Article
Multidisciplinary Sciences
Xu Shi, Xiao Wang, Andrew F. Neuwald, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Summary: BayesDenovo addresses the challenge of de novo transcriptome assembly by accurately reconstructing splicing graphs using a read-guided and Bayesian strategy, achieving higher accuracy and reducing false positives, especially for alternatively spliced genes and highly/lowly expressed transcripts. Additionally, it is more robust on multiple replicates and can identify phenotype-specific transcripts associated with breast cancer recurrence.
SCIENTIFIC REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
Mengli Cao, Xingdong Wang, Shaoke Guo, Yandong Kang, Jie Pei, Xian Guo
Summary: This study analyzed the differences in testicular tissue development between yak and cattle-yak, and identified the genes related to spermatogenesis and apoptosis that are differentially expressed in cattle-yak. The findings provide a theoretical explanation for the sterility in F1 male cattle-yak and offer insights for improving yak hybridization.
Article
Agriculture, Dairy & Animal Science
Ruobing Han, Lei Han, Yanling Xia, Mengya Guo, Heping Li
Summary: This study identified differentially expressed lncRNAs in male sika deer antler during three growth periods, revealing potential roles of lncRNAs in cell proliferation and differentiation. Co-expression networks were constructed based on the identified lncRNAs and their trans-target genes, showing diverse functions of lncRNAs in antler growth. This provides a novel perspective for understanding the molecular mechanism of antler growth.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
August Guang, Mark Howison, Felipe Zapata, Charles Lawrence, Casey W. Dunn
Summary: treeinform is a method that utilizes phylogenetic information across species to improve transcriptome assemblies within species. It helps identify and correct the error of mistaking different transcripts of the same gene as transcripts from multiple closely related genes.
Article
Biochemical Research Methods
Qianqian Zhang, Xing Xu, Li Lin, Jian Yang, Xing Na, Xin Chen, Lingling Wu, Jia Song, Chaoyong Yang
Summary: Cilo-seq is a high-performance platform for single-cell RNA sequencing library construction. It utilizes digital microfluidics in a single device, enabling convenient single-cell isolation, efficient nucleic acid amplification, low-loss nucleic acid purification, and high-quality library preparation.
Article
Multidisciplinary Sciences
Chaoqiong Ding, Xiang Yan, Mengying Xu, Ran Zhou, Yuancun Zhao, Dan Zhang, Zongyao Huang, Zhenzhong Pan, Peng Xiao, Huifang Li, Lu Chen, Yuan Wang
Summary: This study reports the full-length transcriptome of mouse neural stem cells (NSCs) at different developmental stages, providing an important resource for studying NSC fate determination, neural development, and disease in the neuroscience community.
Article
Biotechnology & Applied Microbiology
Shiyong Yang, Datian Li, Langkun Feng, Chaoyang Zhang, Dandan Xi, Hongli Liu, Chaozhan Yan, Zihan Xu, Yujie Zhang, Yunkun Li, Taiming Yan, Zhi He, Jiayun Wu, Quan Gong, Jun Du, Xiaoli Huang, Xiaogang Du
Summary: In this study, the histopathological changes, plasma ion levels, and transcriptome of gill tissue in Siberian sturgeon subjected to different temperatures were analyzed. The results showed that heat stress increased the levels of reactive oxygen species (ROS) and damage in the gill tissue. Transcriptome analysis revealed various genes related to osmoregulation, DNA repair, and apoptosis. This study provides insight into the effects of heat stress on gill tissue damage and osmoregulation in cold-water fishes.
Article
Biotechnology & Applied Microbiology
Lars E. Borm, Alejandro Mossi Albiach, Camiel C. A. Mannens, Jokubas Janusauskas, Ceren Ozgun, David Fernandez-Garcia, Rebecca Hodge, Francisca Castillo, Charlotte R. H. Hedin, Eduardo J. Villablanca, Per Uhlen, Ed S. Lein, Simone Codeluppi, Sten Linnarsson
Summary: EEL FISH is a method that allows for rapid processing of large tissue samples while maintaining high resolution. By electrophoretically transferring RNA, EEL speeds up data acquisition and preserves single-cell resolution, enabling the study of spatial transcriptomes in the mouse brain and the human visual cortex.
