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Ren J, Xu G, Liu H, He N, Zhao Z, Wang M, Gu P, Chen Z, Deng Y, Wu D, Li S. A Chamber-Based Digital PCR Based on a Microfluidic Chip for the Absolute Quantification and Analysis of KRAS Mutation. BIOSENSORS 2023; 13:778. [PMID: 37622864 PMCID: PMC10452697 DOI: 10.3390/bios13080778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/26/2023]
Abstract
The Kirsten rat sarcoma virus gene (KRAS) is the most common tumor in human cancer, and KRAS plays an important role in the growth of tumor cells. Normal KRAS inhibits tumor cell growth. When mutated, it will continuously stimulate cell growth, resulting in tumor development. There are currently few drugs that target the KRAS gene. Here, we developed a microfluidic chip. The chip design uses parallel fluid channels combined with cylindrical chamber arrays to generate 20,000 cylindrical microchambers. The microfluidic chip designed by us can be used for the microsegmentation of KRAS gene samples. The thermal cycling required for the PCR stage is performed on a flat-panel instrument and detected using a four-color fluorescence system. "Glass-PDMS-glass" sandwich structure effectively reduces reagent volatilization; in addition, a valve is installed at the sample inlet and outlet on the upper layer of the chip to facilitate automatic control. The liquid separation performance of the chip was verified by an automated platform. Finally, using the constructed KRAS gene mutation detection system, it is verified that the chip has good application potential for digital polymerase chain reaction (dPCR). The experimental results show that the chip has a stable performance and can achieve a dynamic detection range of four orders of magnitude and a gene mutation detection of 0.2%. In addition, the four-color fluorescence detection system developed based on the chip can distinguish three different KRAS gene mutation types simultaneously on a single chip.
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Affiliation(s)
- Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (J.R.)
| | - Gangwei Xu
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China
- Hunan Shengzhou Biotechnology Company Limited, Shanghai 200439, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (J.R.)
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (J.R.)
| | - Zhehao Zhao
- Hunan Shengzhou Biotechnology Company Limited, Shanghai 200439, China
| | - Meiling Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (J.R.)
| | - Peipei Gu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (J.R.)
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (J.R.)
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (J.R.)
| | - Dongping Wu
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China
- Hunan Shengzhou Biotechnology Company Limited, Shanghai 200439, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (J.R.)
- Hengyang Medical School, University of South China, Hengyang 421001, China
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Yang S, Chen J, Ding Y, Huang Q, Chen G, Ulhassan Z, Wei J, Wang J. Genome-wide investigation and expression profiling of LOR gene family in rapeseed under salinity and ABA stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1197781. [PMID: 37324688 PMCID: PMC10264818 DOI: 10.3389/fpls.2023.1197781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
The Brassica napus (B. napus) LOR (Lurp-One-Related) gene family is a little-known gene family characterized by a conserved LOR domain in the proteins. Limited research in Arabidopsis showed that LOR family members played important roles in Hyaloperonospora parasitica (Hpa) defense. Nevertheless, there is a paucity of research investigating the role of the LOR gene family towards their responses to abiotic stresses and hormone treatments. This study encompassed a comprehensive survey of 56 LOR genes in B. napus, which is a prominent oilseed crop that holds substantial economic significance in China, Europe, and North America. Additionally, the study evaluated the expression profiles of these genes in response to salinity and ABA stress. Phylogenetic analysis showed that 56 BnLORs could be divided into 3 subgroups (8 clades) with uneven distribution on 19 chromosomes. 37 out of 56 BnLOR members have experienced segmental duplication and 5 of them have undergone tandem repeats events with strong evidence of purifying selection. Cis-regulatory elements (CREs) analysis indicated that BnLORs involved in process such as light response, hormone response, low temperature response, heat stress response, and dehydration response. The expression pattern of BnLOR family members revealed tissue specificity. RNA-Seq and qRT-PCR were used to validate BnLOR gene expression under temperature, salinity and ABA stress, revealing that most BnLORs showed inducibility. This study enhanced our comprehension of the B. napus LOR gene family and could provide valuable information for identifying and selecting genes for stress resistant breeding.
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Affiliation(s)
- Su Yang
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Jialuo Chen
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Yonghe Ding
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Qian Huang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Guangna Chen
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Zaid Ulhassan
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Ji’an Wei
- Mizuda Group Co., Ltd., Huzhou, Zhejiang, China
| | - Jian Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Zhang HX, Zhang C, Lu S, Tong X, Zhang K, Yin H, Zhang Y. Cas12a-based one-pot SNP detection with high accuracy. CELL INSIGHT 2023; 2:100080. [PMID: 37193068 PMCID: PMC10134196 DOI: 10.1016/j.cellin.2023.100080] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 05/18/2023]
Abstract
CRISPR-Cas12a based one-pot detection system has been used in nucleic acid detection and diagnosis. However, it is not sensitive enough to distinguish single nucleotide polymorphisms (SNP), which has greatly restricted its application. To overcome these limitations, we engineered a LbCas12a variant with enhanced sensitivity against SNP, named seCas12a (sensitive Cas12a). SeCas12a-based one-pot SNP detection system is a versatile platform that could use both canonical and non-canonical PAM, and was almost not limited by mutation types to distinguish SNPs located between position 1 to 17. The use of truncated crRNA further improved SNP specificity of seCas12a. Mechanistically, we found only when the cis-cleavage was at low level between 0.01min-1 and 0.0006 min-1, a good signal-to-noise ratio can be achieved in one-pot test. SeCas12a-based one-pot SNP detection system was applied to detect pharmacogenomic SNPs in human clinical samples. Of thirteen donors tested in two different SNPs, the seCas12a mediated one-pot system could faithfully detect the SNPs in 30 min with 100% accuracy.
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Affiliation(s)
- Hong-Xia Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Caixiang Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Shuhan Lu
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Xiaohan Tong
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Kun Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Hao Yin
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Ying Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
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Tripathi DK, Punj V, Singh NK, Guerriero G, Deshmukh R, Sharma S. Recent biotechnological avenues in crop improvement and stress management. J Biotechnol 2022; 349:21-24. [DOI: 10.1016/j.jbiotec.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhang K, Mason AS, Farooq MA, Islam F, Quezada-Martinez D, Hu D, Yang S, Zou J, Zhou W. Challenges and prospects for a potential allohexaploid Brassica crop. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2711-2726. [PMID: 34089067 DOI: 10.1007/s00122-021-03845-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/23/2021] [Indexed: 05/28/2023]
Abstract
The production of a new allohexaploid Brassica crop (2n = AABBCC) is increasingly attracting international interest: a new allohexaploid crop could benefit from several major advantages over the existing Brassica diploid and allotetraploid species, combining genetic diversity and traits from all six crop species with additional allelic heterosis from the extra genome. Although early attempts to produce allohexaploids showed mixed results, recent technological and conceptual advances have provided promising leads to follow. However, there are still major challenges which exist before this new crop type can be realized: (1) incorporation of sufficient genetic diversity to form a basis for breeding and improvement of this potential crop species; (2) restoration of regular meiosis, as most allohexaploids are genetically unstable after formation; and (3) improvement of agronomic traits to the level of "elite" breeding material in the diploid and allotetraploid crop species. In this review, we outline these major prospects and challenges and propose possible plans to produce a stable, diverse and agronomically viable allohexaploid Brassica crop.
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Affiliation(s)
- Kangni Zhang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Muhammad A Farooq
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Faisal Islam
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Daniela Quezada-Martinez
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Dandan Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Su Yang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China.
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