Article
Plant Sciences
Qinglun Li, Yuyang Zhang, Weiguo Lu, Xiaoyu Han, Lingling Yang, Yajuan Shi, Honglian Li, Linlin Chen, Yiqing Liu, Xue Yang, Yan Shi
Summary: In this study, a novel geminivirus named SGVA was identified in soybean stay-green plants. The V2 protein of SGVA was determined as a pathogenicity factor and silencing suppressor.
Article
Plant Sciences
Takatoshi Wakabayashi, Shunsuke Ishiwa, Kasumi Shida, Noriko Motonami, Hideyuki Suzuki, Hirosato Takikawa, Masaharu Mizutani, Yukihiro Sugimoto
Summary: Strigolactones act as endogenous phytohormones regulating shoot branching and mediating symbiotic communications in the rhizosphere. Characterization of sorgomol synthase in sorghum revealed that SbCYP728B35 catalyzes the conversion of 5DS to sorgomol, with the C-8bS configuration in the C-ring being essential for this reaction.
Article
Genetics & Heredity
Juan C. Alvarez-Diaz, Manon M. S. Richard, Vincent Thareau, Gianluca Teano, Christine Paysant-Le-Roux, Guillem Rigaill, Stephanie Pflieger, Ariane Gratias, Valerie Geffroy
Summary: This study identified and analyzed the components and expression patterns of the RNA-guided silencing pathway in the non-model plant common bean. The findings provide insights into the biological processes and stress responses of common bean, which is important for its growth and development.
Article
Plant Sciences
Lihua Wang, Yanlong Liu, Li Gao, Xiaocui Yang, Xu Zhang, Shaoping Xie, Meng Chen, Yi-Hong Wang, Jieqin Li, Yixin Shen
Summary: In this study, association mapping was conducted to study four forage yield traits in sorghum, and dynamic transcriptome expression profiling was used to identify genes related to growth and development. Weighted gene correlation network analysis revealed gene modules significantly correlated with the traits. Candidate genes were identified through the integration of genome-wide association studies and RNA sequencing.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Jeremie Bazin, Emilie Elvira-Matelot, Thomas Blein, Vincent Jauvion, Nathalie Bouteiller, Jun Cao, Martin D. Crespi, Herve Vaucheret
Summary: In addition to regulating splicing, the spliceosome components SmD1 and PRP39 also promote posttranscriptional gene silencing in Arabidopsis thaliana. However, their actions are distinct in both splicing and gene silencing. The double mutant analysis suggests that PRP39 and SmD1 work together to limit degradation of transgene-derived aberrant RNAs, thus promoting the initiation of posttranscriptional gene silencing in the cytoplasm.
Article
Cell Biology
Shanshan Li, Haodong Zhu, Ying He, Ni Hong, Guoping Wang, Liping Wang
Summary: This study identifies a protein, P3, encoded by Botryosphaeria dothidea chrysovirus 1 (BdCV1), as a RNA silencing suppressor and demonstrates its impact on the growth and pathogenicity of B. dothidea, as well as the expression levels of RNA silencing components and virus-derived siRNAs (vsiRNAs).
Article
Biochemistry & Molecular Biology
Luisa Abruzzi De Oliveira-Busatto, Cecilia Paz da Silva Giordano, Marilia Ferreira da Silva, Darci Uhry Junior, Frank Guzman, Beatriz Wiebke-Strohm, Zenglu Li, Christian Bredemeier, Maria Helena Bodanese-Zanettini
Summary: Flooding is a common environmental stress that affects soybean growth and yield. This study focused on characterizing the physiological responses and identifying differentially expressed genes in Brazilian soybean genotypes with contrasting flooding tolerance. SNPs related to flooding tolerance were also identified. This research provides valuable information for developing soybean genotypes adapted to poorly drained soils or areas subject to flooding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Lingjiao Fan, Chengyong He, Dehang Gao, Tengfei Xu, Fei Xing, Jiaqi Yan, Binhui Zhan, Shifang Li, Hongqing Wang
Summary: This study identified two suppressors of RNA silencing, Pro2Glu and P28, encoded by the strawberry mottle virus (SMoV) RNA2 genome. These viral proteins were able to suppress local and systemic RNA silencing, and their stability and suppressive ability were influenced by specific amino acids and motifs. Additionally, Pro2Glu and P28 enhanced the accumulation of other viruses and exacerbated virus symptoms in plants.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Muhammad Azam, Shengrui Zhang, Jing Li, Muhammad Ahsan, Kwadwo Gyapong Agyenim-Boateng, Jie Qi, Yue Feng, Yitian Liu, Bin Li, Lijuan Qiu, Junming Sun
Summary: In this study, the isoflavone content in 1551 soybean accessions was analyzed, and a wide range of phenotypic variations was observed. Through genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA), significant SNPs and key modules associated with isoflavone content were identified. Several key genes related to isoflavone content were also discovered.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Licheng Wang, Wenbao Chen, Huan Ma, Jingyuan Li, Xingan Hao, Yunfeng Wu
Summary: The phytoplasma encoded RSS SWP16 inhibits RNA silencing in plants, leading to viral infection and providing insight into pathogen-plant interaction mechanisms.
