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https://www.readbyqxmd.com/read/28092691/effective-detection-of-variation-in-single-cell-transcriptomes-using-matq-seq
#1
Kuanwei Sheng, Wenjian Cao, Yichi Niu, Qing Deng, Chenghang Zong
The quantification of transcriptional variation in single cells, particularly within the same cell population, is currently limited by the low sensitivity and high technical noise of single-cell RNA-seq assays. We report multiple annealing and dC-tailing-based quantitative single-cell RNA-seq (MATQ-seq), a highly sensitive and quantitative method for single-cell sequencing of total RNA. By systematically determining technical noise, we show that MATQ-seq captures genuine biological variation between whole transcriptomes of single cells...
January 16, 2017: Nature Methods
https://www.readbyqxmd.com/read/28092440/molecular-interactions-between-graphene-and-biological-molecules
#2
Xingquan Zou, Shuai Wei, Joshua Jasensky, Minyu Xiao, Qiuming Wang, Charles L Brooks, Zhan Chen
Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applications based on using graphene and peptides require peptides to interact with (e.g., noncovalently bind to) graphene at one end, while simultaneously exposing the other end to the surrounding medium (e...
January 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28092358/recurrent-rna-motifs-as-scaffolds-for-genetically-encodable-small-molecule-biosensors
#3
Ely B Porter, Jacob T Polaski, Makenna M Morck, Robert T Batey
Allosteric RNA devices are increasingly being viewed as important tools capable of monitoring enzyme evolution, optimizing engineered metabolic pathways, facilitating gene discovery and regulators of nucleic acid-based therapeutics. A key bottleneck in the development of these platforms is the availability of small-molecule-binding RNA aptamers that robustly function in the cellular environment. Although aptamers can be raised against nearly any desired target through in vitro selection, many cannot easily be integrated into devices or do not reliably function in a cellular context...
January 16, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28091639/gold-nanoparticles-stabilized-by-cationic-carbosilane-dendrons-synthesis-and-biological-properties
#4
Cornelia E Peña-González, Elzbieta Pedziwiatr-Werbicka, Dzmitry Shcharbin, Carlos Guerrero-Beltrán, Viktar Abashkin, Svetlana Loznikova, José L Jiménez, M Ángeles Muñoz-Fernández, Maria Bryszewska, Rafael Gómez, Javier Sánchez-Nieves, F Javier de la Mata
Gold nanoparticles (AuNPs) and polycationic macromolecules are used as gene carriers. Their behaviour is dependent on several factors, such as the size and type of the framework, charge, etc. We have combined both types of systems and prepared AuNPs covered with cationic carbosilane dendrons with the aim to evaluate their biocompatibility. Water soluble dendronized cationic AuNPs were prepared following a straightforward procedure from dendrons, a gold precursor and a reducing agent in water and were characterized by (1)H NMR, transmission electron microscopy (TEM), dynamic light scattering (DLS), thermogravimetric analysis (TGA), ultraviolet spectroscopy (UV), and zeta potential (ZP)...
January 16, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28091614/transcriptomic-basis-for-drought-resistance-in-brassica-napus-l
#5
Pei Wang, Cuiling Yang, Hao Chen, Chunpeng Song, Xiao Zhang, Daojie Wang
Based on transcriptomic data from four experimental settings with drought-resistant and drought-sensitive cultivars under drought and well-watered conditions, statistical analysis revealed three categories encompassing 169 highly differentially expressed genes (DEGs) in response to drought in Brassica napus L., including 37 drought-resistant cultivar-related genes, 35 drought-sensitive cultivar-related genes and 97 cultivar non-specific ones. We provide evidence that the identified DEGs were fairly uniformly distributed on different chromosomes and their expression patterns are variety specific...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28091529/long-non-coding-rna-linc-ram-enhances-myogenic-differentiation-by-interacting-with-myod
#6
Xiaohua Yu, Yong Zhang, Tingting Li, Zhao Ma, Haixue Jia, Qian Chen, Yixia Zhao, Lili Zhai, Ran Zhong, Changyin Li, Xiaoting Zou, Jiao Meng, Antony K Chen, Pier Lorenzo Puri, Meihong Chen, Dahai Zhu
Long non-coding RNAs (lncRNAs) are important regulators of diverse biological processes. Here we report on functional identification and characterization of a novel long intergenic non-coding RNA with MyoD-regulated and skeletal muscle-restricted expression that promotes the activation of the myogenic program, and is therefore termed Linc-RAM (Linc-RNA Activator of Myogenesis). Linc-RAM is transcribed from an intergenic region of myogenic cells and its expression is upregulated during myogenesis. Notably, in vivo functional studies show that Linc-RAM knockout mice display impaired muscle regeneration due to the differentiation defect of satellite cells...
January 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28090264/drought-stress-induced-changes-of-micrornas-in-diploid-and-autotetraploid-paulownia-tomentosa
#7
Xibing Cao, Guoqiang Fan, Lin Cao, Minjie Deng, Zhenli Zhao, Suyan Niu, Zhe Wang, Yuanlong Wang
Drought stress adversely affects plant productivity. Growth and timber production of Paulownia trees are limited under drought stress. Changes in gene expression patterns and miRNA in different ploidy of Paulownia tomentosa have been investigated. However, the responses of P. tomentosa to drought stress at the microRNA (miRNA) level have not been reported so far. To identify miRNA candidates and their target genes involved in the drought stress response in diploid and tetraploid P. tomentosa, four small RNA and four degradome libraries from diploid and autotetraploid P...
