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https://www.readbyqxmd.com/read/28531887/expression-and-characterization-of-membrane-type-4-matrix-metalloproteinase-mt4-mmp-and-its-different-forms-in-melanoma
#1
Bettina Hieronimus, Julian Pfohl, Christian Busch, Lutz Graeve
BACKGROUND/AIMS: Membrane-type matrix metalloproteinases (MT-MMPs) are expressed on the cell surface and hydrolyze extracellular matrix components and signaling molecules by which they influence cancer cell migration and metastasis. Two of the six known MT-MMPs are anchored to the plasma membrane via a GPI anchor, one of which is MT4-MMP. Only little is known about MT4-MMP expression, synthesis, regulation and degradation. METHODS: We analyzed several human cancer cell lines as well as tissue homogenates using Western blotting and quantitative PCR for the expression of MT4-MMP...
May 25, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28531156/molecular-techniques-for-the-detection-of-organisms-in-aquatic-environments-with-emphasis-on-harmful-algal-bloom-species
#2
REVIEW
Linda K Medlin, Jahir Orozco
Molecular techniques to detect organisms in aquatic ecosystems are being gradually considered as an attractive alternative to standard laboratory methods. They offer faster and more accurate means of detecting and monitoring species, with respect to their traditional homologues based on culture and microscopic counting. Molecular techniques are particularly attractive when multiple species need to be detected and/or are in very low abundance. This paper reviews molecular techniques based on whole cells, such as microscope-based enumeration and Fluorescence In-Situ Hybridization (FISH) and molecular cell-free formats, such as sandwich hybridization assay (SHA), biosensors, microarrays, quantitative polymerase chain reaction (qPCR) and real time PCR (RT-PCR)...
May 22, 2017: Sensors
https://www.readbyqxmd.com/read/28529717/gene-length-and-detection-bias-in-single-cell-rna-sequencing-protocols
#3
Belinda Phipson, Luke Zappia, Alicia Oshlack
Background: Single cell RNA sequencing (scRNA-seq) has rapidly gained popularity for profiling transcriptomes of hundreds to thousands of single cells. This technology has led to the discovery of novel cell types and revealed insights into the development of complex tissues. However, many technical challenges need to be overcome during data generation. Due to minute amounts of starting material, samples undergo extensive amplification, increasing technical variability. A solution for mitigating amplification biases is to include unique molecular identifiers (UMIs), which tag individual molecules...
2017: F1000Research
https://www.readbyqxmd.com/read/28529033/high-throughput-characterization-of-hiv-1-reservoir-reactivation-using-a-single-cell-in-droplet-pcr-assay
#4
Robert W Yucha, Kristen S Hobbs, Emily Hanhauser, Louise E Hogan, Wildaliz Nieves, Mehmet O Ozen, Fatih Inci, Vanessa York, Erica A Gibson, Cassandra Thanh, Hadi Shafiee, Rami El Assal, Maja Kiselinova, Yvonne P Robles, Helen Bae, Kaitlyn S Leadabrand, ShuQi Wang, Steven G Deeks, Daniel R Kuritzkes, Utkan Demirci, Timothy J Henrich
Reactivation of latent viral reservoirs is on the forefront of HIV-1 eradication research. However, it is unknown if latency reversing agents (LRAs) increase the level of viral transcription from cells producing HIV RNA or harboring transcriptionally-inactive (latent) infection. We therefore developed a microfluidic single-cell-in-droplet (scd)PCR assay to directly measure the number of CD4(+) T cells that produce unspliced (us)RNA and multiply spliced (ms)RNA following ex vivo latency reversal with either an histone deacetylase inhibitor (romidepsin) or T cell receptor (TCR) stimulation...
May 4, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28528577/single-step-pcr-based-genetic-sex-determination-of-rat-tissues-and-cells
#5
Pramod Dhakal, Michael J Soares
The advent of genome editing strategies has expanded the range of animal models available for gene manipulation and renewed research interest in the rat. Gender is a key variable for in vivo gene function analyses. Here, we present a simple PCR-based method to determine genetic sex in the rat.