Article
Plant Sciences
Jesus Perez-Lopez, Ana B. Feria, Jacinto Gandullo, Clara de la Osa, Irene Jimenez-Guerrero, Cristina Echevarria, Jose A. Monreal, Sofia Garcia-Maurino
Summary: Phosphoenolpyruvate carboxylase (PEPC) has crucial functions in various processes including photosynthesis, respiration, amino acid synthesis, and seed development. Its phosphorylation by PEPC-kinase (PEPCk) is well-documented. In this study, the silencing of three sorghum genes encoding PEPCk led to decreased phosphorylation of PEPC, altered metabolic profiles and amino acid content in leaves and seeds, delayed flowering, and reduced seed quantity and quality. These findings highlight the importance of PEPC phosphorylation in sorghum development, stress responses, yield, and seed quality.
Article
Biochemistry & Molecular Biology
Dan-Dan Liu, Hu-Jiao Lan, Hashimi Said Masoud, Mei-Yan Ye, Xian-Yong Dai, Chen-Li Zhong, Sheng-Nan Tian, Jian-Zhong Liu
Summary: Silencing GmBIR1 in soybean using rhizobium-induced gene silencing resulted in an autoimmune phenotype and enhanced resistance to various pathogens.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Hala Al Adhami, Judith Vallet, Celia Schaal, Paul Schumacher, Anais Flore Bardet, Michael Dumas, Johana Chicher, Philippe Hammann, Sylvain Daujat, Michael Weber
Summary: Many germline genes are epigenetically repressed in mammals to prevent inappropriate expression in somatic cells. Through studying chromatin signature and conducting a CRISPR-Cas9 knock-out screen, researchers discovered that germline gene repression depends on the polycomb complex PRC1.6 and DNA methylation in mouse embryonic stem cells. They also identified and characterized new genes, including Usp7, Shfm1, and Erh, that contribute to germline gene repression. These findings provide insights into the mechanisms and factors involved in silencing germline genes in embryonic stem cells.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Can Wang, Lingbo Zhou, Jie Gao, Guobing Zhang, Fangli Peng, Chunlan Zhang, Qiang Zhao, Qiu Peng, Mingbo Shao
Summary: The optimal row ratio configuration of waxy sorghum-soybean intercropping systems significantly affects the accumulation and transportation of nitrogen, phosphorus, and potassium in crops, leading to higher yields and economic benefits.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Na Guo, Ammara Tahir, Xiaoxia Cui, Jianyu Xu, Jutao Sun, Nannan Zhang, Ruidong Sun, Sushuang Deng, Han Xing, Jinming Zhao
Summary: This study analyzed the expression profiles of soybean miRNAs before and after infection with Phytophthora sojae and identified miRNAs related to resistance and susceptibility. Potential target genes of these differentially expressed miRNAs were predicted. The findings contribute to understanding the disease resistance mechanism in soybean.
Article
Food Science & Technology
Mohamed Abdelmoteleb, Chi Zhang, Brian Furey, Mark Kozubal, Hywel Griffiths, Marion Champeaud, Richard E. Goodman
Summary: Potential proteins from three novel food sources were predicted and evaluated for allergic cross-reactivity risks by comparing amino acid sequences against allergens in the AOL database. Despite many proteins exceeding CODEX limits for identity matches, these matches were not predictive of allergy risks based on observed taxonomic cross-reactivity. New methods or changes in allergen databases are recommended for better risk evaluation.
