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https://www.readbyqxmd.com/read/29677441/homologous-mirna-analyses-using-a-combinatorial-nanosensor-array-with-two-dimensional-nanoparticles
#1
Mustafa Salih Hizir, Nidhi Nandu, Mehmet Veysel Yigit
A novel combinatorial nanosensor array for miRNA analyses was assembled using the intrinsic non-covalent interactions of unmodified two-dimensional nanoparticles. Discrimination of nine miRNA analogs with as little as a single nucleotide difference was demonstrated under four hours. All nine targets were identified simultaneously with 95% confidence. The developed nanotechnology offered identification and quantification of unknown targets with unknown concentration. Discrimination of target mixtures from low-to-high ratios was demonstrated...
April 20, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29677208/modeling-the-dynamics-and-kinetics-of-hiv-1-gag-during-viral-assembly
#2
Michael D Tomasini, Daniel S Johnson, Joshua S Mincer, Sanford M Simon
We report a computational model for the assembly of HIV-1 Gag into immature viral particles at the plasma membrane. To reproduce experimental structural and kinetic properties of assembly, a process occurring on the order of minutes, a coarse-grained representation consisting of a single particle per Gag molecule is developed. The model uses information relating the functional interfaces implicated in Gag assembly, results from cryo electron-tomography, and biophysical measurements from fluorescence microscopy, such as the dynamics of Gag assembly at single virions...
2018: PloS One
https://www.readbyqxmd.com/read/29676999/sex-differences-in-transcriptomic-profiles-in-aged-kidney-cells-of-renin-lineage
#3
Yuliang Wang, Diana G Eng, Jeffrey W Pippin, Sina A Gharib, Aaron McClelland, Kenneth W Gross, Stuart J Shankland
Renin expressing cells in the kidney's juxta-glomeruluar compartment likely also serve as progenitors for adult glomerular cells in disease. Although these cells of renin lineage (CoRL) decrease in number with advancing kidney age, accompanied by less responsiveness to typical stimuli such as ACE-inhibition, mechanisms and the impact of sex as a biological variable with age are not known. Accordingly, labeled CoRL were sorted from individual young (2m) and aged (27m) male and female Ren1cCre|ZsGreen reporter mice, and their transcriptomic profiles analyzed by RNA seq...
April 18, 2018: Aging
https://www.readbyqxmd.com/read/29676910/5-phosphorothiolate-dinucleotide-cap-analogs-reagents-for-mrna-modification-and-potent-small-molecular-inhibitors-of-decapping-enzymes
#4
Blazej Andrzej Wojtczak, Pawel J Sikorski, Kaja Fac-Dabrowska, Anna Nowicka, Marcin Warminski, Dorota Kubacka, Elzbieta Nowak, Marcin Nowotny, Joanna Kowalska, Jacek Jemielity
The 5' cap consists of 7-methylguanosine (m7G) linked by a 5'-5'-triphosphate bridge to mRNA and acts as the master regu-lator of mRNA turnover and translation initiation in eukaryotes. Cap analogs that influence mRNA translation and turnover (either as small molecules or as part of an RNA transcript) are valuable tools for studying gene expression, which is often also of therapeutic relevance. Here, we synthesized a series of 15 dinucleotide cap (m7GpppG) analogs containing a 5'-phosphorothiolate (5'-PSL) moiety (i...
April 20, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29676772/functional-roles-of-eriocalyxin-b-in-zebrafish-revealed-by-transcriptome-analysis
#5
Xunian Zhou, Cyanne Ye Cao, Angel Tsz-Yau Wan, Grace Gar-Lee Yue, Frankie Hin-Fai Kwok, Kwok-Pui Fung, Handong Sun, Clara Bik-San Lau, Pema-Tenzin Puno, Stephen Kwok-Wing Tsui
BACKGROUND: Eriocalyxin B (EriB) is a natural ent-kaurane diterpenoid obtained from Isodon eriocalyx var. laxiflora (family Lamiaceae), which has multiple biological activities (e.g. anti-tumor and anti-inflammatory) via the alteration of gene expression and signaling transduction. Recently, RNA sequencing (RNA-seq) has been developed as a dynamic transcriptome approach to analyze the transcriptional profile and in addition use such gene expression profiles to identify novel candidate genes in a zebrafish model...
