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RNA Imaging

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https://www.readbyqxmd.com/read/29779890/high-throughput-screening-enhances-kidney-organoid-differentiation-from-human-pluripotent-stem-cells-and-enables-automated-multidimensional-phenotyping
#1
Stefan M Czerniecki, Nelly M Cruz, Jennifer L Harder, Rajasree Menon, James Annis, Edgar A Otto, Ramila E Gulieva, Laura V Islas, Yong Kyun Kim, Linh M Tran, Timothy J Martins, Jeffrey W Pippin, Hongxia Fu, Matthias Kretzler, Stuart J Shankland, Jonathan Himmelfarb, Randall T Moon, Neal Paragas, Benjamin S Freedman
Organoids derived from human pluripotent stem cells are a potentially powerful tool for high-throughput screening (HTS), but the complexity of organoid cultures poses a significant challenge for miniaturization and automation. Here, we present a fully automated, HTS-compatible platform for enhanced differentiation and phenotyping of human kidney organoids. The entire 21-day protocol, from plating to differentiation to analysis, can be performed automatically by liquid-handling robots, or alternatively by manual pipetting...
May 15, 2018: Cell Stem Cell
https://www.readbyqxmd.com/read/29775753/long-non-coding-rna-biomarker-for-human-laryngeal-squamous-cell-carcinoma-prognosis
#2
Jingjing Chen, Zhisen Shen, Hongxia Deng, Wei Zhou, Qi Liao, Ying Mu
Long non-coding RNAs (lncRNA) were discovered in tumors. The regulation of lncRNA in human laryngeal squamous cell carcinoma (LSCC) remains incomplete. Uncovering the potential of lncRNA to stratify the prognosis of LSCC and streamline the vast amount of clinical information will affect medical interventions. The surgical resected LSCC tissues, adjacent non-cancerous tissues (ANCT) and lymph node metastatic tissue (LNM) were collected from 76 patients for lncRNA AC008440.10 expression assay. The stages of LSCC and LNM were classified accordingly...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29774079/long-non-coding-rnas-ac026904-1-and-uca1-a-one-two-punch-for-tgf-%C3%AE-induced-snai2-activation-and-epithelial-mesenchymal-transition-in-breast-cancer
#3
Guo-Yin Li, Wei Wang, Jian-Yong Sun, Bo Xin, Xiang Zhang, Ting Wang, Qian-Feng Zhang, Li-Bo Yao, Hua Han, Dai-Ming Fan, An-Gang Yang, Lin-Tao Jia, Lei Wang
Transforming growth factor-β (TGF-β) has received much attention as a major inducer of epithelial-mesenchymal transition (EMT) during cancer progression, mainly by activating a set of pleiotropic transcription factors including SNAI2/Slug. However, the involvement of long non-coding RNAs (lncRNAs) in TGF-β-induced Slug activation and EMT remains largely unknown. Methods: In this study, we used microarray analysis to compare lncRNA expression profiles between TGF-β treated and untreated breast cancer cells...
2018: Theranostics
https://www.readbyqxmd.com/read/29769032/live-neighbor-joining
#4
Guilherme P Telles, Graziela S Araújo, Maria E M T Walter, Marcelo M Brigido, Nalvo F Almeida
BACKGROUND: In phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes are hypothetical ancestors. In a live phylogeny, both ancestral and living taxa may coexist, leading to a tree where internal nodes may be living taxa. The well-known Neighbor-Joining heuristic is largely used for phylogenetic reconstruction. RESULTS: We present Live Neighbor-Joining, a heuristic for building a live phylogeny. We have investigated Live Neighbor-Joining on datasets of viral genomes, a plausible scenario for its application, which allowed the construction of alternative hypothesis for the relationships among virus that embrace both ancestral and descending taxa...
May 16, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29767359/simultaneous-multiplexed-detection-of-rna-and-protein-on-the-nanostring-%C3%A2-ncounter-%C3%A2-platform
#5
Sarah Warren
The NanoString nCounter Analysis System uses a digital fluorescent barcode technology that allows for direct multiplexed measurement of gene expression (mRNA), DNA, and protein. The technology uses molecular barcodes and single-molecule imaging to detect and count unique mRNA and protein targets in a single reaction. nCounter-based detection is enzyme-free (no amplification of mRNA is required), fully automated, and allows simultaneous detection of up to 770 mRNA and 30 protein targets from multiple sample types...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29764582/-research-advances-in-the-role-of-aptamers-in-the-diagnosis-and-targeted-therapy-of-pediatric-cancer
#6
Yi-Bin Zhang, Yan-Peng Wang, Jing Liu
Aptamers are single-stranded DNA or RNA which are isolated from synthesized random oligonucleotide library in vitro via systematic evolution of ligands by exponential enrichment (SELEX) and can bind to metal ions, small molecules, carbohydrates, lipids, proteins, and others targets with high affinity and specificity. Aptamers have the advantages of simple preparation, good thermal stability, and low immunogenicity and have great potential in the medical fields such as molecular imaging, biosensing, early diagnosis of diseases, and targeted therapy...
