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1.
Anal Chem ; 96(17): 6692-6699, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38632948

ABSTRACT

The antibodies in the natural biological world utilize bivalency/multivalency to achieve a higher affinity for antigen capture. However, mimicking this mechanism on the electrochemical sensing interface and enhancing biological affinity through precise spatial arrangement of bivalent aptamer probes still pose a challenge. In this study, we have developed a novel self-assembly layer (SAM) incorporating triblock polyA DNA to enable accurate organization of the aptamer probes on the interface, constructing a "lock-and-key-like" proximity hybridization assay (PHA) biosensor. The polyA fragment acts as an anchoring block with a strong affinity for the gold surface. Importantly, it connects the two DNA probes, facilitating one-to-one spatial proximity and enabling a controllable surface arrangement. By precisely adjusting the length of the polyA fragment, we can tailor the distance between the probes to match the molecular dimensions of the target protein. This design effectively enhances the affinity of the aptamers. Notably, our biosensor demonstrates exceptional specificity and sensitivity in detecting PDGF-BB, as confirmed through successful validation using human serum samples. Overall, our biosensor presents a novel and versatile interface for proximity assays, offering a significantly improved surface arrangement and detection performance.


Subject(s)
Aptamers, Nucleotide , Becaplermin , Biosensing Techniques , Nucleic Acid Hybridization , Poly A , Biosensing Techniques/methods , Humans , Aptamers, Nucleotide/chemistry , Becaplermin/blood , Poly A/chemistry , Gold/chemistry , DNA Probes/chemistry
2.
Analyst ; 149(12): 3425-3432, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38720619

ABSTRACT

Antimicrobial resistance poses a serious threat to human health due to the high morbidity and mortality caused by drug-resistant microbial infections. Therefore, the development of rapid, sensitive and selective identification methods is key to improving the survival rate of patients. In this paper, a sandwich-type electrochemical DNA biosensor based on a polyadenine-DNA tetrahedron probe was constructed. The key experimental conditions were optimized, including the length of polyadenine, the concentration of the polyadenine DNA tetrahedron, the concentration of the signal probe and the hybridization time. At the same time, poly-avidin-HRP80 was used to enhance the electrochemical detection signal. Finally, excellent biosensor performance was achieved, and the detection limit for the synthetic DNA target was as low as 1 fM. In addition, we verified the practicability of the system by analyzing E. coli with the MCR-1 plasmid and realized multi-channel detection of the drug resistance genes MCR-1, blaNDM, blaKPC and blaOXA. With the ideal electrochemical interface, the polyA-based biosensor exhibits excellent stability, which provides powerful technical support for the rapid detection of antibiotic-resistant strains in the field.


Subject(s)
Biosensing Techniques , Electrochemical Techniques , Escherichia coli , Biosensing Techniques/methods , Electrochemical Techniques/methods , Electrochemical Techniques/instrumentation , Escherichia coli/genetics , Escherichia coli/drug effects , Limit of Detection , Nucleic Acid Hybridization , Humans , DNA, Bacterial/genetics , DNA, Bacterial/analysis
3.
J Obstet Gynaecol ; 44(1): 2333784, 2024 Dec.
Article in English | MEDLINE | ID: mdl-38602239

ABSTRACT

BACKGROUND: Cervical cancer (CC) is the second most common malignancy in women, and identifying biomarkers of CC is crucial for prognosis prediction. Here, we investigated the expression of AF4/FMR2 Family Member 3 (AFF3) in CC and its association with clinicopathological features and prognosis. METHODS: Tumour and adjacent tissues, along with clinicopathological features and follow-up information, were collected from 78 patients. AFF3 expression was assessed using quantitative real-time polymerase chain reaction and Western blotting. The correlation between AFF3 expression and CC symptoms was using chi-square test. The 5-year overall survival (OS) was analysed using the Kaplan-Meier method. The Univariate analysis of prognostic risk factors was conducted using the COX proportional hazards model, followed by multivariate COX regression analysis including variables with p < 0.01. RESULTS: AFF3 expression was downregulated in CC, and its levels were correlated with lymph node metastasis (LNM) and International Federation of Gynaecology and Obstetrics (FIGO) stage. Patients with low AFF3 expression had a lower 5-year OS rate (52.78%, 19/36). Postoperative survival was reduced in patients with histological grade 3 (G3), myometrial invasion (depth ≥ 1/2), lymphovascular space invasion, LNM, and advanced FIGO stage. Low expression of AFF3 (HR: 2.848, 95% CI: 1.144-7.090) and histological grade G3 (HR: 4.393, 95% CI: 1.663-11.607) were identified as independent prognostic risk factors in CC patients. CONCLUSION: Low expression of AFF3 and histological G3 are independent predictors of poor prognosis in CC patients, suggesting that AFF3 could serve as a potential biomarker for prognostic assessment in CC.