FOOD AND CHEMICAL TOXICOLOGY
(2021)
Article
Plant Sciences
Huihui Yu, Qian Du, Malachy Campbell, Bin Yu, Harkamal Walia, Chi Zhang
Summary: Pre-mRNA splicing is crucial for gene expression regulation. Researchers developed a software tool called VaSP to quantify and visualize splicing variants in plants, and identified genotype-specific splicing events associated with shoot Na+ accumulation under salt stress conditions. VaSP proves to be a versatile and powerful tool for alternative splicing analysis and prioritizing candidate causal pre-mRNA splicing in GWAS.
Article
Plant Sciences
Zhen Wang, Junmei Kang, Juan Armando Casas-Mollano, Yongchao Dou, Shangang Jia, Qingchuan Yang, Chi Zhang, Heriberto Cerutti
Summary: The plant-specific protein kinase MLK4 regulates flowering time by phosphorylating histone H3, which in turn accelerates flowering by repressing the transcription of the negative flowering regulator FLC/MAF.
Article
Multidisciplinary Sciences
Li Han, Carlos P. Jara, Ou Wang, Yu Shi, Xinran Wu, Sandra Thibivilliers, Rafal K. Woycicki, Mark A. Carlson, William H. Velander, Eliana P. Araujo, Marc Libault, Chi Zhang, Yuguo Lei
Summary: This study presents a robust method for isolating and cryopreserving pig skin single cells for scRNA-seq, allowing researchers to identify major skin cell types in pigs.
Article
Multidisciplinary Sciences
Huihui Yu, Mu Li, Jaspreet Sandhu, Guangchao Sun, James C. Schnable, Harkamal Walia, Weibo Xie, Bin Yu, Jeffrey P. Mower, Chi Zhang
Summary: The study developed computational pipelines to identify microexons in plants and showed their importance and diversity in plant evolution.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Shengjun Li, Weilong Yang, Yunfeng Liu, Guangyong Li, Xiang Liu, Yaling Liu, James R. Alfano, Chi Zhang, Bin Yu
Summary: The study revealed that FDDM1 and FDDM2 act as a heterodimer to negatively regulate DNA methylation levels at ROS1-dependent DNA loci in Arabidopsis.
Article
Biotechnology & Applied Microbiology
Cintia Lucia Arias, Truyen Quach, Tu Huynh, Hanh Nguyen, Ademar Moretti, Yu Shi, Ming Guo, Amira Rasoul, Kyujung Van, Leah McHale, Tom Elmo Clemente, Ana Paula Alonso, Chi Zhang
Summary: This study evaluated the metabolic and transcriptional responses to the expression of AtWRI1 and AtDGAT1 in soybean seeds. The results showed that the expression of these genes did not increase the total fatty acid content, but led to changes in the oil and carbohydrate composition. Transcriptomic analysis revealed down-regulation of oil body packaging protein genes and strong induction of lipase and FA biosynthesis inhibitor genes.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Review
Oncology
Kiersten Preuss, Nate Thach, Xiaoying Liang, Michael Baine, Justin Chen, Chi Zhang, Huijing Du, Hongfeng Yu, Chi Lin, Michael A. Hollingsworth, Dandan Zheng
Summary: Pancreatic cancer, with a five-year survival rate of only 3% for the majority of patients, is a global healthcare challenge. Radiomics and deep learning methods utilize data science to mine hidden information in medical images and show promise in advancing personalized management of the disease.
Article
Biochemistry & Molecular Biology
Lucas Busta, Ismail Dweikat, Shirley J. Sato, Haolin Qu, Yong Xue, Bangjun Zhou, Lu Gan, Bin Yu, Thomas E. Clemente, Edgar B. Cahoon, Chi Zhang
Summary: This study investigates the phytochemistry and genomics of feral Cannabis populations collected from Nebraska. It found that both male and female flower tissues produced cannabinoids, with cannabidiol being the primary cannabinoid. The expression of genes related to cannabinoid biosynthesis was higher in female flowers, suggesting transcriptional control of cannabinoid abundance. DNA sequencing revealed that the feral Cannabis plants from Nebraska are more similar to hemp-type Cannabis plants than drug-type plants. This research provides foundational knowledge for future studies of feral Nebraska Cannabis.
