Article
Genetics & Heredity
Juan Li, De Bi, Xin Zhang, Yunpeng Cao, Kun Lv, Lan Jiang
Summary: The study suggests that Siraitia grosvenorii (Luo Han Guo) may serve as a new complementary therapy for treating glioblastoma, exerting anti-tumor effects by targeting CCL5 and potentially influencing the immune microenvironment of the tumor.
FRONTIERS IN GENETICS
(2021)
Article
Agronomy
Ili Nadhirah Jamil, Azhani Abdul-Rahman, Hoe-Han Goh, Wan Mohd Aizat
Summary: Mangosteen exhibits unique ripening behavior and transcriptomic analysis reveals differentially expressed transcripts at different ripening stages. The fruit conserves carbon skeleton rather than energy production at the early ripening stage and upregulates transcripts related to anthocyanin and xanthone biosynthesis. This study provides insights into the regulation of ripening in mangosteen and could contribute to its commercial utilization and preservation.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Nicholas J. Dimonaco, Amanda Clare, Kim Kenobi, Wayne Aubrey, Christopher J. Creevey
Summary: In this study, a tool called StORF-Reporter was developed to identify potentially missing CDS genes in unannotated regions. By extracting unannotated regions from annotated genomes and identifying stop-ORFs in these regions, this method successfully recovered genes that were missing from genome annotations.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Pedro L. Baldoni, Yunshun Chen, Soroor Hediyeh-zadeh, Yang Liao, Xueyi Dong, Matthew E. Ritchie, Wei Shi, Gordon K. Smyth
Summary: Differential expression analysis of RNA-seq is commonly used in bioinformatics. However, transcript-level quantifications are more uncertain due to the ambiguity of sequence reads. To address this issue, a new method is proposed to estimate the overdispersion caused by read-to-transcript ambiguity and generate scaled transcript counts, which improves the efficiency and accuracy of differential analysis.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemical Research Methods
Grete Francesca Privitera, Salvatore Alaimo, Alfredo Ferro, Alfredo Pulvirenti
Summary: This study analyzed eight tools for identifying viruses in RNA-seq data, comparing them using synthetic and real datasets. The analysis showed that no tool was able to recognize all the viruses in the datasets, indicating that the choice of tool depends on the specific application domain.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Jingjing Liao, Lei Xie, Hongwu Shi, Shengrong Cui, Fusheng Lan, Zuliang Luo, Xiaojun Ma
Summary: This study utilized transient expression to successfully manipulate the SgCPR1 and SgCPR2 genes in Siraitia grosvenorii fruit, promoting mogroside biosynthesis and revealing the crucial roles of these genes in secondary metabolite production.
Article
Multidisciplinary Sciences
Parashar Dhapola, Johan Rodhe, Rasmus Olofzon, Thomas Bonald, Eva Erlandsson, Shamit Soneji, Goran Karlsson
Summary: Scarf is a modularly designed Python package that enables memory-efficient single-cell analysis and can run on low-cost devices. It provides efficient implementations for memory and computation and supports accurate reference-anchored mapping and subsampling of large single-cell datasets.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Magdalena Szeliga, Beata Bakera, Magdalena Swiecicka, Miroslaw Tyrka, Monika Rakoczy-Trojanowska
Summary: Wheat flowers can be divided into two groups, one with closed flowers for flowering and pollination, and another with open flowers. The swelling of lodicules is involved in the flowering process and can be differentiated between the two groups. Understanding the mechanism of chasmogamy can help in selecting plants with desired outcrossing rates.
Article
Plant Sciences
Miguel Angel Alcalde, Javier Palazon, Mercedes Bonfill, Diego Hidalgo-Martinez
Summary: This study explored the effects of overexpressing the squalene synthase (SQS) gene and the transcription factor TSAR2 on various aspects of C. asiatica hairy root lines. The transformed lines showed noticeable alterations in morphological traits and content of centelloside, phytosterol, and squalene. The expression of T-DNA genes modulated the centelloside biosynthesis genes. These findings provide valuable information for the biotechnological application of C. asiatica hairy roots.
