Scientific Reports
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2024
·Vol. 14
·期 1
·1-21
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IF 3.8
Zhang Lisheng,Huang Yan,Yang Yanting,Liao Birong,Hou Congyan,Wang Yiqi,Qin Huaiyu,Zeng Huixiang,He Yanli,Gu Jiangyong,Zhang Ren
TIMM9 has been identified as a mediator of essential functions in mitochondria, but its association with pan-cancer is poorly understood. We herein employed bioinformatics, computational chemistry techniques and experiments to investigate the role of TIMM9 in pan-cancer. Our analysis revealed that overexpression of TIMM9 was significantly associated with tumorigenesis, pathological stage progression, and metastasis. Missense mutations (particularly the S49L variant), copy number variations (CNV) and methylation alterations in TIMM9 were found to be associated with poor cancer prognosis. Moreover, TIMM9 was positively related with cell cycle progression, mitochondrial and ribosomal function, oxidative phosphorylation, TCA cycle activity, innate and adaptive immunity. Additionally, we discovered that TIMM9 could be regulated by cancer-associated signaling pathways, such as the mTOR pathway. Using molecular simulations, we identified ITFG1 as the protein that has the strongest physical association with TIMM9 , which show a promising structural complement.
研究领域:
肿瘤学
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生物信息学
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分子生物学
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DOI
PubMed
高影响因子
ANALYTICAL BIOCHEMISTRY
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2025
·
IF 2.5
Jiaxu Wang,Zhengrong Lu,Zhanmin Liu,Qiming Chen
Copy number of cell-free mitochondrial DNA (cf-mtDNA) has garnered significant attention as a biomarker for studying and diagnosing various diseases. However, Quantitative Real-time PCR (qPCR) and Droplet Digital PCR (ddPCR) assays for cf-mtDNA copy number detection require expensive equipment and high experiment conditions. In this study, a colorimetric and fluorescent dual-modality assay was developed for quantitative detection of cf-mtDNA copy number. With G-quadruplex (G4) sequence modified primers, the assay could quantitatively detect cf-mtDNA with spectrophotometry, RGB (Red, Green, Blue) visual method and fluorescence method, which made the application scenarios more diverse. The specificity of dual-mode method was better, and the detection limits of spectrophotometry, RGB visual method and fluorescence method were as low as 1.45 × 10 −1 copies/μL, 1.65 copies/μL and 1.58 × 10 −1 copies/μL, respectively. Compared with qPCR and ddPCR assays developed in previous studies, the dual-modality assay in this study had a lower detection limit. It was also independent of expensive qPCR and ddPCR equipment and the detection cost was low. Therefore, the colorimetric and fluorescent dual-modality assay represent a label-free and sensitive approach for assessing cf-mtDNA levels, offering promising implications for biomedical research and clinical diagnostics.
研究领域:
医学诊断
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分子生物学
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DOI
PubMed
高影响因子
FOOD RESEARCH INTERNATIONAL
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2018
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IF 3.52
Ye Liu,HuanLu Song,Huanzhen Luo
The aim of the study was to analyze the correlation between the key aroma compounds and gDNA copies of Bacillus natto during fermentation and maturation of natto. Solvent-assisted flavor evaporation (SAFE) techniques were employed to extract volatile organic compounds. Aroma compounds were separated and analyzed through gas chromatography-olfactometry-mass spectrometry (GC-MS/O) using DB-5 and DB-Wax capillary columns. Seventy-nine compounds were extracted and identified, including 17 ketones, 17 alcohols, 9 aldehydes, 6 acids, 7 esters, 8 pyrazines, 8 aromatics, and 7 others. Twenty-two compounds were identified as the key aroma compounds of natto by aroma extraction dilution analysis (AEDA). Pyrazines played a key role in the flavor of natto both during the fermentation and maturation. 2,5-Dimethylpyrazine, 2,3,5-trimethylpyrazine, 2,3,5,6-tetramethylpyrazine, and 2,3,5-methyl-6-ethylpyrazine contributed substantially to natto flavor. They presented significant positive and negative correlations with the gDNA copies of Bacillus natto during fermentation and maturation, respectively.
研究领域:
食品科学
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微生物学
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DOI
PubMed
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
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2023
·
IF 13.6
Renzhang Lin,Hao Wu,Xiangyu Kong,Hao Ren,Zhenmei Lu
The lack of universal indicators for predicting microbial biodegradation potential and assessing remediation effects limits the generalization of bioremediation. The community-level ribosomal RNA gene operon (rrn) copy number, an important functional trait, has the potential to serve as a key indicator of the bioremediation of organic pollutants . A meta-analysis based on 1275 samples from 26 hydrocarbon-related studies revealed a positive relationship between the microbial hydrocarbon biodegradation level and the community-level rrn copy number in soil, seawater and culture. Subsequently, a microcosm experiment was performed to decipher the community-level rrn copy number response mechanism during total petroleum hydrocarbon (TPH) biodegradation. The treatment combining straw with resuscitation-promoting factor (Rpf) exhibited the highest community-level rrn copy number and the most effective biodegradation compared with other treatments, and the initial TPH content (20,000 mg kg -1 ) was reduced by 67.67% after 77 days of incubation. TPH biodegradation rate was positively correlated with the average community-level rrn copy number ( p = 0.001, R 2 = 0.5781). Both meta and community analyses showed that rrn copy number may reflect the potential of hydrocarbon degradation and microbial dormancy. Our findings provide insight into the applicability of the community-level rrn copy number to assess bacterial biodegradation for pollution remediation.
