Analytical Methods
·
2024
·
IF 2.7
Chu Cheng,Qingzhou Cheng,Wei Zhou,Yulong Chen,Wenbin Liu,Zhiling Zhang,Jingsi Ye,Pengfeng Xiao
Eliminating errors in next-generation sequencing has proven to be challenging. Here we present a novel strategy for DNA sequencing, called correctable two-color fluorogenic DNA decoding sequencing, which can significantly improve sequencing accuracy and throughput by employing a dual-nucleotide addition combined with fluorogenic sequencing-by-synthesis (SBS) chemistry. This sequencing method involves introducing a mixture of natural nucleotide X, labeled unblocked nucleotide X′, 3′ blocked nucleotide Y*, and labeled 3′ blocked nucleotide Y* into each reaction cycle. By cyclically interrogating a template twice with different nucleotide combinations, two sets of base-encoding are sequentially obtained, enabling accurate deduction of base sequence. We demonstrate the remarkable efficacy of this approach in detecting and correcting sequencing errors, achieving a theoretical error rate of 0.0005%, which is twice as accurate as Sanger sequencing. Furthermore, we show the capability to detect known mutation sites using information from only a single sequencing run. The correctable two-color fluorogenic DNA decoding sequencing approach should enable accurate identification of extremely rare genomic variations in diverse applications in biology and medicine.
研究领域:
分子生物学
·
基因组学
·
医学遗传学
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
·
2024
·
IF 3.1
Chu Cheng,Qingzhou Cheng,Wei Zhou,Yulong Chen,Pengfeng Xiao
We proposed a single-color fluorogenic DNA decoding sequencing method designed to improve sequencing accuracy, increase read length and throughput, as well as decrease scanning time. This method involves the incorporation of a mixture of four types of 3’-O-modified nucleotide reversible terminators into each reaction. Among them, two nucleotides are labeled with the same fluorophore, while the remaining two are unlabeled. Only one nucleotide can be extended in each reaction, and an encoding that partially defines base composition can be obtained. Through cyclic interrogation of a template twice with different nucleotide combinations, two sets of encodings are sequentially obtained, enabling the determination of the sequence. We demonstrate the feasibility of this method using established sequencing chemistry, achieving a cycle efficiency of approximately 99.5 %. Notably, this strategy exhibits remarkable efficacy in the detection and correction of sequencing errors, achieving a theoretical error rate of 0.00016 % at a sequencing depth of ×2, which is lower than Sanger sequencing. This method is theoretically compatible with the existing sequencing-by-synthesis (SBS) platforms, and the instrument is simpler, which may facilitate further reductions in sequencing costs, thereby broadening its applications in biology and medicine. Moreover, we demonstrate the capability to detect known mutation sites using information from only a single sequencing run. We validate this approach by accurately identifying a mutation site in the human mitochondrial DNA.
研究领域:
分子生物学
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遗传学
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医学
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产品关联
DOI
PubMed
高影响因子
POULTRY SCIENCE
·
2021
·
IF 3.352
Chunlin Yu,Mohan Qiu,Zengrong Zhang,Xiaoyan Song,Huarui Du,Han Peng,Qingyun Li,Li Yang,Xia Xiong,Bo Xia,Chenming Hu,Jialei Chen,Xiaosong Jiang,Chaowu Yang
As a ubiquitous heavy metal, cadmium ( Cd ) is highly toxic to various organs. However, the effects and molecular mechanism of Cd toxicity in the chicken heart remain largely unknown. The goal of our study was to investigate the cardiac injury in chickens' exposure to Cd. We detected the levels of oxidative stress–related molecules in the Cd-induced chicken heart, and assessed the histopathological changes by hematoxylin and eosin staining. RNA sequencing was performed to identify differentially expressed mRNAs between the Cd-induced group and control group. The expression of candidate genes involved in oxidative stress was certified by quantitative reverse transcription PCR. Our results showed that the expression of glutathione, peroxidase, and superoxide dismutase was significantly decreased and malondialdehyde was increased in the heart of chickens by Cd induction. The disorderly arranged cardiomyocytes, swelled and enlarged cells, partial cardiomyocyte necrosis, blurred morphological structure, and notable inflammatory cell infiltration were observed in the Cd-induced chicken heart. RNA sequencing identified 23 upregulated and 11 downregulated mRNAs in the heart tissues of the chicken in the Cd-induced group, and functional pathways indicated that they were associated with oxidative stress. Moreover, CREM, DUSP8, and ITGA11 expressions were significantly reduced, whereas LAMA1 expression was induced in heart tissue of chickens by Cd treatment. Overall, our findings revealed that oxidative stress and pathological changes in the chicken heart could be triggered by Cd. The mRNA transcriptional profiles identified differentially expressed genes in the chicken heart by Cd induction, revealing oxidative stress–related key genes and enhancing our understanding of Cd toxicity in the chicken heart.