NATURE BIOTECHNOLOGY
(2023)
Article
Cell Biology
Di Wu
Summary: The germinal vesicle (GV) stage is a critical transition point in mammalian oocyte development that determines oocyte quality through active RNA degradation and transcriptome reprofiling. Oocyte RNA-seq has revealed differences between non-surrounded nucleolus (NSN) and surrounded nucleolus (SN) phases. Single oocyte RNA-seq (soRNA-seq) shows higher reproducibility and a better illustration of gene changes during oocyte development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Olga Amelkina, Andreia M. da Silva, Alexandre R. Silva, Pierre Comizzoli
Summary: The study revealed significant differences in transcriptome dynamics and responses to cryopreservation between juvenile and adult testicular tissues in domestic cats. Early juvenile tissues showed the least response to vitrification, while late juvenile tissues responded most similarly to adult tissues.
Article
Fisheries
Tong Wang, Xi Wu, Leling Song, Yang Yang, Shirui Gong, Leilei Zeng, Yuhao Tao, Chaoyue Zhong, Zining Meng, Xiaochun Liu
Summary: Leopard coral grouper, known for its beautiful color and high economic value, has been less studied for its growth traits. In this study, GWAS and RNA-seq were used to analyze the growth traits of 307 leopard coral groupers, resulting in the identification of significant and suggestive SNPs associated with growth traits. RNA-seq analysis of high- and low-weight groups revealed differentially expressed genes related to fatty acid metabolism and amino acid metabolism. Per2 and acadvl genes were found to play important roles in locomotor activity and metabolism. These findings provide a theoretical basis for molecular assisted breeding of leopard coral grouper.
Article
Biochemistry & Molecular Biology
Yu Wang, Qing Huan, Ke Li, Wenfeng Qian
Summary: This study used single-cell RNA sequencing to analyze the transcriptome features of rice seedlings' leaves and roots, revealing different cell types and cell type-specific transcriptional regulation in response to environmental stresses. Additionally, the research identified changes in cell populations in response to stress and investigated the underlying molecular mechanisms through single-cell reconstruction of the developmental trajectory.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Parasitology
Orawan Phuphisut, Akkarin Poodeepiyasawat, Tippayarat Yoonuan, Dorn Watthanakulpanich, Palang Chotsiri, Onrapak Reamtong, Angela Mousley, Geoffrey N. N. Gobert, Poom Adisakwattana
Summary: This study provides comprehensive transcriptome profiles of discrete reproductive tissue samples in Ascaris lumbricoides, revealing the molecular basis of these important tissues. The findings suggest that genes involved in protein phosphorylation, adhesion molecules, G-protein-coupled receptor signaling pathway, SMA genes, and TGF-beta signaling pathway play crucial roles in the reproductive processes of Ascaris. The enriched KEGG pathway analysis identifies Hippo signaling, oxytocin signaling, and tight junction pathways as important players in the male and female reproductive systems of Ascaris.
PARASITES & VECTORS
(2022)
Article
Biotechnology & Applied Microbiology
Muchun Niu, Wenjian Cao, Yongcheng Wang, Qiangyuan Zhu, Jiayi Luo, Baiping Wang, Hui Zheng, David A. Weitz, Chenghang Zong
Summary: The profiling of individual synapses reveals molecular heterogeneity, which is crucial for signal transmission and shows considerable morphological and electrophysiological heterogeneity. However, there is currently a lack of high-throughput methods to analyze the molecular heterogeneity among individual synapses.
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Rongfa Chen, Yegeng Fan, Huiwen Zhou, Shanping Mo, Zhongfeng Zhou, Haifeng Yan, Ting Luo, Xing Huang, Mengling Weng, Prakash Lakshmanan, Yangrui Li, Lihang Qiu, Jianming Wu
Summary: By obtaining high-quality long transcripts from sugarcane using the PacBio Sequel System, it was found that the inhibitory effects of DPC on plant growth may involve pathways related to plant hormone signal transduction and biosynthesis of several metabolites.
Article
Respiratory System
Zhihao Yang, Guodong Du, Lei Ma, Yunhui Lv, Yang Zhao, Tung On Yau
Summary: The study included 206 ED patients with OSA from seven publications, and the results showed that ED patients receiving CPAP treatment significantly improved their IIEF-5 scores. However, high heterogeneity was mainly due to Zhang's data, who had a higher AHI compared to other studies. A moderate heterogeneity was found after excluding Zhang's data.
