LWT-FOOD SCIENCE AND TECHNOLOGY
·
2024
·
IF 6
Zhiqing Xie,Aohuan Huang,Jihang Xie,Shubo Yu,Mengfei Chen,Jie Cai,Rong Huang,Zhenjun Zhu,Yu Ding
Bacteroides dorei is a promising candidate for the next-generation probiotics (NGP), but its accurate identification remains challenging due to its close taxonomic relationship with other Bacteroides species. This study aimed to mine the novel specific molecular target for detecting Bacteroides dorei . Using pan-genome analysis and PCR validation, species-specific target genes with a size of 193 bp were identified, and the specificity of the designed primer pair (30 bp) for this molecular target was confirmed. The PCR assay demonstrated high applicability for detecting target and/or nontarget strains in three simulated food systems, yielding no false-positive or false-negative results. Additionally, a qPCR method was developed for quantifying Bacteroides dorei , with a linear detection range from 1 × 10 8 to 1 × 10 1 CFU/mL and an R 2 value greater than 0.98. This method exhibited accurate and sensitive detection capabilities suitable for both food and feces samples. Overall, our study established PCR and qPCR assays for the rapid identification of Bacteroides dorei , advancing the exploration of Bacteroides species and the application of detection for NGPs in functional foods across various product forms.
研究领域:
微生物学
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分子生物学
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食品科学
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益生菌
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产品关联
DOI
高影响因子
ANALYST
·
2022
·Vol. 147
·期 24
·5623-5632
·
IF 5.227
Jiahai Wang,Le Luo,Yunhui Li,Lanfang Chen,Cenlin Gui,Jianji Zhu,Huizhen Li,Wenlong Wang,Daqi Chen
Solid-state nanopores have been proven as a powerful platform for label-free single-molecule analysis. However, due to its relatively low resolution and selectivity, developing biosensors with good translocation signals faces two significant challenges: (1) small-sized chemical or biological targets show difficulty in producing recognizable translocation signals because of their weak interaction with the nanopore and (2) protein interferents that widely exist in biological samples or buffers would considerably deteriorate the noise level of the nanopore, submerging the translocation signal. Herein, we demonstrate an effective way to overcome both the challenges. DNA cubes were used as signal transducers that can achieve an ultra-high (>50 : 1) signal-to-noise ratio (SNR) translocation signal, which is maintained even in protein interferent-rich buffers. A sensing strategy was constructed via hepatitis B virus (HBV) target-triggered cleavage of the component elements of the DNA cube with the assistance of the CRISPR–Cas12a technology, which caused a great drop in the translocation rate. The elements to cleave were optimized, and the sensor performance was tested in different protein stabilizer-rich buffers and human serum. Coupling with the polymerase chain reaction (PCR) pre-amplification technology, HBV-positive or -negative classification was achieved with the detection limit reaching 5 aM. It is worth noting that in our method, all reaction buffers were directly used without further optimization, which is of great help for the practical application of solid-state nanopores.
研究领域:
生物技术
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纳米技术
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分子生物学
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病毒学
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产品关联
DOI
PubMed
高影响因子
ANALYST
·
2021
·Vol. 146
·期 22
·6960-6969
·
IF 4.616
Ping Mao,Lei Cao,Zedong Li,Minli You,Bin Gao,Xianghong Xie,Zhenrui Xue,Ping Peng,Chunyan Yao,Feng Xu
Digital PCR has shown great potential for quantitative nucleic acid testing (NAT), but most existing platforms are dependent on large auxiliary equipment (e.g., vacuum pump, amplification instrument, fluorescence microscope) to achieve target dispersion, amplification, signal capture and result analysis. Such complex, expensive and bulky NAT platforms have limited their applications in resource-limited areas, especially for point-of-care testing (POCT). In this work, we designed a digital isothermal NAT platform based on a pump-free open droplet array microfluidic chip. A pump-free microfluidic chip was developed based on an open microdroplet array in the form of thousands of independent microdroplets for spontaneous sample dispersion, without the need for external power. Combined with a handheld fluorescent signal reader based on a smartphone, this digital NAT platform can accurately quantify as low as 1 copy per μL of λDNA. Therefore, our integrated NAT platform, as a potable, robust and low-cost tool for highly accurate NA quantitative analysis, holds great potential for POCT applications.