Article
Multidisciplinary Sciences
Lu Gan, Kiyoul Park, Jin Chai, Evan M. Updike, Hyojin Kim, Adam Voshall, Sairam Behera, Xiao-Hong Yu, Yuanheng Cai, Chunyu Zhang, Mark A. Wilson, Jeffrey P. Mower, Etsuko N. Moriyama, Chi Zhang, Sireewan Kaewsuwan, Qun Liu, John Shanklin, Edgar B. Cahoon
Summary: The seed oils of Thunbergia species contain high levels of petroselinic acid, which is attributed to the functional specialization of specific enzymes. Metabolic engineering demonstrates the utility of these enzymes for the production of unusual monounsaturated fatty acids in engineered plants and bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Guangchao Sun, Nishikant Wase, Shengqiang Shu, Jerry Jenkins, Bangjun Zhou, J. Vladimir Torres-Rodriguez, Cindy Chen, Laura Sandor, Chris Plott, Yuko Yoshinga, Christopher Daum, Peng Qi, Kerrie Barry, Anna Lipzen, Luke Berry, Connor Pedersen, Thomas Gottilla, Ashley Foltz, Huihui Yu, Ronan O'Malley, Chi Zhang, Katrien M. Devos, Brandi Sigmon, Bin Yu, Toshihiro Obata, Jeremy Schmutz, James C. Schnable
Summary: Some crop wild relatives have the ability to tolerate extreme stress beyond what domesticated crops can withstand. This study focuses on Paspalum vaginatum, a self-incompatible and stress-tolerant wild relative of maize and sorghum, and explores the molecular mechanisms that enable it to adapt to nutrient-deficit conditions. The findings suggest that inducing trehalose accumulation in maize, similar to the metabolic phenotype of Paspalum vaginatum, can lead to increased biomass accumulation via autophagy.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Fei Bai, Qian Du, Qingliang Zou, Lin Xu, Wei Dong, Xinlin Lv, Xiaorong Han, Huijun Zhou, Chi Zhang, Tao Lu
Summary: This study examined the association between mutations of genes identified in ctDNAs and ctDNA concentration in the blood of CRC patients. The results showed that mutations in five genes were associated with ctDNA concentrations. By analyzing ctDNA mutations, we can infer tumor burden or size and predict survival time.
Article
Engineering, Biomedical
Ou Wang, Li Han, Haishuang Lin, Mingmei Tian, Shuyang Zhang, Bin Duan, Soonkyu Chung, Chi Zhang, Xiaojun Lian, Yong Wang, Yuguo Lei
Summary: Transplanting injectable microtissues of brown adipocytes can improve cell survival and effectively treat obesity and type 2 diabetes.
BIOACTIVE MATERIALS
(2023)
Article
Biotechnology & Applied Microbiology
Guangchao Sun, Huihui Yu, Peng Wang, Martha Lopez-Guerrero, Ravi V. Mural, Olivier N. Mizero, Marcin Grzybowski, Baoxing Song, Karin van Dijk, Daniel P. Schachtman, Chi Zhang, James C. Schnable
Summary: This study examined how changes in transcriptional regulation allow maize to adapt to temperate environments. Through RNA-seq analysis of maize genotypes, they identified genes with different heritability of expression and alternative splicing. They also discovered loci regulating co-expression modules involved in various biological processes. Additionally, a GWAS identified candidate genes related to adaptation to temperate environments.
Article
Immunology
Yunfan Kong, Mitchell Kuss, Yu Shi, Fang Fang, Wen Xue, Wen Shi, Yutong Liu, Chi Zhang, Peng Zhong, Bin Duan
Summary: The study demonstrated that treadmill running with late initiation could effectively facilitate nerve regeneration, prevent muscle atrophy, improve sensorimotor functions, and enhance walking performance following severe traumatic peripheral nerve injury (PNI). Exercise also had positive effects on reducing inflammation, preventing pain sensor overexpression, and reversing maladaptive plastic changes in the central nervous system.
BRAIN, BEHAVIOR, & IMMUNITY - HEALTH
(2022)