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https://www.readbyqxmd.com/read/28438642/diagnostic-microarray-for-14-water-and-foodborne-pathogens-using-a-flatbed-scanner
#1
Vidya Srinivasan, Robert D Stedtfeld, Dieter M Tourlousse, Samuel W Baushke, Yu Xin, Sarah M Miller, Trinh Pham, Jean-Marie Rouillard, Erdogan Gulari, James M Tiedje, Syed A Hashsham
Parallel detection approaches are of interest to many researchers interested in identifying multiple water and foodborne pathogens simultaneously. Availability and cost-effectiveness are two key factors determining the usefulness of such approaches for laboratories with limited resources. In this study, we developed and validated a high-density microarray for simultaneous screening of 14 bacterial pathogens using an approach that employs gold labeling with silver enhancement (GLS) protocol. In total, 8887 probes (50-mer) were designed using an in-house database of virulence and marker genes (VMGs), and synthesized in quadruplicate on glass slides using an in-situ synthesis technology...
April 21, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28434989/colorimetric-detection-of-microrna-based-hybridization-chain-reaction-for-signal-amplification-and-enzyme-for-visualization
#2
Na Ying, Taifan Sun, Zhibao Chen, Guangping Song, Bingyao Qi, Shengjun Bu, Xiuwei Sun, Jiayu Wan, Zehong Li
MicroRNAs (miRNAs) have key roles in gene expression and can be employed as biomarkers for early diagnosis of various diseases, especially cancers. Detection of miRNAs remains challenging and often requires detection platforms. Here, a horseradish peroxidase (HRP)-assisted hybridization chain reaction (HCR) for colorimetric detection of miR-155 was described. In the presence of target miRNA, the capture probe immobilized on the microplate sandwiched the target miR-155 with the 3' end of the reporter probe. Another exposed part of the RP at the 5'end triggered HCR producing double-stranded DNA polymers with multiple fluorescein isothiocyanates (FITC) for signal amplification...
April 20, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28431642/pcr-based-detection-methods-for-single-nucleotide-polymorphism-or-mutation-real-time-pcr-and-its-substantial-contribution-toward-technological-refinement
#3
Kazuyuki Matsuda
Single-nucleotide polymorphisms (SNPs) and single-nucleotide mutations result from the substitution of only a single base. The SNP or mutation can be relevant to disease susceptibility, pathogenesis of disease, and efficacy of specific drugs. It is important to detect SNPs or mutations clinically. Methods to distinguish/detect SNPs or mutations should be highly specific and sensitive. In this regard, polymerase chain reaction (PCR) has provided the necessary analytical performance for many molecular analyses...
2017: Advances in Clinical Chemistry
https://www.readbyqxmd.com/read/28422199/hybridization-chain-reactions-on-silica-coated-qbeads-for-the-colorimetric-detection-of-multiplex-micrornas
#4
Qingsheng Guo, Feika Bian, Yuqian Liu, Xiaojun Qu, Xianyun Hu, Qingjiang Sun
A robust Qbead platform that integrated with target-binding, hybridization chain reaction and staining was developed for the direct multiplexed detection of endogenous miRNAs by amplified Qbead-colour change.
April 19, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28421985/design-of-a-sensitive-and-selective-electrochemical-aptasensor-for-the-determination-of-the-complementary-cdna-of-mirna-145-based-on-the-intercalation-and-electrochemical-reduction-of-doxorubicin
#5
Maryam Mohamadi, Ali Mostafavi, Masoud Torkzadeh-Mahani
<p>The aim of this research was the determination of a microRNA (miRNA) using a DNA electrochemical aptasensor. In this biosensor, the complementary complementary DNA (cDNA) of miRNA-145 (a sense RNA transcript) was the target strand and the cDNA of miRNA-145 was the probe strand. Both cDNAs can be the product of the reverse transcriptase-polymerase chain reaction of miRNA. The proposed aptasensor's function was based on the hybridization of target strands with probes immobilized on the surface of a working electrode and the subsequent intercalation of doxorubicin (DOX) molecules functioning as the electroactive indicators of any double strands that formed...