研究领域:
分子生物学
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生物医学工程
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医学诊断
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DOI
PubMed
高影响因子
Evidence-based Complementary and Alternative Medicine
·
2019
·
IF 1.984
Liwen Han,Haotian Kong,Fasheng Liu,Xiaobin Li,Shanshan Zhang,Xuanming Zhang,Yong Wu,Hua Yang,Aiping Zhang,Kechun Liu
The aim of the study is to explore the protective effect of new gelatin (NG, Xin’ejiao in China) on hematopoietic injury caused by chemotherapy. Zebrafish, at 48 hours post fertilization (hpf), was treated with different chemotherapeutic drugs to establish the zebrafish hematopoietic damage model with reduced thrombocytes and erythrocytes. The protecting effects of NG on the thrombocytes and erythrocytes were observed, respectively, on zebrafish models. Then, the RT-PCR method was used to detect the change of mRNA level of the hematopoiesis-related cytokines scl1, c-myb, pu.1, GATA1, and runx1 genes. The results showed that 50 μg·mL−1 and 100 μg·mL−1 NG rescued and increased the thrombocytes numbers induced by vinorelbine (NVB) and chloramphenicol (CHL) and the erythrocytes numbers induced by methotrexate (MTX), doxorubicin (ADM), and mechlorethamine hydrochloride (MH) in zebrafish models. Meanwhile, the mRNA expression of scl1, c-myb, and GATA1 genes in the NG treatment group was raised compared with the MTX treatment group. Also, the mRNA expression of pu.1 and Runx1 in the NG treatment group was reduced compared with the MTX treatment group. In consequence, traditional Chinese medicine NG showed a certain degree protective effect on hematopoiesis injury induced by chemotherapy in this study, which may depend on the promotion of erythrocytes proliferation and the regulation of the hematopoietic genes level.
研究领域:
药理学
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血液学
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分子生物学
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斑马鱼研究
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产品关联
DOI
PubMed
高影响因子
BMC PLANT BIOLOGY
·
2023
·Vol. 23
·期 1
·1-17
·
IF 5.3
Sun Meiyu,Zhu Li,Zhang Yanan,Liu Ningning,Zhang Jinzheng,Li Hui,Bai Hongtong,Shi Lei
Background
Thyme derived essential oil and its components have numerous applications in pharmaceutical, food, and cosmetic industries, owing to their antibacterial, antifungal, and antiviral properties. To obtain thyme essential oil with different terpene composition, we developed new germplasm resources using the conventional hybridization approach. Results Phenotypic characteristics, including essential oil yield and composition, glandular trichome density, plant type, and fertility, of three wild Chinese and seven European thyme species were evaluated. Male-sterile and male-fertile thyme species were crossed in different combinations, and two F 1 populations derived from Thymus longicaulis (Tl) × T. vulgaris ‘Fragrantissimus’ (Tvf) and T. vulgaris ‘Elsbeth’ (Tve) × T. quinquecostatus (Tq) crosses were selected, with essential oil yield and terpene content as the main breeding goals. Simultaneously, simple sequence repeat (SSR) primers were developed based on the whole-genome sequence of T. quinquecostatus to authenticate the F 1 hybrids. A total of 300 primer pairs were selected, and polymerase chain reaction (PCR) was carried out on the parents of the two hybrid populations (Tl, Tvf, Tve, and Tq). Based on the chemotype of the parents and their F 1 progenies, we examined the expression of genes encoding two γ-terpinene synthases, one α-terpineol synthase, and maybe one geraniol synthase in all genotypes by quantitative real-time PCR (qRT-PCR). Conclusion We used hybridization to create new germplasm resources of thyme, developed SSR markers based on the whole-genome sequence of T. quinquecostatus , and screened the expression of monoterpene synthase genes in thyme. The results of this study provide a strong foundation for the creation of new germplasm resources, construction of the genetic linkage maps, and identification of quantitative trait loci (QTLs), and help gain insight into the mechanism of monoterpenoids biosynthesis in thyme.