April 20, 2018: Molecular omics
https://www.readbyqxmd.com/read/29676619/cysteinyl-leukotriene-receptor-1-and-health-effects-of-particulate-exposure-in-asthma
#6
Nathan Rabinovitch, Meaghan J Jones, Anna Faino, Matthew Strand, Alexander M Morin, Julia MacIsaac, Paul R Reynolds, Amrit Singh, Michael S Kobor, Erwin W Gelfand, Christopher Carlsten
RATIONALE: Acute exposure to ambient particle matter is associated with increased levels of the cysteinyl leukotriene (CysLT) biomarker, urinary leukotriene E4 (uLTE4 ), in subjects with asthma. OBJECTIVES: The role of CysLTs in mediating asthma worsening after particulate matter exposures was explored. METHODS: Daily concentrations of particulate matter of 2.5 μm and smaller diameter (PM2.5 ) and repeated measurements of albuterol use over a 5-month period were collected in 44 urban school children with persistent asthma...
April 2018: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29676245/structure-and-interaction-prediction-in-prokaryotic-rna-biology
#7
Patrick R Wright, Martin Mann, Rolf Backofen
Many years of research in RNA biology have soundly established the importance of RNA-based regulation far beyond most early traditional presumptions. Importantly, the advances in "wet" laboratory techniques have produced unprecedented amounts of data that require efficient and precise computational analysis schemes and algorithms. Hence, many in silico methods that attempt topological and functional classification of novel putative RNA-based regulators are available. In this review, we technically outline thermodynamics-based standard RNA secondary structure and RNA-RNA interaction prediction approaches that have proven valuable to the RNA research community in the past and present...
April 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29675784/isolation-of-normal-fibroblasts-and-their-cancer-associated-counterparts-cafs-for-biomedical-research
#8
Barbora Dvořánková, Lukáš Lacina, Karel Smetana
Cancer-associated fibroblasts (CAFs) represent a crucial component of cancer microenvironment. CAFs significantly influence biological properties of various types of cancer in terms of local aggressiveness, recurrence, and metastatic behaviour. This chapter summarizes a simple protocol for isolation of normal fibroblasts and their cancer-associated counterparts from normal human skin and mucosa, respectively, as well as from samples of human tumours such as basal/squamous carcinoma, melanoma, and breast cancer, and employment of this procedure for other types of cancer is possible...
April 20, 2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29674954/bioinformatic-integration-of-molecular-networks-and-major-pathways-involved-in-mice-cochlear-and-vestibular-supporting-cells
#9
Teresa Requena, Alvaro Gallego-Martinez, Jose A Lopez-Escamez
Background : Cochlear and vestibular epithelial non-hair cells (ENHCs) are the supporting elements of the cellular architecture in the organ of Corti and the vestibular neuroepithelium in the inner ear. Intercellular and cell-extracellular matrix interactions are essential to prevent an abnormal ion redistribution leading to hearing and vestibular loss. The aim of this study is to define the main pathways and molecular networks in the mouse ENHCs. Methods : We retrieved microarray and RNA-seq datasets from mouse epithelial sensory and non-sensory cells from gEAR portal (http://umgear...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29674686/evolutionary-plasticity-of-the-nhl-domain-underlies-distinct-solutions-to-rna-recognition
#10
Pooja Kumari, Florian Aeschimann, Dimos Gaidatzis, Jeremy J Keusch, Pritha Ghosh, Anca Neagu, Katarzyna Pachulska-Wieczorek, Janusz M Bujnicki, Heinz Gut, Helge Großhans, Rafal Ciosk
RNA-binding proteins regulate all aspects of RNA metabolism. Their association with RNA is mediated by RNA-binding domains, of which many remain uncharacterized. A recently reported example is the NHL domain, found in prominent regulators of cellular plasticity like the C. elegans LIN-41. Here we employ an integrative approach to dissect the RNA specificity of LIN-41. Using computational analysis, structural biology, and in vivo studies in worms and human cells, we find that a positively charged pocket, specific to the NHL domain of LIN-41 and its homologs (collectively LIN41), recognizes a stem-loop RNA element, whose shape determines the binding specificity...
