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Streamlined human antibody generation and optimization by exploiting designed immunoglobulin loci in a B cell line

Cellular & Molecular Immunology 2021年第6期18卷 1545-1561页

作者： Hidetaka Seo Hitomi Masuda Kenjiro Asagoshi Tomoaki Uchiki Shigehisa Kawata Goh Sasaki Takashi Yabuki Shunsuke Miyai Naoki Takahashi Shu-ichi Hashimoto Atsushi Sawada Aki Takaiwa Chika Koyama Kanako Tamai Kohei Kurosawa Ke-Yi Lin Kunihiro Ohta Yukoh Nakazaki Department of life sciences Graduate School of Arts and SciencesThe University of TokyoTokyoJapan Research Laboratories Chiome Bioscience IncTokyoJapan

Monoclonal antibodies(mAbs)are widely utilized as therapeutic drugs for various diseases,such as cancer,autoimmune diseases,and infectious *** the avian-derived B cell line DT40,we previously developed an antibody display technology,namely,the ADLib system,which rapidly generates antigen-specific ***,we report the development of a human version of the ADLib system and showcase the streamlined generation and optimization of functional human *** libraries were first constructed by replacing endogenous immunoglobulin genes with designed human *** these libraries,clones producing full-length human IgGs against distinct antigens can be isolated,as exemplified by the selection of antagonistic *** advantage of avian biology,effective affinity maturation was achieved in a straightforward manner by seamless diversification of the parental clones into secondary libraries followed by single-cell sorting,quickly affording mAbs with improved affinities and ***,we demonstrate that the human ADLib system could serve as an integrative platform with unique diversity for rapid de novo generation and optimization of therapeutic or diagnostic antibody ***,our results suggest that libraries can be constructed by introducing exogenous genes into DT40 cells,indicating that the ADLib system has the potential to be applied for the rapid and effective directed evolution and optimization of proteins in various fields beyond biomedicine.

关键词： Immunoglobulin rearrangements homologous recombination antibody therapeutics antibody engineering drug discovery

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Effect of complex hydraulic variables and physicochemical factors on freshwater mussel density in the largest floodplain lake,China

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Ecological Processes 2023年第1期12卷 232-245页

作者： Chenchen Jia Chenhuizi Wu Xiaochen Huang Chunhua Zhou Shan Ouyang Xiongjun Liu Xiaoping Wu school of life sciences Nanchang UniversityNanchang 330031China Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic agricultural Resources in Mountainous Areas School of Life SciencesJiaying UniversityMeizhou 514015China

Background Habitat degradation and flow regime alterations are two of the most prominent and common impact factors to freshwater mussel *** of the correlation between freshwater mussel distribution,density and habitat characteristics is important for maintaining and restoring their biodiversity and ecological *** on predicting habitat suitability of freshwater mussels is lacking in ***,we aimed to analyze the correlation between freshwater mussel density and complex hydraulic and physicochemical variables to predict habitat *** The results showed that four complex hydraulic variables(boundary Reynolds number,critical shear stress,bed roughness and mean sediment particle size)and four physicochemical variables(water temperature,chlorophylla,transparency and pH)were key factors for predicting habitat suitability of freshwater *** mussel density was significantly correlated with Froude number,water temperature and *** Our results confirmed that higher freshwater mussel density would be associated with areas that are stable in complex hydraulic and physicochemical *** results provide an important insight into the conservation of freshwater mussel diversity and their habitat restoration in China and globally.

关键词： Habitat suitability Freshwater mussel Complex hydraulic variable Habitat degradation

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The haplotype-resolved T2T genome assembly of the wild potato species Solanum commersonii provides molecular insights into its freezing tolerance

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Plant Communications 2024年第10期5卷 1-4页

作者： Yang Feng Jie Zhou Dianjue Li Zhen Wang Cheng Peng Guangtao Zhu school of life sciences Yunnan Key Laboratory of Potato BiologyYunnan Normal UniversitySouthwest United Graduate SchoolKunmingYunnan 650500China Yunnan Key Laboratory of Cell Metabolism and Disease Center for Life SciencesSchool of Life SciencesYunnan UniversityKunmingYunnan 650500China school of life sciences Anhui Agricultural UniversityHefeiAnhui 230036China

Dear Editor,The potato is the most important tuber crop,playing an important role in ensuring world food *** genome of the cultivated species(DM,a doubled monoploid type)was first released in 2011 and has been continually updated as the most popular reference(Yang et al.,2023).Recently,a high-quality assembly of tetraploid C88 was released(Bao et al.,2022).