研究领域:
植物科学
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分子生物学
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遗传学
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药学
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农业遗传学
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DOI
PubMed
高影响因子
PEST MANAGEMENT SCIENCE
·
2020
·Vol. 76
·期 12
·4036-4045
·
IF 3.75
Yifan Li,Hong Sun,Zhen Tian,Xinxin Su,Yue Li,Xuan Ye,Yifei Zhou,Shengli Zheng,Jiyuan Liu,Yalin Zhang
BACKGROUND Insect glutathione S-transferases (GSTs) play a crucial role in insecticide detoxification. However, there remains a distinct lack of information regarding the role of GSTs in the detoxification of Tolfenpyrad (TFP) in insects. RESULTS Real-time quantitative PCR showed significant upregulation of PxGSTs after exposure to TFP for 6 h. An in vitro inhibition assay showed that TFP could inhibit PxGSTδ, PxGSTε and PxGSTσ, and the most pronounced inhibitory effect was on PxGSTσ. Metabolism assays displayed that PxGSTσ was superior to other test PxGSTs in metabolizing TFP. The molecular docking of TFP and PxGSTσ revealed that the H-bond provided by the sidechains of Tyr107 and Tyr162 were key to the detoxification of TFP by PxGSTσ. Further tests using mutant PxGSTσ proteins at the sites of Tyr107 (PxGSTσY107A) and Tyr162 (PxGSTσY162A) corroborated that the individual replacement of Tyr107 and Tyr162 could greatly weaken the binding and metabolic abilities to TFP. CONCLUSION Metabolic interactions between the Plutella xylostella (L.) GSTs (PxGSTs) and TFP were deciphered. This study illustrates the molecular metabolism mechanism of PxGSTσ towards TFP and provides theoretical underpinnings for the design and optimization of novel TFP-like insecticides. © 2020 Society of Chemical Industry
研究领域:
昆虫学
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分子生物学
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农药科学
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产品关联
DOI
PubMed
高影响因子
Foods
·
2021
·Vol. 10
·期 5
·1073
·
IF 4.35
Meng-Bo Tian,Lin Yuan,Ming-Yuan Zheng,Zhu-Mei Xi
Anthocyanins are vital components of plant secondary metabolites, and are also the most important coloring substances in wine. Teinturier cultivars are rich in anthocyanins. However, the differences in anthocyanin accumulation and profiles between teinturier and non-teinturier cultivars have not been reported. In this study, Yan 73 and Dunkelfelder were selected as the experimental materials, and three non-teinturier cultivars were used for comparison. LC-MS and qRT-PCR were used to determine the individual anthocyanin contents and the relative gene expression. The results show that the total anthocyanin content of the teinturier cultivars was considerably higher than that in non-teinturier cultivars, and the levels of individual anthocyanins increased gradually during ripening. Lower ratios of modified anthocyanins were found in the teinturier cultivars, which was not only due to the high expression level ofVvUFGTandVvGST4, but also due to the relatively low expression ofVvOMTin these cultivars. Cluster analysis of gene expression and anthocyanin accumulation showed thatVvUFGTis related to anthocyanin accumulation, and thatAM1is related to the synthesis and transport of methylated anthocyanins. Our results will be useful for further clarifying the pathways of anthocyanin synthesis, modification, and transport in teinturier cultivars.Keywords:grape;Yan 73;Dunkelfelder;anthocyanin;cluster analysis
研究领域:
植物学
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植物生理学
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分子生物学
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DOI
PubMed
高影响因子
JOURNAL OF NANOPARTICLE RESEARCH
·
2014
·Vol. 16
·期 11
·1-13
·
IF 2.278
Liu Wenjuan,Yao Jun,Cai Minmin,Chai Hankuai,Zhang Chi,Sun Jingjing,Chandankere Radhika,Masakorala Kanaji
A new nanopesticide, carboxymethyl-β-cyclodextrin-Fe 3 O 4 magnetic nanoparticles-Diuron (CM-β-CD-MNPs-Diuron), was synthesized from an inclusion complex of CM-β-CD-MNPs as host and diuron as guest molecules. The transmission electron microscopy revealed it had an average diameter of 25 nm which is more or less the same as that of MNPs (average diameter ~23 nm). The CM-β-CD grafting was confirmed by infrared spectroscopy, and the amount of CM-β-CD grafted on the surface of MNPs was determined to be 144.1 mg/g by thermogravimetry. The feasibility of using CM-β-CD-MNPs as a nanocarrier for loading diuron was verified by investigating the formation of inclusion complex. The complexation of CM-β-CD-MNPs with diuron followed the Langmuir adsorption isotherm. In this work, the potential toxic effect of CM-β-CD-MNPs-Diuron on soil microbial was evaluated by microcalorimetry, urease enzyme and real-time quantitative PCR (qPCR). The thermokinetic parameters were observed to decrease with increase in the loading of CM-β-CD-MNPs-Diuron in soil. The urease activity data showed that there was a significant effect ( p < 0.05) of CM-β-CD-MNPs-Diuron on the enzyme activity. The microcalorimetric analysis was in agreement with qPCR, confirming the toxic effect of this nanopesticide on microorganism in soil.
