Article
Plant Sciences
Kaitong Wang, Ning Zhang, Xue Fu, Huanhuan Zhang, Shengyan Liu, Xue Pu, Xiao Wang, Huaijun Si
Summary: The study found that the TCP transcription factor StTCP15 regulates the dormancy and sprouting of potato tubers by affecting the balance between ABA and GA(3). Through cloning and regulating expression at the transcription level, it was found that StTCP15 overexpression promotes early sprouting of tubers, while down-regulation delays sprouting. In addition, the study also found that StTCP15 overexpression reduces the ABA/GA(3) ratio, decreases superoxide dismutase activity, and increases peroxidase and catalase activity.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Nikol Hadjieva, Elena Apostolova, Vesselin Baev, Galina Yahubyan, Mariyana Gozmanova
Summary: The study on two pepper cultivars' response to PSTVd infection revealed that DS plants had more downregulated genes compared to KK plants, potentially leading to more severe symptoms. Additionally, the contrasting gene expression patterns in different cultivars highlight the diverse defense mechanisms plants employ to overcome PSTVd infection.
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
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
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
Plant Sciences
Hao Jiang, Wei Gao, Bing-li Jiang, Xue Liu, Ya-ting Jiang, Li-tian Zhang, Yue Zhang, Sheng-nan Yan, Jia-Jia Cao, Jie Lu, Chuan-xi Ma, Cheng Chang, Hai-ping Zhang
Summary: Under high temperature conditions, seed dormancy decreases and pre-harvest sprouting damage occurs during wheat harvest. The molecular mechanism behind this high temperature-mediated seed dormancy reduction is still unknown.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Forestry
Fabiano Sillo, Cecilia Brunetti, Fabio Marroni, Federico Vita, Luana Beatriz dos Santos Nascimento, Alfredo Vizzini, Antonietta Mello, Raffaella Balestrini
Summary: The European hazelnut forms a symbiotic relationship with ectomycorrhizal fungi, and this study suggests that this symbiosis can help plants adapt to stress and regulate defense responses. This research has important implications for understanding novel aspects of ectomycorrhizal symbiosis.
Article
Microbiology
Xueyan Sun, Junyue Wu, Shuhui Zhang, Lu Luo, Cuiyuan Mo, Li Sheng, Aimin Ma
Summary: The mechanism of sclerotium formation in Pleurotus tuber-regium was studied using comparative transcriptomic analysis, revealing differentially expressed genes associated with substrate decomposition, oxidation-reduction process, cell wall synthesis, and other biological processes.
FRONTIERS IN MICROBIOLOGY
(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
Immunology
Catherine Vilcheze, Bo Yan, Rosalyn Casey, Suzie Hingley-Wilson, Laurence Ettwiller, William R. Jacobs
Summary: This study provides detailed insights into the transcriptome changes of Mycobacterium tuberculosis under persisting stresses, highlighting genes and gene cohorts involved in stress response. These findings are valuable for the design of novel drug targets and vaccine development.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Plant Sciences
Sang Yong Park, Woo Joo Jung, Geul Bang, Heeyoun Hwang, Jae Yoon Kim
Summary: This study conducted transcriptomic and proteomic analysis to reveal the differentially expressed genes and proteins in wheat spikes treated with PHS. Results showed differences in spliceosome and proteasome pathways between PHS-sensitive and tolerant cultivars, with alternative splicing and ubiquitin-proteasome supporting germination and seed dormancy regulation. The findings provide insight into the mechanisms and pathways related to PHS in wheat.
Article
Plant Sciences
Maria N. Muniz Garcia, Juan Cortelezzi, Daniela A. Capiati
Summary: Overexpression of StPP2Ac2b delays potato tuber sprouting, promotes sprout branching and growth, and alters the source-sink balance.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Review
Plant Sciences
Tatsuro Suzuki, Takahiro Hara, Kenjiro Katsu
Summary: Buckwheat is an important traditional crop that supports local economies in various regions by being used as cereal grain, noodle, bread, and sprout. Pre-harvest sprouting can affect food quality, leading to a decrease in yield and deteriorated noodle quality. Research on breeding buckwheat for quality, sprouting, and subsequent sprout growth is summarized in this review.
