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1.
Chem Commun (Camb) ; 60(34): 4593-4596, 2024 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-38577866

RESUMO

This work developed DNA amplifier logic gates (AND-OR, OR-AND, FAN-IN, FAN-OUT, and 4-bit square-root circuits) using a flap endonuclease 1 (FEN1)-catalyzed signal amplification reaction, for the fastest and compact DNA computing. Moreover, the logic circuit can use input strands with concentrations of less than 1 nM, which is more than 100 times lower than the input concentration of other DNA logic circuits, providing a promising methodology for constructing fast and compact DNA computations.

2.
Adv Sci (Weinh) ; 11(17): e2307034, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38353386

RESUMO

Exchange bias is extensively studied and widely utilized in spintronic devices, such as spin valves and magnetic tunnel junctions. 2D van der Waals (vdW) magnets, with high-quality interfaces in heterostructures, provide an excellent platform for investigating the exchange bias effect. To date, intrinsic modulation of exchange bias, for instance, via precise manipulation of the magnetic phases of the antiferromagnetic layer, is yet to be fully reached, owing partly to the large exchange fields of traditional bulk antiferromagnets. Herein, motivated by the low-field spin-flop transition of a 2D antiferromagnet, CrPS4, exchange bias is explored by modulating the antiferromagnetic spin-flop phase transition in all-vdW magnetic heterostructures. The results demonstrate that undergoing the spin-flop transition during the field cooling process, the A-type antiferromagnetic ground state of CrPS4 turns into a canted antiferromagnetic one, therefore, it reduces the interfacial magnetic coupling and suppresses the exchange bias. Via conducting different cooling fields, one can select the exchange bias effect switching among the "ON", "depressed", and "OFF" states determined by the spin flop of CrPS4. This work provides an approach to intrinsically modulate the exchange bias in all-vdW heterostructures and paves new avenues to design and manipulate 2D spintronic devices.

3.
J Pharm Biomed Anal ; 240: 115964, 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38219442

RESUMO

Approximately 25% of breast cancer patients with HER2 overexpression tend to have a high risk of disease progression and death. Various HER2-targeting therapies have been approved for treatment. Recently, a novel antibody-drug conjugate, SHR-A1201, is being researched and developed. For the pharmacokinetic study of SHR-A1201, suitable bioanalytical methods are needed for quantifying unconjugated cytotoxin, cytotoxin-conjugated antibodies and total antibodies. In this research, bioanalytical methods involving a highly sensitive LC-MS/MS assay for unconjugated cytotoxic payload DM1 in human plasma, ELISA strategies for DM1-conjugated trastuzumab and total trastuzumab in human serum were developed, validated and successfully applied to a phase I dose-escalation pharmacokinetic study of SHR-A1201. The pharmacokinetic properties and exposure-to-dose proportionality was evaluated for SHR-A1201. According to the bioanalytical method validation guidance, the bioanalytical methods were fully validated and the validation results met the acceptance criteria. The nonspecific binding of DM1 and dimer was avoided for the LC-MS/MS assay. In the dose-escalation pharmacokinetic study of SHR-A1201, a potential dose-proportional pharmacokinetics was observed over the dose from 1.2 mg/kg to 4.8 mg/kg. The validated bioanalytical strategies are robust and reproducible and these bioanalytical methods will contribute to better understanding of the pharmacokinetic properties of SHR-A1201.