研究领域:
环境科学
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微生物学
·
纳米技术
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产品关联
DOI
高影响因子
Frontiers in Genetics
·
2023
·
IF 3.7
Huang Hui,Ye Zhifang,Li Zhengzhao,Wang Bo,Li Ke,Zhou Kai,Cao Huiyuan,Zheng Jiaxuan,Wang Guangji
Identifying effective biomarkers in osteosarcoma (OS) is important for predicting prognosis. We investigated the prognostic value of ferroptosis-related genes (FRGs) in OS. Transcriptome and clinical data were obtained from The Cancer Genome Atlas and Gene Expression Omnibus. FRGs were obtained from the ferroptosis database. Univariate COX regression and LASSO regression screening were performed and an FRG-based prognostic model was constructed, which was validated using the Gene Expression Omnibus cohort. The predictive power of the model was assessed via a subgroup analysis. A nomogram was constructed using clinical markers with independent prognostic significance and risk score results. The CIBERSORT algorithm was used to detect the correlation between prognostic genes and 22 tumor-infiltrating lymphocytes. The expression of prognostic genes in erastin-treated OS cell lines was verified via real-time PCR. Six prognostic FRGs (ACSL5, ATF4, CBS, CDO1, SCD, and SLC3A2) were obtained and used to construct the risk prognosis model. Subjects were divided into high- and low-risk groups. Prognosis was worse in the high-risk group, and the model had satisfactory prediction performance for patients younger than 18 years, males, females, and those with non-metastatic disease. Univariate COX regression analysis showed that metastasis and risk score were independent risk factors for patients with OS. Nomogram was built on independent prognostic factors with superior predictive power and patient benefit. There was a significant correlation between prognostic genes and tumor immunity. Six prognostic genes were differentially expressed in ferroptosis inducer-treated OS cell lines. The identified prognostic genes can regulate tumor growth and progression by affecting the tumor microenvironment.
研究领域:
肿瘤学
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基因组学
·
生物信息学
·
分子生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
BMC PLANT BIOLOGY
·
2019
·Vol. 19
·期 1
·1-16
·
IF 3.67
Cao Yunpeng,Meng Dandan,Han Yahui,Chen Tianzhe,Jiao Chunyan,Chen Yu,Jin Qing,Cai Yongping
Background Studies have demonstrated that BBX (B-BOX) genes play crucial roles in regulatory networks controlling plant growth, developmental processes and stress response. Nevertheless, comprehensive study of BBX genes in orchids (Orchidaceae) is not well studied. The newly released genome sequences of Dendrobium officinale and Phalaenopsis equestris have allowed a systematic analysis of these important BBX genes in orchids. Results Here we identified 19 ( DoBBX01 – 19 ) and 16 ( PeBBX01–16 ) BBX genes from D. officinale and P. equestris , respectively, and clustered into five clades (I-V) according to phylogenetic analysis. Thirteen orthologous, two DoBBXs paralogous and two PeBBXs paralogous gene pairs were validated. This gene family mainly underwent purifying selection, but five domains experienced positive selection during evolution. Noteworthy, the expression patterns of root, root_tips, stem, leaf, speal, column, lip, and flower_buds revealed that they might contribution to the formation of these tissues. According to the cis-regulatory elements analysis of BBX genes, qRT-PCR experiments were carried out using D. officinale PLBs (protocorm-like bodies) and displayed that these BBX genes were differentially regulated under AgNO 3 , MeJA (Methyl Jasmonate), ABA (abscisic acid) and SA (salicylic acid) treatments. Conclusions Our analysis exposed that DoBBX genes play significant roles in plant growth and development, and response to different environmental stress conditions of D. officinale , which provide aid in the selection of appropriate candidate genes for further functional characterization of BBX genes in plants.