May 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28525954/construction-of-various-%C3%AE-34-5-deleted-fluorescent-expressing-oncolytic-herpes-simplex-type-1-ohsv-for-generation-and-isolation-of-hsv-based-vectors
#6
Shahriyar Abdoli, Farzin Roohvand, Ladan Teimoori-Toolabi, Mohammad Ali Shokrgozar, Mina Bahrololoumi, Kayhan Azadmanesh
Background: Oncolytic herpes simplex virus (oHSV)-based vectors lacking γ34.5 gene, are considered as ideal templates to construct efficient vectors for (targeted) cancer gene therapy. Herein, we reported the construction of three single/dually-flourescence labeled and γ34.5-deleted, recombinant HSV-1 vectors for rapid generation and easy selection/isolation of different HSV-Based vectors. Methods: Generation of recombinant viruses was performed with conventional homologous recombination methods using green fluorescent protein (GFP) and BleCherry harboring shuttle vectors...
July 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28522818/efficient-modification-of-%C3%AE-dna-substrates-for-single-molecule-studies
#7
Yoori Kim, Armando de la Torre, Andrew A Leal, Ilya J Finkelstein
Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28521774/correlation-of-cell-free-dna-plasma-concentration-with-severity-of-non-alcoholic-fatty-liver-disease
#8
Thomas Karlas, Lara Weise, Stephanie Kuhn, Felix Krenzien, Matthias Mehdorn, David Petroff, Nicolas Linder, Alexander Schaudinn, Harald Busse, Volker Keim, Johann Pratschke, Johannes Wiegand, Katrin Splith, Moritz Schmelzle
BACKGROUND: The assessment of fibrosis and inflammatory activity is essential to identify patients with non-alcoholic fatty liver disease (NAFLD) at risk for progressive disease. Serum markers and ultrasound-based methods can replace liver biopsy for fibrosis staging, whereas non-invasive characterization of inflammatory activity remains a clinical challenge. Cell-free DNA (cfDNA) is a novel non-invasive biomarker for assessing cellular inflammation and cell death, which has not been evaluated in NAFLD...
May 19, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28515100/detection-of-chromosomal-translocation-in-hematologic-malignancies-by-a-novel-dna-based-looped-ligation-assay-lola
#9
Shuko Harada, Emily Sizzle, Ming-Tseh Lin, Christopher D Gocke
BACKGROUND: Disease-defining chromosomal translocations are seen in various neoplasms, especially in lymphomas and leukemias. Translocation detection at the DNA level is often complicated by chromosomal breakpoints that are distributed over very large regions. We have developed a ligation-based assay [the looped ligation assay (LOLA)] to detect translocations from diseases with multiple widely spaced breakpoint hot spots. METHODS: Oligonucleotide sets that probe breakpoints of IGH-BCL2 (immunoglobulin heavy-apoptosis regulator) in follicular lymphoma (FL), MYC-IGH (MYC proto-oncogene, bHLH transcription factor- immunoglobulin heavy) in Burkitt lymphoma (BL) and BCR-ABL1 (RhoGEF and GTPase activating protein-ABL proto-oncogene 1, non-receptor tyrosine kinase) in chronic myelogenous leukemia (CML) were designed...
May 17, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28509576/her2-positivity-may-confer-resistance-to-therapy-with-paclitaxel-in-breast-cancer-cell-lines
#10
Navideh Haghnavaz, Faezeh Asghari, Daniel Elieh Ali Komi, Dariush Shanehbandi, Behzad Baradaran, Tohid Kazemi
INTRODUCTION: MicroRNAs (miRNAs) are short non-coding single-stranded RNAs. Involving in post-transcriptional gene silencing, miRNAs are thought to play important roles in many cancers such as breast cancer. Paclitaxel is used widely in the treatment of breast cancer. In this study, we investigated the effect of paclitaxel treatment on the expression levels of two oncomirs (oncomiRs), miR-21 and miR-203, in breast cancer cell lines. MATERIALS AND METHODS: MTT assay was performed to determine IC50 of paclitaxel for human breast cancer cell lines including MCF-7, MDA-MB-231, SKBR3 and BT-474...
May 16, 2017: Artificial Cells, Nanomedicine, and Biotechnology
https://www.readbyqxmd.com/read/28505207/immuno-related-polymorphisms-and-cervical-cancer-risk-the-iarc-multicentric-case-control-study
#11
James McKay, Vanessa Tenet, Silvia Franceschi, Amélie Chabrier, Tarik Gheit, Valérie Gaborieau, Sandrine Chopin, Patrice H Avogbe, Massimo Tommasino, Michelle Ainouze, Uzma Hasan, Salvatore Vaccarella
A small proportion of women who are exposed to infection with human-papillomavirus (HPV) develop cervical cancer (CC). Genetic factors may affect the risk of progression from HPV infection to cervical precancer and cancer. We used samples from the International Agency for Research on Cancer (IARC) multicentric case-control study to evaluate the association of selected genetic variants with CC. Overall, 790 CC cases and 717 controls from Algeria, Morocco, India and Thailand were included. Cervical exfoliated cells were obtained from control women and cervical exfoliated cells or biopsy specimens from cases...