May 2018: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/29760585/mir-93-5p-enhance-lacrimal-gland-adenoid-cystic-carcinoma-cell-tumorigenesis-by-targeting-brms1l
#7
Jie Hao, Xin Jin, Yan Shi, Hong Zhang
Background: Lacrimal adenoid cystic carcinoma (LACC) is one of the most common malignancies that affects lacrimal gland. MicroRNAs are known to play a crucial role as oncogenes or tumor suppressors. Specifically, miR-93 has been reported to play a crucial role in colorectal, breast, pancreatic, lung cancer and hepatocellular carcinoma. However, the role of miR-93 in LACC and the potential molecular mechanisms involved remain unknown. Therefore, we took the challenge to determine the involvement of miR-93 in the LACC by targeting BRMS1L...
2018: Cancer Cell International
https://www.readbyqxmd.com/read/29759328/a-novel-applicator-design-for-intracavitary-brachytherapy-of-the-nasopharynx-simulated-reconstruction-image-guided-adaptive-brachytherapy-planning-and-dosimetry
#8
Warren R Bacorro, Ryan Anthony F Agas, Stellar Marie R Cabrera, Maureen R Bojador, Paolo G Sogono, Michael Benedict A Mejia, Teresa T Sy Ortin
PURPOSE: In nasopharyngeal cancer, brachytherapy is given as boost in primary treatment or as salvage for recurrent or persistent disease. The Rotterdam nasopharyngeal applicator (RNA) allows for suboptimal reduction of soft palate radiation dose, based on image-guided brachytherapy plans. Building on the RNA, we propose a novel design, the Benavides nasopharyngeal applicator (BNA). METHODS AND MATERIALS: The virtual BNA was reconstructed on two cases (one T1, one T2) previously treated with intracavitary brachytherapy using the RNA...
May 11, 2018: Brachytherapy
https://www.readbyqxmd.com/read/29759327/immunotherapy-responsive-childhood-neurodegeneration-with-systemic-and-central-nervous-system-inflammation
#9
Mario Sa, Yael Hacohen, Lucy Alderson, W K Kling Chong, Glenn Anderson, Thomas S Jacques, David Neubauer, Elzbieta Szczepanik, Ming Lim, Marios Kaliakatsos
Subacute neuroregression in association with raised neopterin and overexpression of interferon stimulated genes (ISGs) could indicate a type 1 interferonopathy. Here we describe a novel immunotherapy-responsive, clinico-immunological and imaging phenotype with evidence of innate immune activation. Three children (patient 1: 22-month-old boy; patient 2: 5-year-old girl; patient 3: 4-year-old girl) presented with asymmetric bilateral mixed dystonia and spasticity, regression in language (expressive more than receptive) and bulbar symptoms with no evidence of seizures...
April 27, 2018: European Journal of Paediatric Neurology: EJPN
https://www.readbyqxmd.com/read/29752287/-rnaset2-knockout-rats-exhibit-hippocampal-neuropathology-and-deficits-in-memory
#10
Kerstin W Sinkevicius, Thomas R Morrison, Praveen Kulkarni, Martha K Caffrey Cagliostro, Sade Iriah, Samantha Malmberg, Julia Sabrick, Jennifer A Honeycutt, Kim L Askew, Malav Trivedi, Craig F Ferris
RNASET2 deficiency in humans is associated with infant cystic leukoencephalopathy, which causes psychomotor impairment, spasticity, and epilepsy. A zebrafish mutant model suggests that loss of RNASET2 function leads to neurodegeneration due to the accumulation of non-degraded RNA in the lysosomes. The goal of this study was to characterize the first rodent model of RNASET2 deficiency. The brains of 3- and 12-month-old RNaseT2 knockout rats were studied using multiple magnetic resonance imaging modalities and behavioral tests...
May 10, 2018: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/29748557/recombinant-amelogenin-regulates-the-bioactivity-of-mouse-cementoblasts-in-vitro
#11
Sema S Hakki, S Buket Bozkurt, Emre Türkay, Michel Dard, Nuhan Purali, Werner Götz
Amelogenin (AMG) is a cell adhesion molecule that has an important role in the mineralization of enamel and regulates events during dental development and root formation. The purpose of the present study was to investigate the effects of recombinant human AMG (rhAMG) on mineralized tissue-associated genes in cementoblasts. Immortalized mouse cementoblasts (OCCM-30) were treated with different concentrations (0.1, 1, 10, 100, 1000, 10,000, 100,000 ng · mL-1 ) of recombinant human AMG (rhAMG) and analyzed for proliferation, mineralization and mRNA expression of bone sialoprotein (BSP), osteocalcin (OCN), collagen type I (COL I), osteopontin (OPN), runt-related transcription factor 2 (Runx2), cementum attachment protein (CAP), and alkaline phosphatase (ALP) genes using quantitative RT-PCR...
