Article
Plant Sciences
Indrani K. Baruah, Shahin S. Ali, Jonathan Shao, David Lary, Bryan A. Bailey
Summary: Black pod rot, caused by Phytophthora palmivora, is a devastating disease of cacao trees. In this study, the resistance responses of different cacao genotypes to P. palmivora were investigated. Transcriptome analysis revealed the differential expression of genes involved in plant defense in response to the pathogen. Several candidate genes potentially associated with resistance were identified.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Horticulture
Pornprapa Kongtragoul, Koichiro Ishikawa, Hideo Ishii
Summary: Research has shown the presence of metalaxyl-resistant strains in populations of Phytophthora palmivora in Thailand, posing challenges for disease management.
Article
Agriculture, Multidisciplinary
Fumika Kato, Yuka Ando, Aiko Tanaka, Takamasa Suzuki, Daigo Takemoto, Makoto Ojika
Summary: Phytophthora is a microorganism that damages important crops like potatoes and tomatoes. Natural products like naringenin and flazin can inhibit the asexual reproduction of Phytophthora and protect agricultural products.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Microbiology
Junjie Xu, Yilin Li, Jinbu Jia, Wenjing Xiong, Chengcheng Zhong, Guiyan Huang, Xiuhong Gou, Yuling Meng, Weixing Shan
Summary: A study found that the PpAGO3 gene plays a crucial role in regulating the pathogenicity of Phytophthora parasitica. Mutants with deletions in the RGG motif of PpAGO3 showed increased pathogenicity and different accumulation of sRNAs associated with effector genes compared to the wild-type. Overexpression of specific genes in the mutants enhanced the susceptibility of plants to P. parasitica infection.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kangkai Zheng, Jie Lu, Jie Li, Yin Yu, Jia Zhang, Ziwei He, Omayma M Ismail, Jie Wu, Xuejun Xie, Xiaobo Li, Guangyuan Xu, Daolong Dou, Xiaodan Wang
Summary: The study demonstrated that chitosan can enhance potato resistance and reduce Phytophthora infestans infection by activating important plant defence response pathways. In addition, chitosan triggers pattern recognition immune responses, induces systemic resistance, and alters gene expression related to plant defence in potato. These findings provide insights into chitosan-mediated activation of the immune system in potato and offer a potential eco-friendly strategy for controlling late blight in the field.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Plant Sciences
Yumeng Xiong, Di Zhao, Shengnan Chen, Lan Yuan, Die Zhang, Hongyang Wang
Summary: This study focuses on a nuclear-targeted effector Pi07586 released by the highly destructive plant oomycete pathogen Phytophthora infestans. It is found that Pi07586 can effectively suppress plant immunity by inhibiting the expression of specific genes and reducing the levels of plant hormones. These findings enhance our understanding of the intricate relationship between P. infestans and host plants and shed new light on plant immune modulation.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Richard C. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas
Summary: The single-cell transcriptional profile of a human embryo between 16 and 19 days after fertilization shows similarities and differences in gastrulation compared to mouse and non-human primate models. This study provides new insights into human development and offers valuable information for directed differentiation of human cells in vitro.
Article
Biochemistry & Molecular Biology
Jie Lu, Tingli Liu, Xiong Zhang, Jie Li, Xun Wang, Xiangxiu Liang, Guangyuan Xu, Maofeng Jing, Zhugang Li, Ingo Hein, Daolong Dou, Yanju Zhang, Xiaodan Wang
Summary: By analyzing RNA-seq data, this study revealed distinct response models adopted by three Solanaceae hosts in their interactions with Phytophthora infestans, with different infection processes and gene expression characteristics observed. Comparative analysis also identified overlapping but distinct immune response and hormone regulation mechanisms in the host-specific infection processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Shumei Wang, Ramesh R. Vetukuri, Sandeep K. Kushwaha, Pete E. Hedley, Jenny Morris, David J. Studholme, Lydia R. J. Welsh, Petra C. Boevink, Paul R. J. Birch, Stephen C. Whisson
Summary: Phytophthora kernoviae was found to infect Nicotiana benthamiana by expressing green fluorescent protein (GFP) and forming haustoria in host cells. Analysis of P. kernoviae transcriptome revealed 1052 transcripts encoding predicted secreted proteins, potentially functioning as effectors to promote disease development. Identification of 87 expressed RXLR effectors showed significant enhancement of P. kernoviae disease progression in plant cells.
