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RNA Imaging

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https://www.readbyqxmd.com/read/28103687/live-cell-imaging-of-endogenous-mrna-using-rna-based-fluorescence-turn-on-probe
#1
Wei Qiang Ong, Y Rose Citron, Sayaka Sekine, Bo Huang
Messenger RNA (mRNA) plays a critical role in cellular growth and development. However, there have been limited methods available to visualize endogenous mRNA in living cells with ease. We have designed RNA-based fluorescence "turn-on" probes that target mRNA by fusing an unstable form of Spinach with target-complementary sequences. These probes have been demonstrated to be selective, stable, and capable of targeting various mRNAs for live E. coli imaging.
January 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28103302/crude-extracts-flavokawain-b-and-alpinetin-compounds-from-the-rhizome-of-alpinia-mutica-induce-cell-death-via-uck2-enzyme-inhibition-and-in-turn-reduce-18s-rrna-biosynthesis-in-ht-29-cells
#2
Ibrahim Malami, Ahmad Bustamam Abdul, Rasedee Abdullah, Nur Kartinee Bt Kassim, Rozita Rosli, Swee Keong Yeap, Peter Waziri, Imaobong Christopher Etti, Muhammad Bashir Bello
Uridine-cytidine kinase 2 is an enzyme that is overexpressed in abnormal cell growth and its implication is considered a hallmark of cancer. Due to the selective expression of UCK2 in cancer cells, a selective inhibition of this key enzyme necessitates the discovery of its potential inhibitors for cancer chemotherapy. The present study was carried out to demonstrate the potentials of natural phytochemicals from the rhizome of Alpinia mutica to inhibit UCK2 useful for colorectal cancer. Here, we employed the used of in vitro to investigate the effectiveness of natural UCK2 inhibitors to cause HT-29 cell death...
2017: PloS One
https://www.readbyqxmd.com/read/28098980/ruthenium-ii-complex-based-luminescent-bifunctional-probe-for-ag-and-phosphate-ions-ag-assisted-detection-and-imaging-of-rrna
#3
Sanjoy Kumar Sheet, Bhaskar Sen, Romita Thounaojam, Kripamoy Aguan, Snehadrinarayan Khatua
A new bis-heteroleptic Ru(II) complex (1) of benzimidazole-substituted 1,2,3-triazole pyridine ligand has been designed and constructed for the photoluminescent detection of cationic and anionic analytes, Ag(+) and phosphate ions. Compound, 1[PF6]2 was fully characterized by various spectroscopic techniques and the solid-state structure was determined via single-crystal X-ray diffraction. The cation and anion sensing properties in 50% aqueous buffer (pH 9.2) and pure acetonitrile were carefully examined in photoluminescence (PL) spectroscopy...
January 18, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28097054/hydrogel-scaffolds-promote-neural-gene-expression-and-structural-reorganization-in-human-astrocyte-cultures
#4
V Bleu Knight, Elba E Serrano
Biomaterial scaffolds have the potential to enhance neuronal development and regeneration. Understanding the genetic responses of astrocytes and neurons to biomaterials could facilitate the development of synthetic environments that enable the specification of neural tissue organization with engineered scaffolds. In this study, we used high throughput transcriptomic and imaging methods to determine the impact of a hydrogel, PuraMatrix™, on human glial cells in vitro. Parallel studies were undertaken with cells grown in a monolayer environment on tissue culture polystyrene...
2017: PeerJ
https://www.readbyqxmd.com/read/28094815/drd2-co-expression-network-and-a-related-polygenic-index-predict-imaging-behavioral-and-clinical-phenotypes-linked-to-schizophrenia
#5
G Pergola, P Di Carlo, E D'Ambrosio, B Gelao, L Fazio, M Papalino, A Monda, G Scozia, B Pietrangelo, M Attrotto, J A Apud, Q Chen, V S Mattay, A Rampino, G Caforio, D R Weinberger, G Blasi, A Bertolino
Genetic risk for schizophrenia (SCZ) is determined by many genetic loci whose compound biological effects are difficult to determine. We hypothesized that co-expression pathways of SCZ risk genes are associated with system-level brain function and clinical phenotypes of SCZ. We examined genetic variants related to the dopamine D2 receptor gene DRD2 co-expression pathway and associated them with working memory (WM) behavior, the related brain activity and treatment response. Using two independent post-mortem prefrontal messenger RNA (mRNA) data sets (total N=249), we identified a DRD2 co-expression pathway enriched for SCZ risk genes...