April 19, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28421451/mathematical-model-of-polymerase-chain-reaction-with-temperature-dependent-parameters
#6
D G Sochivko, A A Fedorov, Y I Alekseev, V E Kurochkin, M V Dubina
The course of the real-time polymerase chain reaction (PCR) is determined by the temperature dependence of the kinetics of the component reactions, particularly the DNA strand hybridization. To investigate the effect of thermal processes on the reaction behavior, a mathematical model in which the variable rate constant of dissociation of "primer-single strand" complexes depends on temperature was proposed. The reaction medium temperature, which depends on time, was also introduced into the model. The proposed model of real-time PCR makes it possible to analyze different aspects of the reaction, which are important for the development of instruments and reagents for PCR...
January 2017: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28420424/a-novel-lncrna-uc-134-represses-hepatocellular-carcinoma-progression-by-inhibiting-cul4a-mediated-ubiquitination-of-lats1
#7
Wen Ni, Yuqin Zhang, Zetao Zhan, Feng Ye, Yonghao Liang, Jing Huang, Keli Chen, Longhua Chen, Yi Ding
BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, and tumor recurrence and metastasis are major factors that contribute to the poor outcome of patients with HCC. Long noncoding RNAs (lncRNAs) are known to regulate different tumorigenic processes, and a growing body of evidence indicates that Hippo kinase signaling is inactivated in many cancers. However, the upstream lncRNA regulators of Hippo kinase signaling in HCC are poorly understood. METHODS: Using a lncRNA microarray, we identified a novel lncRNA, uc...
April 19, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28415646/combination-of-immunohistochemistry-fish-and-rt-pcr-shows-high-incidence-of-xp11-translocation-rcc-comparison-of-three-different-diagnostic-methods
#8
Hyun Jung Lee, Dong Hoon Shin, GyuYou Noh, Young Keum Kim, Ahrong Kim, Nari Shin, Jung Hee Lee, Kyung Un Choi, Jee Yeon Kim, Chang Hun Lee, Mee Young Sol, Seo Hee Rha, Sung Woo Park
We evaluated the frequency of translocation renal cell carcinoma (RCC) by reverse transcription polymerase chain reaction (RT-PCR) and how well the TFE3 immunoreactivity is concordant with TFE3 gene translocation status proved by fluorescence in situ hybridization (FISH) assay and RT-PCR. TFE3 and Cathepsin K expression was analyzed by immunohistochemistry in 185 RCC cases, and 48 cases either of more than weak expression of TFE3 or of positivity for Cathepsin K were done for FISH analysis and RT-PCR. All the RT-PCR positive cases were confirmed by cloning and sequencing...
March 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28414417/graphene-nanoprobes-for-real-time-monitoring-of-isothermal-nucleic-acid-amplification
#9
Fan Li, Xiaoguo Liu, Bin Zhao, Juan Yan, Qian Li, Ali Aldalbahi, Jiye Shi, Shiping Song, Chunhai Fan, Lihua Wang
Isothermal amplification is an efficient way to amplify DNA with high accuracy, however, the real-time monitoring for quantification analysis mostly relied on expensive and precisely designed probes. In the present study, Graphene oxide (GO)-based nano probe was used to real-time monitor the isothermal amplification process. The interaction between GO and different DNA structures was systematically investigated, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), DNA 3-helix, and long rolling circle amplification (RCA) and hybridization chain reaction (HCR) products, which existed in one-, two- and three-dimensional structures...
April 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28412658/cds-mn-quantum-dot-functionalized-g-c3n4-nanohybrids-as-signal-generation-tags-for-photoelectrochemical-immunoassay-of-prostate-specific-antigen-coupling-dnazyme-concatamer-with-enzymatic-biocatalytic-precipitation
#10
Kangyao Zhang, Shuzhen Lv, Zhenzhen Lin, Dianping Tang
A new photoelectrochemical (PEC) immunosensor based on Mn-doped CdS quantum dots (CdS:Mn QDs) on g-C3N4 nanosheets was developed for the sensitive detection of prostate specific antibody (PSA) in biological fluids. The signal derived from the as-synthesized Cd:Mn QDs-functionalized g-C3N4 nanohybrids via a hydrothermal method and was amplified through DNAzyme concatamers on gold nanoparticles accompanying enzymatic biocatalytic precipitation. Experimental results by UV-vis absorption spectra and photoluminescence revealed that CdS:Mn QDs/g-C3N4 nanohybrids exhibited higher photocurrent than those of CdS:Mn QDs and g-C3N4 alone...