May 9, 2018: International Journal of Oral Science
https://www.readbyqxmd.com/read/29742191/gene-expression-analysis-differentiates-melanomas-from-spitz-nevi
#12
Burkhard Jansen, Doyle Hansen, Ronald Moy, Maesa Hanhan, Zuxu Yao
INTRODUCTION: Pediatric Spitz nevi can pose significant diagnostic challenges to both clinicians and dermatopathologists when the current image-recognition based gold standard is employed. PRAME (preferentially expressed antigen in melanoma) and/or LINC (long intergeneic non-coding RNA 518) gene expression in adult patients in samples obtained non-invasively via adhesive patches differentiates primary melanomas from atypical nevi and other pigmented lesions with a NPV of over 99%, a sensitivity of 91%, and a specificity of 69%, to help clinicians rule out melanoma and the need for surgical biopsies of atypial pigmented lesions with suspicion for melanoma...
May 1, 2018: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/29741745/prospective-feasibility-and-safety-assessment-of-surgical-biopsy-for-patients-with-newly-diagnosed-diffuse-intrinsic-pontine-glioma
#13
Nalin Gupta, Liliana C Goumnerova, Peter Manley, Susan N Chi, Donna Neuberg, Maneka Puligandla, Jason Fangusaro, Stewart Goldman, Tadanori Tomita, Tord Alden, Arthur DiPatri, Joshua B Rubin, Karen Gauvain, David Limbrick, Jeffrey Leonard, J Russel Geyer, Sarah Leary, Samuel Browd, Zhihong Wang, Sandeep Sood, Anne Bendel, Mahmoud Nagib, Sharon Gardner, Matthias A Karajannis, David Harter, Kanyalakshmi Ayyanar, William Gump, Daniel C Bowers, Bradley Weprin, Tobey J MacDonald, Dolly Aguilera, Barunashish Brahma, Nathan J Robison, Erin Kiehna, Mark Krieger, Eric Sandler, Philipp Aldana, Ziad Khatib, John Ragheb, Sanjiv Bhatia, Sabine Mueller, Anu Banerjee, Amy-Lee Bredlau, Sri Gururangan, Herbert Fuchs, Kenneth J Cohen, George Jallo, Kathleen Dorris, Michael Handler, Melanie Comito, Mark Dias, Kellie Nazemi, Lissa Baird, Jeff Murray, Neal Lindeman, Jason L Hornick, Hayley Malkin, Claire Sinai, Lianne Greenspan, Karen D Wright, Michael Prados, Pratiti Bandopadhayay, Keith L Ligon, Mark W Kieran
Background: Diagnosis of diffuse intrinsic pontine gliomas (DIPG) has relied on imaging studies since the appearance is pathognomonic, and surgical risk was felt to be high and unlikely to affect therapy. The DIPG Biology and Treatment Study (DIPG-BATS) reported here incorporated a surgical biopsy at presentation and stratified subjects to receive FDA-approved agents chosen on the basis of specific biologic targets. Methods: Subjects were eligible for the trial if the clinical features and imaging appearance of a newly diagnosed tumor were consistent with a DIPG...
May 5, 2018: Neuro-oncology
https://www.readbyqxmd.com/read/29732074/highly-multiplexed-single-cell-in-situ-rna-and-dna-analysis-with-bioorthogonal-cleavable-fluorescent-oligonucleotides
#14
Manas Mondal, Renjie Liao, Christopher D Nazaroff, Adam D Samuel, Jia Guo
The ability to profile transcripts and genomic loci comprehensively in single cells in situ is essential to advance our understanding of normal physiology and disease pathogenesis. Here we report a highly multiplexed single-cell in situ RNA and DNA analysis approach using bioorthogonal cleavable fluorescent oligonucleotides. In this approach, oligonucleotides tethered to fluorophores through an azide-based cleavable linker are used to detect their nucleic acids targets by in situ hybridization. After fluorescence imaging, the fluorophores in the whole specimen are efficiently cleaved in 30 minutes without loss of RNA or DNA integrity...
