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hybridization chain reaction

Simone B S P Terra, Scott W Aesif, Joseph J Maleszewski, Andrew L Folpe, Jennifer M Boland
Synovial sarcoma (SS), a translocation-associated sarcoma characterized by SS18-SSX1/2 fusion, presents most often in the extremities of young adults. While SS regularly occurs in the pleuropulmonary parenchyma, the mediastinum is an exceedingly rare primary site; the literature on this subject is predominantly composed of case reports and small series, mostly without molecular confirmation. Cases of mediastinal SS were selected from our institutional and consultation archives. Diagnoses were confirmed by either SS18 fluorescence in situ hybridization (n=6) or reverse transcription polymerase chain reaction for SS18-SSX1/2 (n=15)...
March 14, 2018: American Journal of Surgical Pathology
Mohammad Taghi Kardi, Elham Yousefian, Azra Allahveisi, Sanaz Alaee
Background: Maternal thrombophilia has been identified as a risk factor for recurrent pregnancy loss (RPL). The aim of this study was to investigate the association between prothrombin G20210A and factor V Leiden (FVL) polymorphisms in women with RPL and a control group of parous women in Isfahan province of Iran. Methods: We studied 250 women with idiopathic RPL and 116 control cases. Prothrombin and FVL different genotypes were determined using polymerase chain reaction and reverse hybridization technique...
2018: International Journal of Preventive Medicine
Sellappan Selvaraju, Sivashanmugam Parthipan, Lakshminarayana Somashekar, B Krishnan Binsila, Atul P Kolte, Arunachalam Arangasamy, Janivara Parameshwaraiah Ravindra, Stephen A Krawetz
With artificial insemination (AI) and other precision dependent assisted reproductive technologies (ART) being followed in large scale in human and animal reproduction, assessing semen quality and fertilizability is under continuous scrutiny. Various tests have been developed to predict semen quality, but so far no single, highly reliable test is available. In this regard, transcriptomic profiling of spermatozoa assumes significance as it carries the information about spermatogenesis, sperm function, and paternal roles in post-fertilization events...
March 14, 2018: Systems Biology in Reproductive Medicine
Zhijun Chen, Xiaoliang Wang, Yang Liu, Jiao Liu
Protein-polymer microcapsules attracted much attention due to their special feature and potential in biological use. How to make the most of this type of bio-abiotic hybrid material is an intriguing question. Nevertheless, several unsatisfactory technical issues significantly limited the application of these materials. For instance, introducing various biomolecules and cross-linking for the capsules remain challenging and problematic. In this report, recombinant mCherry protein was covalently linked with PNIPAAm to form amphiphilic protein-polymer conjugates, assembled into microcapsules...
March 14, 2018: Chembiochem: a European Journal of Chemical Biology
Cristina Aguado, Maria-de-Los-Llanos Gil, Zaira Yeste, Ana Giménez-Capitán, Cristina Teixidó, Niki Karachaliou, Santiago Viteri, Rafael Rosell, Miguel A Molina-Vila
Fusion of the anaplastic lymphoma receptor tyrosine kinase gene ( ALK ) with the echinoderm microtubule-associated protein 4 gene ( EML4 ) is the second most common actionable alteration in non-small-cell lung cancer, with a frequency of 5%. Here, we present a case of an EML4-ALK-positive patient with an atypical in-frame insertion from the LTBP1 gene in the canonical junction of variant 1 . The patient was a 39-year-old never-smoker female diagnosed with Stage IV lung adenocarcinoma. A core biopsy was negative for EGFR and KRAS mutations but positive for ALK immunohistochemistry and fluorescence in situ hybridization...