关键词： cultivated freezing doubled

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Impact of Drought on Farmers' Livelihood Vulnerability:A Case Study of County-level Units in Western Jilin Province, China

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Chinese Geographical Science 2025年第2期 279-294页

作者： ZHANG Jiani HAN Yang FANG Yangang XU Yaping CHEN Chunlin LIU Zhuxin WANG Feiyu ZHUANG Lijuan HUANG Fang Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains Ministry of Education School of Geographical Sciences Northeast Normal University Department of Environmental and Geosciences Sam Houston State University school of Economics and Management Northeast Normal University

agricultural drought, a prolonged disaster with widespread impacts, exerts tremendous pressure on farm household activities,agricultural production, and economic development. The western region of Jilin Province, China, located in a semi-arid zone, where persistents drought exacerbates ecological fragility. With a larger proportion of its population living in rural areas, the life and production activities of households are particularly susceptible to drought-related challenges. This study focuses on the western part of Jilin Province, utilizing remote sensing data to calculate the temperature vegetation dryness index(TVDI) as a soil moisture monitoring indicator for drought assessment. The livelihood vulnerability index(LVI) and the improved LVI-Intergovernmental Panel on Climate Change(IPCC) index are employed to comprehensively assess the livelihood vulnerability of communes in the region and the impact of drought conditions on farmers' livelihood vulnerability. The results reveal a spatial trend of increasing drought severity from northeast to southwest, with temporally minor fluctuations observed in drought levels from 2005 to 2022. Livelihood vulnerability results indicate significant spatial and temporal variations, with education, health, food, and water playing key roles. Correlation analysis indicates a strong relationship between TVDI and LVI, highlighting the detrimental impact of drought on farmers' livelihoods. The study aims to provide a scientific foundation for managing livelihood vulnerability in the western part of Jilin Province and similar arid areas. Additionally, it seeks to offer strategic recommendations for policymakers to mitigate the adverse effects of drought, thereby reducing farmers' vulnerability and fostering sustainable socio-economic development.

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Robust Surface Reconstruction of Plant Leaves from 3D Point Clouds

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Plant Phenomics 2021年第1期3卷 28-42页

作者： Ryuhei Ando Yuko Ozasa Wei Guo graduate school of Science and Technology Keio UniversityJapan school of System Design and Technology Tokyo Denki UniversityJapan International Field Phenomics Research Laboratory Institute for Sustainable Agro-ecosystem ServicesGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan

The automation of plant phenotyping using 3D imaging techniques is ***,conventional methods for reconstructing the leaf surface from 3D point clouds have a trade-off between the accuracy of leaf surface reconstruction and the method’s robustness against noise and missing *** mitigate this trade-off,we developed a leaf surface reconstruction method that reduces the effects of noise and missing points while maintaining surface reconstruction accuracy by capturing two components of the leaf(the shape and distortion of that shape)separately using leaf-specific *** separation simplifies leaf surface reconstruction compared with conventional methods while increasing the robustness against noise and missing *** evaluate the proposed method,we reconstructed the leaf surfaces from 3D point clouds of leaves acquired from two crop species(soybean and sugar beet)and compared the results with those of conventional *** result showed that the proposed method robustly reconstructed the leaf surfaces,despite the noise and missing points for two different leaf *** evaluate the stability of the leaf surface reconstructions,we also calculated the leaf surface areas for 14 consecutive days of the target *** result derived from the proposed method showed less variation of values and fewer outliers compared with the conventional methods.

关键词： shape separation sugar

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How Useful Is Image-Based Active Learning for Plant Organ Segmentation?