2017: PloS One
https://www.readbyqxmd.com/read/28505181/overexpression-of-pyruvate-dehydrogenase-kinase-1-in-retinoblastoma-a-potential-therapeutic-opportunity-for-targeting-vitreous-seeds-and-hypoxic-regions
#12
Swatishree Sradhanjali, Devjyoti Tripathy, Suryasnata Rath, Ruchi Mittal, Mamatha M Reddy
Pyruvate dehydrogenase kinase 1 (PDK1), a key enzyme implicated in metabolic reprogramming of tumors, is induced in several tumors including glioblastoma, breast cancer and melanoma. However, the role played by PDK1 is not studied in retinoblastoma (RB). In this study, we have evaluated the expression of PDK1 in RB clinical samples, and studied its inhibition as a strategy to decrease cell growth and migration. We show that PDK1 is specifically overexpressed in RB patient samples especially in vitreous seeds and hypoxic regions and cell lines compared to control retina using immunohistochemistry and real-time PCR...
2017: PloS One
https://www.readbyqxmd.com/read/28504693/cyclin-dependent-kinase-7-is-a-therapeutic-target-in-high-grade-glioma
#13
S A Greenall, Y C Lim, C B Mitchell, K S Ensbey, B W Stringer, A L Wilding, G M O'Neill, K L McDonald, D J Gough, B W Day, T G Johns
High-grade glioma (HGG) is an incurable brain cancer. The transcriptomes of cells within HGG tumors are highly heterogeneous. This renders the tumors unresponsive or able to adapt to therapeutics targeted at single pathways, thereby causing treatment failure. To overcome this, we focused on cyclin-dependent kinase 7 (CDK7), a ubiquitously expressed molecule involved in two major drivers of HGG pathogenesis: cell cycle progression and RNA polymerase-II-based transcription. We tested the activity of THZ1, an irreversible CDK7 inhibitor, on patient-derived primary HGG cell lines and ex vivo HGG patient tissue slices, using proliferation assays, microarray analysis, high-resolution respirometry, cell cycle analysis and in vivo tumor orthografts...
May 15, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28504553/aavs1-targeted-plasmid-integration-in-aav-producer-cell-lines
#14
Yuxia Luo, Amy Frederick, John M Martin, Abraham Scaria, Seng H Cheng, Donna Armentano, Samuel C Wadsworth, Karen A Vincent
Adeno-associated virus (AAV) producer cell lines are created via transfection of HeLaS3 cells with a single plasmid containing three components (the vector sequence, the AAV rep and cap genes, and a selectable marker gene). As this plasmid contains both the cis (Rep binding sites) and trans (Rep protein encoded by the rep gene) elements required for site-specific integration, it was predicted that plasmid integration might occur within the AAVS1 locus on human chromosome 19 (chr19). The objective of this study was to investigate whether integration in AAVS1 might be correlated with vector yield...
April 14, 2017: Human Gene Therapy Methods
https://www.readbyqxmd.com/read/28502728/technical-validation-of-a-next-generation-sequencing-assay-for-detecting-clinically-relevant-levels-of-breast-cancer-related-single-nucleotide-variants-and-copy-number-variants-using-simulated-cell-free-dna
#15
Xin Yang, Yuxing Chu, Rui Zhang, Yanxi Han, Lucheng Zhang, Yu Fu, Dan Li, Rongxue Peng, Dongdong Li, Jiansheng Ding, Ziyang Li, Meiru Zhao, Kuo Zhang, Tian Lu, Lang Yi, Qisheng Wu, Guigao Lin, Jiehong Xie, Tao Liu, Ling Yang, Xin Yi, Jinming Li
Next-generation sequencing (NGS) is commonly used in a clinical setting for diagnostic and prognostic testing of genetic mutations to select optimal targeted therapies. Herein, we describe the development of a custom NGS assay for detecting single-nucleotide variants (SNVs) and copy number variations (CNVs) in a panel of 51 genes related to breast cancer. We designed and implemented a validation strategy in accordance with principles and guidelines developed by the Next-Generation Sequencing: Standardization of Clinical Testing work group using artificial, cell-free DNA (cfDNA) with mutant fragments prepared in a simple, rapid, and cost-effective manner...