2018: OncoTargets and Therapy
Zhi-Mei Li, Xiao Zhang, Ru-Ping Liang, Xiang-Juan Zheng, Jian-Ding Qiu
In this work, a newly developed surface plasma resonance (SPR) system for the sensitive detection of M.SssI activity has been designed based on double signal amplification with DNA chain cyclic reactions and AuNPs. In the absence of M.SssI, hairpin DNA 1 (HP1) can be cleaved into s1 fragments catalyzed by HpaII. The s1 fragments can then trigger a recycling process of hairpin DNA 2 (HP2) hybridization and subsequently release massive s2 and s3 in the solution of Nt.AlwI and HPII. AuNPs-DNA can be captured on gold film by the released s2 and s3 to produce a strong SPR signal...
August 3, 2018: Analytica Chimica Acta
Wanying Li, Dan Yu, Jingjuan Yu, Dengyun Zhu, Qian Zhao
ZmbZIP25 ( Zea mays bZIP (basic leucine zipper) transcription factor 25) is a function-unknown protein that belongs to the D group of the bZIP transcription factor family. RNA-seq data showed that the expression of ZmbZIP25 was tissue-specific in maize silks, and this specificity was confirmed by RT-PCR (reverse transcription-polymerase chain reaction). In situ RNA hybridization showed that ZmbZIP25 was expressed exclusively in the xylem of maize silks. A 5' RACE (rapid amplification of cDNA ends) assay identified an adenine residue as the transcription start site of the ZmbZIP25 gene...
March 12, 2018: International Journal of Molecular Sciences
Nicoletta Coccaro, Antonella Zagaria, Paola Orsini, Luisa Anelli, Giuseppina Tota, Paola Casieri, Luciana Impera, Angela Minervini, Crescenzio F Minervini, Cosimo Cumbo, Elisa Parciante, Anna Mestice, Mario Delia, Claudia Brunetti, Giorgina Specchia, Francesco Albano
Most Acute Promyelocytic Leukemia (APL) patients express PML-RARA fusion; in rare cases RARA is rearranged with partner genes other than PML. To date, only two patients presenting features similar to APL showing the RARG gene rearrangement have been described. We report an Acute Myeloid Leukemia (AML) patient with morphology resembling APL without involvement of the RARA gene. Molecular and Fluorescent In Situ Hybridization (FISH) analyses excluded PML-RARA fusion and variant rearrangements involving RARA and RARG loci...
March 9, 2018: Human Pathology
Khadega A Abuelgasim, Hinna Rehan, Maha Alsubaie, Nasser Al Atwi, Mohammed Al Balwi, Saeed Alshieban, Areej Almughairi
BACKGROUND: Chronic lymphocytic leukemia and chronic myeloid leukemia are the most common types of adult leukemia. However, it is rare for the same patient to suffer from both. Richter's transformation to diffuse large B-cell lymphoma is frequently observed in chronic lymphocytic leukemia. Purine analog therapy and the presence of trisomy 12, and CCND1 gene rearrangement have been linked to increased risk of Richter's transformation. The coexistence of chronic myeloid leukemia and diffuse large B-cell lymphoma in the same patient is extremely rare, with only nine reported cases...
March 11, 2018: Journal of Medical Case Reports
Jing Lu, Lin Wu, Yufang Hu, Sui Wang, Zhiyong Guo
In this study, a novel electrochemiluminescence (ECL) biosensor for sensitive detection of femtomolar miRNA-141 was constructed on the basis of Faraday cage-type strategy via graphene oxide (GO) and hybridization chain reaction (HCR)-assisted cascade amplification. A capture probe (CP) was immobilized on Fe3 O4 @SiO2 @Au nanoparticles as capture unit, which could catch the miRNA-141, and the immobilization of the signal unit (Ru(phen)3 2+ -HCR/GO) was allowed via nucleic acid hybridization. The prepared biosensor exhibited two advantages for signal amplification: firstly, GO could lap on the electrode surface directly, extending Outer Helmholtz Plane (OHP) of the sensor due to the large surface area and good electronic transport property; secondly, HCR-assisted cascade amplification was designed by anchoring all HCR products on the GO surface, then embedding Ru(phen)3 2+ as a signal readout pathway...