CLINICAL RESPIRATORY JOURNAL
(2021)
Article
Gastroenterology & Hepatology
Tanya M. Monaghan, Anna M. Seekatz, Nicholas O. Markham, Tung On Yau, Maria Hatziapostolou, Tahseen Jilani, Niki Christodoulou, Brandi Roach, Eleni Birli, Odette Pomenya, Thomas Louie, D. Borden Lacy, Peter Kim, Christine Lee, Dina Kao, Christos Polytarchou
Summary: The study found that FMT for rCDI can lead to changes in miRs, which affect inflammatory genes and cellular protective effects, revealing potential therapeutic targets.
Review
Biochemistry & Molecular Biology
Marco Bocchetti, Maria Grazia Ferraro, Filippo Ricciardiello, Alessandro Ottaiano, Amalia Luce, Alessia Maria Cossu, Marianna Scrima, Wing-Yan Leung, Marianna Abate, Paola Stiuso, Michele Caraglia, Silvia Zappavigna, Tung On Yau
Summary: This review summarizes the major dysregulated miRNAs in CAC and their potential applications in early diagnosis, therapy prediction, and precision treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Xin Li, Jia Chang, Shunmei Chen, Liangge Wang, Tung On Yau, Qiang Zhao, Zhangyong Hong, Jishou Ruan, Guangyou Duan, Shan Gao
Summary: The study identified the recombinant strain RmYN02 across the SARS1 and SARS2 classes within the betacoronavirus subgroup B, which has potential to generate a new strain with similar risk as SARS-CoV and SARS-CoV-2. Recombination, receptor binding abilities, junction furin cleavage sites, among other factors, contribute to the transmission, virulence, and host adaptability of betacoronavirus. The strong recombination ability of coronaviruses integrated with other factors resulted in the emergence of SARS-CoV and SARS-CoV-2, leading to the SARS and COVID-19 pandemics.
FRONTIERS IN MICROBIOLOGY
(2021)
Letter
Cell Biology
Jinghui Lei, Xiaoyu Jiang, Wei Li, Jie Ren, Datao Wang, Zhejun Ji, Zeming Wu, Fang Cheng, Yusheng Cai, Zheng-Rong Yu, Juan Carlos Izpisua Belmonte, Chunyi Li, Guang-Hui Liu, Weiqi Zhang, Jing Qu, Si Wang
Article
Microbiology
Tanya M. Monaghan, Rima N. Biswas, Rupam R. Nashine, Samidha S. Joshi, Benjamin H. Mullish, Anna M. Seekatz, Jesus Miguens Blanco, Julie A. K. McDonald, Julian R. Marchesi, Tung On Yau, Niki Christodoulou, Maria Hatziapostolou, Maja Pucic-Bakovic, Frano Vuckovic, Filip Klicek, Gordan Lauc, Ning Xue, Tania Dottorini, Shrikant Ambalkar, Ashish Satav, Christos Polytarchou, Animesh Acharjee, Rajpal Singh Kashyap
Summary: Non-communicable diseases have become a major cause of morbidity and mortality in India, particularly among susceptible Asian Indians. This study identified multiple dysmetabolic traits in urbanites and young overweight adults, highlighting the complex interactions between host-microbiome and metabolic factors in predicting risk of metabolic disorders like diabetes. Further exploration of these links may help in designing early interventions to manage and prevent NCDs.
Article
Gastroenterology & Hepatology
Tung On Yau, Jayakumar Vadakekolathu, Gemma Ann Foulds, Guodong Du, Benjamin Dickins, Christos Polytarchou, Sergio Rutella
Summary: This study collected transcriptomic data from inflammatory bowel disease patients receiving anti-TNF-alpha therapy and found that hyperactive neutrophil chemotaxis influenced the response to anti-TNF-alpha treatment. IL13RA2 was identified as a potential biomarker to predict the response to anti-TNF-alpha treatment.
JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY
(2022)
Article
Microbiology
Jia Chang, Jinlong Bei, Qi Shao, Hemu Wang, Huan Fan, Tung On Yau, Wenjun Bu, Jishou Ruan, Dongsheng Wei, Shan Gao
Summary: The present study successfully assembled the full-length genome of O. polymorpha HU-11/CBS4732 using high-depth PacBio and Illumina data, and determined important genomic differences between HU-11/CBS4732 and NCYC495. The relationship between CBS4732, NCYC495, and DL-1 has been preliminarily revealed, and the findings provide new opportunities for understanding genome evolution in methylotrophic yeasts and for industrial applications of O. polymorpha strains.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Cell Biology
Guangcai Liang, Dong Mi, Jia Chang, Tung On Yau, Guofeng Xu, Jishou Ruan, Wenjun Bu, Shan Gao
Summary: In this study, we annotated the mitochondrial genomes of Drosophila melanogaster, D. simulans, D. grimshawi, and Bactrocera oleae using pan RNA-seq analysis. We identified conserved polyA(+) and polyA(-) motifs associated with Transcription Initiation Sites (TISs) in the control region (CRs) of the mt genomes. Our findings provide insights into the regulation of mt transcription in invertebrates and suggest the existence of multiple TISs and TTSs in invertebrate mt genomes.
Article
Cell & Tissue Engineering
Hengxing Ba, Xin Wang, Datao Wang, Jing Ren, Zhen Wang, Hai-Xi Sun, Pengfei Hu, Guokun Zhang, Shengnan Wang, Chao Ma, Yusu Wang, Enpeng Wang, Liang Chen, Tianbin Liu, Ying Gu, Chunyi Li
Summary: This study used single-cell RNA sequencing to identify the cell types and composition of deer antler tissues, revealing the differences between antler generation and regeneration, and discovering the role of the androgen-RXFP2 axis in full antler regeneration.
Editorial Material
Multidisciplinary Sciences
Datao Wang, Tomas Landete-Castillejos
Review
Gastroenterology & Hepatology
Marco Bocchetti, Maria Grazia Ferraro, Federica Melisi, Piera Grisolia, Marianna Scrima, Alessia Maria Cossu, Tung On Yau
Summary: Clostridioides difficile infection is listed as an urgent threat due to antibiotic resistance and early detection and appropriate management are crucial. Community-acquired cases are increasing and not limited to immunocompromised patients. Stool-based non-invasive screening is the first-line approach, but improving reliability is necessary.
WORLD JOURNAL OF GASTROENTEROLOGY
(2023)
Article
Microbiology
Jia Chang, Guangyou Duan, Wenjing Li, Tung On Yau, Chang Liu, Jianlin Cui, Huaijun Xue, Wenjun Bu, Yanping Hu, Shan Gao
Summary: In this study, two intact Tc1 transposons were discovered in yeast and filamentous fungi, named Tc1-OP1 and Tc1-MP1, respectively. Tc1-OP1 is the first reported Tc1 transposon in yeast and a nonclassical one with significant differences from others. Tc1-OP1, Tc1-MP1, and IS630-AB1 can be used as reference sequences for the identification of IS630/Tc1/mariner transposons.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Agriculture, Multidisciplinary
Matthew J. Ryan, Tim H. Mauchline, Jacob G. Malone, Susan Jones, Catriona M. A. Thompson, J. Miguel Bonnin, Helen Stewart, Payton T. O. Yau, Rodrigo G. Taketani, Ian M. Clark, Nicola Holden
Summary: Plant microbiomes are crucial for the functioning of plant communities and play a vital role in crop health and food quality. Unfortunately, there is limited research on crop microbiomes, and there is a need for infrastructure to support further research and solutions. The UK Crop Microbiome Cryobank project is addressing this need by developing a comprehensive resource to improve soil and crop health.
CABI AGRICULTURE & BIOSCIENCE
(2023)
Article
Medicine, Research & Experimental
Sergio Rutella, Jayakumar Vadakekolathu, Francesco Mazziotta, Stephen Reeder, Tung -On Yau, Rupkatha Mukhopadhyay, Benjamin Dickins, Heidi Altmann, Michael Kramer, Hanna A. Knaus, Bruce R. Blazar, Vedran Radojcic, Joshua F. Zeidner, Andrea Arruda, Bofei Wang, Hussein A. Abbas, Mark D. Minden, Sarah K. Tasian, Martin Bornhaeuser, Ivana Gojo, Leo Luznik
Summary: This study demonstrates the promoting effect of acute myeloid leukemia (AML) on the generation of senescent-like CD8+ T cells and their negative correlation with overall survival (OS) of patients. The researchers defined new immune effector dysfunction (IED) signatures that were associated with adverse molecular lesions, stemness, and poor outcomes, and found that IED scores were a more accurate predictor of OS than existing risk stratification systems. The IED expression signatures also identified an unresponsive tumor microenvironment and predicted shorter OS. These findings can contribute to improved risk stratification and personalized immunotherapies for AML patients.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
