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Discovering peptides and computational investigations of a multiepitope vaccine target Mycobacterium tuberculosis

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Synthetic and Systems Biotechnology 2024年第3期9卷 391-405页

作者： Truc Ly Nguyen Heebal Kim Department of Agricultural Biotechnology and research Institute of Agriculture and Life Sciences Seoul National UniversitySeoul08826Republic of Korea Interdisciplinary Program in Bioinformatics Seoul National UniversitySeoul08826Republic of Korea eGnome Inc.Seoul05836Republic of Korea

Mycobacterium tuberculosis(MTB)is the causative agent of tuberculosis(TB),a prevalent airborne infectious *** the availability of the Bacille Calmette-Guerin vaccine,its global efficacy remains modest,and tuberculosis persists as a significant global public health *** this challenge and advancing towards the End MTB Strategy,we developed a multiepitope vaccine(MEV)based on immunoinformatics and compu-tational *** screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex(MHC)allele binding,immunogenicity,antigenicity,allergenicity,toxicity,and cytokine *** epitopes were integrated into an MEV construct with adjuvant and linkers,forming a fully immunogenic vaccine *** analyses encompassed the evaluation of immunological and physicochemical properties,determination of tertiary structure,molecular docking with Toll-Like Receptors(TLR),molecular dynamics(MD)simulations for all atoms,and immune *** MEV comprises 534 amino acids,featuring 6 cytotoxic T lymphocyte,8 helper T lymphocyte,and 7 linear B lymphocyte epitopes,demonstrating high antigenicity and ***,molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to *** addition,the immune simulation indicated the capacity to effectively induce elevated levels of an-tibodies and cytokines,emphasizing the vaccine’s robust immunogenic *** study presents a promising MEV against TB,exhibiting favorable immunological and physicochemical *** findings provide theoretical support for TB vaccine *** study aligns with the global initiative of the End MTB Strategy,emphasizing its potential impact on addressing persistent challenges in TB control.

关键词： Mycobacterium tuberculosis Tuberculosis Multiepitope vaccine Docking molecular Molecular dynamics simulation Immune simulation

Defining and tracing subtypes of patient-derived xenograft models in pancreatic ductal adenocarcinoma

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Cancer Communications 2024年第8期44卷 915-920页

作者： Sangyeop Hyun Youngmin Han Jae Yun Moon Young-Ah Suh Won-Gun Yun Wooil Kwon Jong-Eun Lee Daeun Kim Ja-Lok Ku Jin-Young Jang Daechan Park Department of Molecular Science and Technology Ajou UniversitySuwonRepublic of Korea Department of Surgery and Cancer research Institute Seoul National University College of MedicineSeoulRepublic of Korea Molecular Science and Technology research Center Ajou UniversitySuwonRepublic of Korea DNA Link inc. SeoulRepublic of Korea Korean Cell Line Bank Laboratory of Cell BiologyCancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea

Patient-derived xenograft(PDX)models have been used to explore therapeutic opportunities for pancreatic ductal adenocarcinoma(PDAC)[1].Although original tumor characteristics are altered by cancer-stromal interactions... 详细信息

关键词： adenocarcinoma ductal xenograft

Oxidized organic molecules in the tropical free troposphere over Amazonia

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National Science Review 2024年第1期11卷 174-184页

作者： Qiaozhi Zha Diego Aliaga Radovan Krejci Victoria A.Sinclair Cheng Wu Giancarlo Ciarelli Wiebke Scholz Liine Heikkinen Eva Partoll Yvette Gramlich Wei Huang Markus Leiminger Joonas Enroth Otso Per?kyl? Runlong Cai Xuemeng Chen Alkuin Maximilian Koenig Fernando Velarde Isabel Moreno Tuukka Pet?j? Paulo Artaxo Paolo Laj Armin Hansel Samara Carbone Markku Kulmala Marcos Andrade Douglas Worsnop Claudia Mohr Federico Bianchi Institute for Atmospheric and Earth System research/Physics University of Helsinki Joint International research Laboratory of Atmospheric and Earth System Sciences Nanjing University Department of Environmental Science & Bolin Centre for Climate research Stockholm University Department of Chemistry and Molecular Biology University of Gothenburg Institute for Ion and Applied Physics University of Innsbruck Ionicon Analytik GmbH Laboratory for Atmospheric Physics Institute for Physics Research Universidad Mayor de San Andrés Institute of Physics University of Sao Paulo Institute for Geosciences and Environmental research (IGE) University of Grenoble Alpes Agrarian Sciences Institute Federal University of Uberl?ndia Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Department of Atmospheric and Oceanic Sciences University of Maryland Aerodyne research Inc. Department of Environmental System Science ETH Zürich Switzerland and Laboratory of Atmospheric Chemistry Paul Scherrer Institute