Assuntos
Neoplasias da Mama , Imunoconjugados , Maitansina , Humanos , Feminino , Ado-Trastuzumab Emtansina , Imunoconjugados/uso terapêutico , Cromatografia Líquida , Anticorpos Monoclonais Humanizados/farmacocinética , Receptor ErbB-2/metabolismo , Espectrometria de Massas em Tandem , Trastuzumab/uso terapêutico , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/metabolismo , Citotoxinas
4.
Anal Chem ; 96(2): 756-765, 2024 01 16.
Artigo em Inglês | MEDLINE | ID: mdl-38170958

RESUMO

In situ monitoring of the actions of correlated enzymes in living cells is crucial for expanding our understanding of disease progression and evaluating drug efficacy. However, due to the diverse functions of different enzymes, currently available methods for comprehensive analysis of these events are limited. Here, we present an in situ track-generated DNA walker for AND-gate logic imaging of telomerase (TE) and flap endonuclease 1 (FEN1) activities in live cells. TE is in charge of generating the tracks for the walking strands by extending the TE primer on a gold nanoparticle, while FEN1 is responsible for recognizing the overlapping structure formed by the walking strands and the tracks and then cleaving the fluorescent reporter to produce signals. By utilizing the DNA walker, we successfully determined the expression levels and activities of TE and FEN1 in various cancer cell lines, offering promising prospects for screening inhibitors and investigating the biomolecular mechanisms of diseases.


Assuntos
Nanopartículas Metálicas , Telomerase , Endonucleases Flap/genética , Telomerase/metabolismo , Ouro/química , Nanopartículas Metálicas/química , DNA/química
5.
Anal Chem ; 95(22): 8621-8631, 2023 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-37218062

RESUMO

In situ observation of changes in the activity of marker proteins in living cells is crucial for both biomarker-based disease diagnosis and drug screening. Flap endonuclease 1 (FEN1) has been recognized as a broad-spectrum cancer biomarker and therapeutic target. However, simple and reliable methods for in situ studying the FEN1 activity changes in living cells are limited. Here, we introduce a nano firework as a fluorescent sensor to sense and report FEN1 activity changes in living cells through FEN1 recognizing the substrates on the surface of the nano firework to release and restore the fluorescence of the prequenched fluorophores. We verified the high selectivity, anti-interference ability, stability, and quantitative performance of the nano firework in tubes and living cells, respectively. A series of controlled experiments have demonstrated that the nano firework could accurately report changes in FEN1 activity in different cells, enabling "sensors in, results out" in the manner of simple addition to the cell culture medium. Using an in silico molecular docking study and experiments, we also explored the ability of the nano firework for rapid screening of FEN1 inhibitors and found two new candidate compounds myricetrin and neoisoliquritin, which could be used as FEN1 inhibitors for further research. These performances of the nano firework suggest that it can be used in high-throughput screening applications, providing a promising tool for biomarker-based new drug discovery.


Assuntos
Endonucleases Flap , Ensaios de Triagem em Larga Escala , Endonucleases Flap/genética , Simulação de Acoplamento Molecular , Biomarcadores Tumorais , DNA/química
6.
Xenobiotica ; 52(6): 567-574, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-36129160

RESUMO

Lubiprostone, a derivative of prostaglandin E1, is the first chemical-type constipation treatment approved by FDA. Lubiprostone has low systemic exposure after oral administration. Therefore, it is recommended that 15-hydroxylubiprostone, which is a dominant active metabolite of lubiprostone, be used as the pharmacokinetic evaluation indicator. Due to the microdosage of the lubiprostone capsules, it is difficult to develop a highly sensitive bioanalytical method for 15-hydroxylubiprostone.In this study, a highly sensitive and selective liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) method has been established and fully validated for the quantification of 15-hydroxylubiprostone in human plasma, and the validated bioanalytical method has been applied to a pharmacokinetic study of lubiprostone capsules successfully.The pharmacokinetics of 15-hydroxylubiprostone were observed after fed administration in healthy Chinese volunteers. The Cmax and AUC0-t were 75.8 ± 57.6 pg/mL and 222 ± 68.0 pg·h/mL for 15-hydroxylubiprostone.This study investigated the pharmacokinetic properties of 15-hydroxylubiprostone under fed conditions in healthy Chinese volunteers and would provide clinical guidance for the application and further development of lubiprostone capsules.


