Cheng Peng

Chengdu University of Traditional Chinese Medicine

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Junfeng Xu

Ministry of Agriculture and Rural Affairs

Xiaofu Wang

ZheJiang Academy of Agricultural Sciences

Xiaoli Xu

ZheJiang Academy of Agricultural Sciences

Jian Wu

Zhejiang University

Xiaoyun Chen

Nanjing Agricultural University

Yanju Chen

Zhejiang University of Science and Technology

Xiaoyun Chen

Fujian Agriculture and Forestry University

Lin Ding

Nanjing University

Siwenjie Qian

Zhejiang University

Yihua Wang

Nanjing Agricultural University

Cooperative Institutions

Ministry of Agriculture and Rural Affairs

Nanjing Agricultural University

Chinese Academy of Agricultural Sciences

ZheJiang Academy of Agricultural Sciences

Zhejiang University

Chinese Academy of Sciences

Shanghai Jiao Tong University

China National Rice Research Institute

Chinese Academy of Medical Sciences & Peking Union Medical College

University of Chinese Academy of Sciences

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Association between Serum Homocysteine and Erectile Dysfunction: A Systematic Review and Meta-Analysis

Cheng Peng Huimin Li Yajun Shen Yun-wu Wang Xiaolei Tang

Objectives: To detect the relationship between erectile dysfunction (ED) and serum homocysteine (Hcy).Methods: A comprehensive search was done using databases such as Web of Science, Pubmed, and Cochrane Library to identify suitable studies for publication by July 2023. The statistical analysis involved calculating the standardized mean difference (SMD) along with 95% confidence intervals (CI) using the STATA software.Results:17 studies with 2165 ED patients and 3023 non-ED controls were included in this meta-analysis. Pooled results indicated that ED patients’ Hcy levels were obviously higher than the controls (SMD (95% CI) =1.07 (0.68,1.46), p<0.001). Subgroup analysis showed a higher SMD in age>40, IIEF-5 (score: 8-11), BMI> 24 kg/m2, subjects without diabetes and location in China, (1.27 (0.66,1.88), p<0.001; 1.87 (0.71,3.04), p<0.001; 1.01 (0.54,1.48), p<0.001; 0.97 (0.51,1.43), p<0.001; 1.25 (0.66,1.84), p<0.001), respectively.Conclusions: Our meta-analysis indicates that subjects with ED exhibit higher levels of serum Hcy. However, due to the existence of publication bias, more rigorous and large-sample studies are demanded to support it.

Plasma homocysteine

Association (psychology)

10.2139/ssrn.4599362

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Development of DNA Reference Materials of Citrus Huanglongbing Candidatus Liberibacter asiaticus

ACS Agricultural Science & Technology (2024)

Xiaoyun Chen Kai Li Yi Ji Ziyue Zhang Xin Qi

Citrus Huanglongbing (HLB) is a devastating disease within the Citrus industry. Candidatus Liberibacter asiaticus (CLas) is one of the most prevalent HLB-associated strains that has not been cultured in vitro. To ensure the accuracy and comparability of the molecular diagnostic method for HLB detection, certified reference materials urgently need to be developed for CLas detection. Here, we developed a series of DNA reference materials of CLas using 16S rDNA as the target gene and the SAND gene as the Citrus reference gene. The 16S rDNA gene fragment cloned by the NCBI sequence and Citrus DNA extracted by healthy Citrus leaves are thoroughly mixed for preparation. Droplet digital PCR (ddPCR) was used as an accurate quantification method for 16S rDNA, and the SAND was established and optimized through this study. Nine laboratories collaborated in determining these two parameters, and the homogeneity and stability were adequate. The quantification results demonstrated that the copy number certified values and expanded uncertainty of 16S rDNA and SAND in the high-concentration reference material were (3.86 ± 0.34) × 103 and (4.43 ± 0.39) × 103 cp/μL, respectively. The copy number certified values and expanded uncertainty of 16S rDNA and SAND in the low-concentration reference material were (3.98 ± 0.36) × 102 and (4.34 ± 0.37) × 103 cp/μL, respectively. In addition, this certified reference material will provide reliable quality control for detecting CLas.