研究领域:
毒理学
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分子生物学
·
心脏病学
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DOI
PubMed
高影响因子
Cell Reports
·
2024
·
IF 7.5
Yinghao Yin,Yuzhuo Chen,Jiarong Xu,Biao Liu,Yifan Zhao,Xiaoli Tan,Ming Xiao,Yihong Zhou,Xiaoping Zheng,Yanghua Xu,Zhitao Han,Hongji Hu,Zitaiyu Li,Ningjing Ou,Wenfei Lian,Yawei Li,Zhongzhen Su,Yingbo Dai,Yuxin Tang,Liangyu Zhao
The composition and cellular heterogeneity of the corpus cavernosum (CC) microenvironment have been characterized, but the spatial heterogeneity at the molecular level remains unexplored. In this study, we integrate single-cell RNA sequencing (scRNA-seq) and spatial transcriptome sequencing to comprehensively chart the spatial cellular landscape of the human and rat CC under normal and disease conditions. We observe differences in the proportions of cell subtypes and marker genes between humans and rats. Based on the analysis of the fibroblast (FB) niche, we also find that the enrichment scores of mechanical force signaling vary across different regions and correlate with the spatial distribution of FB subtypes. In vitro , the soft and hard extracellular matrix (ECM) induces the differentiation of FBs into apolipoprotein (APO)+ FBs and cartilage oligomeric matrix protein (COMP)+ FBs, respectively. In summary, our study provides a cross-species and physiopathological transcriptomic atlas of the CC, contributing to a further understanding of the molecular anatomy and regulation of penile erection.
研究领域:
分子生物学
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医学
·
生理学
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产品关联
DOI
PubMed
高影响因子
Food & Function
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2025
·
IF 5.4
Dapeng Chen,Jiayi Li,Xinyu Li,Kexin Zhang,Shujie Zeng,Shenjun Zhang,Longyun Li,Yongjian Xiong
Hispidulin, a dietary flavonoid occurring naturally in brown algae, has attracted considerable interest owing to its functions in modulating inflammatory responses and neutralizing reactive oxygen species. This study examined the consequences of hispidulin in a model of chemically induced acute colitis. RNA sequencing (RNA-seq), 16s rRNA-seq, and non-targeted metabolome were conducted to determine the mechanisms underlying hispidulin-induced effects on colitis. The findings revealed that hispidulin exhibited significant therapeutic benefits against colitis. In addition, treatment with hispidulin led to a decrease in pro-inflammatory cytokine levels as well as serum FITC-dextran concentrations. RNA-seq analysis demonstrated a notable increase in colonic ACAT2 expression in mice with colitis following hispidulin treatment. Furthermore, hispidulin administration resulted in the upregulation of GPX4, a reduction in ROS levels, and inhibition of epithelial ferroptosis in mice with colitis. Both genetic inhibition of ACAT2 in vitro and AAV-mediated knockdown of ACAT2 in vivo substantially negated the effects of hispidulin on GPX4/GSH levels, ROS levels, and lipid hydroperoxide accumulation in both NCM460 cells and epithelial cells derived from DSS exposed murine models. 16s rRNA-seq results showed that hispidulin increased abundance of Lactobacillus, NK4A136_group, Oscillibacter, Peptococcus, Adlercreutzia and decreased abundance of Turicimonas in colitic mice. Non-targeted metabolome results showed that hispidulin facilitated the metabolism of galactose and promoted unsaturated fatty acid biosynthesis in colitic mice. In summary, hispidulin reduced the advancement of acute colitis in mice by lessening ACAT2-mediated ferroptosis in epithelial cells, as well as altering composition of gut microbiota.