April 19, 2018: Nature Communications
https://www.readbyqxmd.com/read/29674431/cell-type-transcriptome-atlas-for-the-planarian-schmidtea-mediterranea
#11
Christopher T Fincher, Omri Wurtzel, Thom de Hoog, Kellie M Kravarik, Peter W Reddien
The transcriptome of a cell dictates its unique cell-type biology. We used single-cell RNA sequencing to determine the transcriptomes for essentially every cell type of a complete animal: the regenerative planarian Schmidtea mediterranea. Planarians contain a diverse array of cell types, possess lineage progenitors for differentiated cells (including pluripotent stem cells), and constitutively express positional information, making them ideal for this undertaking. We generated data for 66,783 cells, defining transcriptomes for known and many previously unknown planarian cell types and for putative transition states between stem and differentiated cells...
April 19, 2018: Science
https://www.readbyqxmd.com/read/29673865/tagging-snps-in-the-hotair-gene-are-associated-with-bladder-cancer-risk-in-a-chinese-population
#12
Xiang Wang, Wenying Wang, Qiang Zhang, Damin Gu, Ke Zhang, Yuqiu Ge, Haiyan Chu, Mulong Du, Bin Xu, Meilin Wang, Xu Lv, Zhengdong Zhang, Lin Yuan, Weida Gong
BACKGROUND: The HOX transcript antisense intergenic RNA (HOTAIR) is a well-known long noncoding RNA (lncRNA) that plays a critical role in biological processes in most cancers. However, the function of HOTAIR in bladder cancer remains largely unknown. In this study, we hypothesize that tag single nucleotide polymorphisms (tagSNPs) in HOTAIR are associated with bladder cancer (BCa) risk. METHODS: We performed a hospital-based case-control study of 1050 cases and 1407 controls to investigate the associations between tagSNPs and the risk of BCa in a Chinese population...
April 16, 2018: Gene
https://www.readbyqxmd.com/read/29673664/high-throughput-silencing-identifies-novel-genes-in-endometrioid-endometrial-cancer
#13
Afiqah Alyaa Md Fuzi, Siti Zawiah Omar, Zahurin Mohamed, Noor Azmi Mat Adenan, Norfilza Mohd Mokhtar
OBJECTIVE: To validate the gene expression profile obtained from the previous microarray analysis and to further study the biological functions of these genes in endometrial cancer. From our previous study, we identified 621 differentially expressed genes in laser-captured microdissected endometrioid endometrial cancer as compared to normal endometrial cells. Among these genes, 146 were significantly up-regulated in endometrial cancer. MATERIALS AND METHODS: A total of 20 genes were selected from the list of up-regulated genes for the validation assay...
April 2018: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/29673400/long-noncoding-rna-h19-upregulates-vascular-endothelial-growth-factor-a-to-enhance-mesenchymal-stem-cells-survival-and-angiogenic-capacity-by-inhibiting-mir-199a-5p
#14
Jingying Hou, Lingyun Wang, Quanhua Wu, Guanghui Zheng, Huibao Long, Hao Wu, Changqing Zhou, Tianzhu Guo, Tingting Zhong, Lei Wang, Xuxiang Chen, Tong Wang
BACKGROUND: Currently, the overall therapeutic efficiency of mesenchymal stem cells (MSCs) transplantation for the treatment of cardiovascular disease is not satisfactory. The low viability and angiogenic capacity of the implanted cells in the local infarct tissues restrict their further application. Evidence shows that long noncoding RNA H19 (lncRNA-H19) mediates cell survival and angiogenesis. Additionally, it is also involved in MSCs biological activities. This study aimed to explore the functional role of lncRNA-H19 in MSCs survival and angiogenic capacity as well as the underlying mechanism...
April 19, 2018: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29672513/rna-seq-reveals-differentially-expressed-genes-affecting-polyunsaturated-fatty-acids-percentage-in-the-huangshan-black-chicken-population
#15
Shaohua Yang, Ying Wang, Lulu Wang, Zhaoyuan Shi, Xiaoqian Ou, Dan Wu, Xinmiao Zhang, Hao Hu, Jia Yuan, Wei Wang, Fuhu Cao, Guoqing Liu
Fatty acids metabolic products determine meat quality in chickens. Identifying genes associated with fatty acids composition could provide valuable information for the complex genetic networks of genes with underlying variations in fatty acids synthesis. RNA sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the thigh muscle tissue of 6 Huangshan Black Chickens with 3 extremely high and low phenotypic values for percentage of polyunsaturated fatty acids (PUFAs). In total, we obtained 41,139,108-44,901,729 uniquely mapped reads, which covered 74...
