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In situ hybridization

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https://www.readbyqxmd.com/read/28934690/butyl-benzyl-phthalate-bbp-induces-caudal-defects-during-embryonic-development
#1
Nicole M Roy, Ewelina Zambrzycka, Jenna Santangelo
Butyl benzyl phthalate (BBP) is commonly added during the manufacturing of plastics to increase flexibility and elasticity. However, BBP leaches off of plastic and environment presence has been detected in soil, groundwater and sediment potentially effecting organisms in the environment. Given the widespread uses of BBP in household, consumer goods and the presence of BBP in the environment, studies on developmental toxicity are needed. Here, we use a zebrafish model to investigate the early developmental toxicity of BBP...
September 18, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28934515/utility-of-fluorescence-in-situ-hybridization-panel-for-myelodysplastic-syndrome-in-evaluation-of-cytopenia-in-a-pediatric-hospital-a-5-year-retrospective-review-and-utilization-management
#2
Cynthia T Bunting, Tal Senior, Yehuda Susson, Alethia Rivera, Debra Saxe, Silvia T Bunting
Background: MDS FISH was routinely ordered together with chromosome analysis for patients with cytopenia in our hospital. The utility of MDS FISH in the pediatric population is unknown. Objective: To analyze the utility of fluorescence in situ hybridization panel for myelodysplastic syndrome (MDS FISH) in the management of patients with cytopenia. Methods: We performed a retrospective review over a 5-year period, from 2009 to 2014 to determine whether chromosome analysis (CA) plus MDS FISH added useful information compared to chromosome analysis alone...
August 1, 2017: Laboratory Medicine
https://www.readbyqxmd.com/read/28934307/amplification-of-the-egfr-gene-can-be-maintained-and-modulated-by-variation-of-egf-concentrations-in-in-vitro-models-of-glioblastoma-multiforme
#3
Doreen William, Poroshista Mokri, Nora Lamp, Michael Linnebacher, Carl Friedrich Classen, Andreas Erbersdobler, Björn Schneider
Glioblastoma multiforme (GBM) is the most common and lethal brain tumor in adults. It is known that amplification of the epidermal growth factor receptor gene (EGFR) occurs in approximately 40% of GBM, leading to enhanced activation of the EGFR signaling pathway and promoting tumor growth. Although GBM mutations are stably maintained in GBM in vitro models, rapid loss of EGFR gene amplification is a common observation during cell culture. To maintain EGFR amplification in vitro, heterotopic GBM xenografts with elevated EGFR copy number were cultured under varying serum conditions and EGF concentrations...
2017: PloS One
https://www.readbyqxmd.com/read/28932696/an-automated-workflow-for-quantifying-rna-transcripts-in-individual-cells-in-large-data-sets
#4
Matthew C Pharris, Tzu-Ching Wu, Xinping Chen, Xu Wang, David M Umulis, Vikki M Weake, Tamara L Kinzer-Ursem
Advanced molecular probing techniques such as single molecule fluorescence in situ hybridization (smFISH) or RNAscope can be used to assess the quantity and spatial location of mRNA transcripts within cells. Quantifying mRNA expression in large image sets usually involves automated counting of fluorescent spots. Though conventional spot counting algorithms may suffice, they often lack high-throughput capacity and accuracy in cases of crowded signal or excessive noise. Automatic identification of cells and processing of many images is still a challenge...
2017: MethodsX
https://www.readbyqxmd.com/read/28932414/hox-gene-cluster-of-the-ascidian-halocynthia-roretzi-reveals-multiple-ancient-steps-of-cluster-disintegration-during-ascidian-evolution
#5
Yuka Sekigami, Takuya Kobayashi, Ai Omi, Koki Nishitsuji, Tetsuro Ikuta, Asao Fujiyama, Noriyuki Satoh, Hidetoshi Saiga
BACKGROUND: Hox gene clusters with at least 13 paralog group (PG) members are common in vertebrate genomes and in that of amphioxus. Ascidians, which belong to the subphylum Tunicata (Urochordata), are phylogenetically positioned between vertebrates and amphioxus, and traditionally divided into two groups: the Pleurogona and the Enterogona. An enterogonan ascidian, Ciona intestinalis (Ci), possesses nine Hox genes localized on two chromosomes; thus, the Hox gene cluster is disintegrated...