MOLECULAR PLANT PATHOLOGY
(2021)
Article
Plant Sciences
Jinsen Cai, Songguang Yang, Wenrui Liu, Jinqiang Yan, Biao Jiang, Dasen Xie
Summary: In this study, the gene expression profiles of two Benincasa hispida cultivars with different resistance to Phytophthora melonis were analyzed. The results showed that phenylpropanoid biosynthesis, plant-pathogen interaction, the MAPK signaling pathway-plant, and plant hormone signal transduction played important roles in the response of Benincasa hispida to Phytophthora melonis infection.
FRONTIERS IN PLANT SCIENCE
(2022)
Editorial Material
Biochemical Research Methods
John P. Chute, Joshua P. Sasine
Summary: Image-seq combines high-resolution microscopy with single-cell transcriptomics to spatially resolve and isolate viable bone marrow and leukemia cells, achieving a long-sought integration of single-cell molecular profiling and cellular spatial localization.
Article
Multidisciplinary Sciences
Kai Battenberg, S. Thomas Kelly, Radu Abu Ras, Nicola A. Hetherington, Makoto Hayashi, Aki Minoda
Summary: Single-cell RNA-sequencing analysis has gained popularity, and UniverSC is a universal tool for processing single-cell RNA-seq data on any platform. It provides a command-line tool, docker image, and containerized graphical application for consistent and comprehensive integration, comparison, and evaluation of data from various platforms. Additionally, a cross-platform application with a graphical user interface is available to address the bottleneck of data processing for researchers without bioinformatics expertise.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Malte D. Luecken, M. Buettner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, L. Zappia, M. Dugas, M. Colome-Tatche, Fabian J. Theis
Summary: This study benchmarked 68 method and preprocessing combinations on 85 batches of gene expression data, highlighting the importance of highly variable gene selection in improving method performance. When dealing with complex integration tasks, scANVI, Scanorama, scVI, and scGen consistently performed well, while the performance of single-cell ATAC-sequencing integration was strongly influenced by the choice of feature space.
Article
Biochemical Research Methods
Tal Ashuach, Mariano I. Gabitto, Rohan V. Koodli, Giuseppe-Antonio Saldi, Michael I. Jordan, Nir Yosef
Summary: Jointly profiling the transcriptome, chromatin accessibility, and other molecular properties of single cells can enhance the study of cellular diversity. MultiVI, a probabilistic model, allows the analysis of multiomic data and enhances single-modality datasets by creating a joint representation. It can be accessed at scvi-tools.org.
Article
Biochemistry & Molecular Biology
Sonia Garcia-Ruiz, Emil K. Gustavsson, David Zhang, Regina H. Reynolds, Zhongbo Chen, Aine Fairbrother-Browne, Ana Luisa Gil-Martinez, Juan A. Botia, Leonardo Collado-Torres, Mina Ryten
Summary: Dysregulation of RNA splicing is implicated in rare and complex diseases. We have developed IntroVerse, a comprehensive resource for exploring intron usage by providing a catalogue of annotated introns and novel junctions. This dataset, generated from extensive RNA sequencing analysis, offers insights into novel transcripts and assessment of splicing noise in introns.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Hangjun Sun, Lili Shen, Yuanxia Qin, Xiaowei Liu, Kaiqiang Hao, Ying Li, Jie Wang, Jinguang Yang, Fenglong Wang
Article
Biochemistry & Molecular Biology
X. Gao, J. Y. Zhu, S. Ma, Z. Zhang, C. Xiao, Q. Li, Z. Y. Li, G. X. Wu
GENETICS AND MOLECULAR RESEARCH
(2014)
Article
Entomology
Guo-Xing Wu, Xi Gao, Qing Tan, Zheng-Yue Li, Cui Hu, Gong-Yin Ye
JOURNAL OF ASIA-PACIFIC ENTOMOLOGY
(2014)
Article
Multidisciplinary Sciences