10.1021/acsagscitech.4c00001

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A PAM-Free One-Step Asymmetric RPA and CRISPR/Cas12b Combined Assay (OAR-CRISPR) for Rapid and Ultrasensitive DNA Detection

Analytical Chemistry (2024)

Lei Yang Guanwei Chen Jian Wu Wei Wei Cheng Peng

Current research endeavors have focused on the combination of various isothermal nucleic acid amplification methods with CRISPR/Cas systems, aiming to establish a more sensitive and reliable molecular diagnostic approach. Nevertheless, most assays adopt a two-step procedure, complicating manual operations and heightening the risk of contamination. Efforts to amalgamate both assays into a single-step procedure have faced challenges due to their inherent incompatibility. Furthermore, the presence of the protospacer adjacent motif (PAM) motif (e.g., TTN or TTTN) in the target double-strand DNA (dsDNA) is an essential prerequisite for the activation of the Cas12-based method. This requirement imposes constraints on crRNA selection. To overcome such limitations, we have developed a novel PAM-free one-step asymmetric recombinase polymerase amplification (RPA) coupled with a CRISPR/Cas12b assay (OAR-CRISPR). This method innovatively merges asymmetric RPA, generating single-stranded DNA (ssDNA) amenable to CRISPR RNA binding without the limitations of the PAM site. Importantly, the single-strand cleavage by PAM-free crRNA does not interfere with the RPA amplification process, significantly reducing the overall detection times. The OAR-CRISPR assay demonstrates sensitivity comparable to that of qPCR but achieves results in a quarter of the time required by the latter method. Additionally, our OAR-CRISPR assay allows the naked-eye detection of as few as 60 copies/μL DNA within 8 min. This innovation marks the first integration of an asymmetric RPA into one-step CRISPR-based assays. These advancements not only support the progression of one-step CRISPR/Cas12-based detection but also open new avenues for the development of detection methods capable of targeting a wide range of DNA targets.

Trans-activating crRNA

Recombinase Polymerase Amplification

10.1021/acs.analchem.3c05545

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Effect on metabolome of the grains of transgenic rice containing insecticidal cry and glyphosate tolerance epsps genes

Plant Growth Regulation (2019)

Cheng Peng Lin Ding Chaoyang Hu Xiaoyun Chen Xiaofu Wang

Metabolome

Genetically modified rice

10.1007/s10725-019-00482-6

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Using Combined Methods of Genetic Mapping and Nanopore-Based Sequencing Technology to Analyze the Insertion Positions of G10evo-EPSPS and Cry1Ab/Cry2Aj Transgenes in Maize

Frontiers in Plant Science (2021)

Cheng Peng Yingting Mei Lin Ding Xiaofu Wang Xiaoyun Chen

The insertion position of the exogenous fragment sequence in a genetically modified organism (GMO) is important for the safety assessment and labeling of GMOs. SK12-5 is a newly developed transgenic maize line transformed with two trait genes [i.e., G10evo -5-enolpyrul-shikimate-3-phosphate synthase (EPSPS) and Cry1Ab/Cry2Aj ] that was recently approved for commercial use in China. In this study, we tried to determine the insertion position of the exogenous fragment for SK12-5. The transgene–host left border and right border integration junctions were obtained from SK12-5 genomic DNA by using the thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) and next-generation Illumina sequencing technology. However, a Basic Local Alignment Search Tool (BLAST) analysis revealed that the flanking sequences in the maize genome are unspecific and that the insertion position is located in a repetitive sequence area in the maize genome. To locate the fine-scale insertion position in SK12-5, we combined the methods of genetic mapping and nanopore-based sequencing technology. From a classical bulked-segregant analysis (BSA), the insertion position in SK12-5 was mapped onto Bin9.03 of chromosome 9 between the simple sequence repeat (SSR) markers umc2337 and umc1743 (26,822,048–100,724,531 bp). The nanopore sequencing results uncovered 10 reads for which one end was mapped onto the vector and the other end was mapped onto the maize genome. These observations indicated that the exogenous T-DNA fragments were putatively integrated at the position from 82,329,568 to 82,379,296 bp of chromosome 9 in the transgenic maize SK12-5. This study is helpful for the safety assessment of the novel transgenic maize SK12-5 and shows that the combined method of genetic mapping and the nanopore-based sequencing technology will be a useful approach for identifying the insertion positions of transgenic sequences in other GM plants with relatively large and complex genomes.