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Plant Phenomics 2022年第1期4卷 384-394页

作者： Shivangana Rawat Akshay L.Chandra Sai Vikas Desai Vineeth N.Balasubramanian Seishi Ninomiya Wei Guo Department of Computer Science and Engineering Indian Institute of TechnologyHyderabadIndia Department of Computer Science University of FreiburgGermany graduate school of agricultural and life sciences The University of TokyoJapan

Training deep learning models typically requires a huge amount of labeled data which is expensive to acquire,especially in dense prediction tasks such as semantic ***,plant phenotyping datasets pose additional challenges of heavy occlusion and varied lighting conditions which makes annotations more time-consuming to *** learning helps in reducing the annotation cost by selecting samples for labeling which are most informative to the model,thus improving model performance with fewer *** learning for semantic segmentation has been well studied on datasets such as PASCAL VOC and ***,its effectiveness on plant datasets has not received much *** bridge this gap,we empirically study and benchmark the effectiveness of four uncertainty-based active learning strategies on three natural plant organ segmentation *** also study their behaviour in response to variations in training configurations in terms of augmentations used,the scale of training images,active learning batch sizes,and train-validation set splits.

关键词： consuming lighting sizes

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Strawberry vein banding virus P6 protein intracellular transport and an important domain identification

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Journal of Integrative Agriculture 2018年第9期17卷 2031-2041页

作者： PAN Yuan ZHOU Xiu-hong LI Shuai FENG Ming-feng SHI Man-ling ZUO Deng-pan JIANG Xi-zi CHEN Jing HU Ya-hui ZHANG Xiang-xiang JIANG Tong school of Plant Protection Anhui Agricultural University Biotechnology Center Anhui Agricultural University College of life and Environmental sciences Hangzhou Normal University

Strawberry vein banding virus （SVBV）-infected strawberry cells contain cytoplasmic inclusions with isometric particles. To identify the components of the inclusions, green fluorescent protein （GFP） was fused to the carboxy-terminus （C-terminus） of SVBV open reading frames, these constructs were separately transformed into Agrobacterium tumefaciens and infiltrated into Nicotiana benthamiana leaves. Results showed that the SVBV P6 protein assembled into prominent and amorphous inclusion bodies （IBs）. To investigate P6 subcellular localization, P6-GFP was ectopically expressed in N. benthamiana leaves by agroinfiltration and then stained with 4＂,6-diamidino-2-phenylindole （DAPI）. We found the P6 protein accumulated in the nuclei and also formed cytoplasmic IBs with different sizes. To further determine the location of P6 IBs in the cytoplasm, and explore whether the P6 IBs move freely or depend on cytoskeleton and endoplasmic reticulum （ER）, the microfilament marker protein （GFP-ABD2-GFP）, microtubules marker protein （mCherry-MAP65-1） and ER marker protein （mCherry-HDEL） were separately coexpressed with P6-GFP and into N. benthamiana leaves by agroinfiltration, exhibiting that P6 IBs aligned with cytoskeleton and endoplasmic reticulum. Meanwhile, coinfiltration of P1 and P6 indicated the P6 colocalized with the P1 protein at periphery of cells. The P6 protein contains one C-terminal nuclear localization signal （NLS） region, a P6 protein mutant with a deleted NLS did not localize in the nucleus, did not form IBs, and was unable to facilitate exogenous GFP expression. These results demonstrate that the deleted NLS region is an important P6 domain required for biological functions. In summary, the mobile P6 IBs are associated with ER, microfilaments and microtubules and move along microfilaments to the SVBV P1 protein in the PD.

关键词： SVBV IBs intracellular transport cytoskeleton ER P6 mutant

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Two haplotype-resolved,gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit

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Molecular Plant 2023年第2期16卷 452-470页

作者： Xue Han Yilin Zhang Qiong Zhang Ni Ma Xiaoying Liu Wenjing Tao Zhiying Lou Caihong Zhong Xing Wang Deng Dawei Li Hang He Peking University Institute of Advanced agricultural sciences Shandong Laboratory of Advanced Agricultural Sciences in WeifangShandong 261325China school of Advanced agricultural sciences and school of life sciences Peking UniversityBeijing 100871China Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenThe Chinese Academy of SciencesWuhanHubei 430074China State Key Laboratory of Cellular Stress Biology School of Life SciencesFaculty of Medicine and Life SciencesXiamen UniversityXiamen 361102China