Cervical cancer is a significant health concern worldwide, responsible for over 300,000 deaths annually and ranking as the fourth most common cancer in women. Existing screening methods have limitations, highlighting the need for innovative therapies. In our research, we identified a specific genetic material that varied significantly among cervical cancer patients with varying survival outcomes, detected in tissue samples obtained post-surgery. Our study demonstrates the considerable potential of this marker for accurately predicting outcomes in our study population. By analysing differences in the expression of this genetic marker, we can forecast the prognosis and progression of cervical cancer. These findings offer valuable insights for advancing cervical cancer treatment strategies, potentially improving outcomes for patients. Early detection and targeted treatment based on this genetic marker could extend patients' lives and prevent fatalities by enabling timely medical intervention and management.


Subject(s)
Uterine Cervical Neoplasms , Humans , Female , Uterine Cervical Neoplasms/pathology , Neoplasm Staging , Prognosis , Proportional Hazards Models , Real-Time Polymerase Chain Reaction , Lymphatic Metastasis , Nuclear Proteins
4.
Plant J ; 110(5): 1305-1318, 2022 06.
Article in English | MEDLINE | ID: mdl-35293046

ABSTRACT

Rice (Oryza sativa) is a leading source of dietary cadmium (Cd), a non-essential heavy metal that poses a serious threat to human health. There are significant variations in grain-Cd levels in natural rice populations, which make the breeding of low-Cd rice a cost-effective way to mitigate grain-Cd accumulation. However, the genetic factors that regulate grain-Cd accumulation have yet to be fully established, thereby hindering the development of low-Cd varieties. Here, we reported a low-Cd quantitative trait locus, CF1, that has the potential to reduce Cd accumulation in rice grains. CF1 is allelic to the metal transporter OsYSL2, which transports Fe from the roots to the shoots. However, it is incapable of binding Cd, and thus, reduces grain-Cd levels indirectly rather than directly in the form of upward delivery. Further analysis showed that high expression levels of CF1 improve Fe nutrition in the shoots, subsequently inhibiting Cd uptake by systemically inhibiting expression of the main Cd uptake gene OsNramp5 in the roots. Compared with the CF1 allele from '02428' (CF102428 ), higher expression levels of CF1 from 'TQ' (CF1TQ ) increased the Fe contents and decreased Cd levels in rice grains. In natural rice populations, CF1TQ was found to be a minor allele, while CF102428 is present in most japonica rice, suggesting that CF1TQ could be widely integrated into the japonica rice genome to generate low-Cd varieties. Overall, these results broaden our mechanistic understanding of the natural variation in grain-Cd accumulation, supporting marker-assisted selection of low-Cd rice.