January 17, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28088972/-critical-roles-of-matrix-metalloproteinases-secreted-by-leukemic-cells-in-the-pathogenesis-of-central-nervous-system-leukemia
#6
S R Feng, Z X Chen, J N Cen, H J Shen, Y Y Wang, L Yao
Objective: To observe the effects of matrix metalloproteinases (MMP)-2 and MMP-9 secreted by leukemic cells on tight junction proteins ZO-1, claudin-5 and occluding and the permeability of the blood-brain barrier (BBB) and explore the mechanisms of MMP-2 and MMP-9 in leukemic cell infiltration of the central nervous system (CNS). Methods: The mRNA expressions of MMP-2 and MMP-9 in leukemic cell lines SHI-1, HL-60 and U937 were detected by quantitative RT-PCR. The MMP inhibitor GM6001 was used to inhibit the secretion of MMP-2 and MMP-9...
December 14, 2016: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
https://www.readbyqxmd.com/read/28078793/insights-into-nuclear-dynamics-using-live-cell-imaging-approaches
#7
REVIEW
Rachel B Bigley, Alexander Y Payumo, Jeffrey M Alexander, Guo N Huang
The nucleus contains the genetic blueprint of the cell and myriad interactions within this subcellular structure are required for gene regulation. In the current scientific era, characterization of these gene regulatory networks through biochemical techniques coupled with systems-wide 'omic' approaches has become commonplace. However, these strategies are limited because they represent a mere snapshot of the cellular state. To obtain a holistic understanding of nuclear dynamics, relevant molecules must be studied in their native contexts in living systems...
January 12, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28077066/the-essential-requirement-of-an-animal-heme-peroxidase-protein-during-the-wing-maturation-process-in-drosophila
#8
Dondra Bailey, Mohammed Abul Basar, Sanjay Nag, Nivedita Bondhu, Shaloei Teng, Atanu Duttaroy
BACKGROUND: Thus far, a handful of genes have been shown to be related to the wing maturation process in insects. A novel heme peroxidase enzyme known as curly suppressor (Cysu)(formerly CG5873), have been characterized in this report because it is involved in wing morphogenesis. Using bioinformatics tools we found that Cysu is remarkably conserved in the genus Drosophila (>95%) as well as in invertebrates (>70%), although its vertebrate orthologs show poor homology. Time-lapse imaging and histochemical analyses have confirmed that the defective wing phenotype of Cysu is not a result of any underlying cellular alterations; instead, its wings fail to expand in mature adults...
January 11, 2017: BMC Developmental Biology
https://www.readbyqxmd.com/read/28076321/secretion-modification-region-derived-peptide-blocks-exosome-release-and-mediates-cell-cycle-arrest-in-breast-cancer-cells
#9
Ming-Bo Huang, Ruben R Gonzalez, James Lillard, Vincent C Bond
PURPOSE: Discovery and development of a novel anticancer PEG-SMR-Clu peptide to prevent breast cancer metastasis. How breast cancer cells and primary mammary epithelial cells interact and communicate with each other to promote tumorigenesis and how to prevent tumor metastasis has long been a concern of researchers. Cancer cells secrete exosomes containing proteins and RNA. These factors can influence tumor development by directly targeting cancer cells and tumor stroma. In this study, we determined the effects of a peptide as an inhibitor of exosome secretion on breast tumors...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28073004/epigenetic-sirna-and-chemical-screens-identify-setd8-inhibition-as-a-therapeutic-strategy-for-p53-activation-in-high-risk-neuroblastoma
#10
Veronica Veschi, Zhihui Liu, Ty C Voss, Laurent Ozbun, Berkley Gryder, Chunhua Yan, Ying Hu, Anqi Ma, Jian Jin, Sharlyn J Mazur, Norris Lam, Barbara K Souza, Giuseppe Giannini, Gordon L Hager, Cheryl H Arrowsmith, Javed Khan, Ettore Appella, Carol J Thiele
Given the paucity of druggable mutations in high-risk neuroblastoma (NB), we undertook chromatin-focused small interfering RNA and chemical screens to uncover epigenetic regulators critical for the differentiation block in high-risk NB. High-content Opera imaging identified 53 genes whose loss of expression led to a decrease in NB cell proliferation and 16 also induced differentiation. From these, the secondary chemical screen identified SETD8, the H4(K20me1) methyltransferase, as a druggable NB target. Functional studies revealed that SETD8 ablation rescued the pro-apoptotic and cell-cycle arrest functions of p53 by decreasing p53(K382me1), leading to activation of the p53 canonical pathway...
