36 results on '"Naibo Yang"'
Search Results
2. Development and characterization of a camelid derived antibody targeting a linear epitope in the hinge domain of human PCSK9 protein
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Xinyang Li, Jun Hong, Xiaoyan Gao, Meiniang Wang, and Naibo Yang
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Medicine ,Science - Abstract
Abstract PCSK9 is an effective target for lowering LDL-c. Previously, a camelid-human chimeric heavy chain antibody VHH-B11-Fc targeting human PCSK9 was designed. It had a potent hypolipidemic effect. However, the nanobody VHH-B11 interacts with PCSK9 at low affinity, while camelid VHH exhibits some immunogenicity. Moreover, the interacting epitope is yet to be identified, although VHH-B11 was shown to have distinct hPCSK9-binding epitopes for Evolocumab. This might impede the molecule’s progress from bench to bedside. In the present study, we designed various configurations to improve the affinity of VHH-B11 with hPCSK9 (
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- 2022
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3. Diversity of Mycoviruses Present in Strains of Binucleate Rhizoctonia and Multinucleate Rhizoctonia, Causal Agents for Potato Stem Canker or Black Scurf
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Yuting Li, Naibo Yang, Tongyu Mu, Xuehong Wu, and Can Zhao
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binucleate Rhizoctonia ,multinucleate Rhizoctonia ,metatranscriptome sequencing ,mycoviral diversity ,positive single-stranded RNA ,Biology (General) ,QH301-705.5 - Abstract
In this study, the diversity of putative mycoviruses present in 66 strains of binucleate Rhizoctonia (BNR, including anastomosis group (AG)-A, AG-Fa, AG-K, and AG-W) and 192 strains of multinucleate Rhizoctonia (MNR, including AG-1-IA, AG-2-1, AG-3 PT, AG-4HGI, AG-4HGII, AG-4HGIII, and AG-5), which are the causal agents of potato stem canker or black scurf, was studied using metatranscriptome sequencing. The number of contigs related to mycoviruses identified from BNR and MNR was 173 and 485, respectively. On average, each strain of BNR accommodated 2.62 putative mycoviruses, while each strain of MNR accommodated 2.53 putative mycoviruses. Putative mycoviruses detected in both BNR and MNR contained positive single-stranded RNA (+ssRNA), double-stranded RNA (dsRNA), and negative single-stranded RNA (-ssRNA) genomes, with +ssRNA genome being the prevalent nucleic acid type (82.08% in BNR and 75.46% in MNR). Except for 3 unclassified, 170 putative mycoviruses found in BNR belonged to 13 families; excluding 33 unclassified, 452 putative mycoviruses found in MNR belonged to 19 families. Through genome organization, multiple alignments, and phylogenetic analyses, 4 new parititviruses, 39 novel mitoviruses, and 4 new hypoviruses with nearly whole genome were detected in the 258 strains of BNR and MNR.
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- 2023
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4. The novel llama-human chimeric antibody has potent effect in lowering LDL-c levels in hPCSK9 transgenic rats
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Xinyang Li, Meiniang Wang, Xinhua Zhang, Chuxin Liu, Haitao Xiang, Mi Huang, Yingying Ma, Xiaoyan Gao, Lin Jiang, Xiaopan Liu, Bo Li, Yong Hou, Xiuqing Zhang, Shuang Yang, and Naibo Yang
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PCSK9 ,Antibody ,LDL-c ,VHH-Fc ,sdAb ,Pichia pastoris ,Medicine (General) ,R5-920 - Abstract
Abstract Background The advent of proprotein convertase subtilisin/kexin type 9 (PCSK9)–inhibiting drugs have provided an effective, but extremely expensive treatment for the management of low density lipoprotein (LDL). Our aim was to explore a cost-effective application of camelid anti-PCSK9 single domain antibodies (sdAbs), which are high variable regions of the camelid heavy chain antibodies (VHHs), as a human PCSK9 (hPCSK9) inhibitor. One female llama was immunized with hPCSK9. Screening of high affinity anti-PCSK9 VHHs was carried out based on surface plasmon resonance (SPR) technology. We reported a lysate kinetic analysis method improving the screening efficiency. To increase the serum half-life and targeting properties, the constant region fragment of the human immunoglobulin gamma sub-type 4 (IgG4 Fc) was incorporated to form a novel llama-human chimeric molecule (VHH-hFc). Results The PCSK9 inhibiting effects of the VHH proteins were analyzed in two human liver hepatocellular cells (HepG2 and Huh7) and in the hPCSK9 transgenic Sprague–Dawley (SD) rat model. The hPCSK9 antagonistic potency of the bivalent VHH-hFc exceeded the monovalent VHH (P
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- 2020
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5. Bamboo Shark as a Small Animal Model for Single Domain Antibody Production
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Likun Wei, Meiniang Wang, Haitao Xiang, Yuan Jiang, Jinhua Gong, Dan Su, M. A. R. Al Azad, Hongming Dong, Limin Feng, Jiajun Wu, Leo Lai Chan, Naibo Yang, and Jiahai Shi
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single domain antibody ,bamboo shark ,IgNAR ,immunization ,vNAR ,immune repertoire ,Biotechnology ,TP248.13-248.65 - Abstract
The development of shark single domain antibodies (sdAbs) is hindered by the high cost and tediousness of large-sized shark farming. Here, we demonstrated white-spotted bamboo sharks (Chiloscyllium plagiosum) being cultivated commercially as a promising small animal model to produce sdAbs. We found that immunoglobulin new antigen receptor (IgNAR) presented in bamboo shark genome, transcriptome, and plasma. Four complete IgNAR clusters including variable domains (vNARs) were discovered in the germline, and the Variable–Joining pair from IgNAR1 cluster was dominant from immune repertoires in blood. Bamboo sharks developed effective immune responses upon green fluorescent protein (GFP), near-infrared fluorescent protein iRFP713, and Freund’s adjuvant immunization revealed by elevated lymphocyte counts and antigen specific IgNAR. Before and after immunization, the complementarity determining region 3 (CDR3) of IgNAR were the major determinant of IgNAR diversity revealed by 400-bp deep sequencing. To prove that bamboo sharks could produce high-affinity IgNAR, we isolated anti-GFP and anti-iRFP713 vNARs with up to 0.3 and 3.8 nM affinities, respectively, from immunized sharks. Moreover, we constructed biparatopic vNARs with the highest known affinities (20.7 pM) to GFP and validated the functions of anti-GFP vNARs as intrabodies in mammalian cells. Taken together, our study will accelerate the discovery and development of bamboo shark sdAbs for biomedical industry at low cost and easy operation.
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- 2021
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6. Comparative analysis of sequencing technologies for single-cell transcriptomics
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Kedar Nath Natarajan, Zhichao Miao, Miaomiao Jiang, Xiaoyun Huang, Hongpo Zhou, Jiarui Xie, Chunqing Wang, Shishang Qin, Zhikun Zhao, Liang Wu, Naibo Yang, Bo Li, Yong Hou, Shiping Liu, and Sarah A. Teichmann
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Single-cell RNA sequencing ,Sequencing platforms ,Benchmarking scRNA-seq ,Illumina sequencing ,BGISEQ-500 ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Single-cell RNA-seq technologies require library preparation prior to sequencing. Here, we present the first report to compare the cheaper BGISEQ-500 platform to the Illumina HiSeq platform for scRNA-seq. We generate a resource of 468 single cells and 1297 matched single cDNA samples, performing SMARTer and Smart-seq2 protocols on two cell lines with RNA spike-ins. We sequence these libraries on both platforms using single- and paired-end reads. The platforms have comparable sensitivity and accuracy in terms of quantification of gene expression, and low technical variability. Our study provides a standardized scRNA-seq resource to benchmark new scRNA-seq library preparation protocols and sequencing platforms.