Subject(s)
Cadmium , Oryza , Cadmium/metabolism , Edible Grain/metabolism , Oryza/metabolism , Plant Breeding , Plant Roots
5.
Anal Chem ; 95(23): 8816-8824, 2023 06 13.
Article in English | MEDLINE | ID: mdl-37194113

ABSTRACT

The development of electrochemical DNA biosensors has been limited by their reliability and reproducibility due to many interfering factors such as electrode properties, DNA surface densities, and complex biological samples. In this work, we developed a nanobalance polyA hairpin probe (polyA-HP), which was effectively assembled onto the gold electrode surface through the affinity between the central polyA fragment and the Au surface. One flanking probe of the polyA-HP captured the target sequence together with a MB-labeled signal probe, and the other flanking probe captured a reference probe simultaneously. The MB signal related to the amount of target was normalized by the reference Fc signal; thus, the signal-to-noise (S/N) was as high as 2000, and the reproducibility was remarkably improved to 2.77%, even facing deliberately changed experiment conditions. By designing a hairpin structure at the terminal of the polyA-HP, the selectivity and specificity were dramatically improved for the analysis of mismatched sequences. The analysis performance of biological samples was dramatically improved after normalization, which is critical for its practicability. Our novel biosensor is a universal single-molecule platform for ratiometric biosensors with excellent performance in real samples, indicating great potential for next-generation high-precision electrochemical sensors.


Subject(s)
Biosensing Techniques , Electrochemical Techniques , Reproducibility of Results , DNA/analysis , Gold/chemistry , Limit of Detection
6.
BMC Infect Dis ; 23(1): 381, 2023 Jun 07.
Article in English | MEDLINE | ID: mdl-37286981

ABSTRACT

BACKGROUND: There is a mutual influence between COVID-19, diabetes ketoacidosis, and acute pancreatitis, with clinical manifestations overlapping each other, which can lead to misdiagnosis and delayed treatment that could aggravate the condition and affect the prognosis. COVID-19-induced diabetes ketoacidosis and acute pancreatitis are extremely rare, with only four case reports in adults and no cases yet reported in children. CASE PRESENTATION: We reported a case of acute pancreatitis associated with diabetic ketoacidosis in a 12-year-old female child post novel coronavirus infection. The patient presented with vomiting, abdominal pain, shortness of breath, and confusion. Laboratory findings showed elevated levels of inflammatory markers, hypertriglyceridemia, and high blood glucose. The patient was treated with fluid resuscitation, insulin, anti-infection treatments, somatostatin, omeprazole, low-molecular-weight heparin, and nutritional support. Blood purification was administered to remove inflammatory mediators. The patient's symptoms improved, and blood glucose levels stabilized after 20 days of admission. CONCLUSION: The case highlights the need for greater awareness and understanding of the interrelated and mutually promoting conditions of COVID-19, diabetes ketoacidosis, and acute pancreatitis among clinicians, to reduce misdiagnosis and missed diagnoses.


Subject(s)
COVID-19 , Diabetes Mellitus , Diabetic Ketoacidosis , Pancreatitis , Adult , Female , Humans , Child , Diabetic Ketoacidosis/complications , Diabetic Ketoacidosis/diagnosis , Diabetic Ketoacidosis/therapy , Pancreatitis/complications , Pancreatitis/diagnosis , Acute Disease , Blood Glucose , COVID-19/complications
7.
Ren Fail ; 45(1): 2171886, 2023 Dec.
Article in English | MEDLINE | ID: mdl-36715439

ABSTRACT

OBJECTIVES: Subfornical organ (SFO) is vital in chronic kidney disease (CKD) progression caused by high salt levels. The current study investigated the effects of high salt on phosphoproteomic changes in SFO in CKD rats. METHODS: 5/6 nephrectomized rats were fed a normal-salt diet (0.4%) (NC group) or a high-salt diet (4%) (HC group) for three weeks, while sham-operated rats were fed a normal-salt diet (0.4%) (NS group). For phosphoproteomic analysis of SFO in different groups, TiO2 enrichment, isobaric tags for relative and absolute quantification (iTRAQ) labeling, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used. RESULTS: There were 6808 distinct phosphopeptides found, which corresponded to 2661 phosphoproteins. NC group had 168 upregulated and 250 downregulated phosphopeptides compared to NS group. Comparison to NC group, HC group had 154 upregulated and 124 downregulated phosphopeptides. Growth associated protein 43 (GAP43) and heat shock protein 27 (Hsp27) were significantly upregulated phosphoproteins and may protect against high-salt damage. Differential phosphoproteins with tight functional connection were synapse proteins and microtubule-associated proteins, implying that high-salt diet disrupted brain's structure and function. Furthermore, differential phosphoproteins in HC/NC comparison group were annotated to participate in GABAergic synapse signaling pathway and aldosterone synthesis and secretion, which attenuated inhibitory neurotransmitter effects and increased sympathetic nerve activity (SNA). DISCUSSION: This large scale phosphoproteomic profiling of SFO sheds light on how salt aggravates CKD via the central nervous system.