2018: PloS One
https://www.readbyqxmd.com/read/29672161/tissue-expression-analysis-and-characterization-of-smad3-promoter-in-bovine-myoblasts-and-preadipocytes
#16
Le Zhang, Yue Ning, Peiwei Li, Hongfang Guo, Linsen Zan
The transforming growth factor-β (TGFβ) pathway plays many key roles in regulating numerous biological processes. In addition, the effects of TGFβ are mediated by the transcription factor Smad3. However, the regulation of Smad3 activity is not well understood. In the present study, quantitative real-time PCR revealed that the Smad3 gene was expressed ubiquitously in 11 bovine tissues and displayed different expression patterns between muscle and adipose tissue. We further explored the expression and regulation of Smad3 gene by cloning the bovine Smad3 gene promoter; a dual-luciferase reporter assay identified that the core promoter region -337 to -41 bp was located in a CpG island...
April 19, 2018: DNA and Cell Biology
https://www.readbyqxmd.com/read/29671950/comparative-transcriptomics-across-14-drosophila-species-reveals-signatures-of-longevity
#17
Siming Ma, Andrei S Avanesov, Emily Porter, Byung Cheon Lee, Marco Mariotti, Nadezhda Zemskaya, Roderic Guigo, Alexey A Moskalev, Vadim N Gladyshev
Lifespan varies dramatically among species, but the biological basis is not well understood. Previous studies in model organisms revealed the importance of nutrient sensing, mTOR, NAD/sirtuins, and insulin/IGF1 signaling in lifespan control. By studying life-history traits and transcriptomes of 14 Drosophila species differing more than sixfold in lifespan, we explored expression divergence and identified genes and processes that correlate with longevity. These longevity signatures suggested that longer-lived flies upregulate fatty acid metabolism, downregulate neuronal system development and activin signaling, and alter dynamics of RNA splicing...
April 19, 2018: Aging Cell
https://www.readbyqxmd.com/read/29671889/two-long-non-coding-rnas-prcat17-3-and-prcat38-could-efficiently-discriminate-benign-prostate-hyperplasia-from-prostate-cancer
#18
Hamid Bayat, Behzad Narouie, Seyed-Amir Mohsen Ziaee, Seyed Javad Mowla
BACKGROUND: Long non-coding RNAs (lncRNAs) have recently appeared as new players in cancer biology. Recently, a number of new prostate cancer-associated lncRNAs has been listed via RNA-seq approach by Mitranscriptome project. By analyzing this data we chose four lncRNAs (Prcat17.3, Prcat38, Prcat47, and Cat2184.4) and evaluated their expressions and their abilities to discriminate prostate tumors from benign prostate hyperplasia (BPH). METHODS: Fresh Prostate tissue samples (30 BPH, and 30 tumor samples) and urine samples (19 BPH, and 19 tumor samples) were collected and their total RNA extracted for cDNA syntheses...
April 19, 2018: Prostate
https://www.readbyqxmd.com/read/29671390/bcdforest-a-boosting-cascade-deep-forest-model-towards-the-classification-of-cancer-subtypes-based-on-gene-expression-data
#19
Yang Guo, Shuhui Liu, Zhanhuai Li, Xuequn Shang
BACKGROUND: The classification of cancer subtypes is of great importance to cancer disease diagnosis and therapy. Many supervised learning approaches have been applied to cancer subtype classification in the past few years, especially of deep learning based approaches. Recently, the deep forest model has been proposed as an alternative of deep neural networks to learn hyper-representations by using cascade ensemble decision trees. It has been proved that the deep forest model has competitive or even better performance than deep neural networks in some extent...
April 11, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29670881/impact-of-transcriptomics-on-our-understanding-of-pulmonary-fibrosis
#20
REVIEW
Milica Vukmirovic, Naftali Kaminski
Idiopathic pulmonary fibrosis (IPF) is a lethal fibrotic lung disease characterized by aberrant remodeling of the lung parenchyma with extensive changes to the phenotypes of all lung resident cells. The introduction of transcriptomics, genome scale profiling of thousands of RNA transcripts, caused a significant inversion in IPF research. Instead of generating hypotheses based on animal models of disease, or biological plausibility, with limited validation in humans, investigators were able to generate hypotheses based on unbiased molecular analysis of human samples and then use animal models of disease to test their hypotheses...
2018: Frontiers in Medicine
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