Assuntos
Alprostadil , Espectrometria de Massas em Tandem , Cápsulas , China , Cromatografia Líquida/métodos , Voluntários Saudáveis , Humanos , Lubiprostona , Reprodutibilidade dos Testes , Espectrometria de Massas em Tandem/métodos
7.
Anal Chem ; 93(27): 9593-9601, 2021 07 13.
Artigo em Inglês | MEDLINE | ID: mdl-34191475

RESUMO

DNA walkers have shown superior performance in biosensing due to their programmability to design molecular walking behaviors with specific responses to different biological targets. However, it is still challenging to make DNA walkers capable of distinguishing DNA targets with single-base differences, so that DNA walkers that can be used for circulating tumor DNA sensing are rarely reported. Herein, a flap endonuclease 1 (FEN 1)-assisted DNA walker has been proposed to achieve mutant biosensing. The target DNA is captured on a gold nanoparticle (AuNP) as a walking strand to walk by hybridizing to the track strands on the surface of the AuNP. FEN 1 is employed to report the walking events by cleaving the track strands that must form a three-base overlapping structure recognized by FEN 1 after hybridizing with the captured target DNA. Owing to the high specificity of FEN 1 for structure recognition, the one-base mutant DNA target can be discriminated from wild-type DNA. By constructing a sensitivity-enhanced DNA walker system, as low as 1 fM DNA targets and 0.1% mutation abundance can be sensed, and the theoretical detection limits for detecting the DNA target and mutation abundance achieve 0.22 fM and 0.01%, respectively. The results of epidermal growth factor receptor (EGFR) L858R mutation detection on cell-free DNA samples from 15 patients with nonsmall cell lung cancer were completely consistent with that of next-generation sequencing, indicating that our DNA walker has potential for liquid biopsy.


Assuntos
Técnicas Biossensoriais , Carcinoma Pulmonar de Células não Pequenas , DNA Tumoral Circulante/análise , Neoplasias Pulmonares , Nanopartículas Metálicas , Endonucleases Flap , Ouro , Humanos
8.
Anal Chem ; 93(13): 5529-5536, 2021 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-33752323

RESUMO

Cervical cancer is the fourth leading cause of death in women, especially in developing countries. Specific and economic methodologies for HPV typing are crucial in cancer diagnosis and further disease control. However, routine assays based on real-time polymerase chain reaction (qPCR) or DNA-chip hybridization are either incapable of offering detailed subtype information or involve tedious open-tube operations with the risk of cross-contamination from PCR amplicons. Herein, we proposed a multiplex visualized closed-tube PCR (Multi-Vision) for HPV typing. Using gold nanoparticle probes (AuNPs) as a color change indicator combined with a Hamming distance 2 coding scheme, 13 high-risk HPVs and two subtypes associated with high-incidence benign lesions were successfully typed by performing six closed-tube PCRs. The assay demonstrates high specificity with no cross-reaction among different subtypes under several artificial sample concentrations (from 100 to 103 copies per reaction) and enables highly sensitive detection of as low as 0.5 copies/µL. Further, 105 clinical samples were successfully analyzed using our method with a high concordance rate of 99.05% (104/105) compared to a HPV typing kit. The inconsistent sample was confirmed by sequencing to be consistent with the typing results determined by our method, indicating that Multi-Vision could be a useful tool for HPV detection, especially in resource-limited regions.


Assuntos
Nanopartículas Metálicas , Infecções por Papillomavirus , DNA Viral/genética , Feminino , Ouro , Humanos , Papillomaviridae/genética , Infecções por Papillomavirus/diagnóstico , Sensibilidade e Especificidade
9.
J Pharm Biomed Anal ; 197: 113959, 2021 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-33626444