Subject(s)
Renal Insufficiency, Chronic , Subfornical Organ , Rats , Animals , Rats, Sprague-Dawley , Chromatography, Liquid , Subfornical Organ/physiology , Phosphopeptides/pharmacology , Tandem Mass Spectrometry , Sodium Chloride, Dietary/pharmacology , Phosphoproteins/metabolism , Phosphoproteins/pharmacology
8.
Analyst ; 147(11): 2452-2459, 2022 May 30.
Article in English | MEDLINE | ID: mdl-35521826

ABSTRACT

RNA interference (RNAi) is currently under fast development, which brings improved crop quality and new activity against pests in agriculture, by producing RNAs to specifically inhibit gene expression. This technology, in turn, creates a pressing need for sensitive and specific analytical methods of exogenous RNA molecules in genetically modified (GM) crops for safety assessment and regulation of RNAi plants and their products. In this work, we developed a novel RNA electrochemical biosensor for the analysis of GM maize samples based on a polyA-DNA capturing probe containing three DNA segments: the central polyA segment combined onto a gold electrode surface with adjustable configuration and density, and two flanking DNA probes simultaneously captured the RNA targets through hybridization. Both the assembling and hybridization capability of our probe were demonstrated, and we systematically optimized the analytical conditions. Finally, the ultrasensitive detection of 10 fM RNA was realized without any amplification processes, and the specificity was verified by analyzing non-target maize samples. Our electrochemical biosensor provided a reliable and convenient measurement strategy for RNAi safety and quality assessment, and more importantly, our PAP (probe-polyA-probe) capturing probe exhibited an innovative design for the detection of large RNA molecules with complex secondary structures.


Subject(s)
Biosensing Techniques , Poly A , Biosensing Techniques/methods , DNA , Electrochemical Techniques/methods , Gold/chemistry , Limit of Detection , Poly A/chemistry , RNA , RNA Interference
9.
Proc Natl Acad Sci U S A ; 116(9): 3494-3501, 2019 02 26.
Article in English | MEDLINE | ID: mdl-30808744

ABSTRACT

Rice (Oryza sativa L.) is a chilling-sensitive staple crop that originated in subtropical regions of Asia. Introduction of the chilling tolerance trait enables the expansion of rice cultivation to temperate regions. Here we report the cloning and characterization of HAN1, a quantitative trait locus (QTL) that confers chilling tolerance on temperate japonica rice. HAN1 encodes an oxidase that catalyzes the conversion of biologically active jasmonoyl-L-isoleucine (JA-Ile) to the inactive form 12-hydroxy-JA-Ile (12OH-JA-Ile) and fine-tunes the JA-mediated chilling response. Natural variants in HAN1 diverged between indica and japonica rice during domestication. A specific allele from temperate japonica rice, which gained a putative MYB cis-element in the promoter of HAN1 during the divergence of the two japonica ecotypes, enhances the chilling tolerance of temperate japonica rice and allows it to adapt to a temperate climate. The results of this study extend our understanding of the northward expansion of rice cultivation and provide a target gene for the improvement of chilling tolerance in rice.


