Article
Food Science & Technology
Wenrui Ma, Xiaojie Geng, Fuchen Jia, Xiaomeng Zhang, Yuhong Zhang, Jie Xue
Summary: The microbial composition and function of Zangqu, a saccharifying starter used in the production of highland barley wine, were studied using high throughput sequencing technology. The analysis revealed predominant presence of four fungal and six bacterial phyla in Zangqu samples. Rhizopus oryzae M12 had the highest saccharifying ability, while Bacillus amyloliquefaciens Q4 had the highest protease activity among the isolated strains. This research aims to support the establishment of a microbial database and screening of functional microorganisms for Zangqu production.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Immunology
Lauren M. Walker, Andrea R. Shiakolas, Rohit Venkat, Zhaojing Ariel Liu, Steven Wall, Nagarajan Raju, Kelsey A. Pilewski, Ian Setliff, Amyn A. Murji, Rebecca Gillespie, Nigel A. Makoah, Masaru Kanekiyo, Mark Connors, Lynn Morris, Ivelin S. Georgiev
Summary: The development of novel technologies for discovering human monoclonal antibodies has been extremely valuable in combating infectious diseases. LIBRA-seq with epitope mapping is a next-generation sequencing technology that can determine residue-level epitopes for thousands of single B cells simultaneously, making it an efficient tool for high-throughput identification of antibodies against specific antigen epitopes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Aziz M. Al'Khafaji, Jonathan T. Smith, Kiran V. Garimella, Mehrtash Babadi, Victoria Popic, Moshe Sade-Feldman, Michael Gatzen, Siranush Sarkizova, Marc A. Schwartz, Emily M. Blaum, Allyson Day, Maura Costello, Tera Bowers, Stacey Gabriel, Eric Banks, Anthony A. Philippakis, Genevieve M. Boland, Paul C. Blainey, Nir Hacohen
Summary: Full-length RNA-sequencing methods using long-read technologies are limited in throughput. We introduce MAS-ISO-seq, a technique that programmably concatenates cDNAs for long-read sequencing, increasing throughput by >15-fold to nearly 40 million cDNA reads per run. Applied to single-cell RNA sequencing of tumor-infiltrating T cells, MAS-ISO-seq showed a 12- to 32-fold increase in the discovery of differentially spliced genes.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Joao Gervasio, Alice Ferreira, Liza F. Felicori
Summary: Researchers have developed YClon, a fast and efficient method for clonotyping immunoglobulin repertoire data. This method outperforms others in terms of sensitivity and specificity, and can handle large sequencing datasets much faster.
JOURNAL OF IMMUNOLOGICAL METHODS
(2023)
Article
Biochemistry & Molecular Biology
Yan Zhu, Xiujia Yang, Cuiyu Ma, Haipei Tang, Qilong Wang, Junjie Guan, Wenxi Xie, Sen Chen, Yuan Chen, Minhui Wang, Chunhong Lan, Deqiang Sun, Lai Wei, Caijun Sun, Xueqing Yu, Zhenhai Zhang
Summary: The study revealed that the diversity of AUS sequences affects antibody engineering and PCR quantification, with leader sequences being more conserved than 50 UTR and potentially coevolving with downstream V genes. Single-nucleotide polymorphisms in leader regions are position dependent and may impact the functional reversal of downstream V genes.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Biochemical Research Methods
Chun-Miao Ji, Xiao-Feng Yang, Pan Qin, Bin Wang, Yao-Wei Huang
Summary: High-throughput sequencing was used to study the antibody repertoire in pigs, revealing that specific V gene segments were preferentially used under normal conditions, while PEDV-infected pigs showed different patterns of IGHV usage.
JOURNAL OF VIROLOGICAL METHODS
(2021)
Article
Biochemistry & Molecular Biology
Hao Xiong, Liyan Ji, Jin Yang, Jianji Wan, Mengmeng Song, Guangren Liu, Ling Yang, Xiuqin Dong
Summary: This study assessed the TCRβ repertoire diversity and composition of CD8+ T cells in blood of 9 nonsegmental vitiligo patients via high-throughput sequencing. Vitiligo patients showed low TCRβ diversity with highly expanded clones. Differential usage of TRBV, the TRBJ gene, and the TRBV/TRBJ combination were observed between vitiligo patients and healthy controls. A set of TRBV/TRBJ combinations could differentiate vitiligo patients from healthy controls. This study revealed distinct TCRβ repertoires of CD8+ T cells in vitiligo and may contribute to the exploration of immune biomarkers and therapeutic targets.