研究领域:
环境科学
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微生物学
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DOI
PubMed
高影响因子
Pharmaceuticals
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2025
·Vol. 18
·期 7
·1077
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IF 4.8
Xinyi Lv,Yuehan Song,Tianhua Liu,Dingdan Zhang,Xinpeng Ye,Qingqing Wang,Rongrong Li,Jiayi Chen,Shujing Zhang,Xue Yu,Chunying Hou
Background : Lung cancer has the highest morbidity and mortality of all tumors, and the development of TKI drugs targeting EGFR activating mutations has brought lung cancer treatment into the targeted era. In view of their low efficacy and susceptibility to drug resistance, there is an urgent need to find strategies to increase their efficacy and reduce the incidence of drug resistance. Methods : In this study, we examined the distribution and probability of EGFR mutations in non-small cell lung cancer patients in the cBioPortal database and compared the survival prognosis of patients with normal and abnormal EGFR, NSCLC patients treated with and without TKI, and NSCLC patients with different EGFR gene copy numbers. We established a mouse lung cancer model and examined the histomorphological characteristics of lung tissues via hematoxylin and eosin staining. Additionally, changes in the copy number of the EGFR gene and its protein expression levels were detected using RT-qPCR and Western blotting. Furthermore, we quantified the concentration of the EGFR protein using ELISA. Results : We found no significant advantage of EGFR-TKI therapy over first-line chemotherapeutic agents in patients with EGFR-abnormal NSCLC. The reason for this may be related to the abnormal EGFR gene copy number; the higher the copy number increases, the worse the survival prognosis of the patients. In molecular biology experiments, we demonstrated that ginsenoside Rg3 down-regulated the copy number of 18, 19, 20, and 21 exons and protein expression of EGFR in lung adenocarcinoma cells. The results of in vivo pharmacodynamic assays confirmed that sequential administration of ginsenoside Rg3 with TKI drugs could achieve a gainful complementary effect. Conclusions : Ginsenoside Rg3 down-regulates the copy number of EGFR important exons in EGFR-mutant cells of lung adenocarcinoma and reduces EGFR protein expression, thus providing a high gainful complementary effect in combination with EGFR-TKI.
研究领域:
肿瘤学
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药理学
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分子生物学
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遗传学
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药物研发
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DOI
PubMed
高影响因子
CLINICA CHIMICA ACTA
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2024
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IF 3.2
Xiao Bao,Yuxia Yang,Wenbin Niu,Yimin Wang,Hao Shi,Yangyun Zou,Yidong Liu,Cheng Wan,Jun Ren,Sijia Lu,Yingpu Sun
Background Chromosome abnormalities are a leading cause of conception failure and pregnancy loss. While traditional cytogenetics technologies like karyotyping have been helpful in identifying structural variations (SVs), they face challenges in detecting complex rearrangements and cryptic structures. In this study, we developed a new method called chromosome conformation based karyotyping (C-MoKa) to comprehensively detect different types of chromosomal abnormalities in patients with conception failure and pregnancy loss. Methods A total of 70 clinical samples exhibiting known results of SVs, mosaic aneuploidies, copy number variations （CNVs） and uniparental disomy (UPD) were included in our cohort and underwent C-MoKa analysis. The results obtained from different techniques, including karyotyping, CNV-seq, and CMA were compared and analyzed. Results Distinct chromosomal conformation patterns of various variations were observed and analyzed in clinical samples. Our C-MoKa method not only validated all the findings of karyotyping, CNV-seq and CMA, but also provided more detailed results. It demonstrated superior fragment resolution (<500 Kb) and more precise breakpoints (>100 kb). Moreover, C-MoKa showed higher sensitivity in decoding intricate rearrangements in a single test. Conclusions Our results highlight the potential utility of C-MoKa in precisely unraveling SVs, mosaic aneuploidies, CNVs, and UPD in clinical settings, which can significantly impact further clinical decision-making.
研究领域:
遗传学
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生殖医学
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分子生物学
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DOI
高影响因子
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
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2012
·Vol. 96
·期 3
·763-772
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IF 3.425
Shen Qi,Wu Ming,Wang Hai-Bin,Naranmandura Hua,Chen Shu-Qing
Interleukin-1 receptor antagonist (IL1ra) is known to treat a number of diseases such as rheumatoid arthritis and type 2 diabetes. However, the biological half-life of IL1ra is very short due to its rapid renal clearance. Our present study aimed to increase the biological half-life of IL1ra through fusion with human serum albumin (HSA), and then augmented expression of the IL1ra and HSA fusion protein (IH) in Pichia pastoris strain by increasing IH gene copy number or was co-expressed with chaperone. By comparing clones containing varying copy numbers of IH fusion gene, it was observed that higher levels of secretory IH fusion protein was produced in strain with higher IH gene copy number. In addition, IH protein yield was further improved after being co-expressed with protein disulfide isomerase (PDI). Conversely, it was significantly decreased (i.e., secretory IH in the culture medium) by co-expression of immunoglobulin binding protein. We have also discussed whether the multi-copy strain and co-expressed of PDI could enhance the levels of other secretory albumin fusion protein (e.g., HSA and human growth hormone fusion protein). Interestingly, the level of this fusion protein was apparently also increased by these approaches. In conclusion, our results have demonstrated that increasing copy number and co-expression of PDI may raise yield of albumin fusion protein in P. pastoris , which might probably contribute to the industry for the development of proteinous drugs.