RESUMO

Acquired estrogen receptor 1 (ESR1) mutation is being promoted as a key mechanism of resistance to endocrine therapies in breast cancers. It is significative to monitor ESR1 mutations in real time, which provide an opportunity to alter therapy as these mutations emerge. Previous assays based on next-generation sequencing (NGS) and digital PCR (dPCR) usually due to high costs and complicated workflows hampered their clinical adoption in general medical institutions. Here, we proposed a new strategy using base-specific invasive reaction assisted qPCR measure for ESR1 mutations in cfDNA. Two pivotal steps involved in this strategy are target-specific signal generation and the quantification without adding any internal reference or making standard calibration curves. The strategy enabled a high specificity of 0.1% (better than traditional NGS-based method) and a minimum sensitivity of 0.1 copies µL-1. As validation, with the strategy, cfDNA from endocrine therapy-resistant breast cancers and untreated ones were successfully analyzed (20% mutation rate (2/10) with mutation abundance of 0.54-1.65% vs. 0% mutation rate (0/5)). By virtue of cost-effective, highly flexible and precise, the strategy could be readily implemented in general laboratory, showing promising application perspectives in analysis of other types of mutations.


Assuntos
Neoplasias da Mama , Ácidos Nucleicos Livres , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/genética , Ácidos Nucleicos Livres/genética , Receptor alfa de Estrogênio/genética , Feminino , Humanos , Mutação , Reação em Cadeia da Polimerase em Tempo Real
10.
Sens Actuators B Chem ; 327: 128919, 2021 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-32963421

RESUMO

Nucleic acid detection is important for clinical diagnostics; however, it is challenging to perform genetic testing at the point-of-care due to the tedious steps involved in DNA extraction and the risk of cross-contamination from amplicons. To achieve a fully-automated and contamination-free nucleic acid detection, we propose a closed-type cassette system which enables the following steps to be operated automatically and sequentially: sample preparation based on magnetic beads, target amplification using multiplex polymerase chain reaction, and colorimetric detection of amplicons using a serial invasive reaction coupled with the aggregation of gold nanoparticle probes. The cassette was designed to be round and closed, and 10 targets in a sample could be simultaneously detected by the naked eye or using a spectrophotometer in the system. In addition, a cassette-driven device was fabricated to transfer reagents between wells, to control the temperature of each reaction, and to sense the colour in the detection wells. The cassette system was sensitive enough to detect 10 genotypes at 5 single nucleotide polymorphism sites related to the anticoagulant's usage, by using a 0.5 µL blood sample. The accuracy of the system was evaluated by detecting 12 whole blood samples, and the results obtained were consistent with those obtained using pyrosequencing. The cassette is airtight and the whole system is fully automatic; the only manual operation is the addition of the sample to the cassette, performing point-of-care genetic testing in a sample-in/answer-out way.

11.
Anal Methods ; 12(26): 3344-3350, 2020 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-32930221

RESUMO

Exon 19 deletions (19-Del) on the epidermal growth factor receptor (EGFR) gene are vital biomarkers for guiding tyrosine kinase inhibitor (TKI) treatment and the diagnosis of non-small cell lung cancer (NSCLC). However, it is difficult for conventional qPCR to quantitatively detect all 19-Del targets of EGFR, especially for cfDNA samples. Herein, a multiplex invasive reaction-assisted qPCR was proposed by employing a multiplex invasive reaction to distinguish 19-Del DNA targets from wild DNA targets and report them with different fluorescence signals in each PCR cycle. As all 19-Del targets have the same amplification efficiency and very similar invasive reaction efficiencies, the 19-Del abundance in a sample could be quantified by using the difference between the Ct values (ΔCt) of the deletion targets and the wild targets without the requirement of a standard calibration curve. Combining the high sensitivity of PCR and the high specificity of the invasive reaction, this method can detect 10 copies of the deletion targets and lower than 0.1% deletion abundance. The results were 100% consistent with ARMS-PCR for the 38 tumor tissues tested and were in good agreement with next-generation sequencing for quantifying the abundance of EGFR 19-Del in 15 cfDNA samples, showing the great potential of the method for liquid biopsies.