MOLECULAR IMMUNOLOGY
(2023)
Review
Microbiology
Amy H. Fitzpatrick, Agnieszka Rupnik, Helen O'Shea, Fiona Crispie, Sinead Keaveney, Paul Cotter
Summary: This review assesses and recommends approaches for targeted and agnostic High Throughput Sequencing of RNA viruses, highlighting the challenges and biases that method choice can impart to sequencing results. Methodology choices from RNA extraction to library preparation have a significant impact on the detection or characterization of RNA viruses.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Medicine, General & Internal
Roberta Amoriello, Maria Chernigovskaya, Victor Greiff, Alberto Carnasciali, Luca Massacesi, Alessandro Barilaro, Anna M. Repice, Tiziana Biagioli, Alessandra Aldinucci, Paolo A. Muraro, David A. Laplaud, Andreas Lossius, Clara Ballerini
Summary: CSF repertoires in MS patients show a significantly higher percentage of public clones and sequence similarity compared to peripheral blood, but the repertoire polarization between CSF and PB is not significantly different. One PPMS CSF repertoire differs in TCR similarity architecture. Cluster analysis distinguishes MS from HD.
Article
Biotechnology & Applied Microbiology
Tongtong Zhang, Qian Li, Xiaoqing Li, Li Kang, Yunliang Jiang, Yi Sun
Summary: This study provides the first comprehensive characterization of the TCR gamma repertoire in chicken thymus, revealing similar features among the four chickens analyzed. Specific V gamma segments and V gamma-J gamma pairs were preferentially utilized by all individuals, and the CDR3 gamma sequences encoded a wider length distribution with a longer mean length compared to human, mice, and other animal species.
Article
Immunology
Guangyu Wang, Weiguo Sui, Wen Xue, Junning Zhang, Xueli Yang, Chune Mo, Xiaoping Pan, Minglin Ou, Xianliang Hou
Summary: This study investigates the dynamic changes in the BCR-H (TCR-beta) CDR3 repertoire of kidney transplant patients. Specific gene subfamilies and sequence combinations were identified at different time points during the transplantation process.
CLINICAL IMMUNOLOGY
(2022)
Article
Plant Sciences
Malyaj R. Prajapati, Aakansha Manav, Jitender Singh, Pankaj Kumar, Amit Kumar, Ravindra Kumar, Satya Prakash, Virendra Kumar Baranwal
Summary: A study identified a virus named GarV-E in garlic plants in India, and conducted research on it using high-throughput sequencing. Sequence analysis showed a close relationship of this Indian isolate with GarV-E isolates from China. This study is the first report of GarV-E in Indian garlic.
Article
Forestry
Zhiquan Wang, Fengjiao Zhang, Qin Shi, Rui Zhang, Yunlong Yin, Chaoguang Yu
Summary: This study aimed to discover the miRNAs responding to salt stress. Small RNA sequencing was performed in the salt-tolerant Taxodium hybrid 'Zhongshanshan 405' and 52 differentially expressed miRNAs were found. Enrichment analysis of target genes showed that miRNAs may play key roles in regulating the tolerance to salt stress in 'Zhongshanshan 405'. The study also identified two important genes regulated by miRNAs under salt treatment, which can be selected for future research.
Article
Biochemistry & Molecular Biology
Kadri Runnel, Kessy Abarenkov, Ovidiu Copot, Vladimir Mikryukov, Urmas Koljalg, Irja Saar, Leho Tedersoo
Summary: This study assessed the efficiency of long-read high throughput sequencing (HTS) for taxonomic identification of fungal specimens and found that PacBio HTS had a higher success rate and lower cost compared to Sanger sequencing. It also enabled the detection of gene polymorphism within the specimens, providing crucial information for species delimitation and population-level studies.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Chemistry, Analytical
Shifeng Yu, Yongjia Wu, Shuyu Wang, Michael Siedler, Peter M. Ihnat, Dana Filoti, Ming Lu, Lei Zuo
Summary: This paper presents a novel MEMS-based differential scanning calorimeter (DSC) for direct thermal characterization of protein samples. The DSC exhibited high sensitivity, low noise, high scanning rate, and low sample consumption volume. The study demonstrated that the MEMS DSC is an effective tool for directly understanding the thermal stability of antibodies in a high-throughput and low-cost manner compared to conventional calorimeters.
