Article
Biotechnology & Applied Microbiology
Kangwuk Kyung, Jamin Ku, Eunbin Cho, Junhyung Ryu, Jin Woo, Woong Jung, Dong-Eun Kim
Summary: We developed a fluorometric method for the accurate detection of single-nucleotide mutations in SARS-CoV-2 RNA using RNA sequence-dependent DNA ligation and tandem isothermal gene amplification methods. This method allows for high sensitivity identification of SARS-CoV-2 variants.
BIOENGINEERING-BASEL
(2023)
Article
Multidisciplinary Sciences
Qiangyuan Zhu, Yichi Niu, Michael Gundry, Chenghang Zong
Summary: A novel single-cell whole-genome amplification method was reported in this study, which efficiently captures spontaneous DNA damage in single cells. The study identified high-damage genes and found significant enrichment of these genes in differentially expressed genes (DEGs) detected in both Alzheimer's disease (AD) and autism spectrum disorder (ASD) single-cell transcriptomes. This discovery shed new lights on the role of DNA damage in human diseases and disorders.
Article
Biochemistry & Molecular Biology
Kailing Tu, Keying Lu, Qilin Zhang, Wei Huang, Dan Xie
Summary: A new variant detection method SCOUT was developed for single-cell genotyping, which does not require external data for SNV detection. By utilizing base count information from the neighboring genomic region, SCOUT improves variant detection performance and shows increased operating efficiency compared to other methods.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Analytical
Jialun He, Xiaolong Li, Lei Liao, Wenjiao Zhou, Bingying Jiang
Summary: A non-enzymatic and label-free sensing method is developed for accurate and ultrasensitive differentiation of SNP in the K-ras gene, showing high sensitivity with a detection limit of 3.63 fM and high selectivity to discriminate MtDNA from a mixture with a concentration ratio of WtDNA to MtDNA as high as 5000:1. This approach has the potential application for future clinical diagnostics by analyzing target MtDNA in diluted serum samples.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Chemistry, Analytical
Wenjun Jiang, Rashid Aman, Zahir Ali, Gundra S. Rao, Magdy Mahfouz
Summary: This study presents a new peptide nucleic acid (PNA)-based nucleic acid detection toolkit, PNA-Pdx, which provides accurate and rapid detection of specific nucleic acid sequences, including pathogens and genomic sequences, such as SARS-CoV-2, in clinical samples.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Wenjun Jiang, Rashid Aman, Zahir Ali, Gundra S. Rao, Magdy Mahfouz
Summary: PNA-Pdx is a novel peptide nucleic acid (PNA)-based nucleic acid detection toolkit that can accurately and rapidly detect specific nucleic acid sequences. It can also invade double-stranded DNA to produce single-stranded DNA for precise detection of genomic SNPs.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Fanwei Luo, Fei Chen, Yi Xiong, Zhen Wu, Xiuhua Zhang, Wei Wen, Shengfu Wang
Summary: The integration of magnetic separation and DNA walker amplification has resulted in a robust and sensitive single-particle electrochemical biosensor. This method effectively captures and separates targets from complex samples, avoiding interference and aggregation, leading to cyclic amplification and greatly enhanced detection sensitivity. The ultrasensitive detection of HIV DNA in complex systems demonstrates promising potential for real sample applications and the development of new single-entity biosensors.
ANALYTICAL CHEMISTRY
(2021)
Article
Urology & Nephrology
Wei Zhu, Xin Zhang, Zhen Zhou, Yin Sun, Guangyuan Zhang, Xiaolu Duan, Zhicong Huang, Guoyao Ai, Yang Liu, Zhijian Zhao, Wen Zhong, Guohua Zeng
Summary: This study found a significant association between single nucleotide polymorphisms (SNPs) and kidney stone recurrence, and SNPs can provide prognostic value in addition to traditional clinical risk factors. A predictive model combining clinical and genetic variables shows potential as an assessment tool for evaluating the recurrence risk of kidney stones.
CLINICAL KIDNEY JOURNAL
(2023)
Article
Chemistry, Analytical
Juneseok You, Kuewhan Jang, Hyunjun Park, Seonwoo Lee, Ahreum Lim, Chanho Park, Kyonghwa Park, Sungsoo Na
Summary: This study developed a method using PNA and RNase H II for real-time PCR to detect KRAS single nucleotide polymorphism. The method exhibited high sensitivity and selectivity, and achieved a synergistic effect by combining the advantages of both techniques. Validation tests with different samples showed the potential of this method in detecting cancer mutations and its applicability in breath biopsy.
ANALYTICA CHIMICA ACTA
(2022)
Article
Chemistry, Analytical
Zhang Zhang, Luhao Guan, Juan Yao, Lijia Li, Chunfang Liu, Yongcan Guo, Guoming Xie
Summary: In this study, a closed-tube, dual-labeled RNA-modified probes and RNase H II-assisted real-time LAMP (RART-LAMP) method was proposed for SNP genotyping. This method allows for rapid and accurate nucleic acid analysis in resource-limited settings, and can be applied to various sample types including blood, saliva, and swabs.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
David Laehnemann, Johannes Koester, Ute Fischer, Arndt Borkhardt, Alice C. McHardy, Alexander Schoenhuth
Summary: ProSolo is a tool for calling single nucleotide variants from MDA single cell DNA sequencing data, which integrates all relevant MDA biases to achieve higher accuracy and reliability in single cells compared to existing tools.