May 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28498310/selective-expression-of-flt3-within-the-mouse-hematopoietic-stem-cell-compartment
#16
Ciaran James Mooney, Alan Cunningham, Panagiotis Tsapogas, Kai-Michael Toellner, Geoffrey Brown
The fms-like tyrosine kinase 3 (Flt3) is a cell surface receptor that is expressed by various hematopoietic progenitor cells (HPC) and Flt3-activating mutations are commonly present in acute myeloid and lymphoid leukemias. These findings underscore the importance of Flt3 to steady-state and malignant hematopoiesis. In this study, the expression of Flt3 protein and Flt3 mRNA by single cells within the hematopoietic stem cell (HSC) and HPC bone marrow compartments of C57/BL6 mice was investigated using flow cytometry and the quantitative reverse transcription polymerase chain reaction...
May 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28497977/effect-of-amino-acid-substitutions-within-the-v3-region-of-hiv-1-crf01_ae-on-interaction-with-ccr5-coreceptor
#17
Sayamon Hongjaisee, Martine Braibant, Francis Barin, Nicole Ngo-Giang-Huong, Wasna Sirirungsi, Tanawan Samleerat
Specific amino acids within the V3 loop of HIV-1 CRF01_AE envelope glycoprotein that are involved in the interaction with CCR5/CXCR4 coreceptors, are not well characterized. We generated V3 mutants using PCR-based site-directed mutagenesis of HIV-1 CRF01_AE R5-env plasmids at specific positions. Mutant viruses were produced by env-pseudotyped virus assay, tested for coreceptor usage using U373.R5 and U373.X4 cells, and viral entry was assessed with luciferase activity measurement. All viruses, harboring either single or double mutations, used the CCR5 coreceptor...
May 12, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28497617/association-of-npr3-polymorphism-with-risk-of-essential-hypertension-in-a-chinese-population
#18
D-B Kuang, J-P Zhou, M-P Li, J Tang, X-P Chen
WHAT IS KNOWN AND OBJECTIVE: Essential hypertension (EH) is a common disease exhibiting large individual difference in occurrence, development and treatment response. Genetic factors are implicated in the development and progression of EH. This study aimed to explore the association between NPR3 single nucleotide polymorphism rs2270915 (A/G, Asn521Asp) and the risk of EH in a Chinese Han population by a case-control study. METHODS: The study was a single-centre, case-control trial, in which a total of 287 EH patients and 289 age- and sex-matched healthy controls were enrolled...
May 11, 2017: Journal of Clinical Pharmacy and Therapeutics
https://www.readbyqxmd.com/read/28495200/genotyping-of-theileria-lestoquardi-from-sheep-and-goats-in-sudan-to-support-control-of-malignant-ovine-theileriosis
#19
A M Ali, D A Salih, M N Njahira, S K Hassan, A M El Hussein, Z Liu, H Yin, R Pelle, R A Skilton
Theileriosis, caused by parasitic protozoa of the genus Theileria parasites, are among the major tick-borne diseases of ruminant livestock. The largest economic losses are attributed in particular to those caused by the leukoproliferative species of Theileria: T. parva, T. annulata and T. lestoquardi. Theileria lestoquardi is transmitted by Hyalomma ticks and causes malignant ovine theileriosis (MOT), a disease that is particularly prevalent in Sudan. The disease is considered of a high economic importance in Sudan, where export of sheep is a major component of the national economy...
May 30, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28494187/the-screening-of-the-functional-microrna-binding-site-snps-in-sporadic-colorectal-cancer-genes
#20
Hongjuan He, Lei Lei, Erfei Chen, Xiaona Xu, Lili Wang, Junqiang Pan, Fangfang Yang, Min Wang, Jing Dong, Jin Yang
Sporadic colorectal cancer (sCRC) is one of the most commonly diagnosed cancers worldwide, but few genetic markers have been identified and utilized for its early detection. MicroRNAs are diverse cellular regulators in cancer pathogenesis that bind to the 3'-untranslated region (3'-UTR) of their target mRNAs, and variants within the miRNA target sites on sCRC-related genes may influence its pathogenesis. To investigate this possibility, we used a bioinformatical method to screen SNPs for putative changes in miRNA recognition sites within the 3'-UTR of sCRC-related genes...
May 11, 2017: Cancer Biology & Therapy
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