New particle formation(NPF) in the tropical free troposphere(FT) is a globally important source of cloud condensation nuclei, affecting cloud properties and climate. Oxidized organic molecules(OOMs)produced from biogenic volatile organic compounds are believed to contribute to aerosol formation in the tropical FT, but without direct chemical observations. We performed in situ molecular-level OOMs measurements at the Bolivian station Chacaltaya at 5240 m above sea level, on the western edge of Amazonia. For the first time, we demonstrate the presence of OOMs, mainly with 4–5 carbon atoms, in both gas-phase and particle-phase(in terms of mass contribution) measurements in tropical FT air from Amazonia. These observations, combined with air mass history analyses, indicate that the observed OOMs are linked to isoprene emitted from the rainforests hundreds of kilometers away. Based on particle-phase measurements, we find that these compounds can contribute to NPF, at least the growth of newly formed nanoparticles, in the tropical FT on a continental scale. Thus, our study is a fundamental and significant step in understanding the aerosol formation process in the tropical FT.

关键词： oxidized organic molecules tropical aerosol formation Amazon free troposphere

Emerging technological developments to address pest resistance in Bt cotton

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Journal of Cotton research 2024年第3期7卷 318-333页

作者： NAGARAJ Selvarani RAJASEKARAN Ravikesavan PALANIAPPAN Jayamani RANGASAMY Selvakumar NARAYANASAMY Chitra NARAYANAN Manikanda Booapathi Department of Genetics and Plant Breeding Centre for Plant Breeding and Genetics(CPBG)Tamil Nadu Agricultural University(TNAU)Coimbatore 641003India Centre for Plant Breeding and Genetics TNAUCoimbatore 641003India Department of Pulses CPBGTNAUCoimbatore 641003India research and Development Centre Rasi Seeds(P)Ltd.SalemAttur 636102India Department of Cotton TNAUCoimbatore 641003India Department of Plant Biotechnology Centre for Plant Molecular Biology and Biotechnology(CPMB&B)TNAUCoimbatore 641003India

Cotton plays a crucial role in shaping Indian economy and rural *** cotton crop is prone to numerous insect pests,necessitating insecticidal application,which increases production *** advent of the expression of Bacillus thuringiensis(Bt)insecticidal protein in cotton has significantly reduced the burden of pest without compromising environmental or human *** the introduction of transgenic cotton,the cultivated area expanded to 22 million hectares,with a 64% increase in adoption by farmers ***,Bt cotton accounts for 93% of the cultivated cotton area in ***,extensive use of Bt cotton has accelerated resistance development in pests like the pink ***,the overreliance on Bt cotton has reduced the use of broad-spectrum pesticides,favouring the emergence of secondary pests with significant *** emphasizes the urgent necessity for developing novel pest management *** high-dose and refuge strategy was initially effective for managing pest resistance in Bt cotton,but its implementation in India faced challenges due to misunderstandings about the use of non-Bt refuge *** gene pyramiding was introduced as a solution,combining mono toxin also led to instances of ***,there is a need for further exploration of biotechnological approaches to manage insect resistance in Bt *** biotechnological strategies,such as sterile insect release,RNA interference(RNAi)-mediated gene silencing,stacking Bt with RNAi,and genome editing using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein(CRISPR-Cas),offer promising tools for identifying and managing resistance genes in ***,CRISPR-mediated gene drives and the development of novel biopesticides present potential avenues for effective pest management in cotton *** innovative approaches could significantly enhance the sustainability and efficacy of

关键词： Bt Cotton Gene pyramiding RNAi Modified toxin Genome editing Plant derived insecticidal protein Gene drive

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Drought-Tolerant Rice at Molecular Breeding Eras:An Emerging Reality

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Rice science 2024年第2期31卷 179-189页