研究领域:
植物生物学
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基因组学
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分子遗传学
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生物信息学
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DOI
PubMed
高影响因子
ANALYST
·
2015
·Vol. 140
·期 13
·4566-4575
·
IF 4.107
Jacky F. C. Loo,S. S. Wang,F. Peng,J. A. He,L. He,Y. C. Guo,D. Y. Gu,H. C. Kwok,S. Y. Wu,H. P. Ho,W. D. Xie,Y. H. Shao,S. K. Kong
As in all RNA viruses, influenza viruses change and mutate constantly because their RNA polymerase has no proofreading ability. This poses a serious threat to public health nowadays. In addition, traditional pathogen-based detection methods may not be able to report an infection from an unknown type or a subtype of virus if its nucleotide sequence is not known. Because of these factors, targeting host microRNA signatures may be an alternative to classify infections and distinguish types of pathogens as microRNAs are produced in humans shortly after infection. Although this approach is in its infant stage, there is an urgent need to develop a rapid reporter assay for microRNA for disease control and prevention. As a proof of concept, we report herein for the first time a non-PCR MARS (MicroRNA-RNase-SPR) assay to detect the microRNA miR-29a-3p from human subjects infected with influenza virus H1N1 by surface plasmon resonance (SPR). In our MARS assay, RNase H is employed to specifically hydrolyze the RNA probes immobilized on the gold surface where they hybridize with its cognate target cDNAs miR-29a-3p, where it was formed from reverse transcription with mature miR-29a-3p specific stem-looped primers. After the digestion of the RNA probe by RNase H, the intact cDNA was released from the RNA–DNA hybrid and bound to a new RNA probe for another enzymatic reaction cycle to amplify signals. With assay optimization, the detection limit of our MARS assay for miR-29a-3p was found to be 1 nM, and this new assay could be completed within 1 hour without thermal cycling. This non-PCR assay with high selectivity for mature microRNA provides a new platform for rapid disease diagnosis, quarantine and disease control.
研究领域:
病毒学
·
分子生物学
·
诊断学
·
公共卫生
✓ 已验证
DOI
PubMed
高影响因子
TALANTA
·
2020
·
IF 5.339
Wancun Zhang,Kangbo Liu,Pin Zhang,Weyland Cheng,Yaodong Zhang,Linfei Li,Zhidan Yu,Mengmeng Chen,Lin Chen,Lifeng Li,Xianwei Zhang
Rapid, simple, specific and sensitive approaches for single nucleotide polymorphisms (SNPs) detection are essential for clinical diagnosis. In this study, all-in-one approaches, consisting of the whole detection process including ligase detection reaction (LDR) and real time quantitative polymerase chain reaction performed in one PCR tube by a one-step operation on a real-time PCR system using molecular beacon (MB) as turn-on probe, were developed for rapid, simple, specific and sensitive quantifcation of SNPs. High specificity of the all-in-one approach was achieved by using the LDR, which employs a thermostable and single-base discerning Hifi Taq DNA ligase to ligate adjacently hybridized LDR-specific probes. In addition, a highly specific probe, MB, was used to detect the products of all-in-one approach, which doubly enhances the specificity of the all-in-one approach. The linear dynamic range and high sensitivity of mutant DNA (MutDNA) and wild-type DNA (WtDNA) all-in-one approaches for the detection of MutDNA and WtDNA were studied in vitro , with a broad linear dynamic range of 0.1 fM to 1 pM and detection limits of 65.3 aM and 31.2 aM, respectively. In addition, the MutDNA and WtDNA all-in-one approaches were able to accurately detect allele frequency changes as low as 0.1%. In particular, the epidermal growth factor receptor T790M MutDNA frequency in the tissue of five patients with non-small cell lung cancer detected by all-in-one approaches were in agreement with clinical detection results, indicating the excellent practicability of the developed approaches for the quantification of SNPs in real samples. In summary, the developed all-in-one approaches exhibited promising potential for further applications in clinical diagnosis.
研究领域:
分子生物学
·
医学诊断
·
遗传学
✓ 已验证
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）