Article
Multidisciplinary Sciences
Zih-Ting Chang, Yu-Feng Huang, Yue-Wen Chen, Ming-Ren Yen, Po-Ya Hsu, Tzu-Han Chen, Yi-Hsuan Li, Kuo-Ping Chiu, Yu-Shin Nai
Summary: Deformed wing virus (DWV) has a high prevalence in honey bee populations, infecting bees through vertical and horizontal transmission. Infection with DWV in artificially reared honey bee larvae did not cause significant mortality, but survival rates decreased at the pupal stage. Transcriptomic analysis revealed differentially expressed genes (DEGs) related to metabolic pathways and stress responses, indicating potential impacts on gene expression levels from larval to pupal stages.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Peng Liu, Jessica Ewald, Zhiqiang Pang, Elena Legrand, Yeon Seon Jeon, Jonathan Sangiovanni, Orcun Hacariz, Guangyan Zhou, Jessica A. Head, Niladri Basu, Jianguo Xia
Summary: ExpressAnalyst is a web-based platform that efficiently processes and analyzes RNA-sequencing data from any eukaryotic species, providing statistical and functional analysis. It includes modules for processing and annotating FASTQ files, as well as analyzing count tables or gene lists. By integrating ultra-fast read mapping algorithms with high-resolution ortholog databases, ExpressAnalyst enables researchers to obtain global expression profiles and gene-level insights within 24 h.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Nikita R. Raje, Janelle R. Noel-MacDonnell, Katherine A. Shortt, Nicole M. Gigliotti, Marcia A. Chan, Daniel P. Heruth
Summary: The phenotypic variations of chromosome 22q11.2 deletion syndrome (22qDS) are not well explained. This study investigated gene expression in T cells of individuals with and without 22qDS, and found differentially expressed genes associated with T cell counts and markers. This suggests an important role of T cells in defective communication in 22qDS.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Alex J. La Reau, Noah B. Strom, Ellen Filvaroff, Konstantinos Mavrommatis, Tonya L. Ward, Dan Knights
Summary: The microbiome plays a role in human diseases, but identifying key microbes and their functions requires large studies. 16S sequencing is commonly used for large studies, but has poor resolution. Shallow shotgun sequencing provides a more specific and reproducible alternative to 16S sequencing for large-scale microbiome studies, at a lower cost than deep shotgun sequencing.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Xiaoxi Dong, Kovidh Vegesna, Cory Brouwer, Weijun Luo
Summary: SBGNview is a comprehensive R package that addresses the limitations in pathway analysis and data visualization by adopting the standard SBGN format. It greatly extends pathway coverage and data format, and provides essential infrastructure for manipulating and processing SBGN data.
Article
Horticulture
Xiaonan Dai, Qingyu Li, Fudong Jiang, Zhizhong Song, Xiaoli Tang, Shuqi Su, Ruotong Yao, Haiying Yang, Yanqing Yang, Hongxia Zhang, Jianzhao Li
Summary: This study clarified the mechanism of anthocyanin accumulation in "Red Bartlett" pear through transcriptome analysis, and identified the genes and transcription factors associated with anthocyanin biosynthesis and regulation.
SCIENTIA HORTICULTURAE
(2022)
Article
Environmental Sciences
Jing Guo, Xiuli Song, Caiyue Zheng, Shiqi Sun, Baolong Zhuang, Bo Tao
Summary: In this study, RNA-seq was used to investigate gene expression in a Fusarium verticillioides isolate resistant to glyphosate. Analyzing the transcriptome revealed differentially expressed genes in response to glyphosate treatment, leading to the identification of candidate genes. These findings offer new insights for acquiring glyphosate resistance resources.
JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART B-PESTICIDES FOOD CONTAMINANTS AND AGRICULTURAL WASTES
(2021)
Article
Allergy
Lena Moebus, Elke Rodriguez, Inken Harder, Nicole Boraczynski, Silke Szymczak, Matthias Huebenthal, Dora Stoelzl, Sascha Gerdes, Andreas Kleinheinz, Susanne Abraham, Annice Heratizadeh, Christiane Handrick, Eva Haufe, Thomas Werfel, Jochen Schmitt, Stephan Weidinger
Summary: This study explored the blood transcriptomic features of moderate to severe atopic dermatitis (AD). The results showed that AD patients exhibited pronounced inflammatory expression signatures and could be stratified into eosinophilic and noneosinophilic endotypes. Additionally, treatment strategies for the eosinophil-high endotype may require more attention to the restoration of natural killer cell function.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Plant Sciences
Jagesh Kumar Tiwari, Tanuja Buckseth, Rajesh Kumar Singh, Rasna Zinta, Aastha Saraswati, Manoj Kumar, Swarup Kumar Chakrabarti
Summary: By investigating DNA methylation and transcriptome profiling in potato, our study identified several candidate genes associated with tuber shape variation, including those involved in phytohormone regulation, sugar metabolism, transcription factors, stress responses, and cell wall modification. These candidate genes are suggested to play key roles in shaping potato tubers.
PLANT GROWTH REGULATION
(2021)
Article
Biotechnology & Applied Microbiology
Eslam M. Abdel-Salam, Mohammad Faisal, Abdulrahman A. Alatar, Ahmed A. Qahtan, Perwez Alam
Summary: The study on fringed rue (Ruta chalepensis L.) focused on changes in transcriptomic landscape across leaf, stem, and root tissues to identify genes responsible for rutin biosynthesis. Using comparative transcriptome sequencing, it was found that leaf tissues had the highest rutin content, with up-regulated genes related to rutin biosynthesis compared to roots. This dataset will serve as a valuable public resource for future genomics and transcriptomic studies in R. chalepensis.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Oncology
Alessandra Trojani, Barbara Di Camillo, Luca Emanuele Bossi, Livia Leuzzi, Antonino Greco, Alessandra Tedeschi, Anna Maria Frustaci, Marina Deodato, Giulia Zamprogna, Alessandro Beghini, Roberto Cairoli
Summary: Research found that there are significantly differentially expressed genes in the B cells of WM patients compared to IgM MGUS and controls, suggesting their potential involvement in WM development. Additionally, a small set of genes showed similar expression levels in WM and IgM MGUS, possibly affecting the transformation of IgM MGUS to WM.
Article
Plant Sciences
Mengyun Liu, Li Yang, Miaomiao Cai, Chong Feng, Zhimin Zhao, Depo Yang, Ping Ding
Summary: Transcriptomic analysis was used to investigate the differences in expression genes of oligosaccharides biosynthesis in Morinda officinalis, revealing that several key gene families were closely linked to oligosaccharides biosynthesis.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Horticulture
Yang Li, Youjian Yu, Liai Xu, Erbiao Guo, Yunxiang Zang, Yong He, Zhujun Zhu
Summary: This study identified a total of 184 GSL biosynthetic genes in Brassica nigra, with some key genes showing high expression contributing to sinigrin synthesis, while low expression of certain genes explaining the low content of indolic and aromatic GSLs in B. nigra. The findings provide genetic insights into the unique GSL profile in B. nigra and offer potential for functional analysis and genetic improvement of GSLs in Brassica species.
Article
Biochemistry & Molecular Biology
Wenyu Li, Yi Cao, Zhen Liu, Shouhui Wei, Hongjuan Huang, Yuning Lan, Ying Sun, Zhaofeng Huang
Summary: Redroot amaranth is a noxious weed affecting soybean production in China. Two populations of this weed showed resistance to bentazone, and the resistance was found to be associated with increased expression of the psbA gene and enhanced herbicide metabolism.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Hengame Abbasi Mesrabadi, Karim Faez, Jamshid Pirgazi
Summary: This paper proposes a new computational model for drug-target interaction (DTI) prediction, which consists of three phases: feature extraction, feature selection, and classification. Different features are extracted from protein sequences and drugs, and then combined. The selected features are input to the rotation forest classifier for more efficient prediction. Experimental results show that the proposed model has an acceptable accuracy in DTI prediction and is compatible with methods proposed in other papers.
SCIENTIFIC REPORTS
(2023)