March 6, 2018: Biosensors & Bioelectronics
Masanori Tachikawa, Hidetoh Toki, Masahiko Watanabe, Masatoshi Tomi, Ken-Ichi Hosoya, Tetsuya Terasaki
The A-subclass of ATP-binding cassette (ABC) transporters is a highly conserved superfamily of potent lipid transporters. Although the ABCA1-like subgroup of ABCA1-4, and A7 have been shown to mediate the transport of endogenous lipids, the roles of the ABCA6-like subgroup transporters, which have been identified as a unique gene cluster on human chromosome 17q24 (ABCA5, A6, A8, A9, and A10) and mouse chromosome 11 (Abca5, a6, a8a, a8b, and a9), remains largely unknown. The purpose of the present study was to clarify the spatial and temporal expression profiles of Abca6-like subgroup transporters in embryonic and postnatal mouse brains by a combination of in situ hybridization and quantitative polymerase chain reaction (PCR) using magnetically isolated brain vascular endothelial cells...
March 8, 2018: Anatomical Science International
Ruben Van de Vijver, Maarten K Sabbe, Marie-Françoise Reyniers, Kevin M Van Geem, Guy B Marin
A set of group additivity values for intramolecular hydrogen abstraction reactions of alkanes, alkenes and alkynes is reported. Calculating 448 reaction rate coefficients at the CBS-QB3 level of theory for 1-2 up to 1-7 hydrogen shift reactions allowed the estimation of ΔGAV° values for 270 groups. The influence of substituents on (1) the attacking radical, (2) the attacked carbon atom, and (3) the carbon chain between the attacking and attacked reactive atom has been systematically studied. Substituents have been varied between hydrogen atoms and sp3 , sp2 and sp hybridized carbon atoms...
March 8, 2018: Physical Chemistry Chemical Physics: PCCP
Jan Chalabala, Frank Uhlig, Petr Slavicek
Ionization in the condensed phase and molecular clusters leads to a complicated chain of processes with coupled electron-nuclear dynamics. It is difficult to describe such dynamics with conventional nonadiabatic molecular dynamics schemes since the number of states swiftly increases as the molecular system grows. It is therefore attractive to use a direct electron and nuclear propagation such as the real-time time-dependent density functional theory (RT-TDDFT). Here we report a RT-TDDFT benchmark study on simulations of singly and doubly-ionized states of a water monomer and dimer as a prototype for more complex processes in a condensed phase...
March 7, 2018: Journal of Physical Chemistry. A
Fanfeng Meng, Guiwei Dong, Yubiao Zhang, Sibao Tian, Zhizhong Cui, Shuang Chang, Peng Zhao
In poultry, fowl adenovirus (FAdV) and immunosuppressive virus co-infection is likely to cause decreased egg production, inclusion body hepatitis, and pericardial effusion syndrome. In this study, fowl adenovirus infection was found in parental and descendent generations of chickens. We used quantitative polymerase chain reaction (PCR) and dot blot hybridization to detect the infection of reticuloendotheliosis (REV), avian leukosis virus (ALV), and chicken infectious anemia virus (CIAV) in 480 plasma samples...
March 1, 2018: Poultry Science
Deyin Xing, Gang Zheng, John Kenneth Schoolmeester, Zaibo Li, Aparna Pallavajjala, Lisa Haley, Michael G Conner, Russell Vang, Chien-Fu Hung, Tzyy-Choou Wu, Brigitte M Ronnett
Small cell neuroendocrine carcinoma (SCNEC) of the uterine cervix is a rare but extremely aggressive tumor. While high-risk human papillomavirus (HPV) is involved at an early stage of oncogenesis in many tumors, additional driving events have been postulated to facilitate the progression of SCNECs. Identification of oncogenic drivers could guide targeted therapy of this neoplasm. Clinicopathologic features of 10 cervical SCNECs are reported. Analyses included immunohistochemical evaluation of p16, p53, synaptophysin, and chromogranin expression; in situ hybridizations and polymerase chain reaction for high-risk HPV and/or HPV 18; and next-generation sequencing based on a 637-gene panel...