2017: Zoological Letters
https://www.readbyqxmd.com/read/28932295/expression-of-mdm2-mrna-mdm2-p53-and-p16-proteins-in-urothelial-lesions-in-the-view-of-the-who-4-th-edition-guidelines-as-a-molecular-insight-towards-personalized-medicine
#6
Olfat Hammam, Mona Magdy, Mohamed Badawy, Khalid Al Osili, Amr El Kholy, Tarek El LeitHy
AIM: Here we imposed a multimarker molecular panel composed of P53, MDM2 protein & mRNA & P16 with the identification of sensitive and specific cut offs among the Egyptian urothelial carcinomas bilharzial or not emphasize the pathological and molecular classifications, pathways and prognosis as a privilege for adjuvant therapy. METHODS: Three hundred and ten urothelial lesions were pathologically evaluated and grouped as follows: 50 chronic cystitis as benign, 240 urothelial carcinomas and 20 normal bladder tissue as a control...
August 15, 2017: Open Access Macedonian Journal of Medical Sciences
https://www.readbyqxmd.com/read/28931104/-molecular-diagnostics-of-alk-positive-lung-cancer
#7
József Tímár, Gábor Lotz, Erzsébet Rásó, Judit Moldvay
ALK translocation is the 3rd most frequent genetic aberration in lung adenocarcinoma, and several inhibitors are now clinically available in first and second line settings. Accordingly, molecular diagnostics of ALK-positive lung cancer is very important and can be done with the rational combination of several methods. All international recommendations suggest that, except for cytological samples, screening technology for ALK-positive tumors is immunohistochemistry using a validated test. It is highly recommended that in case of ALK protein positive samples gene translocation must be confirmed by fluorescent in situ hybridization (FISH)...
September 20, 2017: Magyar Onkologia
https://www.readbyqxmd.com/read/28930482/diagnostic-and-prognostic-cytogenetics-of-chronic-myeloid-leukaemia-an-update
#8
Matteo Molica, Fulvio Massaro, Massimo Breccia
Despite the advent of molecular assessment, banding cytogenetics and fluorescence in situ hybridization (FISH) still have a significant role in diagnostic and prognostic approaches to chronic myeloid leukaemia (CML). Area covered. At diagnosis and duringtreatment with tyrosine kinase inhibitors (TKIs), cytogenetics is used to detect the Philadelphia chromosome, with its typical translocation t(9;22)(q34;q11.2), and any additional or other chromosomal aberrations (ACAs and OCAs) that may arise in 5-10% of cases, the latter associated to transformation of the disease in blast phases...
September 20, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28928676/effects-of-immune-activation-during-early-or-late-gestation-on-n-methyl-d-aspartate-receptor-measures-in-adult-rat-offspring
#9
Tasnim Rahman, Katerina Zavitsanou, Tertia Purves-Tyson, Lauren R Harms, Crystal Meehan, Ulrich Schall, Juanita Todd, Deborah M Hodgson, Patricia T Michie, Cyndi Shannon Weickert
BACKGROUND: Glutamatergic receptor [N-methyl-d-aspartate receptor (NMDAR)] alterations within cortex, hippocampus, and striatum are linked to schizophrenia pathology. Maternal immune activation (MIA) is an environmental risk factor for the development of schizophrenia in offspring. In rodents, gestational timing of MIA may result in distinct behavioral outcomes in adulthood, but how timing of MIA may impact the nature and extent of NMDAR-related changes in brain is not known. We hypothesize that NMDAR-related molecular changes in rat cortex, striatum, and hippocampus are induced by MIA and are dependent on the timing of gestational inflammation and sex of the offspring...