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- 2019
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7. The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish
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Yaolei Zhang, Haoyang Gao, Hanbo Li, Jiao Guo, Bingjie Ouyang, Meiniang Wang, Qiwu Xu, Jiahao Wang, Meiqi Lv, Xinyu Guo, Qun Liu, Likun Wei, Han Ren, Yang Xi, Yang Guo, Bingzhao Ren, Shanshan Pan, Chuxin Liu, Xiaoyan Ding, Haitao Xiang, Yingjia Yu, Yue Song, Lingfeng Meng, Shanshan Liu, Jun Wang, Yuan Jiang, Jiahai Shi, Shiping Liu, Jamal S.M. Sabir, Mumdooh J. Sabir, Muhummadh Khan, Nahid H. Hajrah, Simon Ming-Yuen Lee, Xun Xu, Huanming Yang, Jian Wang, Guangyi Fan, Naibo Yang, and Xin Liu
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Biological Sciences ,Genetics ,Genomics ,Phylogenetics ,Evolutionary Biology ,Science - Abstract
Summary: Chondrichthyan (cartilaginous fish) occupies a key phylogenetic position and is important for investigating evolutionary processes of vertebrates. However, limited whole genomes impede our in-depth knowledge of important issues such as chromosome evolution and immunity. Here, we report the chromosome-level genome of white-spotted bamboo shark. Combing it with other shark genomes, we reconstructed 16 ancestral chromosomes of bamboo shark and illustrate a dynamic chromosome rearrangement process. We found that genes on 13 fast-evolving chromosomes can be enriched in immune-related pathways. And two chromosomes contain important genes that can be used to develop single-chain antibodies, which were shown to have high affinity to human disease markers by using enzyme-linked immunosorbent assay. We also found three bone formation-related genes were lost due to chromosome rearrangements. Our study highlights the importance of chromosome rearrangements, providing resources for understanding of cartilaginous fish diversification and potential application of single-chain antibodies.
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- 2020
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8. The complete chloroplast genome sequence of Sauropus spatulifolius Beille
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Shike Cai, Fang Zhou, Yan Gu, Zhina Huang, Yu Mei, Naibo Yang, and Jihua Wang
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sauropus spatulifolius beille ,euphorbia ,chloroplast genome ,medical plant ,Genetics ,QH426-470 - Abstract
Sauropus spatulifolius Beille is one kind of Chinese herbal medicine with anti-inflammatory and analgesic activities. In this study, we reported the complete chloroplast genome of S. spatulifolius Beille, and assembled and annotated with high-throughput sequencing data, which would provide help for its taxonomy research. The chloroplast sequence was 154,707 bp , with two of 87,438 bp and 19,427 bp single-copy regions, which were separated by two inverted repeat regions with 23,921 bp . A total of 129 genes were predicted, with GC content of 36.61%. Phylogenetic analysis showed that S. spatulifolius Beille closest to Glochidion chodoense in Malpighiales.
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- 2020
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9. The Population Genetics of Alternaria tenuissima in Four Regions of China as Determined by Microsatellite Markers Obtained by Transcriptome Sequencing
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Naibo Yang, Guoping Ma, Kenxi Chen, and Xuehong Wu
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Alternaria tenuissima ,SSR marker ,tomato ,population genetic structure ,next-generation sequencing ,Microbiology ,QR1-502 - Abstract
A total of 32,284 unigenes were obtained from the transcriptome of Alternaria tenuissima, a pathogenic fungus causing foliar disease in tomato, using next-generation sequencing (NGS) technology. In total, 24,670 unigenes were annotated using five databases, including NCBI non-redundant protein, Swiss-Prot, euKaryotic Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and the Gene Ontology. A total of 1,140 simple sequence repeats were also identified for use as molecular markers. Sixteen of the simple sequence repeat loci were selected to study the population structure of A. tenuissima. A population genetic analysis of 191 A. tenuissima isolates, sampled from four geographic regions in China, indicated that A. tenuissima had a high level of genetic diversity, and that the selected simple sequence repeat markers could reliably capture the genetic variation. The null hypothesis of random mating was rejected for all four geographic regions in China. Isolation by distance was observed for the entire data set, but not within clusters, which is indicative of barriers to gene flow among geographic regions. The analyses of Bayesian and principal coordinates, however, did not separate four geographic regions into four separate genetic clusters. The different levels of historical migration rates suggest that isolation by distance did not represent a major biological obstacle to the spread of A. tenuissima. The potential epidemic spread of A. tenuissima in China may occur through the transport of plant products or other factors. The presented results provide a basis for a comprehensive understanding of the population genetics of A. tenuissima in China.
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- 2018
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10. Comparative Analysis of Immune Repertoires between Bactrian Camel's Conventional and Heavy-Chain Antibodies.
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Xinyang Li, Xiaobo Duan, Kai Yang, Wei Zhang, Changjiang Zhang, Longfei Fu, Zhe Ren, Changxi Wang, Jinghua Wu, Ruxue Lu, Yanrui Ye, Mengying He, Chao Nie, Naibo Yang, Jian Wang, Huanming Yang, Xiao Liu, and Wen Tan
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Medicine ,Science - Abstract
Compared to classical antibodies, camel heavy chain antibodies (HCAbs) are smaller in size due to lack of the light chain and the first constant domain of the heavy chain (CH1 region). The variable regions of HCAbs (VHHs) are more soluble and stable than that of conventional antibodies (VHs). Even with such simple structure, they are still functional in antigen binding. Although HCAbs have been extensively investigated over the past two decades, most efforts have been based upon low throughput sequence analysis, and there are only limited reports trying to analyze and describe the complete immune repertoire (IR) of camel HCAbs. Here we leveraged the high-throughput data generated by Next Generation Sequencing (NGS) of the variable domains of the antibody heavy chains from three Bactrian camels to conduct in-depth comparative analyses of the immunoglobulin repertoire. These include analyses of the complementary determining region 3 (CDR3) length and distribution, mutation rate, antibody characteristic amino acids, the distribution of the cysteine (Cys) codons, and the non-classical VHHs. We found that there is higher diversity in the CDR2 than in the other sub-regions, and there is a higher mutation rate in the VHHs than in the VHs (P < 0.05). In addition to substitutions at amino acid (AA) residue positions NO.49/50/52 between VH and VHH clones, we also observed other substitutions at the positions NO.40/54/57/96/101 that could lead to additional structural alterations. We also found that VH-derived VHH clones, referred to as non-classical VHH clones in this study, accounted for about 8% of all clones. Further, only 5%-10% clones had the Trp > Arg AA substitution at the first position of framework 4 for all types of clones. We present, for the first time, a relatively complete picture of the Bactrian camel antibody immune repertoire, including conventional antibody (Ab) and HCAbs, using PCR and in silico analysis based on high-throughput NGS data.
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- 2016
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11. Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients
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Penghui Yang, Xiaoshan Wang, Yuhuan Gong, George F. Gao, William J. Liu, Jin Yan, Peipei Liu, Ziqian Xu, Beiwei Ye, Longlong Wang, Ning Zhang, Naibo Yang, Haitao Xiang, Xinyang Li, Zhaohai Wang, Xiaopan Liu, Longqi Liu, Guizhen Wu, Ying Gu, Shaogeng Zhang, Linxiang Yu, Chen Zhu, Fanping Meng, Yingze Zhao, Xiaoju Yuan, Meiniang Wang, Wei Zhang, Pengyan Wang, Chengrong Bian, Kai Gao, Yi Shi, Liang Wu, Changqing Bai, Xun Xu, Haixi Sun, Yuhai Bi, and Lei Tian
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Adult ,Male ,Lineage (genetic) ,Adolescent ,Immunology ,B-cell receptor ,Receptors, Antigen, B-Cell ,BCR, B-cell receptor ,Antibodies, Viral ,Virus ,Immune system ,medicine ,Humans ,Immunology and Allergy ,Gene ,B cell ,COVID-19, coronavirus disease 2019 ,Aged, 80 and over ,B-Lymphocytes ,SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2 ,biology ,SARS-CoV-2 ,Repertoire ,COVID-19 ,B-cell receptor repertoire ,General Medicine ,Middle Aged ,Antibodies, Neutralizing ,Clonal expansion ,medicine.anatomical_structure ,PBMC, peripheral blood mononuclear cells ,SHM, somatic hypermutation ,biology.protein ,Female ,Antibody ,Immunoglobulin Heavy Chains ,CDR3, complementarity determining region 3 ,IGH, immunoglobin heavy chain ,Research Article - Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of coronavirus disease 2019 (COVID-19). Great international efforts have been put into the development of prophylactic vaccines and neutralizing antibodies. However, the knowledge about the B cell immune response induced by the SARS-CoV-2 virus is still limited. Here, we report a comprehensive characterization of the dynamics of immunoglobin heavy chain (IGH) repertoire in COVID-19 patients. By using next-generation sequencing technology, we examined the temporal changes in the landscape of the patient's immunological status and found dramatic changes in the IGH within the patient's immune system after the onset of COVID-19 symptoms. Although different patients have distinct immune responses to SARS-CoV-2 infection, by employing clonotype overlap, lineage expansion, and clonotype network analyses, we observed a higher clonotype overlap and substantial lineage expansion of B cell clones 2-3 weeks after the onset of illness, which is of great importance to B-cell immune responses. Meanwhile, for preferences of V gene usage during SARS-CoV-2 infection, IGHV3-74 and IGHV4-34, and IGHV4-39 in COVID-19 patients were more abundant than those of healthy controls. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic development as well as mechanistic research.
