Article
Biochemistry & Molecular Biology
Xiu-Mei Dong, Wei Zhang, Shi-Bao Zhang
Summary: This study analyzed the expression profiles of anthocyanin and carotenoids biosynthesis genes in Cymbidium lowianum using qRT-PCR. Reference gene selection and validation were conducted before normalization of gene expression. The study provides reference genes in Cymbidium lowianum and valuable information for understanding the molecular mechanisms of flower color formation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Green & Sustainable Science & Technology
Jing Xu, Jing Li, Tianpeng Gao
Summary: This study aims to select suitable reference genes for gene expression quantification in E. crassipes and analyze the expression stability of candidate reference genes in different tissue samples, hormone-treated samples, phosphorus-treated samples, and mixed samples. The results suggest that different reference genes should be selected according to the specific experimental setup.
Article
Biochemistry & Molecular Biology
Sarah Arrowsmith
Summary: This study evaluated the stability of reference genes in pregnant human myometrium and found CYC1, YWHAZ, and ATP5B to be the most stable genes. On the other hand, ACTB, 18s, and B2M were found to be less stable and too variable for accurate normalization.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Microbiology
Lingning Meng, Xiaoli Cao, Chuchu Li, Jia Li, Hui Xie, Jiping Shi, Mei Han, Han Shen, Chang Liu
Summary: This study tested the stability of ten classic housekeeping genes under the pressure of eight commonly used antibiotics in the laboratory. Results showed that the stability of gene expression was indeed affected by the types of antibiotics added, and the best reference gene set varied for different antibiotics. This study provides a comprehensive summary of the effects of laboratory antibiotics on the stability of housekeeping genes in P. aeruginosa, highlighting the necessity to select housekeeping genes according to the type of antibiotics used in the initial stage of experiment.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ines Medina-Lozano, Maria Soledad Arnedo, Jerome Grimplet, Aurora Diaz
Summary: In this study, six candidate reference genes (ADF2, CYB5, iPGAM, SCL13, TRXL3-3, and VHA-H) with low expression variation were selected for gene expression studies. Their stability was evaluated using qPCR and various analytical tools, and CYB5 was found to be the most stable gene in the leaf colour experiment, while TRXL3-3 was the most stable gene in the tissue and drought stress experiments. These findings provide valuable information for gene expression studies in Lactuca spp. under the specified conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Aishuang Hu, Xiuyan Yang, Jianfeng Zhu, Xiuping Wang, Jiaxin Liu, Jiping Wang, Haiwen Wu, Huilong Zhang, Huaxin Zhang
Summary: This study provides a theoretical reference for the standardization and quantification of gene expression in N. sibirica under various abiotic stress conditions, and helps to reveal the molecular mechanisms that confer stress tolerance to N. sibirica.
Article
Plant Sciences
Ragini Sinha, Meenu Bala, Pragya Prabha, Alok Ranjan, Rakesh K. Chahota, Tilak Raj Sharma, Anil Kumar Singh
Summary: The study identified nine candidate reference genes from horse gram RNA-seq data and evaluated their stability in two genotypes under various abiotic stress conditions. TCTP was found to be the most stable gene overall, while profilin was most stable in one genotype and PSMA5 was least stable. TCTP and profilin genes were validated for data normalization in gene expression studies in horse gram.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
Article
Biochemistry & Molecular Biology
Zhiwei Chen, Nigel G. Halford, Chenghong Liu
Summary: Real-time quantitative PCR is a technique for measuring the content of a specific nucleic acid sequence in a sample, and it can be divided into absolute and relative quantitative methods. Relative quantification is mainly used for gene expression in functional genomics and transcriptome studies. However, to accurately use this technology, key points such as designing specific primers, selecting appropriate reference genes, and performing scientific calculations and statistics are crucial. This article proposes a workflow for relative quantitative PCR and introduces relevant points to help beginners better understand and utilize this technology.