NATURE COMMUNICATIONS
(2021)
Article
Agriculture, Dairy & Animal Science
H. Alkhoder, Z. Liu, D. Segelke, R. Reents
Summary: The single-step genomic evaluation model in German Holsteins shows higher prediction correlation and greater genomic breeding values variance compared to the current multistep genomic model. There was no overprediction of young animals for conformation traits by the single-step SNP BLUP model in German Holsteins.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Chemistry, Analytical
Qilin Wen, Dandan Li, Huai Xi, Guidan Huang, Wenyuan Zhu
Summary: A rapid and sensitive fluorescence sensing strategy for the detection of Dam MTase activity was developed based on methylation-blocked enzymatic recycling amplification. This method has a lower detection limit and shorter assay time compared with previously reported similar methodologies.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2022)
Article
Health Care Sciences & Services
Jung Oh Kim, Han Sung Park, Eun Ju Ko, Jung Hoon Sung, Jinkwon Kim, Seung Hun Oh, Ok Joon Kim, Nam Keun Kim
Summary: TS 1100T>C and 1170A>G polymorphisms are strongly associated with the risk of ischemic stroke and SBI in Koreans, with 1100T>C polymorphism also showing synergistic effects with low folic acid levels. These findings suggest that TS 1100T>C and 1170A>G polymorphisms may serve as potential biomarkers for ischemic stroke and SBI.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Agriculture, Dairy & Animal Science
Ahmed M. Sallam
Summary: This study investigated TLR 4 gene polymorphisms in Barki ewes and their correlation with milk traits, identifying a missense mutation with potential effects on milk traits. Results suggest a significant impact of TLR genotype on milk fat and protein percentage, with the presence of the G allele increasing milk yield and decreasing fat, protein, and total solid percentage.
Article
Microbiology
Li-Xiao Sun, Hui Qian, Meng-Yu Liu, Ming-Hua Wu, Yun-Yun Wei, Xue-Ming Zhu, Jian-Ping Lu, Fu-Cheng Lin, Xiao-Hong Liu
Summary: The study identified and characterized Hse1 and Vps27 in M. oryzae, showing that disruption of MoHse1 and MoVps27 caused pleiotropic defects in growth, conidiation, sexual development, and pathogenicity. It was also found that ESCRT-0 is involved in the regulation of autophagy and interacts with COPII, impacting ER homeostasis and UPR. This suggests that ESCRT-0 plays critical roles in regulating fungal development, virulence, autophagy, and ER-phagy in M. oryzae.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Pengyun Huang, Yan Li, Jing Wang, Qing Wang, Zhicheng Huang, Xiaohong Liu, Fucheng Lin, Jianping Lu
Summary: A transcription factor, Pcf1, was found to be inhibited and degraded in nuclei of incipient appressoria in Magnaporthe oryzae, interacting with CK2 and undergoing ubiquitination in hyphae. These findings provide insight into the degradation of TFs during appressorium formation.
Article
Microbiology
Ming-Hua Wu, Lu-Yao Huang, Li-Xiao Sun, Hui Qian, Yun-Yun Wei, Shuang Liang, Xue-Ming Zhu, Lin Li, Jian-Ping Lu, Fu-Cheng Lin, Xiao-Hong Liu
Summary: The MoAlo1 protein plays a crucial role in vegetative growth, conidiogenesis, and pathogenicity in Magnaporthe oryzae.
Article
Microbiology
Ying-Ying Cai, Jing-Yi Wang, Xi-Yu Wu, Shuang Liang, Xue-Ming Zhu, Lin Li, Jian-Ping Lu, Xiao-Hong Liu, Fu-Cheng Lin
Summary: This study reveals that MoOpy2 plays an essential role in fungal development, appressorium penetration, autophagy, and pathogenesis of Magnaporthe oryzae.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Qing Wang, Jing Wang, Pengyun Huang, Zhicheng Huang, Yan Li, Xiaohong Liu, Fucheng Lin, Jianping Lu
Summary: Studies have shown that Nap1 plays a crucial role in Magnaporthe oryzae, participating in regulating fungal development and virulence, especially in appressorium formation and plant penetration.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Pengyun Huang, Jing Wang, Yan Li, Qing Wang, Zhicheng Huang, Hui Qian, Xiao-Hong Liu, Fu-Cheng Lin, Jianping Lu
Summary: In this study, it was found that Vrf1 and Hox7 play vital roles in the regulation of appressorium maturation in Magnaporthe oryzae. They coordinate the formation and development of appressoria by regulating the expression of genes related to cell wall remodeling.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Microbiology
Ming-Hua Wu, Qin Yu, Tian-Yi Tao, Li-Xiao Sun, Hui Qian, Xue-Ming Zhu, Lin Li, Shuang Liang, Jian-Ping Lu, Fu-Cheng Lin, Xiao-Hong Liu
Summary: This study identified and analyzed the AGC kinases in Magnaporthe oryzae, a plant-pathogenic fungus. It revealed the important roles of AGC kinases in the growth, conidiation, germination, appressorium formation, and pathogenicity of the fungus. Furthermore, it discovered the specific functions of MoFpk1, a subfamily protein of AGC kinases, in cell wall integrity and lipid metabolism. The study also provided insights into the mechanisms of plasma membrane homeostasis and autophagy through lipid asymmetry maintenance.