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- 2022
12. SARS-CoV-2 breakthrough infections induce somatically hypermutated broadly neutralizing antibodies against heterologous variants
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Xiaoli Xiong, Haisheng Yu, Yaping Wang, Jingrong Shi, Chengqian Feng, Guofang Tang, Jiaojiao Li, Fengyu Hu, Liliangzi Guo, Feng Li, Xiaoping Tang, Banghui Liu, Qiuluan Chen, Zimu Li, Mengzhen Su, Qihong Yan, Xinwen Chen, Rongjuan Pei, Yudi ZHANG, Qian Wang, Peiyu HU, Pingqian Zheng, Ling Chen, Xijie Gao, Jun He, Haitao Xiang, Caixia Xie, Quan Shi, Longqi Liu, Xiaopan Liu, Xiumei Lin, Chuanyu Liu, Yalin Huang, Naibo Yang, Meiniang Wang, Xiaofang Peng, Dan Liang, Bixia Ke, and Changwen Ke
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Currently circulating SARS-CoV-2 Omicron variants feature highly mutated spike proteins with extraordinary abilities in evading acute-infection-induced germline antibodies isolated earlier in the pandemic. We identified that memory B cells from Delta variant breakthrough-infection patients expressed antibodies with more extensive somatic hypermutations (SHMs) allowing isolation of a number of broadly neutralizing antibodies with activities against heterologous variants of concerns (VOCs) including Omicron variant. Structural studies identified that SHM introduced altered amino acids and highly unusual HCDR2 insertions respectively in two representative broadly neutralizing antibodies - YB9-258 and YB13-292. Previously, insertion/deletion were rarely reported for antiviral antibodies except for those induced by HIV-1 chronic infections. Identified SHMs involved heavily in epitope recognition, they broadened neutralization breadth by rendering antibodies resistant to VOC mutations highly detrimental to previously isolated antibodies targeting similar epitopes. These data provide molecular mechanisms for enhanced immunity to heterologous SARS-CoV-2 variants after repeated antigen exposures with implications for future vaccination strategy.
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- 2022
13. A megadiverse naïve library derived from numerous camelids for efficient and rapid development of VHH antibodies
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Meiniang Wang, Likun Wei, Haitao Xiang, Bingzhao Ren, Xiaopan Liu, Lin Jiang, Naibo Yang, and Jiahai Shi
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Camelus ,Biophysics ,Animals ,Reproducibility of Results ,Cell Biology ,Antigens ,Single-Domain Antibodies ,Immunoglobulin Heavy Chains ,Camelids, New World ,Molecular Biology ,Biochemistry ,Antibodies ,Gene Library - Abstract
The field of antibody development is under pressure to meet rising demands for speed, cost-effectiveness, efficacy, reliability, and large-scale production. It is costly and time-consuming to immunize animals and build a single-domain antibody (sdAb) library for each target. Using the variable domain (VHH) of heavy-chain only antibodies (HcAbs) derived from blood samples of 75 non-immunized camelid animals (51 alpacas, 13 llamas, 11 Bactrian camels), and spleens from two Bactrian camels, a naïve sdAb library with extensive megadiversity and reusability was constructed. The library was evaluated using next-generation DNA sequencing (NGS) and was found to contain hundreds of billions of unique clones. To confirm the availability of target-specific VHHs, a naive library was screened for a variety of targets. At least two VHH candidates were extracted for each target using a 20-day selection pipeline. Some binders had ultrahigh potencies, with binding affinities in the nanomolar range. This naïve library, in particular, offers the possibility of acquiring unique antibodies targeting antigens of interest with low feasible dissociation constant (kD) without the time, effort, and price associated in producing antibodies in animals via antigen injection. Overall, the study shows that the megadiverse naïve library provides a rapid, adaptable, and easy platform for antibody creation, emphasizing its therapeutic and diagnostic implications.
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- 2022
14. Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction
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Zhiqin Huang, Pramod K. Srivastava, Song Liu, Jason A. Greenbaum, Dirk Jäger, Jiaqian Wang, Ognjen Milicevic, Willem-Jan Krebber, Barbara Schrörs, Sean Michael Boyle, Michal Bassani-Sternberg, Ana M. Mijalkovic Lazic, Amit A. Lugade, Kristen K. Dang, Han Si, Alessandro Sette, Jeffrey P. Ward, Irsan Kooi, Michael F. Princiotta, Begonya Comin-Anduix, Thierry Schuepbach, Pia Kvistborg, Julia Kodysh, William Chour, Vladimir B. Kovacevic, Jan H. Kessler, Ariella Sasson, Antoni Ribas, Brian Stevenson, Sriram Sridhar, Prateek Tanden, Robert D. Schreiber, Jason Perera, Kathleen C. F. Sheehan, Hira Rizvi, Sachet A. Shukla, Baikang Pei, Han Chang, Bo Li, Ion I. Mandoiu, Cristina Puig-Saus, Beatriz M. Carreno, Si Qiu, Jennifer M. Shelton, Patrick Jongeneel, Qiang Hu, Taha Merghoub, Matthew D. Hellmann, James P. Conway, Francisco Arcila, Ton N. Schumacher, Mathias Vormehr, Christopher A. Morehouse, Patrice Manning, Jonathon Blake, Pornpimol Charoentong, Angela Frentzen, Christopher A. Miller, Michael A. Kuziora, Bin Song, Lei Wei, Martin Löwer, Gabor Bartha, Justin Guinney, Niels Halama, Rolf Hilker, Yinong Sebastian, Veliborka Josipovic, Jason Harris, Geng Liu, Guilhem Richard, Arjun A. Rao, Nikola M. Skundric, Markus Mueller, Daniel K. Wells, Tatiana Shcheglova, Inka Zörnig, Weixuan Fu, John Sidney, Nadine Defranoux, Gabriela Steiner, Joseph D. Szustakowski, Arbel D. Tadmor, Maxim N. Artyomov, Jianmin Wang, George Coukos, Brandon W. Higgs, Milica R. Kojicic, Siranush Sarkizova, Daphne van Beek, Naibo Yang, Robert Ziman, Mignonette H. Macabali, Thomas Yu, Nicolas Guex, Nina Bhardwaj, Lorenzo F. Fanchi, Bjoern Peters, Christian Iseli, Song Wu, Maren Lang, Juliet Forman, Marit M. van Buuren, David Balli, Steven L. C. Ketelaars, Nir Hacohen, Ekaterina Esaulova, Maarten Slagter, Todd Creasy, Robert A. Petit, Yi-Hsiang Hsu, Ravi Gupta, Katie M. Campbell, Pascal Gellert, David Haussler, Jesse M. Zaretsky, Sofie R. Salama, Vanessa M. Hubbard-Lucey, Joel Greshock, Zeynep Kosaloglu Yalcin, Cornelis J. M. Melief, Priyanka Shah, Ioannis Xenarios, Nevena M. Ilic Raicevic, Andrew Lamb, Suchit Jhunjhunwala, Aly A. Khan, David Gfeller, James R. Heath, Richard Chen, Jia M. Chen, Alphonsus H. C. Ng, Elham Sherafat, Ana Belen Blazquez, Leo J. Lee, Beata Berent-Maoz, Cheryl Selinsky, Jasreet Hundal, Eduardo Cortes, Xengie Doan, Sahar Al Seesi, Adam Kolom, Fred Ramsdell, Nicolas Robine, and Andrew J. Rech
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medicine.medical_treatment ,T cell ,Programmed Cell Death 1 Receptor ,No reference ,Sequencing data ,Computational biology ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Epitope ,Cohort Studies ,Epitopes ,03 medical and health sciences ,0302 clinical medicine ,Antigens, Neoplasm ,Neoplasms ,Research community ,medicine ,Humans ,Alleles ,030304 developmental biology ,Antigen Presentation ,0303 health sciences ,Immunogenicity ,Reproducibility of Results ,Immunotherapy ,medicine.anatomical_structure ,Peptides ,030217 neurology & neurosurgery - Abstract
Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community.