January 9, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28068668/the-hippo-kinases-lats1-and-2-control-human-breast-cell-fate-via-crosstalk-with-er%C3%AE
#11
Adrian Britschgi, Stephan Duss, Sungeun Kim, Joana Pinto Couto, Heike Brinkhaus, Shany Koren, Duvini De Silva, Kirsten D Mertz, Daniela Kaup, Zsuzsanna Varga, Hans Voshol, Alexandra Vissieres, Cedric Leroy, Tim Roloff, Michael B Stadler, Christina H Scheel, Loren J Miraglia, Anthony P Orth, Ghislain M C Bonamy, Venkateshwar A Reddy, Mohamed Bentires-Alj
Cell fate perturbations underlie many human diseases, including breast cancer. Unfortunately, the mechanisms by which breast cell fate are regulated are largely unknown. The mammary gland epithelium consists of differentiated luminal epithelial and basal myoepithelial cells, as well as undifferentiated stem cells and more restricted progenitors. Breast cancer originates from this epithelium, but the molecular mechanisms that underlie breast epithelial hierarchy remain ill-defined. Here, we use a high-content confocal image-based short hairpin RNA screen to identify tumour suppressors that regulate breast cell fate in primary human breast epithelial cells...
January 9, 2017: Nature
https://www.readbyqxmd.com/read/28067416/a-novel-technique-of-delivering-viral-vectors-to-trigeminal-ganglia-in-rats
#12
Hu Long, Lina Liao, Yang Zhou, Di Shan, Meiya Gao, Renhuan Huang, Xin Yang, Wenli Lai
The objective of this study was to develop a viable and reliable technique of delivering viral vectors to rat trigeminal ganglia. Adult Sprague-Dawley rats (200-300 g) were used, and lentiviral vectors containing enhanced green fluorescence protein and calcitonin gene-related peptide short hairpin RNA (shRNA) were generated. Following general anesthesia, viral vectors were delivered to rat trigeminal ganglia using the technique described in this study. Both X-ray and micro-computed tomography (micro-CT) were employed to verify the position of the needles when injecting the vectors...
January 9, 2017: European Journal of Oral Sciences
https://www.readbyqxmd.com/read/28065320/imaging-cytokinesis-of-drosophila-s2-cells
#13
A Kechad, G R X Hickson
Animal cell cytokinesis proceeds through three successive stages: a contractile ring stage, an intercellular bridge stage, and an abscission stage. Many studies have identified a complex network of key proteins required for successful cytokinesis. While each component interacts with, and depends on, several other components, our understanding of how these proteins cooperate in space and time to ensure faithful progression through the stages of cytokinesis remains incomplete. A full understanding of the complexity of the process and its underlying machinery necessitates experimental systems that allow both genetic manipulation and real-time visualization of the various components throughout the successive stages of cytokinesis...
2017: Methods in Cell Biology
https://www.readbyqxmd.com/read/28063496/measuring-phospholipase-d-enzymatic-activity-through-biochemical-and-imaging-methods
#14
F Philip, E E Ha, M A Seeliger, M A Frohman
The phospholipase D (PLD) enzymatic superfamily regulates a wide range of cell biological and physiological pathways, including platelet activation, immune responses, cancer, and spermatogenesis. The three main enzymatic actions of the superfamily entail (i) hydrolyzing membrane phospholipids (phosphatidylcholine (PC) and cardiolipin) to generate choline and the second messenger signaling lipid phosphatidic acid (PA), (ii) using ethanol to transphosphatidylate PC to generate the long-lived metabolite phosphatidylethanol, and (iii) hydrolyzing RNA transcripts to generate piRNAs, the third form of endogenous RNAi...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28062830/dissecting-inherent-intratumor-heterogeneity-in-patient-derived-glioblastoma-culture-models
#15
Jian Teng, Cintia Carla da Hora, Rami S Kantar, Ichiro Nakano, Hiroaki Wakimoto, Tracy T Batchelor, E Antonio Chiocca, Christian E Badr, Bakhos A Tannous
BACKGROUND: Molecular profile of glioblastoma multiforme (GBM) revealed 4 subtypes, 2 of which, proneural and mesenchymal, have been predominantly observed, with the latter displaying a more aggressive phenotype and increased therapeutic resistance. Single-cell RNA sequencing revealed that multiple subtypes actually reside within the same tumor, suggesting cellular heterogeneity in GBM. Further, plasticity between these 2 subtypes is observed during tumor recurrence and in response to radiation therapy...