作者： ZHU Chengqi YE Yuxuan QIU Tian HUANG Yafan YING Jifeng SHEN Zhicheng Institute of Insect Sciences Zhejiang UniversityHangzhou 310058China Performance Plants inc. 1287 Gardiners RoadKingstonOntario K7P 3J6Canada China National Rice research Institute Hangzhou 310006China

Rice(Oryza sativa L.)stands as the most significantly influential food crop in the developing world,with its total production and yield stability affected by environmental *** stress impacts about 45%of the world’s rice area,affecting plants at molecular,biochemical,physiological,and phenotypic *** conventional breeding method,predominantly employing single pedigree selection,has been widely utilized in breeding numerous drought-tolerant rice varieties since the Green *** rapid progress in plant molecular biology,hundreds of drought-tolerant QTLs/genes have been identified and tested in rice crops under both indoor and field *** genes have been introgressed into elite germplasm to develop commercially accepted drought-tolerant varieties,resulting in the development of several drought-tolerant rice varieties through marker-assisted selection and genetically engineered *** review provides up-to-date information on proof-of-concept genes and breeding methods in the molecular breeding era,offering guidance for rice breeders to develop drought-tolerant rice varieties.

关键词： conventional breeding drought stress drought tolerant rice genetic engineering marker-assisted selection breeding

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Quantized Redshift and its Significance for Recent Observation

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research in Astronomy and Astrophysics 2024年第9期24卷 156-166页

作者： Arindam Mal Sarbani Palit Christopher C.Fulton Sisir Roy Indian Space research Organization Space Applications CentreAhmedabadIndia Indian Statistical Institute CVPR UnitKolkataIndia Protostar Inc.15652 Carrousel DriveCanyon CountryCA 91387USA National Institute of Advanced Studies IISC CampusBangaloreIndia

With the recent observational evidence in extragalactic astronomy,the interpretation of the nature of quasar redshift continues to be a research *** high redshifts are being detected for extragalactic objects that are presumably very distant and young while also exhibiting properties that are characteristic of a more mature galaxy such as *** to Halton Arp and Geoffrey Burbidge,redshift disparities consist of an intrinsic component and are related to an evolutionary *** observed redshift periodicity at integer multiples of0.089 in log scale and Burbidge observed redshift periodicity at integer multiples of 0.061 in linear *** Singular Value Decomposition based periodicity estimation is known to be superior for noisy data sets,especially when the data contain multiple harmonics and overtones,mainly irregular in nature,we have chosen it to be our primary tool for analysis of the quasar-galaxy pair redshift *** have observed a fundamental periodicity of0.051 with a confidence interval of 95%in linear scale with the site-available Sloan Digital Sky Survey Data Release 7(SDSS DR7)quasar-galaxy pair data *** have independently generated quasar-galaxy pair data sets from both 2d F and SDSS and found fundamental periodicities of 0.077 and 0.089,respectively,in log scale with a confidence interval of 95%.

关键词： galaxies:distances and redshifts (galaxies:)quasars:absorption lines cosmology:observations

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Neutralization of SARS-CoV-2 infection by antibodies targeting diverse epitopes

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Genes & Diseases 2024年第4期11卷 134-137页

作者： Shusheng Wang Yunji Liao Kaiyong Yang Hang Ma Zhangyi Song Haiqiu Huang Li Zhang Ailing Wang Lei Han Jiawei Zhang Hui Chen Haiyang Yin Yantin Bian Hua Jiang Xiaodong Xiao Yueqing Xie Yunsheng Yuan Jianwei Zhu Engineering research Center of Cell and Therapeutic Antibody Ministry of EducationSchool of PharmacyShanghai Jiao Tong UniversityShanghai 200240China Jecho Laboratories Inc.FrederickMD 21704USA Jecho Institute Co. Ltd.Shanghai 200240China

The CoVID-19 pandemic that started in late 2019 is sweeping through the world,posing historic challenges to global health,and disrupting social and economic *** and recent studies indicate that monoclonal antibodies can be efficacious in preventing and treating SARSCoV-1 and SARS-CoV-2 *** a phage display platform,we have identified dozens of monoclonal antibodies that bind to diverse epitope groups on the SARS-CoV-2 spike *** of them bound to the receptor binding domain(RBD)and inhibited ACE2-RBD interaction.