Assuntos
Carcinoma Pulmonar de Células não Pequenas , Ácidos Nucleicos Livres , Neoplasias Pulmonares , Carcinoma Pulmonar de Células não Pequenas/genética , Ácidos Nucleicos Livres/genética , Receptores ErbB/genética , Éxons/genética , Humanos , Neoplasias Pulmonares/diagnóstico
12.
J Nanosci Nanotechnol ; 20(10): 6140-6147, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-32384963

RESUMO

Detection of blood-borne pathogenic viruses is essential for blood transfusion, and has great significance for epidemiology, as well as clinical practices. Common blood-borne viruses causing infectious diseases include Hepatitis B virus (HBV), Hepatitis C virus (HCV), Human immunodeficiency virus (HIV) and Treponema pallidum (TP). Therefore, multiplex detection of these viruses is more in the line with the needs of clinical testing. Although real-time PCR-based multiplex nucleic acid testing (NAT) was developed for pathogen detection, however, the requirement of multichannel realtime PCR machine increases the instrumental cost and is not suitable for use in resource-limited areas. In this study, we proposed a multiplex and colorimetric assay for detecting viral nucleic acids in blood by using serial invasive reaction assisted gold nanoparticle (AuNPs) probes assembling to identify multiplex PCR amplicons. As low as 2 copies per reaction of HIV and TP targets, and 20 copies per reaction of HBV and HCV targets can be detected. The results can be observed by naked eyes; thus, just a standard PCR machine is required. In addition, the hairpin probe and the AuNPs for signal read out are universal for all the targets, reducing the detection cost. About 20 DNA samples remaining after clinical HBV testing were successfully detected, and the results were consistent with that of commercially available real-time PCR based kit, indicating that this method has a potential for clinical applications.


Assuntos
Hepatite C , Nanopartículas Metálicas , DNA Viral/genética , Ouro , Hepacivirus/genética , Vírus da Hepatite B/genética , Humanos , Reação em Cadeia da Polimerase Multiplex , Sensibilidade e Especificidade
13.
Metabolomics ; 16(3): 41, 2020 03 14.
Artigo em Inglês | MEDLINE | ID: mdl-32172350

RESUMO

INTRODUCTION: Pharmacogenetics and pharmacometabolomics are the common methods for personalized medicine, either genetic or metabolic biomarkers have limited predictive power for drug response. OBJECTIVES: In order to better predict drug response, the study attempted to integrate genetic and metabolic biomarkers for drug pharmacokinetics prediction. METHODS: The study chose celecoxib as study object, the pharmacokinetic behavior of celecoxib was assessed in 48 healthy volunteers based on UPLC-MS/MS platform, and celecoxib related single nucleotide polymorphisms (SNPs) were also detected. Three mathematic models were constructed for celecoxib pharmacokinetics prediction, the first one was mainly based on celecoxib-related SNPs; the second was based on the metabolites selected from a pharmacometabolomic analysis by using GC-MS/MS method, the last model was based on the combination of the celecoxib-related SNPs and metabolites above. RESULTS: The result proved that the last model showed an improved prediction power, the integration model could explain 71.0% AUC variation and predict 62.3% AUC variation. To facilitate clinical application, ten potential celecoxib-related biomarkers were further screened, which could explain 68.3% and predict 54.6% AUC variation, the predicted AUC was well correlated with the measured values (r = 0.838). CONCLUSION: This study provides a new route for personalized medicine, the integration of genetic and metabolic biomarkers can predict drug response with a higher accuracy.