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- 2020
15. The novel llama-human chimeric antibody has potent effect in lowering LDL-c levels in hPCSK9 transgenic rats
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Naibo Yang, Meiniang Wang, Chuxin Liu, Xinhua Zhang, Xiaoyan Gao, Xiaopan Liu, Bo Li, Huang Mi, Xiuqing Zhang, Hou Yong, Lin Jiang, Xinyang Li, Ma Yingying, Shuang Yang, and Haitao Xiang
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0301 basic medicine ,Medicine (miscellaneous) ,VHH-Fc ,Pichia pastoris ,PCSK9 ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Potency ,sdAb ,Antibody ,lcsh:R5-920 ,biology ,Research ,Proprotein convertase ,biology.organism_classification ,Molecular biology ,Evolocumab ,030104 developmental biology ,chemistry ,030220 oncology & carcinogenesis ,Low-density lipoprotein ,biology.protein ,Molecular Medicine ,Kexin ,lcsh:Medicine (General) ,LDL-c - Abstract
Background The advent of proprotein convertase subtilisin/kexin type 9 (PCSK9)–inhibiting drugs have provided an effective, but extremely expensive treatment for the management of low density lipoprotein (LDL). Our aim was to explore a cost-effective application of camelid anti-PCSK9 single domain antibodies (sdAbs), which are high variable regions of the camelid heavy chain antibodies (VHHs), as a human PCSK9 (hPCSK9) inhibitor. One female llama was immunized with hPCSK9. Screening of high affinity anti-PCSK9 VHHs was carried out based on surface plasmon resonance (SPR) technology. We reported a lysate kinetic analysis method improving the screening efficiency. To increase the serum half-life and targeting properties, the constant region fragment of the human immunoglobulin gamma sub-type 4 (IgG4 Fc) was incorporated to form a novel llama-human chimeric molecule (VHH-hFc). Results The PCSK9 inhibiting effects of the VHH proteins were analyzed in two human liver hepatocellular cells (HepG2 and Huh7) and in the hPCSK9 transgenic Sprague–Dawley (SD) rat model. The hPCSK9 antagonistic potency of the bivalent VHH-hFc exceeded the monovalent VHH (P
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- 2020
16. Additional file 4 of The novel llama-human chimeric antibody has potent effect in lowering LDL-c levels in hPCSK9 transgenic rats
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Xinyang Li, Meiniang Wang, Xinhua Zhang, Chuxin Liu, Haitao Xiang, Huang, Mi, Yingying Ma, Xiaoyan Gao, Jiang, Lin, Xiaopan Liu, Li, Bo, Hou, Yong, Xiuqing Zhang, Yang, Shuang, and Naibo Yang
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Additional file 4: Table S1. The sequences of the sdAbs.
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- 2020
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17. Diversity of Fusarium species associated with root rot of sugar beet in China
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Can Zhao, Sha Cao, Chenggui Han, Jia Liu, Naibo Yang, and Xuehong Wu
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0106 biological sciences ,Fusarium ,biology ,food and beverages ,Plant Science ,biology.organism_classification ,01 natural sciences ,Crop ,010602 entomology ,Horticulture ,Fusarium oxysporum ,Root rot ,Sugar beet ,Internal transcribed spacer ,Sugar ,Agronomy and Crop Science ,Ribosomal DNA ,010606 plant biology & botany - Abstract
Sugar beet is widely grown throughout the world and represents the second largest crop used to produce sugar. Root rot in sugar beet, caused by Fusarium, significantly reduces yield, juice purity, and sugar concentration. Here, 307 Fusarium isolates were collected from sugar beet roots exhibiting typical root rot symptoms in eight provinces or autonomous regions of China from 2009 to 2012. Based on morphological characteristics and sequence data of the internal transcribed spacer (ITS) region of ribosomal DNA (rDNA) and the translation elongation factor 1α (EF-1α), Fusarium oxysporum (38.4%) was identified as the most prevalent species, followed by F. solani (20.9%), and F. equiseti (18.9%). These three species were widely distributed in all eight of the provinces and autonomous regions. F. tricinctum (5.9%), F. brachygibbosum (4.6%), F. redolens (3.3%), F. proliferatum (3.3%), F. graminearum (2.3%), F. verticillioides (1.6%), F. nygamai (0.7%), and F. culmorum (0.3%) were less frequently obtained. Of the 307 Fusarium isolates, 117 representing different species and geographic locations were demonstrated to cause tip rot and vascular discoloration in sugar beet roots, with disease incidence ranging from 84.2 to 100.0% and disease index ranging from 41.94 to 75.83. This is the first detailed report of Fusarium species, in particular F. tricinctum, F. brachygibbosum, F. redolens, F. proliferatum, F. nygamai, and F. culmorum, causing sugar beet root rot in China.
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- 2018
18. The complete chloroplast genome sequence of Sauropus spatulifolius Beille
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Fang Zhou, Zhina Huang, Yu Mei, Naibo Yang, Jihua Wang, Shike Cai, and Yan Gu
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0106 biological sciences ,0301 basic medicine ,Genetics ,Whole genome sequencing ,Euphorbia ,food and beverages ,Biology ,biology.organism_classification ,Sauropus spatulifolius ,010603 evolutionary biology ,01 natural sciences ,Genome ,Chloroplast ,03 medical and health sciences ,030104 developmental biology ,Molecular Biology - Abstract
Sauropus spatulifolius Beille is one kind of Chinese herbal medicine with anti-inflammatory and analgesic activities. In this study, we reported the complete chloroplast genome of S. spatulifolius ...
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- 2020
19. Selection of potential cytokeratin-18 monoclonal antibodies following IGH repertoire evaluation in mice
- Author
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Xiuqing Zhang, Xiao Liu, Xinyang Li, Chao Nie, Shuang Yang, Wei Zhang, Naibo Yang, Zhe Ren, and Huang Mi
- Subjects
Male ,Vaccine evaluation ,medicine.drug_class ,Immunology ,Antibody Affinity ,Immunoglobulin Variable Region ,chemical and pharmacologic phenomena ,Enzyme-Linked Immunosorbent Assay ,Complementarity determining region ,Biology ,Monoclonal antibody ,Cytokeratin ,Antibody Specificity ,medicine ,Immunology and Allergy ,Animals ,Mice, Inbred BALB C ,Keratin-18 ,Antibodies, Monoclonal ,High-Throughput Nucleotide Sequencing ,Molecular biology ,Complementarity Determining Regions ,biology.protein ,Immunohistochemistry ,Immunoglobulin heavy chain ,Immunization ,Antibody ,Clone (B-cell biology) ,Immunoglobulin Heavy Chains ,Antibody Diversity - Abstract
Cytokeratin 18 (CK18), the main scaffold protein of keratinocyte, is distributed in epithelial cells. This structural protein maintains the integrity and continuity of epithelial tissue. Cytokeratin is also frequently used as an immunohistochemical marker of tumor growth. In recent years, immune repertoire (IR) evaluation using next-generation sequencing (NGS) have become increasingly efficient. Here we deep sequenced the mouse IR of the immunoglobulin heavy chain (IGH) after CK18 immunization. We comprehensively analyzed the IR based on complementarity determining region 3 (CDR3) abundance, germline gene usage polarization, clone diversity, and lineage. We found many convergence characteristics after CK18 immunization. Convergence represents a phenomenon that antigen stimulation or pathogen exposure induces the antigen specific clone expansion and enrichment. The convergence could be used for the immune evaluation and antibody screen. After immunization, the IGHV5 gene clusters became preponderant. The abundance and length of the most frequent CDR3 both increased, nevertheless the IR diversity level decreased. From the convergent IGH repertoires, we selected and expressed six antibodies with the most frequent CDR3s and IGH V-J combinations. The ELISA results suggested all screened six antibodies bound CK18 specifically. The most potential antibody had 9.424E-10M M affinity for the interaction with the CK18. Therefore, this is the NGS platform has been first used for anti-CK18 monoclonal antibodies (MAbs) discovery. These analyses methods could also be used for vaccine evaluation.