April 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28409525/rare-pyrenophora-teres-hybridization-events-revealed-by-development-of-sequence-specific-pcr-markers
#11
Barsha Poudel, Simon R Ellwood, Alison C Testa, Mark McLean, Mark W Sutherland, Anke Martin
Pyrenophora teres f. teres and P. teres f. maculata cause net form and spot form, respectively, of net blotch on barley (Hordeum vulgare). The two forms reproduce sexually, producing hybrids with genetic and pathogenic variability. Phenotypic identification of hybrids is challenging because lesions induced by hybrids on host plants resemble lesions induced by either P. teres f. teres or P. teres f. maculata. In this study, 12 sequence-specific polymerase chain reaction markers were developed based on expressed regions spread across the genome...
April 14, 2017: Phytopathology
https://www.readbyqxmd.com/read/28403015/hr-hpv-e6-e7-mrna-in-situ-hybridization-validation-against-pcr-dna-in-situ-hybridization-and-p16-immunohistochemistry-in-102-samples-of-cervical-vulvar-anal-and-head-and-neck-neoplasia
#12
COMPARATIVE STUDY
Anne M Mills, Dawn C Dirks, Melinda D Poulter, Stacey E Mills, Mark H Stoler
Dysregulated expression of oncogenic types of E6 and E7 is necessary for human papillomavirus (HPV)-driven carcinogenesis. An HPV E6/E7 mRNA in situ hybridization (ISH) assay covering 18 common high-risk types ("HR-RISH," aka HR-HPV RNA18 ISH) has not been extensively studied in the anogenital tract or validated on automated technology. We herein compare HR-RISH to DNA polymerase chain reaction (PCR), p16 immunohistochemistry, and a previously available HPV DNA ISH assay in HPV-related anogenital and head and neck (H&N) neoplasia...
May 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28402752/the-microrna-mir-210-is-expressed-by-cancer-cells-but-also-by-the-tumor-microenvironment-in-triple-negative-breast-cancer
#13
Isabelle Bar, Ahmad Merhi, Fadi Abdel-Sater, Abduelhakem Ben Addi, Sara Sollennita, Jean-Luc Canon, Paul Delrée
The triple-negative breast cancer (TNBC) subtype occurs in about 15% of breast cancer and is an aggressive subtype of breast cancer with poor outcome. Furthermore, treatment of patients with TNBC is more challenging due to the heterogeneity of the disease and the absence of well-defined molecular targets. Microribonucleic acid (RNA) represents a new class of biomarkers that are frequently dysregulated in cancer. It has been described that the microRNA miR-210 is highly expressed in TNBC, and its overexpression had been linked to poor prognosis...
April 1, 2017: Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society
https://www.readbyqxmd.com/read/28400811/effect-of-electroacupuncture-on-the-mrna-and-protein-expression-of-rho-a-and-rho-associated-kinase-ii-in-spinal-cord-injury-rats
#14
You-Jiang Min, Li-Li-Qiang Ding, Li-Hong Cheng, Wei-Ping Xiao, Xing-Wei He, Hui Zhang, Zhi-Yun Min, Jia Pei
Electroacupuncture is beneficial for the recovery of spinal cord injury, but the underlying mechanism is unclear. The Rho/Rho-associated kinase (ROCK) signaling pathway regulates the actin cytoskeleton by controlling the adhesive and migratory behaviors of cells that could inhibit neurite regrowth after neural injury and consequently hinder the recovery from spinal cord injury. Therefore, we hypothesized electroacupuncture could affect the Rho/ROCK signaling pathway to promote the recovery of spinal cord injury...
February 2017: Neural Regeneration Research
https://www.readbyqxmd.com/read/28397213/-analysis-of-genome-wide-copy-number-variations-among-fetuses-with-abnormalities-detected-by-prenatal-ultrasouography
#15
Ke Wu, Shaohua Tang, Chong Chen, Huanzheng Li, Lili Zhou, Jianxin Lyu
OBJECTIVE: To explore the genetic etiology of fetal abnormalities detected by prenatal ultrasound through single nucleotide polymorphism (SNP array) analysis. METHODS: Two hundred and eight fetuses were tested with SNP array and conventional karyotyping. Complex copy number variations (CNVs) were verified with fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and quantitative fluorescence polymerase chain reaction (QF-PCR)...