Insertion

genomic DNA

Insertion sequence

Bacterial artificial chromosome

10.3389/fpls.2021.690951

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HPLC‐MS/MSにより測定した異なる生育段階におけるActinidia valvata葉中のフラボノイドの動的変化【Powered by NICT】

Qiaohui Du Qiaoyan Zhang Ting Han Jiang Yi-ping Cheng Peng

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A rapid and convenient method for on-site detection of MON863 maize through real-time fluorescence recombinase polymerase amplification

Food Chemistry (2020)

Xiaofu Wang Shilong Xie Xiaoyun Chen Cheng Peng Xiaoli Xu

Recombinase Polymerase Amplification

10.1016/j.foodchem.2020.126821

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Citations (22)

A Localized CRISPR Assay that Detects Short Nucleic Acid Fragments in Unamplified Genetically Modified Samples

ACS Sensors (2023)

Cheng Peng Yuling Wang Xiaoyun Chen Xiaofu Wang Lin Ding

Detecting short genetically modified (GM) nucleic acid fragments in GM crops and associated products is critically important for the global agriculture industry. Although nucleic acid amplification-based technologies have been widely used for genetically modified organism (GMO) detection, they still struggle to amplify and detect these ultra-short nucleic acid fragments in highly processed products. Here, we used a multiple-CRISPR-derived RNA (crRNA) strategy to detect ultra-short nucleic acid fragments. By combining confinement effects on local concentrations, an amplification-free CRISPR-based short nucleic acid (CRISPRsna) system was established to detect the cauliflower mosaic virus 35S promoter in GM samples. Moreover, we demonstrated assay sensitivity, specificity, and reliability by directly detecting nucleic acid samples from GM crops with a wide genomic range. The CRISPRsna assay avoided possible aerosol contamination from nucleic acid amplification and saved time due to an amplification-free approach. Given that our assay displayed distinct advantages over other technologies in detecting ultra-short nucleic acid fragments, it may have wide applications for detecting GM in highly processed products.

Molecular beacon

Nucleic acid detection

Nucleic acid quantitation

10.1021/acssensors.2c01955

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Comparison of droplet digital PCR with quantitative real-time PCR for determination of zygosity in transgenic maize

Transgenic Research (2016)

Xiaoli Xu Cheng Peng Xiaofu Wang Xiaoyun Chen Qiang Wang

Zygosity

10.1007/s11248-016-9982-0

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Rotary Valve-Assisted Fluidic System Coupling with CRISPR/Cas12a for Fully Integrated Nucleic Acid Detection

ACS Sensors (2021)

Hui Wu Siwenjie Qian Cheng Peng Xiaofu Wang Tingzhang Wang

Of late, many nucleic acid analysis platforms have been established, but there is still room for constructing integrated nucleic acid detection systems with high nucleic acid extraction efficiency, low detection cost, and convenient operation. In this work, a simple rotary valve-assisted fluidic chip coupling with CRISPR/Cas12a was established to achieve fully integrated nucleic acid detection. All of the detection reagents were prestored on the fluidic chip. With the aid of the rotary valve and syringe, the liquid flow and stirring can be precisely controlled. The nucleic acid extraction, loop-mediated isothermal amplification (LAMP) reaction, and CRISPR detection could be completed in 80 min. A clean reservoir and an air reservoir on the fluidic chip were designed to effectively remove the remaining ethanol. With Vibrio parahaemolyticus as the targets, the detection sensitivity of the fluidic chip could reach 3.1 × 101 copies of target DNA per reaction. A positive sample could be sensitively detected by CRISPR/Cas12a to produce a green fluorescent signal, while a negative sample generated no fluorescent signal. Further, the fluidic chip was successfully applied for detection of spiked shrimp samples, which showed the same detection sensitivity. A great feasibility for real-sample detection was showed by the fluidic chip. The proposed detection platform did not need expensive centrifugal instruments or pumps, which displayed its potential to become a powerful tool for food safety analysis and clinical diagnostics, especially in the resource-limited areas.

Fluidics

Nucleic acid quantitation

Nucleic acid methods

Lab-on-a-Chip

10.1021/acssensors.1c01468

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Citations (32)