2017: Frontiers in Psychiatry
https://www.readbyqxmd.com/read/28928367/characterization-of-a-new-member-of-iridoviridae-shrimp-hemocyte-iridescent-virus-shiv-found-in-white-leg-shrimp-litopenaeus-vannamei
#10
Liang Qiu, Meng-Meng Chen, Xiao-Yuan Wan, Chen Li, Qing-Li Zhang, Ruo-Yu Wang, Dong-Yuan Cheng, Xuan Dong, Bing Yang, Xiu-Hua Wang, Jian-Hai Xiang, Jie Huang
A newly discovered iridescent virus that causes severe disease and high mortality in farmed Litopenaeus vannamei in Zhejiang, China, has been verified and temporarily specified as shrimp hemocyte iridescent virus (SHIV). Histopathological examination revealed basophilic inclusions and pyknosis in hematopoietic tissue and hemocytes in gills, hepatopancreas, periopods and muscle. Using viral metagenomics sequencing, we obtained partial sequences annotated as potential iridoviridae. Phylogenetic analyses using amino acid sequences of major capsid protein (MCP) and ATPase revealed that it is a new iridescent virus but does not belong to the five known genera of Iridoviridae...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928284/functional-and-evolutionary-insights-from-the-ciona-notochord-transcriptome
#11
Wendy M Reeves, Yuye Wu, Matthew J Harder, Michael T Veeman
The notochord of the ascidian Ciona consists of only 40 cells, and is a longstanding model for studying organogenesis in a small, simple embryo. Here, we perform RNAseq on flow-sorted notochord cells from multiple stages to define a comprehensive Ciona notochord transcriptome. We identify 1364 genes with enriched expression and extensively validate the results by in situ hybridization. These genes are highly enriched for Gene Ontology terms related to the extracellular matrix, cell adhesion and cytoskeleton...
September 15, 2017: Development
https://www.readbyqxmd.com/read/28928214/fishing-out-the-hidden-enemy-advances-in-detecting-and-measuring-latent-hiv-infected-cells
#12
Vinayaka R Prasad, Ganjam V Kalpana
The indomitable aspect of HIV-1 infection is not that HIV-1 proviral DNA is integrated into host DNA but that it can also turn itself off, remaining invisible to drug or immune surveillance. Thus, the goals of eradication include ways to precisely excise HIV-1 DNA or wake up the silent HIV-1 provirus and eliminate the infected cells thus identified. Methods to identify and fish out the latently infected cells or to delineate their characteristics are being rapidly developed. In 2016, Baxter et al. (A. E. Baxter, J...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28927531/discriminating-rna-variants-with-single-molecule-allele-specific-fish
#13
REVIEW
Martyna O Urbanek, Wlodzimierz J Krzyzosiak
DNA mutations of various types often affect the cellular localization and function of gene products. The role of mutant transcripts in the pathogenesis of human disease is increasingly recognized. Among the pathogenic RNA variants are transcripts with single nucleotide substitutions, small insertions or deletions, aberrantly or alternatively spliced transcripts and RNAs derived from fused genes. To discriminate among transcripts, particularly those of low abundance, showing small or large sequence differences, a highly sensitive and specific RNA imaging method is required...
July 2017: Mutation Research
https://www.readbyqxmd.com/read/28927089/chronic-radiation-exposure-of-neuroblastoma-cells-reduces-nmyc-copy-number
#14
Manu Gnanamony, Reuben Antony, Karen S Fernández, Libes Jaime, Julian Lin, Pushpa A Joseph, Christopher S Gondi
Neuroblastoma accounts for >15% of cancer-associated mortalities of children in the USA. Despite aggressive treatment regimens, the long-term survival for these children remains <40%. The identification of v-Myc avian myelocytomatosis viral oncogene neuroblastoma-derived homolog (nMYC) gene amplification during diagnosis is associated with poor prognosis in neuroblastoma. There are limited studies examining changes in nMYC copy numbers in response to therapy and its biological effect on cancer cells. The aim of the present study was to evaluate the effect of radiation on nMYC expression and amplification status in high-risk neuroblastoma...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28927048/mucoepidermoid-carcinoma-of-the-sublingual-gland-harboring-a-translocation-of-the-maml2-gene-a-case-report
#15
Kiminobu Sato, Jun Akiba, Ken Nakamura, Hideyuki Abe, Akihiko Kawahara, Takeichiro Aso, Hirohito Umeno, Hiroshi Harada, Hirohisa Yano
Among tumors of the major salivary glands, tumors in the sublingual gland are rare. Although mucoepidermoid carcinoma (MEC) represents a histological type of salivary gland tumor, it is occasionally difficult to diagnose due to its histological variation. The present study reports a case of MEC harboring a mastermind-like transcriptional coactivator 2 (MAML2) gene translocation in the sublingual gland. A 76-year-old Japanese woman with a mass in the left submandibular region was referred to Kurume University Hospital (Kurume, Japan)...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28926787/a-novel-a-b-process-for-enhanced-biological-nutrient-removal-in-municipal-wastewater-reclamation
#16
Guangjing Xu, Han Wang, Jun Gu, Nan Shen, Zheng Qiu, Yan Zhou, Yu Liu
This study developed an innovative A-B process for enhanced nutrients removal in municipal wastewater reclamation, in which a micro-aerated moving bed biofilm reactor served as A-stage and a step-feed sequencing batch reactor (SBR) as B-stage. In the A-stage, 55% of COD and 15% of ammonia nitrogen was removed, while more than 88% of the total nitrogen was removed via nitritation and denitritation, together with 93% of phosphorous removal at the B-stage where ammonia oxidizing bacteria activity was significantly higher than nitrite oxidizing bacteria activity...