研究领域:
营养科学
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胃肠病学
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分子生物学
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微生物学
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药理学
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生物信息学
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产品关联
DOI
PubMed
高影响因子
Plant Gene
·
2021
·
IF 0
Hu Zhao,Xiaopu Shi,Cheng Shen,Caifeng Chen,Jiyuan Liu,Changqing Qu
Toon bud is rich in polyphenols and flavonoids, which not only have nutritional value but also have health benefits. However, the molecular mechanisms of flavonoid accumulation during storage remain unclear. In our report, small RNA libraries from toon buds were synthesized after three storage period (0, 3, and 5 days) at 4 °C. Overall, 303 homologous sequences with known microRNA (conserved miRNAs homology) and 19 putative novel miRNAs were obtained using Illumina sequencing technology. Furthermore, the potential target unigenes of these miRNAs were predicted. Of the predicted miRNAs and their target unigenes, 17 conserved miRNAs and their target unigenes were confirmed by quantitative real-time PCR (qRT-PCR). Exactly 11 miRNAs involved in the flavonoid pathway and 6 miRNAs targeting transcription factors displayed significant correlation with flavonoid accumulation in toon buds. The findings will be helpful for better understanding flavonoid accumulation in toon buds during storage.
研究领域:
植物科学
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分子生物学
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食品科学
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DOI
MOLECULES
·
2023
·Vol. 28
·期 14
·5496
·
IF 4.6
Ting Li,Chaoyue Yang,Houkang Cao,Siyi Mo,Bo Li,Zhipeng Huang,Ruobing Zhang,Jianzhao Wu,Kefeng Zhang,Ya Gao
Bergenin (BER), a natural component of polyphenols, has a variety of pharmacological activities, especially in improving drug metabolism, reducing cholestasis, anti-oxidative stress and inhibiting inflammatory responses. The aim of this study was to investigate the effects of BER on liver injury induced by isonicotinic acid hydrazide (INH) and rifampicin (RIF) in mice. The mice model of liver injury was established with INH (100 mg/kg)+RIF (100 mg/kg), and then different doses of BER were used to intervene. The pathological morphology and biochemical indicators of mice were detected. Meanwhile, RNA sequencing was performed to screen the differentially expressed genes and signaling pathways. Finally, critical differentially expressed genes were verified by qRT-PCR and Western blot. RNA sequencing results showed that 707 genes were significantly changed in the INH+RIF group compared with the Control group, and 496 genes were significantly changed after the BER intervention. These differentially expressed genes were mainly enriched in the drug metabolism, bile acid metabolism, Nrf2 pathway and TLR4 pathway. The validation results of qRT-PCR and Western blot were consistent with the RNA sequencing. Therefore, BER alleviated INH+RIF-induced liver injury in mice. The mechanism of BER improving INH+RIF-induced liver injury was related to regulating drug metabolism enzymes, bile acid metabolism, Nrf2 pathway and TLR4 pathway.Keywords:bergenin;isonicotinic acid hydrazide;rifampicin;liver injury;RNA sequencing
研究领域:
药理学
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分子生物学
·
毒理学
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产品关联
DOI
PubMed
高影响因子
Processes
·
2025
·Vol. 13
·期 3
·731
·
IF 2.8
Shuanghu Fan,Zihan Feng,Meiting Xu,Zhenxia Shi,Yufeng Zhang,Peipei Zhang,Xiaoqiang Hou
Phthalic acid esters (PAEs) are mainly used as plasticizers and result in serious environmental contamination worldwide. Microbial biodegradation becomes an efficient strategy for PAE elimination. In the current study, the PAE-degrading strainGordoniasp. LUNF6 was isolated from contaminated soil. Strain LUNF6 can efficiently degrade DBP in a wide range of temperatures, pH values, and salinity levels. This strain is also capable of degrading 11 types of PAEs and displays remediation potential in wastewater. The complete genome of strain LUNF6 was sequenced to determine its efficient degradation performance. Its genome comprises a chromosome (3,971,257 bp) and a plasmid (78,813 bp). After gene function annotation, the complete PAE degradation pathway was proposed. The gene of monoalkyl PAE hydrolase MphGd2 was cloned and heterologously expressed. The protein of MphGd2 was purified by infinity chromatography, and we hydrolyzed MBP to produce PA. These results reveal the molecular mechanism of PAE degradation by strain LUNF6, which will contribute to the application of strain LUNF6 and hydrolase MphGd2 in bioremediation.