Article
Plant Sciences
Jing Wang, Qing Wang, Pengyun Huang, Yingmin Qu, Zhicheng Huang, Huan Wang, Xiao-Hong Liu, Fu-Cheng Lin, Jianping Lu
Summary: Defects in endosomal structure and the cAMP-PKA pathway contribute to the defective appressorium maturation and virulence of Magnaporthe oryzae.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Jing Wang, Zhicheng Huang, Pengyun Huang, Qing Wang, Yan Li, Xiao-Hong Liu, Fu-Cheng Lin, Jianping Lu
Summary: This study shows that the Clp1 protein in M. oryzae regulates development and pathogenicity by maintaining autophagy homeostasis and affecting gene transcription in the nucleus.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Meng-Yu Liu, Li-Xiao Sun, Hui Qian, Yun-Ran Zhang, Xue-Ming Zhu, Lin Li, Shuang Liang, Jian-Ping Lu, Fu-Cheng Lin, Xiao-Hong Liu
Summary: The study revealed the importance of de novo purine nucleotide biosynthesis in conidiation, development, and pathogenicity in M. oryzae.
Article
Plant Sciences
Hui Qian, Lixiao Sun, Minghua Wu, Wenhui Zhao, Mengyu Liu, Shuang Liang, Xueming Zhu, Lin Li, Zhenzhu Su, Jianping Lu, Fucheng Lin, Xiaohong Liu
Summary: The endoplasmic reticulum (ER) is the starting point of the secretory pathway and COPII vesicles are responsible for transporting cargo proteins from the ER to the Golgi. This study identified and explored the importance of the inner shell subunit of COPII vesicles (MoSec24B) in the rice blast fungus. The disruption of MoSec24B led to various negative effects on fungal growth, pathogenicity, and autophagy, highlighting the significant role of MoSec24B in fungal development and disease progression.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Zi-Fang Shen, Lin Li, Jing-Yi Wang, Yun-Ran Zhang, Zi-He Wang, Shuang Liang, Xue-Ming Zhu, Jian-Ping Lu, Fu-Cheng Lin, Xiao-Hong Liu
Summary: The COP9 signalosome (CSN) plays an important role in regulating fungal development, pathogenicity, and autophagy in Magnaporthe oryzae. The CSN subunit MoCsn6 is involved in vegetative growth, sporulation, and plant infection. Deletion of MoCSN6 disrupts the Osm1 and Pmk1 phosphorylation pathways and negatively regulates autophagic activity by interacting with MoAtg6 and controlling its ubiquitination level.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Zi-He Wang, Zi-Fang Shen, Jing-Yi Wang, Ying-Ying Cai, Lin Li, Jian Liao, Jian-Ping Lu, Xue-Ming Zhu, Fu-Cheng Lin, Xiao-Hong Liu
Summary: This study identified a novel calcineurin regulatory-subunit-binding protein, MoCbp7, which is involved in calcium signal transduction and is important for the growth, conidiation, appressorium formation, invasive growth, and virulence of Magnaporthe oryzae. MoCbp7 also interacts with calcineurin to regulate endoplasmic reticulum homeostasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Zhicheng Huang, Huijuan Cao, Huan Wang, Pengyun Huang, Jing Wang, Ying-Ying Cai, Qing Wang, Yan Li, Jiaoyu Wang, Xiao-Hong Liu, Fu-Cheng Lin, Jianping Lu
Summary: In this study, the researchers identified a serine/threonine protein phosphatase regulatory subunit called Smek1 that plays a crucial role in the growth, conidiation, and virulence of Magnaporthe oryzae. Deleting SMEK1 resulted in defects in the utilization of lipids, arabinose, glycerol, and ethanol. Additionally, Smek1 was found to directly interact with and dephosphorylate the proteins CreA and Crf1, which are involved in carbon metabolism. Overall, Smek1 acts as a dual-function regulator of lipid and carbohydrate metabolism, coordinating fungal development and virulence.
MOLECULAR PLANT PATHOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Zhicheng Huang, Qing Wang, Irshad Ali Khan, Yan Li, Jing Wang, Jiaoyu Wang, Xiaohong Liu, Fucheng Lin, Jianping Lu
Summary: The methylcitrate cycle and the glyoxylate cycle are important carbon metabolic pathways in fungi, which not only convert toxic intermediates into usable substances, but also play important roles in fungal growth, development, and pathogenic processes.