Subject(s)
Adaptation, Physiological/genetics , Oryza/genetics , Plant Proteins/genetics , Stress, Physiological/genetics , Climate , Cyclopentanes/metabolism , Genetic Variation , Isoleucine/analogs & derivatives , Isoleucine/genetics , Isoleucine/metabolism , Oryza/growth & development , Quantitative Trait Loci/genetics
10.
Small ; 17(48): e2006605, 2021 12.
Article in English | MEDLINE | ID: mdl-33522113

ABSTRACT

Synthesis of high-quality single-walled carbon nanotubes arrays with pure semiconducting type is crucial for the fabrication of integrated circuits in nanoscale. However, the naturally grown carbon nanotubes usually have diverse structures and properties. Here the bicomponent catalyst using Au and ZrO2 is designed and prepared. The Au nanoparticle serves as the catalysts for carbon feedstock cracking and facilitating the nucleation of carbon nanotubes, whereas the close-connected ZrO2 forms a localized etching zone around Au by releasing lattice oxygen and to inhibit the nucleation of metallic carbon nanotubes precisely. The obtained single-walled carbon nanotubes array show a high semiconducting content of >96%, on the basis of good performance of field-effect transistor devices. And such building of localized etching zone is compatible with other catalyst systems as a universal and efficient method for the scalable production of semiconducting carbon nanotubes.


Subject(s)
Metal Nanoparticles , Nanotubes, Carbon , Gold
11.
Eur J Clin Microbiol Infect Dis ; 40(7): 1357-1367, 2021 Jul.
Article in English | MEDLINE | ID: mdl-33768442

ABSTRACT

Human papillomavirus (HPV) infection among men who have sex with men (MSM) in China is underreported. We performed a systematic review and meta-analysis to clarify site-specific HPV prevalence among MSM in China. We searched both English and Chinese databases for all studies published before April 1, 2020, that reported HPV prevalence among MSM in China. Random-effects meta-analysis was used to calculate summary estimates. Thirty-four articles were eligible, where 32, 5, and 2 articles reported HPV prevalence at the anus, penis, and oral cavity, respectively. The estimated prevalence of anal HPV among MSM in China was 85.1% (HIV-positive), 53.6% (HIV-negative), and 59.2% (unknown HIV status), with HPV genotypes being predominated by HPV 6, 11, 16, 18, 52, and 58. Any HPV and high-risk (HR) HPV was more common in northern China, while low-risk HPV was more common in southern China. HPV prevalence increased with age among HIV-negative MSM, from 40.5% (aged < 20 years) to 57.2% (aged ≥ 40 years). High prevalence of any HPV (HIV+: 95.1%; HIV-: 97.7%) and multiple infections (HIV+: 75.9%; HIV-: 41.7%) was found in anogenital warts among MSM. HPV is common among MSM in China. MSM living with HIV and/or anogenital warts were at disproportionate risk for HR HPV. Younger MSM were found to have a lower HPV prevalence. HPV vaccines would have prevented the majority of infections if given before sex debut. HPV at anatomical sites other than the anus, incident HPV infection, and the cost-effectiveness of HPV vaccination in this population are worth further investigation.


Subject(s)
Homosexuality, Male , Papillomaviridae/isolation & purification , Papillomavirus Infections/virology , China/epidemiology , Humans , Male , Papillomavirus Infections/epidemiology
12.
Anal Chem ; 92(6): 4498-4503, 2020 03 17.
Article in English | MEDLINE | ID: mdl-32090545

ABSTRACT

MicroRNAs (miRNAs) have been explored as biomarkers for early diagnosis of diseases like cancers. However, it remains challenging to detect low-level miRNAs in the total RNA from real samples in a facile approach. In this work, we report a two-phase miRNA biosensing strategy based on a modular framework nucleic acid (FNA) platform, which combines the high efficiency of homogeneous reaction and the convenience of heterogeneous biosensing. In the first phase, free DNA probes bind target miRNAs in a homogeneous solution, forming a DNA-RNA complex with high base stacking energy. Then, at the second phase, the universal FNA interface on the electrode selectively mediated the transition of the complex from the solution onto the interface for electrochemical signal generating and transduction. By applying this method, we detected as few as 1 aM of miR-141, a cancer marker miRNA, without the need for nucleic acid amplification. The dynamic range spans 10 orders of magnitude. We demonstrate multiplex miRNA detection and discrimination of highly homologous miRNAs with mismatches as few as a single base. We also show that this system can detect miR-141 in only 50 ng of total RNA samples from real cells, which allows discrimination of prostate cancer cells with normal cells. We envision this platform may satisfy the need for facile and high-throughput screening of early cancer markers.