Article
Multidisciplinary Sciences
Lukas M. Weber, Arkajyoti Saha, Abhirup Datta, Kasper D. Hansen, Stephanie C. Hicks
Summary: nnSVG is a scalable approach based on nearest-neighbor Gaussian processes for identifying spatially variable genes. It can identify genes that show continuous variation in expression across the entire tissue or within specific spatial domains, and it scales linearly with the number of spatial locations. We demonstrate its performance using experimental data and simulations.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Jianbo Li, Congjiao Sun, Jiangxia Zheng, Junying Li, Guoqiang Yi, Ning Yang
Summary: This study provides a comprehensive profile of four representative stages of chicken gonadal development at the transcriptional and chromatin levels. The findings suggest that candidate genes involved in morphogenesis, meiosis, and subcellular structure formation may contribute to asymmetric gonadal development. Further analysis reveals that chromatin accessibility and transcriptional activity of these candidate genes may be regulated by nearby open chromatin regions, acting as potential cis-regulatory elements.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Mitra Darvish, Enrico Seiler, Svenja Mehringer, Rene Rahn, Knut Reinert
Summary: The ever-growing size of sequencing data poses a major challenge in bioinformatics as hardware development fails to keep up. In this paper, a solution called Needle is proposed, which is a fast and space-efficient index for thousands of experiments and can estimate transcript quantification in seconds.
Article
Multidisciplinary Sciences
Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N. Taroni, Vincent J. Carey, Casey S. Greene, Levi Waldron, Sean Davis
Summary: Millions of transcriptomic profiles stored in public archives are often underutilized for interpreting new experiments. In this study, the authors propose GenomicSuperSignature, a method that allows for the interpretation of new transcriptomic datasets by comparing them to public archives without requiring high-performance computing. The method is efficient and robust to batch effects and heterogeneous training data, and exhibits transfer learning capabilities. GenomicSuperSignature facilitates the analysis of new gene expression data in the context of existing databases using minimal computing resources.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Junxiao Ren, Weihua Tian, Keren Jiang, Zhang Wang, Dandan Wang, Zhuanjian Li, Fengbin Yan, Yanbin Wang, Yadong Tian, Kepeng Ou, Hongjun Wang, Xiangtao Kang, Hong Li, Xiaojun Liu
Summary: Using RNA-Seq and ChIP-Seq, a total of 990 estrogen-responsive genes were identified in chicken liver, which are highly enriched in lipid metabolism and biological processes. Integrated analysis also revealed 191 genes directly targeted by estrogen, shedding light on the molecular mechanism of estrogen-related lipid metabolism.
Article
Plant Sciences
Peng Guo, Ziqi Huang, Xinke Li, Wei Zhao, Yihan Wang
Summary: In this study, RNA-seq was used to evaluate the gene expression of B. papyrifera leaves at different developmental stages and discovered important enzyme genes involved in flavonoid production pathways. The results showed that the dynamic change of flavonoid contents is related to the expression pattern of essential genes in the biosynthetic pathway.
Article
Ecology
Zitong Li, Shiming Liu, Warren Conaty, Qian-Hao Zhu, Philippe Moncuquet, Warwick Stiller, Iain Wilson
Summary: Genomic selection has become an important breeding technology for crop improvement. This study focuses on cotton and aims to develop a GP-based breeding system to enhance efficiency. By genotyping 1385 breeding lines using a high-density SNP chip, the study found that combining genomic and pedigree information resulted in the highest prediction accuracies.
Article
Biochemistry & Molecular Biology
Zhixing Qing, Yao Shi, Lida Han, Pengkun Li, Ziou Zha, Chang Liu, Xiubin Liu, Peng Huang, Yisong Liu, Qi Tang, Kewu Zeng, Jianguo Zeng, Yuan Zhou
Summary: This study isolated ten cucurbitacin C analogues, including six compounds with inhibitory effects on tumor cell lines. Cucurbitacin C6 and C7 exhibited significant inhibition on HepG2 cell line. Cucumber is an important source of specialized metabolites in the food and medicinal industries.
Article
Biochemistry & Molecular Biology
Li Chen, Enhui Shen, Yunlei Zhao, Hongmei Wang, Iain Wilson, Qian-Hao Zhu
Summary: This study utilized publicly available RNA-seq datasets to identify the conservativeness and divergence of lincRNAs in different cotton species and their role in responding to biotic stresses. The study provided new insights into the relationship between the conservativeness and Vd responsiveness of lincRNAs and identified candidate lincRNAs for further functional characterization in disease response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Xiaochen Sun, Wenli Wu, Yanfang Yang, Iain Wilson, Fenjuan Shao, Deyou Qiu
Summary: This study provides a comprehensive analysis of m(6)A pathway genes in Poplar 84K, including gene structures, promoter analysis, and expression profiles. The results show tissue-specific expression patterns of m(6)A pathway genes in leaves, xylem, phloem, and roots. Additionally, the transcription factor LBD15 regulates the expression of several m(6)A pathway genes. These findings contribute to the understanding of the functions and epigenetic regulation mechanisms of these genes in Poplar 84K.