- Published
- 2019
20. The Population Genetics of Alternaria tenuissima in Four Regions of China as Determined by Microsatellite Markers Obtained by Transcriptome Sequencing
- Author
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Kenxi Chen, Naibo Yang, X. H. Wu, and Guoping Ma
- Subjects
0106 biological sciences ,0301 basic medicine ,Microbiology (medical) ,Population ,lcsh:QR1-502 ,Population genetics ,Biology ,tomato ,01 natural sciences ,Genetic analysis ,Microbiology ,lcsh:Microbiology ,Gene flow ,03 medical and health sciences ,Genetic variation ,population genetic structure ,education ,SSR marker ,Isolation by distance ,Original Research ,education.field_of_study ,Genetic diversity ,Alternaria tenuissima ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,next-generation sequencing ,010606 plant biology & botany - Abstract
A total of 32,284 unigenes were obtained from the transcriptome of Alternaria tenuissima, a pathogenic fungus causing foliar disease in tomato, using next-generation sequencing (NGS) technology. In total, 24,670 unigenes were annotated using five databases, including NCBI non-redundant protein, Swiss-Prot, euKaryotic Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and the Gene Ontology. A total of 1,140 simple sequence repeats were also identified for use as molecular markers. Sixteen of the simple sequence repeat loci were selected to study the population structure of A. tenuissima. A population genetic analysis of 191 A. tenuissima isolates, sampled from four geographic regions in China, indicated that A. tenuissima had a high level of genetic diversity, and that the selected simple sequence repeat markers could reliably capture the genetic variation. The null hypothesis of random mating was rejected for all four geographic regions in China. Isolation by distance was observed for the entire data set, but not within clusters, which is indicative of barriers to gene flow among geographic regions. The analyses of Bayesian and principal coordinates, however, did not separate four geographic regions into four separate genetic clusters. The different levels of historical migration rates suggest that isolation by distance did not represent a major biological obstacle to the spread of A. tenuissima. The potential epidemic spread of A. tenuissima in China may occur through the transport of plant products or other factors. The presented results provide a basis for a comprehensive understanding of the population genetics of A. tenuissima in China.
- Published
- 2018
21. The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish
- Author
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Yang Guo, Simon Ming-Yuen Lee, Jun Wang, Jiahao Wang, Shanshan Pan, Chuxin Liu, Shanshan Liu, Lingfeng Meng, Han Ren, Yue Song, Shiping Liu, Yingjia Yu, Haitao Xiang, Likun Wei, Qiwu Xu, Jiao Guo, Bingzhao Ren, Yaolei Zhang, Xin Liu, Mumdooh J. Sabir, Qun Liu, Meiniang Wang, Nahid H. Hajrah, Jiahai Shi, Huanming Yang, Hanbo Li, Xiaoyan Ding, Naibo Yang, Haoyang Gao, Yang Xi, Muhummadh Khan, Meiqi Lv, Jamal S. M. Sabir, Bingjie Ouyang, Guangyi Fan, Jian Wang, Xun Xu, Xinyu Guo, and Yuan Jiang
- Subjects
0301 basic medicine ,Genomics ,02 engineering and technology ,Chromosomal rearrangement ,Biology ,Genome ,Article ,03 medical and health sciences ,SDG 3 - Good Health and Well-being ,Phylogenetics ,Genetics ,lcsh:Science ,Gene ,Evolutionary Biology ,Multidisciplinary ,Phylogenetic tree ,Chromosome ,Biological Sciences ,021001 nanoscience & nanotechnology ,White (mutation) ,030104 developmental biology ,Evolutionary biology ,lcsh:Q ,0210 nano-technology - Abstract
Summary Chondrichthyan (cartilaginous fish) occupies a key phylogenetic position and is important for investigating evolutionary processes of vertebrates. However, limited whole genomes impede our in-depth knowledge of important issues such as chromosome evolution and immunity. Here, we report the chromosome-level genome of white-spotted bamboo shark. Combing it with other shark genomes, we reconstructed 16 ancestral chromosomes of bamboo shark and illustrate a dynamic chromosome rearrangement process. We found that genes on 13 fast-evolving chromosomes can be enriched in immune-related pathways. And two chromosomes contain important genes that can be used to develop single-chain antibodies, which were shown to have high affinity to human disease markers by using enzyme-linked immunosorbent assay. We also found three bone formation-related genes were lost due to chromosome rearrangements. Our study highlights the importance of chromosome rearrangements, providing resources for understanding of cartilaginous fish diversification and potential application of single-chain antibodies., Graphical Abstract, Highlights • Inferred ancestral chromosome karyotypes of cartilaginous fish • Chromosome rearrangements resulted in fast-evolving chromosomes and immune genes • Chromosome rearrangements led to deletion of bone formation-related genes • Proved that single-domain antibodies in shark have great potential application, Biological Sciences; Genetics; Genomics; Phylogenetics; Evolutionary Biology
- Published
- 2020
22. [A set of methods of amplification of human monoclonal antibody heavy and light chain genes from one single B cell]
- Author
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Xinyang, Li, Peiyao, Yang, and Naibo, Yang
- Subjects
B-Lymphocytes ,Antibodies, Monoclonal ,Humans ,Immunoglobulin Light Chains ,Cloning, Molecular ,Flow Cytometry ,Immunoglobulin Heavy Chains ,Polymerase Chain Reaction ,Cell Line ,DNA Primers - Abstract
Objective To develop a set of methods of amplifying the natural paring heavy and light chain genes from one single B cell. Methods Yanhuang (YH) cells were the first whole genome sequenced human cells of Asian origin. With the immortalized cell lines as the raw material, single CD19
- Published
- 2018
23. PSSMHCpan:a novel PSSM-based software for predicting class I peptide-HLA binding affinity
- Author
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Geng Liu, Zhen Cheng, Yong Hou, Dongli Li, Wenhui Li, Cheng-chi Chao, Handong Li, Bo Li, Si Qiu, Naibo Yang, Le Cheng, Jian Wang, Huanming Yang, Zhang Li, Xin Song, Xiuqing Zhang, and Kun Ma
- Subjects
0301 basic medicine ,medicine.medical_treatment ,Health Informatics ,Peptide ,Peptide binding ,Plasma protein binding ,Human leukocyte antigen ,Computational biology ,Biology ,Genome ,03 medical and health sciences ,Cancer immunotherapy ,Antigens, Neoplasm ,Neoplasms ,Antitumor vaccine ,Technical Note ,medicine ,Humans ,Allele ,Alleles ,chemistry.chemical_classification ,PSSMHCpan ,Histocompatibility Antigens Class I ,Cancer ,peptide-HLA binding affinity ,medicine.disease ,neoantigen ,Computer Science Applications ,030104 developmental biology ,chemistry ,Peptides ,Software ,Protein Binding - Abstract
Predicting peptide binding affinity with human leukocyte antigen (HLA) is a crucial step in developing powerful antitumor vaccine for cancer immunotherapy. Currently available methods work quite well in predicting peptide binding affinity with HLA alleles such as HLA-A*0201, HLA-A*0101, and HLA-B*0702 in terms of sensitivity and specificity. However, quite a few types of HLA alleles that are present in the majority of human populations including HLA-A*0202, HLA-A*0203, HLA-A*6802, HLA-B*5101, HLA-B*5301, HLA-B*5401, and HLA-B*5701 still cannot be predicted with satisfactory accuracy using currently available methods. Furthermore, currently the most popularly used methods for predicting peptide binding affinity are inefficient in identifying neoantigens from a large quantity of whole genome and transcriptome sequencing data. Here we present a Position Specific Scoring Matrix (PSSM)-based software called PSSMHCpan to accurately and efficiently predict peptide binding affinity with a broad coverage of HLA class I alleles. We evaluated the performance of PSSMHCpan by analyzing 10-fold cross-validation on a training database containing 87 HLA alleles and obtained an average area under receiver operating characteristic curve (AUC) of 0.94 and accuracy (ACC) of 0.85. In an independent dataset (Peptide Database of Cancer Immunity) evaluation, PSSMHCpan is substantially better than the popularly used NetMHC-4.0, NetMHCpan-3.0, PickPocket, Nebula, and SMM with a sensitivity of 0.90, as compared to 0.74, 0.81, 0.77, 0.24, and 0.79. In addition, PSSMHCpan is more than 197 times faster than NetMHC-4.0, NetMHCpan-3.0, PickPocket, sNebula, and SMM when predicting neoantigens from 661 263 peptides from a breast tumor sample. Finally, we built a neoantigen prediction pipeline and identified 117 017 neoantigens from 467 cancer samples of various cancers from TCGA. PSSMHCpan is superior to the currently available methods in predicting peptide binding affinity with a broad coverage of HLA class I alleles.