Assuntos
Anti-Inflamatórios não Esteroides/metabolismo , Celecoxib/metabolismo , Polimorfismo de Nucleotídeo Único/genética , Adulto , Anti-Inflamatórios não Esteroides/farmacocinética , Biomarcadores/análise , Celecoxib/farmacocinética , Cromatografia Líquida de Alta Pressão , Voluntários Saudáveis , Humanos , Masculino , Metabolômica , Medicina de Precisão , Espectrometria de Massas em Tandem , Adulto Jovem
14.
RSC Adv ; 10(27): 16094-16100, 2020 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-35493641

RESUMO

A mass barcode mediated signal amplification strategy was developed and applied to the determination of protein. A new compound, N'-((2-aminopyridin-3-yl)methylene)-5-(1,2-dithiolan-3-yl)pentanehydrazide (TAPA), was synthesized from the linker and the signal barcode, and used as the bonding barcode. For the realization of signal transduction, TAPAs and the target catcher aptamers, were both modified on gold nanoparticles (AuNPs) to establish the relationship between TAPAs and the target. Owing to the fact that the amount of TAPAs was much greater than the target, the signal of the target was not only transduced to the signal of the mass barcodes, but also amplified greatly. Thrombin, an important biomarker for coagulation abnormality diseases, was selected as a model analyte. Two kinds of thrombin recognition aptamers, aptamer 29 (apt29) and aptamer 15 (apt15), were modified onto the magnetic beads (MBs) and AuNPs, respectively. The modified AuNPs were further functionalized with lots of TAPA and formed apt15-AuNPs-TAPA. MBs-apt29 and apt15-AuNPs-TAPA could both recognize the target thrombin and form the sandwich complex (MBs-apt29/thrombin/apt15-AuNPs-TAPA). After the complex was separated by an extra magnetic field, NaClO oxidant solution was added to release the signal barcodes, 2-Amino-3-pyridinecarboxaldehyde (APA), which were then collected after centrifuging and analyzed by LC-MS/MS. Under optimized conditions, the mass response intensity was proportional to thrombin concentration in the range of 0.05-10 nM, with a 0.007 nM detection limit. This method was applied to the determination of thrombin in spiked serum samples, and the average recoveries ranged from 89.6% to 110.4%, which confirmed the applicability of this method.

15.
J Proteome Res ; 19(1): 119-128, 2020 01 03.
Artigo em Inglês | MEDLINE | ID: mdl-31617722

RESUMO

Individual variation in pharmacokinetics of faropenem is significant. We attempted to predict drug response of faropenem using a pharmacometabonomic approach. Metabolic profiling was performed on predose plasma samples from 36 healthy volunteers by gas chromatography-mass spectrometry (GC/MS), with 204 endogenous metabolites detected. Plasma concentration was measured after drug administration, using high pressure liquid chromatography-tandem mass spectroscopy (LC/MS/MS), and the pharmacokinetic parameters were calculated. Then a two-stage partial least squares strategy was employed to screen potential biomarkers and predict the pharmacokinetic parameters of faropenem. The results showed a good prediction of AUC and Cmax with the screened biomarkers, and metabolites such as valine, proline, aspartic acid, gluconic acid, glucuronic acid, and 2-ketoisocaproic acid were indicated as candidate biomarkers. Finally, we explored the mechanism of individual variation by pathway enrichment analysis, and it suggested that organic anion transporter 1 (OAT1) and 3 (OAT3) might be responsible for individual variation of faropenem, and this hypothesis was verified by an experiment in rats.


Assuntos
Metabolômica , Espectrometria de Massas em Tandem , Animais , Cromatografia Líquida de Alta Pressão , Cromatografia Líquida , Ratos , beta-Lactamas
16.
Analyst ; 144(19): 5775-5784, 2019 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-31460526

RESUMO

Accurately quantifying hepatitis B virus DNA (HBV-DNA) in serum is important in dynamic monitoring and prognosis evaluation for patients with hepatitis B. Routine assays based on real-time polymerase chain reaction (qPCR) for HBV-DNA quantification usually require laborious calibration curves and may bring bias from the biological samples. To enable absolute quantification of HBV-DNA in a single tube, we described a modification of the conventional Q-Invader assay by separately encoding targeted DNA and artificially designed internal quantitative-standard DNA (QS-DNA) at the flaps of the corresponding downstream probes. Quantification of targeted HBV-DNA was readily achieved by the difference in the quantification cycle value (Ct) between itself and QS-DNA. Furthermore, spiked-in QS-DNA before DNA extraction allowed errors caused by DNA extraction to be corrected. Two different gene regions covering eight genotypes were encoded with the same flap to avoid false-negative results. The method demonstrates a high sensitivity, which enables accurate detection of as low as 2 copies of the HBV-DNA plasmid or 20 IU mL-1 HBV-DNA in serum in a single tube. Successful quantification of 50 clinical samples indicates that our method is cost-effective, labor-saving and reproducible, and promising for the ultra-sensitive quantification analysis of many types of pathogens other than HBV.