March 21, 2018: Chemical Science
https://www.readbyqxmd.com/read/29729405/efficient-sirna-transfer-to-knockdown-a-placenta-specific-lncrna-using-rgd-modified-nano-liposome-a-new-preeclampsia-like-mouse-model
#15
Qianwen Yu, Yue Qiu, Xuhui Wang, Jiajing Tang, Yayuan Liu, Ling Mei, Man Li, Ming Yang, Li Tang, Huile Gao, Zhirong Zhang, Wenming Xu, Qin He
Preeclampsia is one of the most serious pregnancy complications. Many animal models have already been developed by researchers to study the pathogenesis and treatment of preeclampsia. However, most of these animal models were established by systemic administration or by surgery in the uterine cavity, which could lead to unwanted systemic toxicity or operative wounds and affect the accuracy of the results. Because of the high expression level of integrin αvβ3 on the placenta, arginine-glycine-aspartic acid peptide (RGD) modified PEGylated cationic liposome (RGD-Lip) was designed as a novel gene delivery system to target the placenta safely and efficiently, and a new animal model of preeclampsia was established through targeting of long noncoding RNA (lncRNA)...
May 2, 2018: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/29728644/ca-2-imaging-and-gene-expression-profiling-of-lonicera-confusa-in-response-to-calcium-rich-environment
#16
Wenwen Jin, Yan Long, Chunhua Fu, Libin Zhang, Jun Xiang, Baoshan Wang, Maoteng Li
As a medicinal plant widely planted in southwest karst of China, the study of adaptation mechanisms of Lonicera confusa, especially to karst calcium-rich environment, can provide important theoretical basis for repairing desertification by genetic engineering. In this study, the Ca2+ imaging in the leaves of L. confusa was explored by LSCM (Laser Scanning Confocal Microscopy) and TEM (Transmission Electron Microscopy), which revealed that the calcium could be transported to gland, epidermal hair and stoma in the leaves of L...
May 4, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29725066/isothermal-folding-of-a-light-up-bio-orthogonal-rna-origami-nanoribbon
#17
Emanuela Torelli, Jerzy Wieslaw Kozyra, Jing-Ying Gu, Ulrich Stimming, Luca Piantanida, Kislon Voïtchovsky, Natalio Krasnogor
RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter...
May 3, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29721384/low-dose-gemcitabine-increases-the-cytotoxicity-of-human-v%C3%AE-9v%C3%AE-2-t-cells-in-bladder-cancer-cells-in-vitro-and-in-an-orthotopic-xenograft-model
#18
Teruki Shimizu, Mako Tomogane, Masatsugu Miyashita, Osamu Ukimura, Eishi Ashihara
Human γδT cell immunotherapy is well tolerated and has shown promising results in clinical trials; however, its antitumor efficacy is limited, including results in solid tumors. Ex-vivo expanded γδT cell stimulated by zoledronic acid (ZOL) activates the γδT cell subpopulation of so called Vγ9Vδ2 T cells. To improve the clinical outcomes of Vγ9Vδ2 T cell (abbreviated as γδT cell here) immunotherapy, we aimed to increase the cytotoxicity of γδT cells by focusing on two issues: recognition of tumor cells by γδT cells and the effector (γδT cell)-to-target (tumor cell) (E/T) ratio...
2018: Oncoimmunology
https://www.readbyqxmd.com/read/29721240/mexican-patients-with-hiv-have-a-high-prevalence-of-vertebral-fractures
#19
José Antonio Mata-Marín, Carla I Arroyo-Anduiza, María de Los Ángeles Berrospe-Silva, Alberto Chaparro-Sánchez, Ana Gil-Avila, Jesús Gaytán-Martínez
Low bone mineral density (BMD) and fragility fractures are common in individuals infected with HIV, who are undergoing antiretroviral therapy (ART). In high-income countries, dual energy X-ray absorptiometrry is typically used to evaluate osteopenia or osteoporosis in HIV infected individuals. However, this technology is unavailable in low andmiddle income countries, so a different approach is needed. The aim of this study was to use X-ray scans of the spine to determine the prevalence of and associated risk factors for vertebral fractures in HIVinfected patients in a tertiary-care hospital in Mexico...
March 29, 2018: Infectious Disease Reports
https://www.readbyqxmd.com/read/29721197/backtracked-analysis-of-preleukemic-fusion-genes-and-dna-repair-foci-in-umbilical-cord-blood-of-children-with-acute-leukemia
#20
Milan Škorvaga, Matúš Durdík, Pavol Košík, Eva Marková, Marek Holop, Miroslav Kubeš, Judita Puškáčová, Alexandra Kolenová, Igor Belyaev
The first event in origination of many childhood leukemias is a specific preleukemic fusion gene (PFG) that arises, often in utero, in hematopoietic stem/progenitor cells (HSPC) from misrepaired DNA double strand break (DSB). An immanently elevated level of DSB and impaired apoptosis may contribute to origination and persistence of PFG and donor cell-derived leukemia in recipients of allogeneic transplantation of umbilical cord blood (UCB). We investigated DSB, apoptosis and PFG in the backtracked UCB cells of leukemic patients...
April 10, 2018: Oncotarget
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