研究领域:
分子生物学
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生物技术
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药学
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DOI
PubMed
高影响因子
Nature Protocols
·
2021
·Vol. 16
·期 7
·3522-3546
·
IF 13.491
Liu Jia,He Hui,Xie Dan,Wen Yanrong,Liu Zhen
Cellular heterogeneity is pervasive and of paramount importance in biology. Single-cell analysis techniques are indispensable for understanding the heterogeneity and functions of cells. Low-copy-number proteins (fewer than 1,000 molecules per cell) perform multiple crucial functions such as gene expression, cellular metabolism and cell signaling. The expression level of low-copy-number proteins of individual cells provides key information for the in-depth understanding of biological processes and diseases. However, the quantitative analysis of low-copy-number proteins in a single cell still remains challenging. To overcome this, we developed an approach called single-cell plasmonic immunosandwich assay (scPISA) for the quantitative measurement of low-copy-number proteins in single living cells. scPISA combines in vivo microextraction for specific enrichment of target proteins from cells and a state-of-the-art technique called plasmon-enhanced Raman scattering for ultrasensitive detection of low-copy-number proteins. Plasmon-enhanced Raman scattering detection relies on the plasmonic coupling effect (hot-spot) between silver-based plasmonic nanotags and a gold-based extraction microprobe, which dramatically enhances the signal intensity of the surface-enhanced Raman scattering of the nanotags and thereby enables sensitivity at the single-molecule level. scPISA is a straightforward and minimally invasive technique, taking only ~6–15 min (from in vivo extraction to Raman spectrum readout). It is generally applicable to all freely floating intracellular proteins provided that appropriate antibodies or alternatives (for example, molecularly imprinted polymers or aptamers) are available. The entire protocol takes ~4–7 d to complete, including material fabrication, single-cell manipulation, protein labeling, signal acquisition and data analysis.
研究领域:
生物学
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生物技术
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分析化学
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分子生物学
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DOI
PubMed
高影响因子
ANALYST
·
2019
·Vol. 144
·期 16
·4757-4771
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IF 4.019
Xiurui Zhu,Shisheng Su,Mingzhu Fu,Zhiyong Peng,Dong Wang,Xiao Rui,Fang Wang,Xiaobin Liu,Baoxia Liu,Lingxiang Zhu,Wenjun Yang,Na Gao,Guoliang Huang,Gaoshan Jing,Yong Guo
Droplet digital PCR (ddPCR) is a single-molecule amplification technology with broad applications in precision medicine and clinical diagnosis. Dual-fluorescence and four-cluster ddPCR (two/four-ddPCR) assay is an effective way to quantify copy numbers. Currently, two/four-ddPCR data are usually classified with manual thresholds. For clinical applications, automatic and accurate methods are required to avoid subjectivity in diagnosis. Although there are some automatic classification algorithms, their accuracy and robustness still need to be improved to meet the needs of clinical diagnosis. Therefore, a new method is in high demand to automatically classify two/four-ddPCR data in an accurate and robust way. Here, a novel density-watershed algorithm (DWA) method was developed for the accurate, automatic and unsupervised classification of two/four-ddPCR data. First, data gridding was applied to a scatter plot of the fluorescence signal intensity to calculate data densities. Based on the data densities, the watershed algorithm was used to divide the gridded scatter plot into isolated regions automatically. Next, an optimal cluster pattern was determined based on these isolated regions, and excess regions were merged. Finally, the two/four-ddPCR data were classified based on the merged regions, and DNA template copy numbers were calculated accordingly. Using the DWA method for the quantification of both wild types and mutants of epidermal growth factor receptor (EGFR) L858R and T790M, the classification results were highly consistent with expectations, and significantly better than commonly-used automatic algorithms for now. The computed template copy numbers scaled proportionally to the relative concentration of input templates (r2 > 0.998) in four orders of magnitude with a good reproducibility, and achieved a limit of detection over 40 times lower than the commonly-used automatic algorithms. Furthermore, the DWA method was validated on 254 clinical DNA samples derived from frozen tissues, formalin-fixed paraffin-embedded tissues and peripheral blood. In most cases, the DWA method derived accurate and valid classification results. This highly effective DWA method may be widely used for automatically classifying two/four-ddPCR data, and it will greatly promote the application of ddPCR in clinical diagnosis.
研究领域:
生物信息学
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分子生物学
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临床诊断
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精准医疗
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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）