研究领域:
环境微生物学
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分子生物学
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DOI
高影响因子
FISH & SHELLFISH IMMUNOLOGY
·
2019
·
IF 3.298
Yafei Duan,Yun Wang,Dalin Xiong,Jiasong Zhang
The intestine is important for nutrition, metabolism and immunity. Succinate (SA) plays a vital role in the physiological homeostasis of animal intestines. However, the effects of dietary SA on the intestinal immunity and metabolism in shrimp are not clear. In this study, we investigated the immune and metabolic responses in the intestine of Litopenaeus vannamei that were fed diets consisting of different levels of SA: 0 g/kg (Con) and 10 g/kg (SA) for 56 days. The results from a RNA-seq analysis identified 6005 differentially expressed genes (DEGs), including 2728 upregulated genes and 3277 downregulated genes, which were grouped into 312 pathways. The DEGs were most enriched in pathways related to protein synthesis and amino acid metabolism , including “ribosome”, “aminoacyl-tRNA biosynthesis”, “pyrimidine metabolism”, and “arginine and proline metabolism”; additionally, carbohydrate and lipid metabolism pathways were also activated. A large number of immune-related genes were associated with mucus barrier modification, antimicrobial activity , pathogen attachment and recognition, antioxidant activity , and apoptosis. The expression patterns of several candidate genes involved in the immune response and nutrition metabolism were detected by qPCR. This study provides insight into the transcriptomic modulating mechanisms associated with intestinal immunity and the metabolism of L. vannamei in response to the intake of dietary SA.
研究领域:
水产养殖学
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分子生物学
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营养学
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产品关联
DOI
PubMed
高影响因子
CELLULAR SIGNALLING
·
2024
·
IF 4.4
Jingwen Shi,Wenda Jing,Yueyun He,Ying Huang
Despite decades of research, endometriosis remains a mysterious gynecological disease with unknown etiology and pathogenesis. Krüppel-like Factor 6 (KLF6), a transcription factor, has a wide expression profile and regulates a variety of biological processes. Here, we investigated the expression and function of KLF6 and its possible regulatory mechanisms in endometriosis. To determine the function of KLF6, knockdown and overexpression experiments were performed in eutopic endometrial stromal cells (EU-ESCs) and ectopic endometrial stromal cells (EC-ESCs), respectively. Cell viability, apoptosis, migration, invasion, and angiogenesis assays were conducted in ESCs. ChIP-sequencing and mRNA-sequencing were performed to investigate the functional mechanism of KLF6 in regulating ESCs. We found that KLF6 was highly expressed in eutopic endometrium of endometriosis patients, compared with ectopic endometrium. Similarly, the same was true in EU-ESCs, which was compared with EC-ESCs. Overexpression of KLF6 significantly suppressed EC-ESC proliferation, migration and invasion and induced cell apoptosis, while knockdown of KLF6 resulted in the opposite effects on EU-ESCs. Overexpression of KLF6 significantly inhibited EC-ESC angiogenesis. Mechanistically, the results of ChIP sequencing and mRNA sequencing revealed that CTNNB1 may be a transcriptional target regulated by KLF6. Reintroduction of KLF6 reversed the effects of KLF6 knockdown on EU-ESCs. KLF6 inhibited the proliferation, migration and angiogenesis of EC-ESCs by inhibiting the expression of CTNNB1. Our findings provided a new perspective on the role of KLF6 in endometriosis progression and inspire potential targeted therapeutic strategies.