- Published
- 2017
24. Comparative analysis of immune repertoires between Bactrian camel's conventional and heavy-chain antibodies
- Author
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Yanrui Ye, Changjiang Zhang, Changxi Wang, Kai Yang, Chao Nie, Ruxue Lu, Zhe Ren, Jinghua Wu, Mengying He, Xiaobo Duan, Wei Zhang, Huanming Yang, Jian Wang, Naibo Yang, Wen Tan, Xiao Liu, Xinyang Li, and Long-Fei Fu
- Subjects
0301 basic medicine ,Mutation rate ,Physiology ,Immunoglobulin Variable Region ,lcsh:Medicine ,Artificial Gene Amplification and Extension ,Biochemistry ,Polymerase Chain Reaction ,0302 clinical medicine ,Camels ,Immune Physiology ,Medicine and Health Sciences ,lcsh:Science ,Mammals ,Multidisciplinary ,Immune System Proteins ,Genes, Immunoglobulin ,High-Throughput Nucleotide Sequencing ,Vertebrates ,Amino Acid Analysis ,Antibody ,Immunoglobulin Heavy Chains ,Sequence Analysis ,Research Article ,Camelus ,Sequence analysis ,In silico ,Immunology ,Nucleotide Sequencing ,Sequence alignment ,Computational biology ,Biology ,Molecular cloning ,Immunoglobulin light chain ,Research and Analysis Methods ,Antibodies ,03 medical and health sciences ,Animals ,Bactrian camel ,Molecular Biology Techniques ,Sequencing Techniques ,Molecular Biology ,Molecular Biology Assays and Analysis Techniques ,lcsh:R ,Organisms ,Biology and Life Sciences ,Proteins ,biology.organism_classification ,Molecular biology ,030104 developmental biology ,Amniotes ,biology.protein ,lcsh:Q ,Sequence Alignment ,030215 immunology ,Cloning - Abstract
Compared to classical antibodies, camel heavy chain antibodies (HCAbs) are smaller in size due to lack of the light chain and the first constant domain of the heavy chain (CH1 region). The variable regions of HCAbs (VHHs) are more soluble and stable than that of conventional antibodies (VHs). Even with such simple structure, they are still functional in antigen binding. Although HCAbs have been extensively investigated over the past two decades, most efforts have been based upon low throughput sequence analysis, and there are only limited reports trying to analyze and describe the complete immune repertoire (IR) of camel HCAbs. Here we leveraged the high-throughput data generated by Next Generation Sequencing (NGS) of the variable domains of the antibody heavy chains from three Bactrian camels to conduct in-depth comparative analyses of the immunoglobulin repertoire. These include analyses of the complementary determining region 3 (CDR3) length and distribution, mutation rate, antibody characteristic amino acids, the distribution of the cysteine (Cys) codons, and the non-classical VHHs. We found that there is higher diversity in the CDR2 than in the other sub-regions, and there is a higher mutation rate in the VHHs than in the VHs (P < 0.05). In addition to substitutions at amino acid (AA) residue positions NO.49/50/52 between VH and VHH clones, we also observed other substitutions at the positions NO.40/54/57/96/101 that could lead to additional structural alterations. We also found that VH-derived VHH clones, referred to as non-classical VHH clones in this study, accounted for about 8% of all clones. Further, only 5%-10% clones had the Trp > Arg AA substitution at the first position of framework 4 for all types of clones. We present, for the first time, a relatively complete picture of the Bactrian camel antibody immune repertoire, including conventional antibody (Ab) and HCAbs, using PCR and in silico analysis based on high-throughput NGS data.
- Published
- 2016
25. Population Patch Clamp Improves Data Consistency and Success Rates in the Measurement of Ionic Currents
- Author
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Jan Hughes, Shawn D. Handran, Andrew Wittel, Naibo Yang, Alan Finkel, and James Costantin
- Subjects
ERG1 Potassium Channel ,Cell Membrane Permeability ,Patch-Clamp Techniques ,Data consistency ,Computer science ,Population ,Muscle Proteins ,CHO Cells ,Models, Biological ,Biochemistry ,Sodium Channels ,NAV1.5 Voltage-Gated Sodium Channel ,Analytical Chemistry ,Potassium Channels, Tandem Pore Domain ,Tetracaine ,Automated patch clamp ,Consistency (statistics) ,Cricetinae ,Animals ,Humans ,Computer Simulation ,4-Aminopyridine ,education ,Throughput (business) ,Ion channel ,education.field_of_study ,Kv1.3 Potassium Channel ,Subtraction ,Lidocaine ,Reproducibility of Results ,Ether-A-Go-Go Potassium Channels ,Electrophysiology ,Molecular Medicine ,Biological system ,Biotechnology ,Communication channel - Abstract
Present whole-cell patch-clamp methodology has only moderate consistency and throughput, rendering impractical functional measurements on large numbers of ion channel ligands or on large numbers of unknown or mutant channel genes. In the population patch clamp (PPC) described herein, a single voltage-clamp amplifier sums the whole-cell currents from multiple cells at once, each sealed to a separate aperture in a planar substrate well. The resulting ensemble currents are more consistent from well to well, and the success rate for each recording attempt is >95%. The PPC was implemented by modifying the PatchPlate substrate and amplifiers in the IonWorks patch-clamp instrument. The increased data consistency and likelihood of a successful recording in each well, combined with 384-well measurements in parallel, allow the direct electrophysiological recording of thousands of ensemble ionic currents per day. Therapeutic groups in drug discovery programs require this order of throughput to screen directed compound libraries against ion channel targets. The potential for studying the function of large numbers of ion channel mutants may be realized with the technique. The procedure incorporates subtraction methods that correct for expected distortions and also reliably produces data that agree with previous patch-clamp studies.