April 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28395057/early-mir-223-upregulation-in-gastroesophageal-carcinogenesis
#16
Matteo Fassan, Deborah Saraggi, Laura Balsamo, Stefano Realdon, Marco Scarpa, Carlo Castoro, Irene Coati, Roberta Salmaso, Fabio Farinati, Vincenza Guzzardo, Diletta Arcidiacono, Giada Munari, Pierluigi Gasparini, Nicola Veronese, Claudio Luchini, Nicola Valeri, Massimo Rugge
Objectives: To test miR-223 upregulation during gastric (intestinal-type) and Barrett esophageal carcinogenesis. Methods: miR-223 expression was assessed by quantitative reverse transcription polymerase chain reaction in a series of 280 gastroesophageal biopsy samples representative of the whole spectrum of phenotypic changes involved in both carcinogenetic cascades. The results were further validated by in situ hybridization on multiple tissue specimens obtained from six surgically treated gastroesophageal adenocarcinomas...
March 1, 2017: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28388364/piezo2-expression-in-mechanosensitive-dental-primary-afferent-neurons
#17
J Won, H Vang, P R Lee, Y H Kim, H W Kim, Y Kang, S B Oh
Mechanosensitive ion channels have been suggested to be expressed in dental primary afferent (DPA) neurons to transduce the movement of dentinal fluid since the proposal of hydrodynamic theory. Piezo2, a mechanosensitive, rapidly inactivating (RI) ion channel, has been recently identified in dorsal root ganglion (DRG) neurons to mediate tactile transduction. Here, we examined the expression of Piezo2 in DPA neurons by in situ hybridization, single-cell reverse transcriptase polymerase chain reaction, and whole-cell patch-clamp recordings...
April 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28385057/a-comprehensive-molecular-investigation-of-%C3%AE-thalassemia-in-an-iranian-cohort-from-different-provinces-of-north-iran
#18
Hajar Eftekhari, Ahmad Tamaddoni, Hassan Mahmoudi Nesheli, Mohsen Vakili, Sadegh Sedaghat, Ali Banihashemi, Mandana Azizi, Reza Youssefi Kamangar, Haleh Akhavan-Niaki
α-Thalassemia (α-thal) is the most common monogenic disease that is caused by the absence or reduced expression of α-globin genes. The aim of this study was to investigate common α-globin mutations and their associated haplotypes in four northern provinces of Iran (Gilan, Mazandaran, Golestan, Khorasan). One thousand, one hundred and ninety-one persons were tested for α-thal mutations by gap-polymerase chain reaction (PCR), reverse dot-blot hybridization, restriction fragment length polymorphism (RFLP) analysis and sequencing...
April 7, 2017: Hemoglobin
https://www.readbyqxmd.com/read/28384399/molecular-analysis-of-genetic-markers-for-non-hodgkin-lymphomas
#19
Lynette M Sholl, Janina Longtine, Frank C Kuo
Molecular analysis complements the clinical and histopathologic tools used to diagnose and subclassify hematologic malignancies. The presence of clonal antigen-receptor gene rearrangements can help to confirm the diagnosis of a B or T cell lymphoma and can serve as a fingerprint of that neoplasm to be used in identifying concurrent disease at disparate sites or recurrence at future time points. Certain lymphoid malignancies harbor a characteristic chromosomal translocation, a finding that may have significant implications for an individual's prognosis or response to therapy...
April 6, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28384287/genome-wide-profiling-in-oral-squamous-cell-carcinoma-identifies-a-four-genetic-marker-signature-of-prognostic-significance
#20
Vui King Vincent-Chong, Iman Salahshourifar, Kar Mun Woo, Arif Anwar, Rozaimi Razali, Ranganath Gudimella, Zainal Ariff Abdul Rahman, Siti Mazlipah Ismail, Thomas George Kallarakkal, Anand Ramanathan, Wan Mahadzir Wan Mustafa, Mannil Thomas Abraham, Keng Kiong Tay, Rosnah Binti Zain
BACKGROUND: Cancers of the oral cavity are primarily oral squamous cell carcinomas (OSCCs). Many of the OSCCs present at late stages with an exceptionally poor prognosis. A probable limitation in management of patients with OSCC lies in the insufficient knowledge pertaining to the linkage between copy number alterations in OSCC and oral tumourigenesis thereby resulting in an inability to deliver targeted therapy. OBJECTIVES: The current study aimed to identify copy number alterations (CNAs) in OSCC using array comparative genomic hybridization (array CGH) and to correlate the CNAs with clinico-pathologic parameters and clinical outcomes...
2017: PloS One
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