Article
Agronomy
Wenjing Yu, Yuan Tao, Liping Luo, Jonathan Hrovat, Ahui Xue, Huolin Luo
Summary: In this study, three computational statistical methods were used to evaluate the expression stability of 12 commonly-used reference genes in Dianthus caryophyllus. The results showed significant variations in the expression stability of candidate genes across different experimental conditions. TIP41 and UBQ10 were identified as relatively stable reference genes, while CYP and TUA could serve as reliable internal controls. Additionally, certain gene pairs were found to be suitable reference genes under specific treatments, such as hormone, heavy metal, salt, heat, cold, flooding, and drought.
NEW ZEALAND JOURNAL OF CROP AND HORTICULTURAL SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Nina Franko, Lucija Ana Vrscaj, Taja Zore, Barbara Ostanek, Janja Marc, Jasna Lojk
Summary: RT-qPCR is the gold standard method for measuring gene expression, and selection of appropriate reference genes for normalization is crucial. This study identified the most stable reference genes during osteogenic differentiation of human osteosarcoma cell lines using statistical algorithms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Kathannan Sankar, Hyung Joo Yoon, Young Bo Lee, Kyeong Yong Lee
Summary: Bumble bees are important alternative pollinators and model insects. This study identified stable reference genes for the bumble bee species and their different lines and tissues using RT-qPCR procedures and four analysis programs. The results emphasized the need to evaluate the stability of candidate reference genes for any differently designed lines and tissue conditions in bumble bee species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Horticulture
Chenjie Zhang, Chengwei Song, Linfeng Chen, Huili Ma, Yabing Zhang, Dalong Guo, Lili Guo, Xiaogai Hou
Summary: The aim of this study was to identify suitable reference genes for normalizing the expression levels of miRNA in different developmental stages and tissues. Five algorithms were used for stability analysis, and the results identified mtr-MIR160b-p3 and gma-miR394a-5p as the most stable miRNAs during bud development in early-flowering tree peony 'Feng dan', while PC-5p-19095 was the most stable during bud development in late-flowering tree peony 'Lian he'. Additionally, mtr-miR159a was found to be the most stable miRNA during flower development stages of different tree peony varieties.
Article
Plant Sciences
Rohit Bharati, Madhab Kumar Sen, Ram Kumar, Aayushi Gupta, Jana Ziarovska, Eloy Fernandez-Cusimamani, Olga Leuner
Summary: This study assessed the suitability of ten commonly used reference genes as optimal reference genes in M. officinalis under different abiotic stress conditions and plant organs. The combination of EF-1 alpha and GAPDH was recommended as the best reference genes for gene expression studies in M. officinalis.
Article
Horticulture
Rundong Yao, Xiaolou Huang, Hanqing Cong, Fei Qiao, Yunjiang Cheng, Yeyuan Chen
Summary: Real-Time PCR is a rapid and sensitive technique widely used to determine gene expression. This study identified 10 candidate reference genes in mangos and evaluated their stability using professional software. TUBB gene was found to be the most stable and suitable reference gene.