September 12, 2017: Chemosphere
https://www.readbyqxmd.com/read/28925924/in-situ-preparation-of-fe-sub-3-sub-o-sub-4-sub-in-a-carbon-hybrid-of-graphene-nanoscrolls-and-carbon-nanotubes-as-high-performance-anode-material-for-lithium-ion-batteries
#17
Yuewen Liu, Ahmad Hassan Siddique, Heran Huang, Qile Fang, Wei Deng, Xufeng Zhou, Huanming Lu, Z P Liu
A new conductive carbon hybrid combining both graphene nanoscrolls and carbon nanotubes (rGNSs-CNTs) is prepared, and used to host Fe3O4 nanoparticles through an in situ synthesis method. As an anode material for LIBs, the obtained Fe3O4@rGNSs-CNTs shows good electrochemical performance. At a current density of 0.1 A g-1, the anode material shows a high reversible capacity of 1232.9 mAh g-1 after 100 cycles. Even at a current density of 1 A g-1, it still achieves a high reversible capacity of 812.3 mAh g-1 after 200 cycles...
September 19, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28924861/role-of-bdnf-and-neurotrophic-receptors-in-human-inner-ear-development
#18
L Johnson Chacko, M J F Blumer, E Pechriggl, H Rask-Andersen, W Dietl, A Haim, H Fritsch, R Glueckert, J Dudas, A Schrott-Fischer
The expression patterns of the neurotrophin, brain-derived neurotrophic factor, BDNF, and the neurotrophic receptors-p75NTR and Trk receptors-in the developing human fetal inner ear between the gestational weeks (GW) 9 to 12 are examined via in situ hybridization and immunohistochemistry. BDNF mRNA expression was highest in the cochlea at GW 9 but declined in the course of development. In contrast to embryonic murine specimens, a decline in BDNF expression from the apical to the basal turn of the cochlea could not be observed...
September 19, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28924860/facial-nerve-palsy-secondary-to-epstein-barr-virus-infection-of-the-middle-ear-in-pediatric-population-may-be-more-common-than-we-think
#19
Katarina Vogelnik, Aleš Matos
BACKGROUND: Facial nerve palsy is a rare complication of acute otitis media (AOM). The general understanding is that this complication has a bacterial cause although bacteria can be isolated from the middle ear only in approximately two-thirds of cases of AOM. Detection of viral agents from specimens obtained during myringotomy in patients with AOM suggests a possible role of viruses in the etiology of this disease. CASE PRESENTATIONS: We studied 5 otherwise healthy 17- to 27-month-old children who were referred to the Department of Otorhinolaryngology and Cervicofacial Surgery from December 2012 to January 2016 because of AOM and ipsilateral facial nerve palsy...
September 18, 2017: Wiener Klinische Wochenschrift
https://www.readbyqxmd.com/read/28924672/in-situ-super-resolution-imaging-of-genomic-dna-with-oligostorm-and-oligodna-paint
#20
Brian J Beliveau, Alistair N Boettiger, Guy Nir, Bogdan Bintu, Peng Yin, Xiaowei Zhuang, C-Ting Wu
OligoSTORM and OligoDNA-PAINT meld the Oligopaint technology for fluorescent in situ hybridization (FISH) with, respectively, Stochastic Optical Reconstruction Microscopy (STORM) and DNA-based Point Accumulation for Imaging in Nanoscale Topography (DNA-PAINT) to enable in situ single-molecule super-resolution imaging of nucleic acids. Both strategies enable ≤20 nm resolution and are appropriate for imaging nanoscale features of the genomes of a wide range of species, including human, mouse, and fruit fly (Drosophila)...
2017: Methods in Molecular Biology
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