Kiwifruit is a recently domesticated horticultural fruit crop with substantial economic and nutritional value,especially because of the high content of vitamin C in its *** this study,we de novo assembled two telomere-to-telomere kiwifruit genomes from Actinidia chinensis var.‘Donghong’(DH)and Actinidia latifolia‘Kuoye’(KY),with total lengths of 608327852 and 640561626 bp for 29 chromosomes,*** a burst of structural variants involving inversion,translocations,and duplications within 8.39 million years,the metabolite content of DH and KY exhibited differences in saccharides,lignans,and vitamins.A regulatory ERF098 transcription factor family has expanded in KY and Actinidia eriantha,both of which have ultra-high vitamin C *** each assembly phased into two complete haplotypes,we identified allelic variations between two sets of haplotypes,leading to protein sequence variations in 26494 and 27773 gene loci and allele-specific expression of 4687 and 12238 homozygous gene *** metabolome and transcriptome changes during DH fruit development revealed the same dynamic patterns in expression levels and metabolite contents;free fatty acids and flavonols accumulated in the early stages,but sugar substances and amino acids accumulated in the late *** AcSWEET9b gene that exhibits allelic dominance was further identified to positively correlate with high sucrose content in *** with wild varieties and other Actinidia species,AcSWEET9b promoters were selected in red-flesh kiwifruits that have increased fruit sucrose content,providing a possible explanation on why red-flesh kiwifruits are ***,these two gap-free kiwifruit genomes provide a valuable genetic resource for investigating domestication mechanisms and genome-based breeding of kiwifruit.

关键词： kiwifruit genome telomere-to-telomere allele-specific expression vitamin C sugar metabolism

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Recombinant Bivalent Vaccine against Foot-and-Mouth Disease Virus Serotype O/A Infection in Guinea Pig

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Acta Biochimica et Biophysica Sinica 2004年第9期36卷 589-596页

作者： Jian-Zhong YI1, Ming-Qiu LIU1, Cai-Zhu ZHU2, Qiang ZHANG1, Zu-Tian SHENG3, Qing-Yun DU3, Wei-Yao YAN1, and Zhao-Xin ZHENG1* State Key Laboratory of Genetics Engineering, life Science school, Fudan University, Shanghai 200433, China 1The Veterinary Institute of Chinese Academy of agricultural sciences, Lanzhou 730046, China 2The Virus Research Institute of Zhejiang Academy of agricultural sciences, Hangzhou 310021, China State Key Laboratory of Genetics Engineering Life Science School Fudan University The Veterinary Institute of Chinese Academy of agricultural sciences

In this study, two DNA fragments encoding amino acid (141–160)-(21–40)-(141–160) of the VP1 of FMDV (foot-and-mouth disease virus) serotype O and (138–160)-(21–40)-(138–160) of the serotype A FMDV were chemically synthesized. These two tandem-repeat fragments were ligated and transfected into prokaryotic expression vector pTrcHis A to construct pTH-O-A. The other vector called pTH-O-scIgG-A was constructed similarly only that the two tandem-repeat DNA fragments were linked by the bovine- IgG heavy chain coding sequence. Guinea pigs immunized with the two bivalent vaccines pTH-O-A and pTH-O-scIgG-A showed both specific antibody activity and T cell proliferation responses. FMDV challenge tests showed that 85% and 70% of guinea pigs vaccinated twice with 200 μg of the fusion protein of pTH-O-A were protected from FMDV serotype O and serotype A infection respectively. 70% and 57% of the guinea pigs immunized with the fusion protein of pTH-O-scIgG-A were protected from FMDV serotype O and serotype A infection respectively.

关键词： foot-and-mouth disease FMDV serotype O FMDV serotype A VP1 protein bivalent vaccine guinea pig

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Germline-competent stem cell in avian species and its application

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Asian Journal of Andrology 2015年第3期17卷 421-426页

作者： Jae Yong Han Hyung Chul Lee Tae Sub Park Department of agricultural Biotechnology College of Agriculture and Life Sciences and Research Institute of Agriculture and Life Sciences Seoul National University Seoul 151-921 Korea graduate school of International agricultural Technology and Institute of Green-Bio Science and Technology Seoul National University Pyeongchang-gun Gangwon-do 232-916 Korea

Germ cells are the only cell type in the body that can transfer genetic information to the next generation. Germline-competent stem cells can self-renew and contribute to the germ cell lineage giving rise to pluripotent stem cells under specific conditions. Hence far, studies on germline-competent stem cells have contributed to,the generation of avian model systems and the conservation of avian genetic resources. In this review, we focus on previous studies on germline-competent stem cells from avian species, mainly chicken germline-competent stem cells, which have been well established and characterized. We discuss different sources of germline-competent stem cells and recent advances for the future applications in birds.

关键词： birds germline-competent stem cells primordial germ cells spermatogonial stem cells

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