Article
Food Science & Technology
Yao Liu, Ling Li, Yuanmiao Wei, Hanyue Zhang, Shuna Xiang, Ying Shang
Summary: The article introduces a detection method for T. albuminosus mushrooms using the TSA gene as an endogenous reference gene. The method is validated through qualitative and quantitative PCR, providing a fast and accurate way to detect T. albuminosus and protect consumers' rights while promoting the industry.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Gastroenterology & Hepatology
Fengchao Wang, David Scoville, Xi C. He, Maxime M. Mahe, Andrew Box, John M. Perry, Nicholas R. Smith, Nan Ye Lei, Paige S. Davies, Megan K. Fuller, Jeffrey S. Haug, Melainia McClain, Adam D. Gracz, Sheng Ding, Matthias Stelzner, James C. Y. Dunn, Scott T. Magness, Melissa H. Wong, Martin G. Martin, Michael Helmrath, Linheng Li
Article
Biochemistry & Molecular Biology
Jiong Ren, Zhibin Niu, Xiaoqin Li, Jie Yang, Meijiao Gao, Xudong Li, Tao Zhang, Lei Fang, Boyang Zhang, Junping Wang, Yongping Su, Fengchao Wang
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2018)
Article
Medicine, Research & Experimental
Tao Zhang, Qilong Wang, Yeqi Wang, Junping Wang, Yongping Su, Fengchao Wang, Guixue Wang
JOURNAL OF TRANSLATIONAL MEDICINE
(2019)
Article
Chemistry, Multidisciplinary
Chenwen Li, Yang Zhao, Juan Cheng, Jiawei Guo, Qixiong Zhang, Xiangjun Zhang, Jiong Ren, Fengchao Wang, Jun Huang, Houyuan Hu, Ruibing Wang, Jianxiang Zhang
Article
Endocrinology & Metabolism
Shilei Chen, Yan Qi, Song Wang, Yang Xu, Mingqiang Shen, Mengjia Hu, Changhong Du, Fang Chen, Mo Chen, Yukai Lu, Zihao Zhang, Yong Quan, Cheng Wang, Fengchao Wang, Junping Wang
JOURNAL OF PINEAL RESEARCH
(2020)
Article
Cell Biology
Hao Du, Chen Chen, Yan Wang, Yang Yang, Zhuanzhuan Che, Xiaoxu Liu, Siyan Meng, Chenghao Guo, Manman Xu, Haitong Fang, Fengchao Wang, Chengqi Lin, Zhuojuan Luo
JOURNAL OF MOLECULAR CELL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Na Zhao, Guojian Wang, Shuang Long, Dengqun Liu, Jining Gao, Yang Xu, Cheng Wang, Aiping Wang, Fengchao Wang, Yuhui Hao, Xinze Ran, Junping Wang, Yongping Su, Tao Wang
Summary: The study identifies an endogenous pattern involving Spink7 in the immune compartment as a key player in controlling chemokines/cytokines production, contributing to the resolution of inflammation in colitis.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2021)
Article
Biochemistry & Molecular Biology
Mengjia Hu, Yukai Lu, Song Wang, Zihao Zhang, Yan Qi, Naicheng Chen, Mingqiang Shen, Fang Chen, Mo Chen, Lijing Yang, Shilei Chen, Dongfeng Zeng, Fengchao Wang, Yongping Su, Yang Xu, Junping Wang
Summary: The study identifies CD63 as a novel functional marker of HSCs in mice, showing that high CD63 expression is associated with more quiescent HSCs with robust self-renewal and myeloid differentiation abilities. CD63 deficiency leads to reduced HSC numbers, impaired quiescence, and increased sensitivity to irradiation and 5-fluorouracil treatment. Further investigations reveal that CD63 interacts with TGF beta receptors to sustain TGF beta signaling activity and regulate HSC quiescence.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Biochemistry & Molecular Biology
Zixiao Jiang, Zhenqing Li, Fengchao Wang, Zhiqin Zhou
Summary: The study revealed that PMFs in sour orange protected mice from radiation-induced injury by maintaining intestinal structure and showing high radio-resistance potential.
Article
Multidisciplinary Sciences
Xin Wu, Yun Wang, Rui Huang, Qujing Gai, Haofei Liu, Meimei Shi, Xiang Zhang, Yonglin Zuo, Longjuan Chen, Qiwen Zhao, Yu Shi, Fengchao Wang, Xiaowei Yan, Huiping Lu, Senlin Xu, Xiaohong Yao, Lin Chen, Xia Zhang, Qiang Tian, Ziyan Yang, Bo Zhong, Chen Dong, Yan Wang, Xiu-Wu Bian, Xindong Liu
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)