Subject(s)
Biosensing Techniques , DNA/chemistry , Electrochemical Techniques , MicroRNAs/analysis , Nucleic Acid Amplification Techniques , Electrodes , Humans
13.
BMC Cancer ; 19(1): 957, 2019 Oct 15.
Article in English | MEDLINE | ID: mdl-31615475

ABSTRACT

BACKGROUND: Circular RNAs (circRNAs) have emerged as a special subset of endogenous RNAs that are implicated in tumorigenesis and cancer progression. Herein we aim to carry out a meta-analysis to evaluate the clinicopathologic, diagnostic and prognostic significance of circRNA expression in colorectal cancer (CRC). METHODS: A systematic search of online databases was performed for original articles published in English, which investigated the diagnostic accuracy, prognostic utility, and clinicopathologic association of circRNA(s) in CRC. Data were strictly extracted and study bias was judged using the Quality Assessment for Studies of Diagnostic Accuracy II (QUADAS II) and Newcastle-Ottawa Scale (NOS) checklists. RESULTS: A total of 13 studies, involving 1430 patients with CRC, were included in the meta-analysis. The clinicopathologic study showed that abnormally expressed circRNAs were correlated with tumor diameter (P = 0.0350), differentiation (P = 0.0038), lymphatic metastasis (P = 0.0119), distant metastasis (P < 0.0001), TNM stage (P = 0.0002), and depth of invasion (P = 0.001) in patients with CRC. The summary area under the curve (AUC) of circRNA for the discriminative efficacy between patients with and without CRC was estimated to be 0.79, corresponding to a weighted sensitivity of 0.77 [95% confidence interval (CI): 0.74-0.79], specificity of 0.67 (95%CI: 0.64-0.70), and diagnostic odds ratio (DOR) of 7.52 (95%CI: 4.66-12.12). Survival analysis showed that highly expressed circRNAs were correlated with significantly worse overall survival (OS) [hazard ratio (HR) = 2.66, 95%CI: 2.03-3.50, P = 0.000; X2 = 4.34, P = 0.740, I2 = 0.0%], whereas lower expression of circRNAs was associated with prolonged OS (weighted HR = 0.30, 95%CI: 0.17-0.53, P = 0.000; X2 = 1.34, P = 0.909, I2 = 0.0%). Stratified analysis in circRNA expression status, and test matrix also showed robust results. CONCLUSION: Abnormally expressed circRNAs may be auxiliary biomarkers facilitating CRC diagnosis, and promising prognostic biomarkers in predicting the survival of CRC patients.


Subject(s)
Colorectal Neoplasms/diagnosis , Colorectal Neoplasms/genetics , RNA, Circular/genetics , Area Under Curve , Biomarkers, Tumor/genetics , Colorectal Neoplasms/pathology , Gene Expression/genetics , Humans , Lymphatic Metastasis/genetics , Neoplasm Staging , Prognosis , Proportional Hazards Models , Publication Bias , Real-Time Polymerase Chain Reaction , Sensitivity and Specificity , Sequence Analysis, RNA , Tumor Burden/genetics
15.
Analyst ; 141(18): 5304-10, 2016 Sep 21.
Article in English | MEDLINE | ID: mdl-27460969

ABSTRACT

Fast, portable and sensitive analysis of E. coli is becoming an important challenge in many critical fields (e.g., food safety, environmental monitoring and clinical diagnosis). Thus, electrochemical biosensing of PCR amplicons from the bacterial genome has attracted reasonable research attention. In this work, we utilized a 3D DNA tetrahedral probe to establish a "sandwich-type" electrochemical DNA biosensor for sensitive and specific analysis of a 250 bp unpurified PCR amplicon from the uidA gene of the E. coli genome. Asymmetric PCR was used to produce single-stranded PCR products. Streptavidin-polyHRP80 was employed to improve the signal gain during electrochemical detection. We optimized important experimental conditions for DNA sensing, including the streptavidin-polyHRP, the signal probe and the ion strength. Finally, we achieved a remarkable sensitivity of 10 fM synthetic DNA target, and successfully performed the analysis of PCR amplicons from as low as 0.2 pg µL(-1) of E. coli genome. Compared with traditional single stranded DNA (ssDNA) probe based detection, our present work demonstrated 3 orders of magnitude improvement in sensitivity. In addition, our electrochemical DNA biosensor was 4 orders of magnitude more sensitive than normal electrophoretic analysis of PCR products. Our work made important progress in DNA nanostructured probe-based biosensors toward application in real applications.