Article
Plant Sciences
Qian-Hao Zhu, Shuangxia Jin, Yuman Yuan, Qing Liu, Xianlong Zhang, Iain Wilson
Summary: This study successfully generated a collection of cotton miR482 mutants using CRISPR/Cas9 technology, resulting in lower disease index in response to pathogen infection. The study provides a valuable resource for the cotton community to uncover the role of miR482-NLR module(s) in the interaction between cotton and different pathogens.
Editorial Material
Plant Sciences
Linghe Zeng, Iain Wilson, Fred M. Bourland
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Tianlu Zhang, Dong Zhou, Xin Wang, Tian Xiao, Lingxi Wu, Qi Tang, Ying Lu
Summary: This study investigated the effects of adding Kadsura coccinea fruit extract on broilers, and the results showed that adding 200 mg/kg Kadsura coccinea fruit extract can replace traditional antibiotics as a growth promoter, improving the growth performance, slaughter performance, antioxidant capacity, and regulating intestinal microorganisms of broilers. This indicates that Kadsura coccinea fruit extract is a feasible feed additive.
Article
Biochemistry & Molecular Biology
Yingying Shao, Detian Mu, Limei Pan, Iain W. Wilson, Yajie Zheng, Lina Zhu, Zhiguo Lu, Lingyun Wan, Jine Fu, Shugen Wei, Lisha Song, Deyou Qiu, Qi Tang
Summary: An optimized protocol for the isolation, purification, and transient gene expression of Uncaria rhynchophylla protoplasts was developed, resulting in a highly efficient protoplast-based transient expression system with a transfection rate of 71%.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Rong-Ju Yang, Na Wang, Xiao Ma, Meng-Die Gong, Yi-Rong Wang, Si-Yu Meng, Zhao-Ying Liu, Qi Tang
Summary: In this study, a two-dimensional liquid chromatography-UV detector was used to establish a method for simultaneous detection of PLP, PA, and PL. The method exhibited good performance in sample processing, separation, and detection, making it suitable for applications in pharmacological, pharmaceutical, and clinical research.
Article
Biochemistry & Molecular Biology
Detian Mu, Yingying Shao, Jialong He, Lina Zhu, Deyou Qiu, Iain W. Wilson, Yao Zhang, Limei Pan, Yu Zhou, Ying Lu, Qi Tang
Summary: This study reports the stability of reference genes in Uncaria rhynchophylla and their potential role in alkaloid production. The researchers evaluated the expression stability of ten candidate reference genes under stress-related experimental treatments and found that S-adenosylmethionine decarboxylase (SAM) exhibited higher stability. Using SAM as a reference gene, they examined the expression patterns of key alkaloid biosynthetic genes and a transcription factor under stress treatments. The results indicate that the transcription factor WRKY1 may coordinate the expression of tryptophan decarboxylase (TDC), providing a potential method for enhancing alkaloid production in the future through synthetic biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Infectious Diseases
Tianlu Zhang, Dong Zhou, Miaofen Chen, Hui Zou, Qi Tang, Ying Lu, Yajie Zheng
Summary: This study evaluates the effects of fibrous roots of Polygonatum cyrtonema Hua on various parameters of white-feathered broilers and explores the mechanism of immune function improvement through network pharmacology and molecular docking technology. The results show that incorporating P. cyrtonema fibrous roots in broiler diets has positive effects on growth performance, slaughter parameters, meat quality, immune function, antioxidant capacity, and intestinal morphology.
Article
Biochemistry & Molecular Biology
Yao Zhang, Detian Mu, Liya Wang, Xujun Wang, Iain W. Wilson, Wenqiang Chen, Jinghan Wang, Zhaoying Liu, Deyou Qiu, Qi Tang
Summary: Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to analyze Gelsemium elegans leaf tissue and identify suitable reference genes for data normalization. The optimal stable reference genes varied among the different treatments and at least two reference genes were required for accurate quantification. The expression patterns of 15 genes related to gelsenicine biosynthesis pathway were determined using RT-qPCR and three of these genes showed a strong correlation with the amount of gelsenicine measured. This research is crucial for future molecular analyses of G. elegans, a medically important plant species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Medicinal
Meng-ting Zuo, Yan-chun Liu, Zhi-liang Sun, Li Lin, Qi Tang, Pi Cheng, Zhao-ying Liu
Summary: A powerful integrated strategy based on LC-MS was developed for the comprehensive characterization and quantification of multiple components of Gelsemium elegans. The LC-QqQ/MS method was sensitive and reproducible for the simultaneous relative quantification of 41 components of G. elegans, showing potential application value.
CHINESE HERBAL MEDICINES
(2021)