by gavage with hydroethanolic extracts of the plants studied. Phytochemical screening of these extracts made it possible to characterize the major chemical groups, in particular alkaloids, polyphenols including tannins, flavonoids and leucoanthocyanins, as well as reducing compounds and saponosides in the plants studied. Cytotoxic analysis of these extracts on Artemia salina shrimp larvae revealed globally high LC50 values of between 3.14 and 4.64 mg/mL, which testify a priori to the harmlessness of these extracts. The administration of the hydroethanolic extract of each plant to anaemic rats at doses of 2000 mg/kg/d promoted, after 15 days, an increase in hemoglobin levels, the number of red blood cells and hematocrit, going to more than 90% recovery of the hematological parameters involved. The highest rate, 99.06% being that of the species Justicia secunda followed closely by Sorghum bicolor (96.80%) compared to 93.93% obtained by treatment with the Ranferon-12 positive control used. Indeed, these results confirm the therapeutic indication of these plants in the resorption of anemia in traditional medicine.

关键词： Anemia Resorption Tinctorial Plants Phytochemistry Benin

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Differences and similarities between mesenchymal stem cell and endothelial progenitor cell immunoregulatory properties against T cells

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World Journal of Stem Cells 2021年第8期13卷 971-984页

作者： mehdi Razazian maryam Khosravi Sheyda Bahiraii Georges Uzan Sara Shamdani sina Naserian Institut national de la santéet de la recherche médicale(Inserm)Unitémixte de Recherche-Inserm-ministère de la Défense 1197 Hôpital Paul BrousseVillejuif 94800France microenvironment&Immunity Unit Institut PasteurParis 75724France Institut national de la santéet de la recherche médicale(Inserm)Unit 1224 Paris 75724France Department of Pharmacognosy University of ViennaVienna 1090Austria Paris-Saclay University Villejuif 94800France CellmedEx Saint Maur Des Fossés 94100France

Bone-marrow-derived mesenchymal stem cells and endothelial progenitor cells have some interesting biological properties that make them unique for cell therapy of degenerative and cardiovascular *** both cell populations have been already studied and used for their regenerative potentials,recently their special immunoregulatory features have brought much more *** stem cells and endothelial progenitor cells have both proangiogenic functions and have been shown to suppress the immune response,particularly T cell proliferation,activation,and cytokine *** makes them suitable choices for allogeneic stem cell ***,these two cells do not have equal immunoregulatory *** elements including their extraction sources,age/passage,expression of different markers,secretion of bioactive mediators,and some others could change the efficiency of their immunosuppressive ***,to our knowledge,no publication has yet compared mesenchymal stem cells and endothelial progenitor cells for their immunological interaction with T *** review aims to specifically compare the immunoregulatory effect of these two populations including their T cell suppression,deactivation,cytokine production,and regulatory T cells induction ***,it evaluates the implications of the tumor necrosis factor alpha-tumor necrosis factor receptor 2 axis as an emerging immune checkpoint signaling pathway controlling most of their immunological properties.

关键词： Endothelial Progenitor Cells mesenchymal Stem Cells T cells Immunosuppression Immunoregulation TNFα-TNFR2 signaling pathway

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Diversity and Distribution of Staphylococcal Chromosomal Cassettes mec (SCCmec) Types I, II and III in Coagulase-Negative Staphylococcal Strains Isolated from Surfaces and medico-Technical materials of the University Hospital of Abomey-Calavi/Sô-Ava

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American Journal of molecular Biology 2022年第3期12卷 122-133页

作者： Nanoukon Chimene Cachon Fresnel Djèdatin Gustave sina Haziz Socohou Akim Dado Aurel Kougblènou Enorck Badé Farid Agbangla Clémént Baba-moussa Lamine Saïd Laboratoire de Biologie moléculaire et de Bio-Informatique Appliquée à la Génomique Ecole Nationale Supérieure de Bioscience et de Biotechnologies Appliquées Université Nationale des Sciences Technologies Ingénierie et Mathématique Dassa-Zoumè Bénin Laboratoire de Biochimie Biologie Moléculaire et Environnement Faculté des Sciences et Techniques Université d’Abomey-Calavi Abomey-Calavi Bénin Laboratoire de Biologie et de Typage moléculaire en microbiologie Faculté des Sciences et Techniques Université d’Abomey-Calavi Abomey-Calavi Bénin Laboratoire de Génétique moléculaire et d’Analyse des Génomes Faculté des Sciences et Techniques Université d’Abomey-Calavi Abomey-Calavi Bénin

The coagulase-negative staphylococci (CoNS) have long been considered to be low pathogenicity. The possibility of a horizontal transfer of resistance and virulence genes from S. aureus to CoNS could increase the pathogenicity of these bacteria. The objective of this work is to contribute to a better knowledge of the pathogenicity of (CoNS) strains isolated from surfaces and medico-technical materials of the University Hospital of Abomey-Calavi/Sô-Ava. Seventy strains of CoNS isolated from surfaces and medico-technical materials of the University Hospital of Abomey-Calavi were tested for methicillin resistance. The resistance to methicillin was evaluated phenotypically by the resistance of the strains to cefoxitin and then confirmed by the search for the mecA gene using PCR. The genes encoding staphylococcal chromosomal cassette (SCCmec) types I, II and III originally found in S. aureus were tested in CoNS by multiplex PCR using specific primers. All the strains studied showed resistance to methicillin. However, only 28.5% (20/70) carried the mecA gene. SCCmec was identified in only 17.14% (12/70) of these strains. Four strains carried mecA gene as well as one of the three types of SCCmec searched. SCCmec types I, II and III were identified in CoNS strains studied. SCCmec type I was the most frequent chromosomal cassette in mecA+ strains, only or in association with another SCCmec. The study also revealed methicillin-resistant strains carrying SCCmec lacking the mecA gene. Finally, 60% (12/20) of the strains were found to be non-typeable. Our results show that CoNS strains present a high resistance to methicillin and the source of this resistance in the CoNS of our study is not only the mecA gene. There is also a high diversity of SCCmec, justified by a large number of non-typeable CoNS strains. The mecA− SCCmec+ methicillin-resistant strains deserve to be sequenced for further studies.

关键词： Coagulase Negative Staphylococci mecA Staphylococcal Chromosomal Cassette

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