January 6, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28061811/the-nature-and-nurture-of-cell-heterogeneity-accounting-for-macrophage-gene-environment-interactions-with-single-cell-rna-seq
#16
Quin F Wills, Esther Mellado-Gomez, Rory Nolan, Damien Warner, Eshita Sharma, John Broxholme, Benjamin Wright, Helen Lockstone, William James, Mark Lynch, Michael Gonzales, Jay West, Anne Leyrat, Sergi Padilla-Parra, Sarah Filippi, Chris Holmes, Michael D Moore, Rory Bowden
BACKGROUND: Single-cell RNA-Seq can be a valuable and unbiased tool to dissect cellular heterogeneity, despite the transcriptome's limitations in describing higher functional phenotypes and protein events. Perhaps the most important shortfall with transcriptomic 'snapshots' of cell populations is that they risk being descriptive, only cataloging heterogeneity at one point in time, and without microenvironmental context. Studying the genetic ('nature') and environmental ('nurture') modifiers of heterogeneity, and how cell population dynamics unfold over time in response to these modifiers is key when studying highly plastic cells such as macrophages...
January 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28059107/single-cell-time-lapse-analysis-reveals-that-podoplanin-enhances-cell-survival-and-colony-formation-capacity-of-squamous-cell-carcinoma-cells
#17
Tomoyuki Miyashita, Youichi Higuchi, Motohiro Kojima, Atsushi Ochiai, Genichiro Ishii
Tumor initiating cells (TICs) are characterized by high clonal expansion capacity. We previously reported that podoplanin is a TIC-specific marker for the human squamous cell carcinoma cell line A431. The aim of this study is to explore the molecular mechanism underlying the high clonal expansion potential of podoplanin-positive A431cells using Fucci imaging. Single podoplanin-positive cells created large colonies at a significantly higher frequency than single podoplanin-negative cells, whereas no difference was observed between the two types of cells with respect to cell cycle status...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28057790/novel-risk-markers-and-risk-assessments-for-cardiovascular-disease
#18
REVIEW
Mark R Thomas, Gregory Y H Lip
The use of risk markers has transformed cardiovascular medicine, exemplified by the routine assessment of troponin, for both diagnosis and assessment of prognosis in patients with chest pain. Clinical risk factors form the basis for risk assessment of cardiovascular disease and the addition of biochemical, cellular, and imaging parameters offers further refinement. Identifying novel risk factors may allow greater risk stratification and a steady, but gradual progression toward precision medicine. Indeed, the generation of data in this area of research is explosive and when combined with new technologies and techniques provides the potential for more refined, targeted approaches to cardiovascular medicine...
January 6, 2017: Circulation Research
https://www.readbyqxmd.com/read/28052353/temporal-and-spatial-regulation-of-mrna-export-single-particle-rna-imaging-provides-new-tools-and-insights
#19
Stephanie Heinrich, Carina Patrizia Derrer, Azra Lari, Karsten Weis, Ben Montpetit
The transport of messenger RNAs (mRNAs) from the nucleus to cytoplasm is an essential step in the gene expression program of all eukaryotes. Recent technological advances in the areas of RNA-labeling, microscopy, and sequencing are leading to novel insights about mRNA biogenesis and export. This includes quantitative single molecule imaging (SMI) of RNA molecules in live cells, which is providing knowledge of the spatial and temporal dynamics of the export process. As this information becomes available, it leads to new questions, the reinterpretation of previous findings, and revised models of mRNA export...
January 4, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28047590/su-f-r-02-imaging-genomics-for-predicting-gbm-molecular-subclasses-and-survival
#20
F Mahmoudi, L Poisson, H Bagher-Ebadian, M Nazem-Zadeh, H Soltanian-Zadeh
PURPOSE: Glioblastoma (GBM) is the most common and fatal primary intracranial neoplasm. GBM is categorized into five sub-classes (classical, G-CIMP, mesenchymal, proneural and neural) that can only be determined by an invasive brain biopsy followed by RNA and DNA methylation profiling. The goal of this study is to develop imaging features extracted from conventional MRI scans and an ensemble-classification method as a potential noninvasive method to predict the five molecular sub-classes and 12-month survival status...
June 2016: Medical Physics
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