- Published
- 2006
26. Molecular Basis of Charge Movement in Voltage-Gated Sodium Channels
- Author
-
Alfred L. George, Naibo Yang, and Richard Horn
- Subjects
Models, Molecular ,Chemical Phenomena ,Protein Conformation ,Recombinant Fusion Proteins ,Neuroscience(all) ,Molecular Sequence Data ,Transfection ,Sodium Channels ,Cell Line ,Membrane Potentials ,03 medical and health sciences ,0302 clinical medicine ,Protein structure ,Humans ,Channel blocker ,Hanatoxin ,Amino Acid Sequence ,Cysteine ,Muscle, Skeletal ,Ion channel ,030304 developmental biology ,0303 health sciences ,Voltage-gated ion channel ,Base Sequence ,Chemistry ,Chemistry, Physical ,General Neuroscience ,Sodium channel ,Sodium ,Sulfhydryl Reagents ,Depolarization ,Biophysics ,Mutagenesis, Site-Directed ,Ion Channel Gating ,030217 neurology & neurosurgery ,Communication channel - Abstract
Voltage-dependent movement of a sodium channel S4 segment was examined by cysteine scanning mutagenesis and testing accessibility of the residues to hydrophilic cysteine-modifying reagents. These experiments indicate that 2 charged S4 residues move completely from an internally accessible to an externally accessible location in response to depolarization by passage through a short “channel” in the protein. The energetic problems of S4 movement have thus been solved in the same way that many ion channels achieve highly selective and rapid ion permeation through an open pore, by restricting the contact region between the permion and its channel.
- Published
- 1996
- Full Text
- View/download PDF
27. Sodium channel mutations in paramyotonia congenita exhibit similar biophysical phenotypes in vitro
- Author
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Ming Zhou, Louis J. Ptáček, Alfred L. George, Sen Ji, Robert L. Barchi, Richard Horn, and Naibo Yang
- Subjects
Nav1.4 ,Molecular Sequence Data ,Biophysics ,In Vitro Techniques ,Biology ,medicine.disease_cause ,Biophysical Phenomena ,Sodium Channels ,Myotonia ,Paralyses, Familial Periodic ,Structure-Activity Relationship ,medicine ,Humans ,Hyperkalemic periodic paralysis ,DNA Primers ,Genetics ,Mutation ,Multidisciplinary ,Base Sequence ,Sodium channel ,Electric Conductivity ,Temperature ,Skeletal muscle ,Periodic paralysis ,medicine.disease ,Cell biology ,medicine.anatomical_structure ,Paramyotonia congenita ,Mutagenesis, Site-Directed ,biology.protein ,Research Article - Abstract
Mutations in the skeletal muscle voltage-gated Na+ channel alpha-subunit have been found in patients with two distinct hereditary disorders of sarcolemmal excitation: hyperkalemic periodic paralysis (HYPP) and paramyotonia congenita (PC). Six of these mutations have been functionally expressed in a heterologous cell line (tsA201 cells) using the recombinant human skeletal muscle Na+ channel alpha-subunit cDNA hSkM1. PC mutants from diverse locations in this subunit (T1313M, L1433R, R1448H, R1448C, A1156T) all exhibit a similar disturbance in channel inactivation characterized by reduced macroscopic rate, accelerated recovery, and altered voltage dependence. PC mutants had no significant abnormality in activation. In contrast, one HYPP mutation studied (T704M) has a normal inactivation rate but exhibits shifts in the midpoints of steady-state activation and inactivation along the voltage axis. These findings help to explain the phenotypic differences between HYPP and PC at the molecular and biophysical level and contribute to our understanding of Na+ channel structure and function.
- Published
- 1994
28. Validation of high throughput screening assays against three subtypes of Ca(v)3 T-type channels using molecular and pharmacologic approaches
- Author
-
Edward Perez-Reyes, Naibo Yang, Lucinda A. Davies, Amy Van Deusen, Daniella A. Babu, Xinmin Xie, Holden Cheng, Iuliia Vitko, Paula Q. Barrett, and Nhung T. Huynh
- Subjects
Quality Control ,Patch-Clamp Techniques ,Potassium Channels ,Drug Evaluation, Preclinical ,law.invention ,Cell Line ,Cell membrane ,Calcium Channels, T-Type ,law ,Drug Discovery ,medicine ,Extracellular ,Humans ,Fluorometry ,Patch clamp ,Coloring Agents ,Chemistry ,Temperature ,Reproducibility of Results ,Calcium Channel Blockers ,Molecular biology ,Potassium channel ,Cell biology ,medicine.anatomical_structure ,Cell culture ,Data Interpretation, Statistical ,Mibefradil ,Recombinant DNA ,Molecular Medicine ,Calcium ,Intracellular ,Plate reader ,Algorithms - Abstract
T-type Ca(2+) channels encoded by voltage-gated Ca(2+) channel (Ca(v)) 3.1, 3.2, and 3.3 genes play important physiological roles and serve as therapeutic targets for neurological and cardiovascular disorders. Currently there is no selective T-channel blocker. To screen for such a blocker, we developed three stable cell lines expressing human recombinant Ca(v)3.1, 3.2, or 3.3 channels and then examined their usefulness in high throughput screens. All three cell lines displayed an increase in intracellular Ca(2+) in response to changes in extracellular Ca(2+) as detected with Ca(2+)-sensitive dyes using a fluorometric imaging plate reader (FLIPR [Molecular Devices, Sunnyvale, CA] or FlexStation [Molecular Devices]). The signal-to-noise ratio was 2-4. Co-expression of Ca(v)3.2 with a mouse leak K(+) channel, which by virtue of being open at rest hyperpolarizes the cell membrane, blocked the fluorescent signal. Co-addition of KCl to these cells induced a Ca(2+) signal that was similar to that observed in the cell line expressing Ca(v)3.2 alone. These results confirm that the detection of intracellular Ca(2+) increase in cells expressing Ca(v)3.2 alone results from Ca(2+) entry through channels that are open at the resting membrane potential of each cell line (i.e., window currents). Testing known drugs on Ca(v)3 channels showed that block could be reliably detected using the FlexStation assay, FLIPR assay, or voltage clamp recordings using the IonWorks HT system (Molecular Devices). These results support the use of the FLIPR window current assay for primary drug screening and high throughput patch recordings for secondary screening of novel T-channel blockers.
- Published
- 2007
29. PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity.
- Author
-
Geng Liu, Dongli Li, Zhang Li, Si Qiu, Wenhui Li, Cheng-chi Chao, Naibo Yang, Handong Li, Zhen Cheng, Xin Song, Le Cheng, Xiuqing Zhang, Jian Wang, Huanming Yang, Kun Ma, Yong Hou, and Bo Li
- Subjects
LEUCOCYTES ,CANCER immunotherapy - Abstract
Predicting peptide binding affinity with human leukocyte antigen (HLA) is a crucial step in developing powerful antitumor vaccine for cancer immunotherapy. Currently available methods work quite well in predicting peptide binding affinity with HLA alleles such as HLA-A*0201, HLA-A*0101, and HLA-B*0702 in terms of sensitivity and specificity. However, quite a few types of HLA alleles that are present in the majority of human populations including HLA-A*0202, HLA-A*0203, HLA-A*6802, HLA-B*5101, HLA-B*5301, HLA-B*5401, and HLA-B*5701 still cannot be predicted with satisfactory accuracy using currently available methods. Furthermore, currently the most popularly used methods for predicting peptide binding affinity are inefficient in identifying neoantigens from a large quantity of whole genome and transcriptome sequencing data. Here we present a Position Specific Scoring Matrix (PSSM)-based software called PSSMHCpan to accurately and efficiently predict peptide binding affinity with a broad coverage of HLA class I alleles. We evaluated the performance of PSSMHCpan by analyzing 10-fold cross-validation on a training database containing 87 HLA alleles and obtained an average area under receiver operating characteristic curve (AUC) of 0.94 and accuracy (ACC) of 0.85. In an independent dataset (Peptide Database of Cancer Immunity) evaluation, PSSMHCpan is substantially better than the popularly used NetMHC-4.0, NetMHCpan-3.0, PickPocket, Nebula, and SMM with a sensitivity of 0.90, as compared to 0.74, 0.81, 0.77, 0.24, and 0.79. In addition, PSSMHCpan is more than 197 times faster than NetMHC-4.0, NetMHCpan-3.0, PickPocket, sNebula, and SMM when predicting neoantigens from 661 263 peptides from a breast tumor sample. Finally, we built a neoantigen prediction pipeline and identified 117 017 neoantigens from 467 cancer samples of various cancers from TCGA. PSSMHCpan is superior to the currently available methods in predicting peptide binding affinity with a broad coverage of HLA class I alleles. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
30. Evidence for voltage-dependent S4 movement in sodium channels
- Author
-
Richard Horn and Naibo Yang
- Subjects
Adult ,Time Factors ,Arginine ,Neuroscience(all) ,Kinetics ,Sodium Channels ,Membrane Potentials ,Extracellular ,Humans ,Point Mutation ,Cysteine ,Muscle, Skeletal ,Voltage-gated ion channel ,Chemistry ,General Neuroscience ,Sodium channel ,Electric Conductivity ,Depolarization ,Electrophysiology ,Transmembrane domain ,Biochemistry ,Biophysics ,Ion Channel Gating - Abstract
The mutation R1448C substitutes a cysteine for the outermost arginine in the fourth transmembrane segment (S4) of domain 4 in skeletal muscle sodium channels. We tested the accessibility of this cysteine residue to hydrophilic methanethiosulfonate reagents applied to the extracellular surface of cells expressing these mutant channels. The reagents irreversibly increase the rate of inactivation of R1 448C, but not wild-type, channels. Cysteine modification is voltage dependent, as if depolarization extends this residue into the extracellular space. The rate of cysteine modification increases with depolarization and has the voltage dependence and kinetics expected for the movement of a voltage sensor controlling channel gating.