Subject(s)
Biosensing Techniques , DNA Probes , Escherichia coli/genetics , Genome, Bacterial , Polymerase Chain Reaction , Nanostructures
16.
Sensors (Basel) ; 16(12)2016 Dec 16.
Article in English | MEDLINE | ID: mdl-27999248

ABSTRACT

Pb(II) can cause serious damaging effects to human health, and thus, the study of Pb2+ detection methods to sensitively and selectively monitor Pb(II) pollution has significant importance. In this work, we have developed a label-free fluorescence sensing strategy based on a Pb(II) DNAzyme cleavage and the ThT/G-quadruplex complex. In the presence of Pb(II), a G-rich tail was cut and released from the substrate strand, which then would form a G-quadruplex structure by combination with ThT dye. The fluorescence signal increase was then measured for sensitive Pb(II) quantification with a limit of detection of 0.06 nM. Our sensor also demonstrated high selectivity against six different metal ions, which is very important for the analysis of complex samples.


Subject(s)
Biosensing Techniques/instrumentation , DNA, Catalytic/chemistry , G-Quadruplexes , Lead/analysis , Molecular Conformation , Staining and Labeling , Thiazoles/chemistry , Benzothiazoles , Fluorescence , Limit of Detection , Temperature
17.
Theor Appl Genet ; 128(7): 1359-71, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25862679

ABSTRACT

KEY MESSAGE: Dongxiang wild rice is phylogenetically close to temperate japonica and contains multiple cold resistance loci conferring its adaptation to high-latitude habitat. Understanding the nature of adaptation in wild populations will benefit crop breeding in the development of climate-resilient crop varieties. Dongxiang wild rice (DXWR), the northernmost common wild rice known, possesses a high degree of cold tolerance and can survive overwintering in its native habitat. However, to date, it is still unclear how DXWR evolved to cope with low-temperature environment, resulting in limited application of DXWR in rice breeding programs. In this study, we carried out both QTL mapping and phylogenetic analysis to discern the genetic mechanism underlying the strong cold resistance. Through a combination of interval mapping and single locus analysis in two genetic populations, at least 13 QTLs for seedling cold tolerance were identified in DXWR. A phylogenetic study using both genome-wide InDel markers and markers associated with cold tolerance loci reveals that DXWR belongs to the Or-III group, which is most closely related to cold-tolerant Japonica rice rather than to the Indica cultivars that are predominant in the habitat where DXWR grows. Our study paves the way toward an understanding of the nature of adaptation to a northern habitat in O. rufipogon. The QTLs identified in DXWR in this study will be useful for molecular breeding of cold-tolerant rice.


Subject(s)
Adaptation, Physiological/genetics , Cold Temperature , Oryza/genetics , Quantitative Trait Loci , Chromosome Mapping , Crosses, Genetic , DNA, Plant/genetics , Ecosystem , Genetic Linkage , Genetic Markers , Genetics, Population , INDEL Mutation , Oryza/classification , Phylogeny , Polymorphism, Single Nucleotide
18.
Anal Chem ; 86(5): 2285-8, 2014 Mar 04.
Article in English | MEDLINE | ID: mdl-24528092

ABSTRACT

Because of the short size and low abundance of microRNAs, it is challenging to develop fast, inexpensive, and simple biosensors to detect them. In this work, we have demonstrated a new generation (the third generation) of E-DNA sensor for the sensitive and specific detection of microRNAs. Our third generation of E-DNA sensor can sensitively detect microRNA target (microRNA-141) as low as 1 fM. The excellent specificity has been demonstrated by its differential ability to the highly similar microRNA analogues. In our design, the use of DNA tetrahedron ensures the stem-loop structure in well controlled density with improved reactivity. The regulation of the thermodynamic stability of the stem-loop structure decreases the background signal and increases the specificity as well. The enzymes attached bring the electrocatalytic signal to amplify the detection. The combination of these effects improves the sensitivity of the E-DNA sensor and makes it suitable to the microRNA detection. Finally, our third generation of E-DNA sensor is generalizable to the detection of other micro RNA targets (for example, microRNA-21).