March 2, 2018: American Journal of Surgical Pathology
A Palma, B Ortiz, L Mendoza, G Matamoros, J A Gabrie, A L Sánchez, G Fontecha
Ascaris sp. is a soil-transmitted helminth (STH) significantly affecting the health of human and swine populations. Health inequities and poverty, with resulting deficiencies in water, sanitation and hygiene, are directly associated with Ascaris lumbricoides prevalence in humans. Resource constraints also lead to small-scale livestock production under unsanitary conditions. Free-ranging pigs, for instance, are exposed to a number of infectious agents, among which Ascaris suum is one of the most common. Under these conditions, close proximity between people and pigs can result in cross-contamination; that is, pigs harbouring human Ascaris and vice versa...
March 5, 2018: Journal of Helminthology
Cheol-Kyu Park, In-Jae Oh, Yoo-Duk Choi, Tae-Won Jang, Jeong-Eun Lee, Jeong-Seon Ryu, Shin-Yup Lee, Young-Chul Kim
OBJECTIVES: We aimed to evaluate the prevalence and predictive role of c-MET expression and EGFR mutation in the efficacy of erlotinib in non-small-cell lung cancer (NSCLC). METHODS: We prospectively recruited 196 patients with stage IV or recurrent NSCLC treated with erlotinib after failure of first-line chemotherapy. Immunohistochemistry was used to evaluate c-MET overexpression, silver in situ hybridization (SISH) to assess gene copy number, and real-time polymerase chain reaction to detect EGFR mutations, respectively, in tumor tissue...
March 2, 2018: Oncology
Xiaoyu Li, Junjing Li, Caixia Zhu, Xiaohua Zhang, Jinhua Chen
In this work, a new electrochemical immunosensor was developed for prion protein assay based on hybridization chain reaction (HCR) with hemin/G-quadruplex DNAzyme for signal amplification. In this amplification system, the hemin/G-quadruplex DNAzyme simultaneously mimicked the biocatalytic functions for H2 O2 reduction and L-cysteine oxidation. In the presence of L-cysteine, the hemin/G-quadruplex catalyzed the oxidation of L-cysteine to L-cystine. At the same time, H2 O2 was produced under the oxygen condition...
May 15, 2018: Talanta
Chung-Guei Huang, Li-Ang Lee, Tuan-Jen Fang, Hsueh-Yu Li, Chun-Ta Liao, Chung-Jan Kang, Tzu-Chen Yen, Kuo-Chien Tsao, Tse-Ching Chen, Shin-Ru Shih
BACKGROUND/PURPOSE: To examine whether the prevalence rate of human papillomavirus (HPV) infection in Taiwanese patients with primary laryngeal squamous cell carcinoma (LSCC) is different from that in those with a vocal polyp (VP) or vocal fold leukoplakia (VFL). METHODS: This prospective cohort study recruited 41 consecutive patients with primary LSCC and 27 and 20 patients with VP and VFL, respectively. The HPV L1 gene in surgical specimens was detected using polymerase chain reaction...
February 21, 2018: Journal of Microbiology, Immunology, and Infection, Wei Mian Yu Gan Ran za Zhi
Ye Tao, Neil Gross, Xiaojiao Fan, Jianming Yang, Maikun Teng, Xu Li, Guojun Li, Yang Zhang, Zhigang Huang
BACKGROUND: As hybrid RNAs, transcription-induced chimeras (TICs) may have tumor-promoting properties, and some specific chimeras have become important diagnostic markers and therapeutic targets for cancer. METHODS: We examined 23 paired laryngeal cancer (LC) tissues and adjacent normal mucous membrane tissue samples (ANMMTs). Three of these pairs were used for comparative transcriptomic analysis using high-throughput sequencing. Furthermore, we used real-time polymerase chain reaction (RT-PCR) for further validation in 20 samples...
March 2, 2018: BMC Cancer
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