Article
Biochemistry & Molecular Biology
Xiao W. Mao, Stephanie Byrum, Nina C. Nishiyama, Michael J. Pecaut, Vijayalakshmi Sridharan, Marjan Boerma, Alan J. Tackett, Dai Shiba, Masaki Shirakawa, Satoru Takahashi, Michael D. Delp
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2018)
Article
Biochemistry & Molecular Biology
Xiao Wen Mao, Lawrence B. Sandberg, Daila S. Gridley, E. Clifford Herrmann, Guangyu Zhang, Ravi Raghavan, Roman A. Zubarev, Bo Zhang, Louis S. Stodieck, Virginia L. Ferguson, Ted A. Bateman, Michael J. Pecaut
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Multidisciplinary Sciences
Trisha A. Rettig, Bailey A. Bye, Nina C. Nishiyama, Savannah Hlavacek, Claire Ward, Michael J. Pecaut, Stephen K. Chapes
Article
Multidisciplinary Sciences
Xiao W. Mao, Nina C. Nishiyama, Stephanie D. Byrum, Seta Stanbouly, Tamako Jones, Alyson Drew, Vijayalakshmi Sridharan, Marjan Boerma, Alan J. Tackett, David Zawieja, Jeffrey S. Willey, Michael Delp, Michael J. Pecaut
SCIENTIFIC REPORTS
(2019)
Article
Astronomy & Astrophysics
Trisha A. Rettig, Nina C. Nishiyama, Michael J. Pecaut, Stephen K. Chapes
LIFE SCIENCES IN SPACE RESEARCH
(2019)
Article
Multidisciplinary Sciences
Eliah G. Overbey, Willian Abraham da Silveira, Seta Stanbouly, Nina C. Nishiyama, Gina D. Roque-Torres, Michael J. Pecaut, David Carl Zawieja, Charles Wang, Jeffrey S. Willey, Michael D. Delp, Gary Hardiman, Xiao Wen Mao
SCIENTIFIC REPORTS
(2019)
Article
Biochemistry & Molecular Biology
Xiao W. Mao, Nina C. Nishiyama, Stephanie D. Byrum, Seta Stanbouly, Tamako Jones, Jacob Holley, Vijayalakshmi Sridharan, Marjan Boerma, Alan J. Tackett, Jeffrey S. Willey, Michael J. Pecaut, Michael D. Delp
Review
Developmental Biology
Foluwasomi A. Oyefeso, Alysson R. Muotri, Christopher G. Wilson, Michael J. Pecaut
Summary: Oxidative stress is a significant contributor to systemic damage, with implications for various diseases, and can be induced by multiple factors. Studies have shown that oxidative stress contributes to neurodegeneration, and brain organoids have emerged as a promising model to study central nervous system diseases.
DEVELOPMENTAL NEUROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Amber M. Paul, Eliah G. Overbey, Willian A. da Silveira, Nathaniel Szewczyk, Nina C. Nishiyama, Michael J. Pecaut, Sulekha Anand, Jonathan M. Galazka, Xiao Wen Mao
Summary: The study used a ground-based model to simulate spaceflight conditions and found negligible differences in immune differentials but large disparities in red blood cell differentials post-exposure. Analysis of spleen cells revealed expression profiles associated with inflammation and dysregulated immune function persisting to 1-week post-simulated spaceflight. Additionally, specific regulation pathways associated with human blood disease gene orthologs were noted.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Jacob M. Holley, Seta Stanbouly, Michael J. Pecaut, Jeffrey S. Willey, Michael Delp, Xiao Wen Mao
Summary: This study aimed to characterize changes in gene expression profiles associated with neuroinflammation, neuronal function, metabolism, and stress in mouse brain tissue after spaceflight. Results showed that many pathways related to cellular stress, inflammation, apoptosis, and metabolism were significantly altered by the flight conditions. Additionally, the mRNA expression of genes involved in anti-viral signaling, reactive oxygen species generation, and bacterial immune response were significantly downregulated. These findings suggest that altered immune reactions may be closely associated with spaceflight-induced stress responses and can affect neuronal function.
Article
Biochemistry & Molecular Biology
Alicia L. Veliz, Lana Mamoun, Lorelei Hughes, Richard Vega, Bailey Holmes, Andrea Monteon, Jillian Bray, Michael J. Pecaut, Mary Kearns-Jonker
Summary: This study focuses on the transcriptomic changes in the hearts of female C57BL/6J mice flown on the International Space Station (ISS) for 30 days. RNA sequencing revealed that 1147 transcripts were significantly regulated after spaceflight, and the MAPK, PI3K-Akt, and GPCR signaling pathways were predicted to be activated. Transcripts related to cytoskeleton breakdown and organization were upregulated, but no significant change in the expression of extracellular matrix (ECM) components or oxidative stress pathway-associated transcripts occurred. Our findings suggest an absence of cellular senescence and an adaptive response to long-term spaceflight in the cardiovascular transcriptome.
Meeting Abstract
Immunology
Trisha A. Rettig, Nina C. Nishiyama, Michael J. Pecaut, Stephen K. Chapes
JOURNAL OF IMMUNOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Trisha A. Rettig, Michael J. Pecaut, Stephen K. Chapes