- Published
- 1995
31. Probing the outer vestibule of a sodium channel voltage sensor
- Author
-
Naibo Yang, Richard Horn, and Alfred L. George
- Subjects
Alkanesulfonates ,Models, Molecular ,Stereochemistry ,Biophysics ,Protein Structure, Secondary ,Sodium Channels ,03 medical and health sciences ,0302 clinical medicine ,Extracellular ,Humans ,Muscle, Skeletal ,030304 developmental biology ,chemistry.chemical_classification ,Mesylates ,0303 health sciences ,Chemistry ,Sodium channel ,Cationic polymerization ,Depolarization ,Electric Stimulation ,Recombinant Proteins ,Electrophysiology ,Quaternary Ammonium Compounds ,Kinetics ,Membrane ,Cytoplasm ,Thiol ,Mutagenesis, Site-Directed ,Ion Channel Gating ,030217 neurology & neurosurgery ,Cysteine ,Research Article - Abstract
The second and third basic residues of the S4 segment of domain 4 (D4:R2 and D4:R3) of the human skeletal muscle Na+ channel are known to be translocated from a cytoplasmic to an extracellular position during depolarization. Accessibilities of individual S4 residues were assayed by alteration of inactivation kinetics during modification of cysteine mutants by hydrophilic methanethiosulfonate reagents. The voltage dependences of the reaction rates are identical for extracellular application of cationic methanethiosulfonate-ethyltrimethylammonium (MTSET) and anionic methanethiosulfonate-ethylsulfonate (MTSES), suggesting that D4:R3C is situated outside the membrane electric field at depolarized voltages. The absolute rate of R3C modification is 281-fold greater for MTSET than for MTSES, however, suggesting that at depolarized voltages this S4 thiol resides in a negatively charged hydrophilic crevice. The two hydrophobic residues between D4:R2C and D4:R3C in the primary sequence (L1452 and A1453) are not externally exposed at any voltage. An alpha-helical representation of D4/S4 shows that the basic residues D4:R2 and D4:R3 are on the face opposite that of L1452 and A1453. We propose that in the depolarized conformation, the hydrophobic face of this portion of D4/S4 remains in contact with a hydrophobic region of the extracellular vestibule of the S4 channel.
- Full Text
- View/download PDF
32. Additional file 2: of Comparative analysis of sequencing technologies for single-cell transcriptomics
- Author
-
Kedar Natarajan, Zhichao Miao, Miaomiao Jiang, Xiaoyun Huang, Hongpo Zhou, Jiarui Xie, Chunqing Wang, Shishang Qin, Zhikun Zhao, Wu, Liang, Naibo Yang, Li, Bo, Hou, Yong, Shiping Liu, and Teichmann, Sarah
- Subjects
3. Good health - Abstract
Supplementary methods. (PDF 608 kb)
33. Additional file 1: of Comparative analysis of sequencing technologies for single-cell transcriptomics
- Author
-
Kedar Natarajan, Zhichao Miao, Miaomiao Jiang, Xiaoyun Huang, Hongpo Zhou, Jiarui Xie, Chunqing Wang, Shishang Qin, Zhikun Zhao, Wu, Liang, Naibo Yang, Li, Bo, Hou, Yong, Shiping Liu, and Teichmann, Sarah
- Subjects
3. Good health - Abstract
Supplementary figures. (PDF 1140 kb)
34. Additional file 1: of Comparative analysis of sequencing technologies for single-cell transcriptomics
- Author
-
Kedar Natarajan, Zhichao Miao, Miaomiao Jiang, Xiaoyun Huang, Hongpo Zhou, Jiarui Xie, Chunqing Wang, Shishang Qin, Zhikun Zhao, Wu, Liang, Naibo Yang, Li, Bo, Hou, Yong, Shiping Liu, and Teichmann, Sarah
- Subjects
3. Good health - Abstract
Supplementary figures. (PDF 1140 kb)
35. Additional file 2: of Comparative analysis of sequencing technologies for single-cell transcriptomics
- Author
-
Kedar Natarajan, Zhichao Miao, Miaomiao Jiang, Xiaoyun Huang, Hongpo Zhou, Jiarui Xie, Chunqing Wang, Shishang Qin, Zhikun Zhao, Wu, Liang, Naibo Yang, Li, Bo, Hou, Yong, Shiping Liu, and Teichmann, Sarah
- Subjects
3. Good health - Abstract
Supplementary methods. (PDF 608 kb)
36. Validation of High Throughput Screening Assays Against Three Subtypes of Cav3 T-Type Channels Using Molecular and Pharmacologic Approaches.
- Author
-
Xinmin Xie, Amy L. Van Deusen, Iuliia Vitko, Daniella A. Babu, Lucinda A. Davies, Nhung Huynh, Holden Cheng, Naibo Yang, Paula Q. Barrett, and Edward Perez-Reyes
- Subjects
GENES ,BRAIN diseases ,CARDIOVASCULAR diseases ,CELL lines ,FLUORIMETRY ,DRUGS - Abstract
T-type Ca2channels encoded by voltage-gated Ca2channel (Cav) 3.1, 3.2, and 3.3 genes play important physiological roles and serve as therapeutic targets for neurological and cardiovascular disorders. Currently there is no selective T-channel blocker. To screen for such a blocker, we developed three stable cell lines expressing human recombinant Cav3.1, 3.2, or 3.3 channels and then examined their usefulness in high throughput screens. All three cell lines displayed an increase in intracellular Ca2in response to changes in extracellular Ca2as detected with Ca2-sensitive dyes using a fluorometric imaging plate reader (FLIPR®[Molecular Devices, Sunnyvale, CA] or FlexStation®[Molecular Devices]). The signal-to-noise ratio was 2–4. Co-expression of Cav3.2 with a mouse leak Kchannel, which by virtue of being open at rest hyperpolarizes the cell membrane, blocked the fluorescent signal. Co-addition of KCl to these cells induced a Ca2signal that was similar to that observed in the cell line expressing Cav3.2 alone. These results confirm that the detection of intracellular Ca2increase in cells expressing Cav3.2 alone results from Ca2entry through channels that are open at the resting membrane potential of each cell line (i.e., window currents). Testing known drugs on Cav3 channels showed that block could be reliably detected using the FlexStation assay, FLIPR assay, or voltage clamp recordings using the IonWorks®HT system (Molecular Devices). These results support the use of the FLIPR window current assay for primary drug screening and high throughput patch recordings for secondary screening of novel T-channel blockers. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
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