Assuntos
DNA Viral/sangue , Vírus da Hepatite B/química , Reação em Cadeia da Polimerase em Tempo Real/métodos , Humanos , Limite de Detecção , Reprodutibilidade dos Testes
17.
Ecotoxicol Environ Saf ; 164: 618-628, 2018 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-30165339

RESUMO

Understanding the community structure of soil microbes is required to evaluate the potential effects of genetically modified (GM) plants on ecological environments. Bacterial communities in soil planted with conventional cotton (CC) and transgenic cultivar (TC) in a natural ecosystem for three years were characterized by 454 pyrosequencing of the V3-V5 and V5-V9 regions of 16S rDNA from June to September 2013. V3-V5 and V5-V9 regions yielded a total of 12,848 and 10,541 OTUs, respectively. The V5-V9 amplicon was additionally used to detect phyla that were poorly sequenced by V3-V5 (such as Chlamydiae, Crenarchaeota and Archaea). Among the species detected by each primer pair, 46% of the species identified from V3-V5 and 60% of those identified from V5-V9 were detected by both primer pairs. Although distinct bacterial compositions existed between the two amplified regions, statistical analysis revealed no significant difference in the diversity indexes or phylogenetic patterns in TC versus compared to those in the CC control. Further, clustering analysis in both regions indicated that there was no unambiguous aggregation in TC compared to that in CC control. Of all 26 phyla detected by both regions, each region detected 2 distinct phyla exhibiting significant variations in abundance. The species unique to each treatment field accounted for less than 27% of all species and were rare taxa (abundance < 0.15%). However, a small fraction of diagnostic taxa with specific ecological functions differed significantly between TC and CC. These differences were not driven by any obvious environmental factors. The results established a comprehensive inventory of the bacterial communities associated with GM plants and indicated that transgenic cotton may not significantly affect soil microorganisms compared with conventional cotton over a three-year period. Furthermore, diagnostic taxa were provided for monitoring the perturbation in soil, but further verification in future studies is required.


Assuntos
Archaea/classificação , Bactérias/classificação , Gossypium/microbiologia , Plantas Geneticamente Modificadas/microbiologia , DNA Bacteriano/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Solo/química , Microbiologia do Solo
18.
Anal Bioanal Chem ; 410(26): 6751-6759, 2018 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30128808

RESUMO

Detection of EGFR mutations in circulating cell-free DNA (cfDNA) is beneficial to monitor the therapeutic effect, tumor progression, and drug resistance in real time. However, it requires that the mutation detection method has the ability to quantify the mutation abundance accurately. Although the next-generation sequencing (NGS) and digital PCR showed high sensitivity for quantifying mutations in cfDNA, the use of expensive equipment and the high-cost hampered their applications in the clinic. Herein, we propose a highly sensitive and specific real-time PCR by employing serial invasive reaction as a sequence identifier for quantifying EGFR mutation abundance in cfDNA (termed as qPCR-Invader). The mutation abundance can be quantified by using the difference of Ct values between mutant and wild-type targets without the need of making a standard curve. The method can quantify a mutation level as lower as 0.1% (10 copies/tube). Thirty-six tissue samples from non-small-cell lung cancer (NSCLC) patients were detected by our method and 14/36 tissues gave EGFR L858R mutation-positive results, whereas ARMS-PCR just identified 12 of L858R mutant samples. The two inconsistent samples were confirmed as L858R mutant by pyrophosphorolysis-activated polymerization method, indicating that qPCR-Invader is more sensitive than ARMS-PCR for mutation detection. The L858R mutation abundances of 19 cfDNA samples detected by qPCR-Invader were close to that from NGS, indicating our method can precisely quantify mutation abundance in cfDNA. The qPCR-Invader just needs a common real-time PCR device to accomplish quantification of EGFR mutations, and the fluorescence probes are universal for any target detection. Therefore, it could be used in most laboratories to analyze mutations in cfDNA. Graphical abstract ᅟ.