关键词： antibodies inhibited monoclonal

Efficient and multiplex gene upregulation in plants through CRISPR-Cas-mediated knockin of enhancers

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Molecular Plant 2024年第9期17卷 1472-1483页

作者： Qi Yao Rundong Shen Yang Shao Yifu Tian Peijin Han Xuening Zhang Jian-Kang Zhu Yuming Lu Shanghai Collaborative Innovation Center of Agri-seeds Joint Center for Single-Cell BiologySchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai Center for Plant Stress Biology Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 201602China University of the Chinese Academy of Sciences BeijingChina College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China institute of Advanced Biotechnology and School of Medicine Southern University of Science and TechnologyShenzhen 518055China

Geneupregulation through genome editing is important for plant research and *** insertion of short transcriptional enhancers(STEs)into gene promoters may offer a universal solution akin to transgene-mediated overexpression while avoiding the drawbacks associated with ***,we introduce an“in locus activation”technique in rice that leverages well-characterized STEs for refined,heritable,and multiplexed gene *** address the scarcity of potent enhancers,we developed a large-scale mining approach and discovered a suite of STEs that are capable of enhancing gene expression in rice *** in locus integration of these STEs into eight rice genes resulted in substantial tran-scriptional upregulation in the edited plants,with up to 869.1-fold increases in their transcript ***-ploying a variety of STEs,we achieved delicate control of gene expression,enabling the fine-tuning of key phenotypic traits such as plant *** approach also enabled efficient multiplexed gene upregu-lation,with up to four genes activated simultaneously,significantly enhancing the nicotinamide mononucleotide metabolic ***,heritability studies from the To to T3 generations confirmed the stable and heritable nature of STE-driven gene ***,our work demon-strates that coupled with STE mining,leveraging genome editing for in locus activation and gene upregu-lation holds great promise to be widely adopted in fundamental plant research and crop breeding.

关键词： genome editing short transcriptional enhancers gene upregulation crop breeding

Oviposition Site Preference and Its Effects on Subsequent Development of Variegated Grasshopper (Zonocerus variegatus L.) under Laboratory Conditions

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Advances in Entomology 2024年第3期12卷 143-154页

作者： Saffea Joseph Torto Abu James Sundufu Alusaine Edward Samura Sahr Ngoba Fomba Dennis Peter Musa Skeku Alfred Kanu Prince Emmanuel Norman Department of Crop Protection School of Agriculture and Food Sciences Njala Sierra Leone Department of Horticulture School of Natural Resources Management Njala University Njala Sierra Leone Department of Crop Science School of Agriculture and Food Sciences Njala University Njala Sierra Leone Germplasm Enhancement and seeds Systems Sierra Leone Agricultural Research Institute Freetown Sierra Leone

Female grasshoppers can affect the fitness of their offspring through their selection of oviposition site. Knowledge of soil type on oviposition, and its effects on subsequent development can provide guidelines for habitat manipulations that reduce the harmful effects of these pests on farmers fields. The influence of soil types on the oviposition site preference of variegated grasshopper (Zonocerus variegatus L.) reared some cassava (Manihot esculenta Crantz) varieties, was investigated in a cage trial carried out at the Bio factory laboratory, School of Agriculture and Food Sciences, Njala University, Sierra Leone during 2022/2023. The treatments comprised three soil types (Sandy, Loamy and Clay), each with three replications laid out in a randomized complete block design (RCBD) in wooden cages. Data were collected on the following development parameters including, Net reproductive growth ratio (R0), Generation time (Tc), Intrinsic rate of increase (rm), Finite rate of increase (), Doubling time (Dt), and overall survivorship. Findings revealed that, Z. variegatus L. preferred sandy soil in which, on average, most eggs were deposited (338, 6.62 4.40), followed by loamy soil, 286 (5.53 3.96), and then, clayey soil, 200 (3.91 3.85);though, the differences were not significant. This study established that Z. variegatus deposited more eggs in sandy soil > loamy soil > clayey soil, respectively;and subsequent survivorship of the immature unto mature adult insect, revealed a similar order. This indicates that the sandy soil is the most preferred substrate for oviposition and subsequent development into adult insects.

关键词： Development Oviposition Oviposition Site Preference Soil Types Variegated Grasshopper