Lifang Li, Mingxian Lan, Wufeng Lu, Zhaobo Li, Tao Xia, Jiaying Zhu, Min Ye, Xi Gao, Guoxing Wu
Article
Multidisciplinary Sciences
Lifang Li, Xi Gao, Mingxian Lan, Yuan Yuan, Zijun Guo, Ping Tang, Mengyue Li, Xianbin Liao, Jiaying Zhu, Zhengyue Li, Min Ye, Guoxing Wu
Article
Biochemistry & Molecular Biology
Lifang Li, Xi Gao, Huamin Gui, Mingxian Lan, Jiaying Zhu, Yonghui Xie, Youguo Zhan, Zhijiang Wang, Zhengyue Li, Min Ye, Guoxing Wu
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
(2020)
Article
Anatomy & Morphology
Ping Gao, Xianbin Liao, Guoxing Wu, Lifang Li, Mingxian Lan, Mehboob Hussain, Bin Chen, Guowen Tang, Yonghui Xie, Xi Gao
Summary: Eocanthecona furcellataWolff is a native generalist predator that attacks and kills its prey by inserting its stylet and injecting saliva. The salivary glands of this predator include principal glands and accessory glands, with cells rich in rough endoplasmic reticulum and secretory content. The cells have plasma membrane infoldings in the basal region and produce the proteins found in the saliva.
MICROSCOPY RESEARCH AND TECHNIQUE
(2021)
Article
Plant Sciences
Mou Zhang, Hang Wang, Mehboob Hussain, Jinfeng Qi, Canrong Ma, Mingxian Lan, Xi Gao, Guoxing Wu
SOUTH AFRICAN JOURNAL OF BOTANY
(2020)
Article
Microscopy
Hang Zhao, Chen Liang, Ping Gao, Yong-Hui Xie, Zhi-Jiang Wang, Guo-Xing Wu, Guo-Wen Tang, Bin Cheng, Xi Gao
Summary: The study investigated the mechanism underlying chemosensation in Eocanthecona furcellata by observing the external morphology of antennae and sensilla on both sexes of adults and nymphs. The results showed sexual dimorphism in the number of sensilla on adult antennae, with females having more sensilla. These inter-sexual differences may be related to chemoreception.
Article
Virology
Yubing Jiao, Xiuxiang Zhao, Kaiqiang Hao, Xinran Gao, Dan Xing, Zhiping Wang, Mengnan An, Zihao Xia, Yuanhua Wu
Summary: This study identified the profile of vsiRNAs from PMMoV in infected pepper plants, revealing the length distribution and host target pathways. The results also showed that PMMoV infection up-regulated specific gene transcripts in pepper plants, which are important components of the antiviral RNA silencing pathway. These findings suggest the potential roles of vsiRNAs in PMMoV-pepper interactions.
Article
Biotechnology & Applied Microbiology
Jie Wang, Kaiqiang Hao, Fangfei Yu, Lili Shen, Fenglong Wang, Jinguang Yang, Chenyu Su
Summary: This study innovatively combines biological antiviral agents with nanotechnology to control plant virus diseases, significantly improving control efficiency and reducing the use of traditional chemical pesticides. The results demonstrated that quercetin nanoliposomes with excellent stability could effectively inhibit the target genes and proteins associated with plant viruses, outperforming conventional formulations and other antiviral agents in field experiments.
JOURNAL OF NANOBIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kaiqiang Hao, Miaoren Yang, Yakun Cui, Zhiyuan Jiao, Xinran Gao, Zhichao Du, Zhiping Wang, Mengnan An, Zihao Xia, Yuanhua Wu
Summary: This study reveals the resistance mechanism of maize to maize lethal necrosis (MLN) by analyzing gene expression profiles of maize infected with sugarcane mosaic virus (SCMV) and maize chlorotic mottle virus (MCMV) using RNA sequencing. Genes related to photosynthesis, reactive oxygen species scavenging, and disease resistance were found to be differentially expressed. Furthermore, it was demonstrated that vitamin C can suppress viral infections, while vitamins E and K promote MCMV infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Entomology
Guoxing Wu, Xi Gao, Jiaying Zhu, Cui Hu, Gongyin Ye
JOURNAL OF INSECT SCIENCE
(2014)