Assuntos
Ácidos Nucleicos Livres/genética , Receptores ErbB/genética , Mutação , Reação em Cadeia da Polimerase em Tempo Real/métodos , Sequência de Bases , Carcinoma Pulmonar de Células não Pequenas/genética , Difosfatos/química , Fluorescência , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Limite de Detecção , Neoplasias Pulmonares/genética , Polimerização , Reprodutibilidade dos Testes
19.
Chem Sci ; 9(6): 1666-1673, 2018 Feb 14.
Artigo em Inglês | MEDLINE | ID: mdl-29675214

RESUMO

A DNA logic sensor was constructed for gene mutation analysis based on a novel signal amplification cascade by controllably extending a hairpin-structured flap to bridge two invasive reactions. The detection limit was as low as 0.07 fM, and the analytical specificity is high enough to unambiguously pick up 0.02% mutants from a large amount of wild-type DNA. Gene mutations related to the personalized medicine of gefitinib, a typical tyrosine kinase inhibitor, were analyzed by the DNA logic sensor with only a 15 minute response time. Successful assay of tissue samples and cell-free plasma DNA indicates that the new concept we proposed here could benefit clinicians for straightforward prescription of a mutation-targeted drug.

20.
J Pharm Biomed Anal ; 151: 145-150, 2018 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-29328981

RESUMO

As an orally active iron chelator, deferasirox forms its ion complexes in the prepared plasma samples and LC-MS mobile phase where ferric ion exists, and then comparing with the nominal concentration level, a lower detected concentration level of deferasirox would be obtained after LC-MS analysis, if no proper treatment was adopted. Meanwhile, the phenomenon would be observed that multiple repeat injections of the same deferasirox plasma sample in the same tube would show the lower and lower detected concentration levels of deferasirox, which caused by more and more ferric ions from the injection needle dissolved in the sample solution as multiple repeated injections. The addition of a proper concentration of EDTA in the mobile phase and the sample will competitively inhibit deferasirox from complexing with ferric ion, and prevent the decrease of deferasirox concentration. In this paper, an LC-MS/MS method was developed and validated for the determination of deferasirox in human plasma. To achieve the protein precipitation, the analytes were extracted from aliquots of 200 µL human plasma with acetonitrile. Chromatographic separation was performed on an ODS-C18 column with the mobile phase consisted of methanol and 0.1% formic acid containing 0.04 mM ethylenediamine tetraacetate dihydrate (EDTA) (80:20, v/v) at a flow rate of 0.5 mL/min. Deferasirox and the internal standard (IS, mifepristone) were detected using electrospray ionization in positive ion multiple reaction monitoring mode by monitoring the precursor-to-product ion transitions m/z 374.2 → 108.1 for deferasirox and m/z 430.1 → 372.2 for the IS. The method exhibited good linearity over the concentration range of 0.04-40 µg/mL for deferasirox. The method was successfully applied to a pharmacokinetic study in 10 Chinese healthy volunteers after oral administration of deferasirox.


Assuntos
Benzoatos/sangue , Compostos Férricos/sangue , Quelantes de Ferro/análise , Espectrometria de Massas em Tandem/métodos , Triazóis/sangue , Cromatografia Líquida/métodos , Deferasirox , Humanos , Espectrometria de Massas por Ionização por Electrospray/métodos
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