Subject(s)
Biosensing Techniques , DNA/chemistry , MicroRNAs/analysis , Nanostructures , Nucleic Acid Conformation
19.
Tumour Biol ; 35(9): 9311-6, 2014 Sep.
Article in English | MEDLINE | ID: mdl-24943681

ABSTRACT

Conflicting results were implicated in both single case-control studies and meta-analyses of the correlation between p73 G4C14-to-A4T14 polymorphism and lung cancer risk. We designed this study to further assess the association by meta-analysis. A meta-analysis was performed based on five case-control studies (5,467 subjects) retrieved from PubMed and Embase. Odds ratios (ORs) with 95 % confidence intervals (CIs) were measured for the association using the models of random effects and fixed effects. The results showed no evidence between p73 G4C14-to-A4T14 polymorphism and lung cancer risk in any genetic model (allele model: OR, 1.06, 95 % CI, 0.89-1.26; homozygote genotypes: OR, 1.18, 95 % CI, 0.80-1.73; heterozygote genotypes: OR, 1.04, 95 % CI, 0.89-1.23; dominant model: OR, 1.05, 95 % CI, 0.89-1.24; recessive model: OR, 1.17, 95 % CI, 0.93-1.47). Subgroup analyses according to ethnicity, however, detected significant association in Caucasian population. Our study provides evidence that p73 G4C14-to-A4T14 polymorphism may play a major role in susceptibility to lung cancer in Caucasians.


Subject(s)
DNA-Binding Proteins/genetics , Genetic Predisposition to Disease/genetics , Lung Neoplasms/genetics , Nuclear Proteins/genetics , Polymorphism, Genetic , Tumor Suppressor Proteins/genetics , Alleles , Asian People/genetics , Case-Control Studies , Gene Frequency , Genetic Predisposition to Disease/ethnology , Genotype , Humans , Lung Neoplasms/ethnology , Odds Ratio , Risk Factors , Tumor Protein p73 , White People/genetics
20.
Methods ; 64(3): 276-82, 2013 Dec 15.
Article in English | MEDLINE | ID: mdl-23911620

ABSTRACT

MicroRNAs (miRNAs) are key regulators of a wide range of cellular processes, and have been identified as promising cancer biomarkers due to their stable presence in serum. As an surface-based electrochemical biosensors which offer great opportunities for low-cost, point-of-care tests (POCTs) of disease-associated miRNAs. Nevertheless, the sensitivity of miRNA sensors is often limited by mass transport and the surface crowding effect at the water-electrode interface. Here, we present a protocol as well as guidelines for ultrasensitive detection of miRNA with DNA nanostructure-based electrochemical miRNA biosensor. By employing the three-dimensional DNA nanostructure-based interfacial engineering approach, we can directly detect as few as attomolar (<1000 copies) miRNAs with high single-base discrimination ability. Since this ultrasensitive electrochemical miRNA sensor (EMRS) is highly reproducible and essentially free of prior target labeling and PCR amplification, it can conveniently and reliably analyze miRNA expression levels in clinical samples from esophageal squamous cell carcinoma (ESCC) patients.


Subject(s)
Biosensing Techniques , DNA Probes/chemistry , MicroRNAs/genetics , Carcinoma, Squamous Cell/metabolism , Electrochemical Techniques , Esophageal Neoplasms/metabolism , Humans , MicroRNAs/metabolism , Nucleic Acid Conformation , Nucleic Acid Hybridization , Sensitivity and Specificity
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