研究领域:
妇科学
·
分子生物学
·
转录因子
·
疾病发病机制
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产品关联
DOI
PubMed
高影响因子
Foods
·
2022
·Vol. 11
·期 19
·3134
·
IF 5.561
Huahua Qiao,Liwei Chen,Jinsong Yang,Wenbo Zhi,Rong Chen,Tianyu Lu,Haisheng Tan,Zhanwu Sheng
Fermentation technology is of great significance for food preservation; through fermentation, while extending the shelf life of food, it can also improve the sensory quality of food and increase its nutritional value. Compared with natural fermentation, the use of specific microorganisms for fermentation can be used to determine the direction of fermentation. Therefore, in order to better explore the effect of bacterial community structure on the quality of sugarcane juice naturally fermented and inoculated with different lactic acid bacteria in the fermentation process, the most suitable method for sugarcane juice fermentation was found, which provided a theoretical basis for the safe production of fermented sugarcane juice. In this experiment, the sugarcane juice was treated differently and divided into four groups: natural fermentation, fermentation withLactobacillusHNK10, fermentation withLactococcusHNK21, and HNK10 + HNK21 compound fermentation. The changes in bacterial community structure of different treatments of sugarcane juice during fermentation were analyzed by high-throughput sequencing technology, and the quality change of different treatments of sugarcane juice during fermentation was analyzed by high-performance liquid chromatography, and the change in its bacteriostatic ability was explored. The results showed that after the sugarcane juice treated withLactobacillusHNK10 was fermented at 37 °C for 48 h, the final fermented sugarcane juice had a large abundance of lactic acid bacteria and high-quality and strong antibacterial activity. Conclusions: changes in the bacterial community structure during the fermentation of sugarcane juice affect the formation of organic acids and the change of bacteriostatic ability and directly determine the quality and shelf life of fermented sugarcane juice.Keywords:sugarcane juice;fermentation;high-throughput sequencing;high-performance liquid chromatography
研究领域:
食品科学
·
微生物学
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产品关联
DOI
PubMed
高影响因子
Foods
·
2023
·Vol. 12
·期 8
·1588
·
IF 5.2
Jiaqi Luo,Siyu Liu,Hongyun Lu,Qihe Chen,Ying Shi
Soybeans possess unexpected flavors and are difficult to be absorbed by the gastrointestinal tract. Kefir grain fermentation provides diverse strains and bioactive compounds, which may enhance flavor and bioaccessibility. Third-generation sequencing was applied to analyze the microbial diversity in milk and soybean kefir grains in this study. In both types of kefir grains, the most common bacterial genus wasLactobacillus, and their fungal communities were dominated byKazachstania.Lactobacillus kefiranofacienswas the most abundant species in kefir grains, whileLactobacillus kefirishowed a higher proportion in soybean kefir grains. In addition, the quantification of free amino acids and volatile flavor compounds in soybean solution and soybean kefir have shown the increased content of glutamic acid and a decreased amount of unpleasant beany flavor compounds, demonstrating that the nutritive value and sensory properties of soybean can be improved by kefir grain fermentation. Finally, the bioconversion of isoflavones during fermentation and in vitro digestion was evaluated, suggesting that fermentation is beneficial for aglycone formation and absorption. To conclude, kefir fermentation is proposed to change the microbial structure of kefir grains, promote the nutritional value of soybean-based fermented products, and provide possible solutions for the development of soybean products.Keywords:soybean;kefir grains;third-generation sequencing;fermentation;isoflavones
研究领域:
食品科学
·
微生物学
·
营养学
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产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）