2017: Genes & Genomics
https://www.readbyqxmd.com/read/28090037/expression-of-pro-renin-receptor-during-rapamycin-induced-erythropoiesis-in-k562-erythroleukemia-cells-and-its-possible-dual-actions-on-erythropoiesis
#8
Kiriko Kaneko, Koji Ohba, Takuo Hirose, Kazuhito Totsune, Kazumichi Furuyama, Kazuhiro Takahashi
(Pro)renin receptor ((P)RR), a specific receptor for renin and prorenin, is expressed in erythroblastic cells. (P)RR has multiple biological actions: prorenin activation, stimulation of the intracellular signaling including extracellular signal-regulated kinases, and functional complex formation with vacuolar H(+)-ATPase (v-ATPase). However, the functional implication of (P)RR in erythroblast cells has not been clarified. The aim of the present study was to clarify changes of (P)RR expression during erythropoiesis and a role of (P)RR in the heme synthesis...
2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28089386/detection-of-urinary-cell-free-mir-210-as-a-potential-tool-of-liquid-biopsy-for-clear-cell-renal-cell-carcinoma
#9
Guorong Li, An Zhao, Michel Péoch, Michèle Cottier, Nicolas Mottet
BACKGROUND: Recent findings show that cell-free miRNAs are stable in biological fluid. Urine provides an alternative to blood serum or plasma as a potential source of tumor biomarkers. MiR-210 is proven to be overexpressed in patients with a clear cell renal cell carcinoma (ccRCC). The purpose of this pilot study was to examine the urinary cell-free miR-210 as a potential tool of liquid biopsy for ccRCC. METHODS: Overall, 75 patients with a ccRCC and 45 control subjects without a cancer were included in this study...
January 12, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28089131/transcriptome-wide-identification-and-functional-investigation-of-circular-rna-in-the-teleost-large-yellow-croaker-larimichthys-crocea
#10
Shuangbin Xu, Shijun Xiao, Changliang Qiu, Zhiyong Wang
Circular RNA (circRNA) was first reported over thirty years ago. With the development of high-throughput sequencing technologies, circRNA has been identified in an increasing number of species. However, few studies on circRNA have been reported in teleost fish. Accumulating transcriptome and phenotype data enable us to probe the biological functions of circRNA in fish species. Here, we report the identification of circRNAs from RNA sequencing (RNA-seq) data in large yellow croaker (Larimichthys crocea), a commercially important marine fish in China and East Asia...
January 6, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28089042/molecular-screening-of-xerophilic-aspergillus-strains-producing-mycophenolic-acid
#11
Bello Mouhamadou, Lucile Sage, Sophie Périgon, Virginie Séguin, Valérie Bouchart, Patrick Legendre, Mathilde Caillat, Hayet Yamouni, David Garon
Mycophenolic acid (MPA) is the fungal secondary metabolite displaying several biological properties. Up to now, screening of fungal strains producing MPA has mainly been the result of the search of this molecule in their culture medium by chemical methods. Here we developed a molecular approach by targeting the expression level of the MpaC gene encoding the polyketide synthase, one of the key enzymes involved in the MPA synthesis. Thirty xerophilic Aspergillus strains were identified using the RNA polymerase II subunit and the β-tubulin genes...
February 2017: Fungal Biology
https://www.readbyqxmd.com/read/28088836/upregulation-of-long-noncoding-rna-tug1-promotes-cervical-cancer-cell-proliferation-and-migration
#12
Yingying Hu, Xiangwei Sun, Chenchen Mao, Gangqiang Guo, Sisi Ye, Jianfeng Xu, Ruanmin Zou, Jun Chen, Ledan Wang, Ping Duan, Xiangyang Xue
Long noncoding RNAs (lncRNAs), a novel class of transcripts that have critical roles in carcinogenesis and progression, have emerged as important gene expression modulators. Recent evidence indicates that lncRNA taurine-upregulated gene 1 (TUG1) functions as an oncogene in numerous types of human cancers. However, its function in the development of cervical cancer remains unknown. The aim of this research was to investigate the clinical significance and biological functions of TUG1 in cervical cancer. TUG1 was found to be significantly upregulated in cervical cancer tissues and four cervical cancer cell lines by quantitative real-time polymerase chain reaction (qRT-PCR)...
January 15, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28088361/purification-and-characterisation-of-dsrna-using-ion-pair-reverse-phase-chromatography-and-mass-spectrometry
#13
Alison O Nwokeoji, An-Wen Kung, Peter M Kilby, David E Portwood, Mark J Dickman
RNA interference has provided valuable insight into a wide range of biological systems and is a powerful tool for the analysis of gene function. The exploitation of this pathway to block the expression of specific gene targets holds considerable promise for the development of novel RNAi-based insect management strategies. In addition, there are a wide number of future potential applications of RNAi to control agricultural insect pests as well as its use for prevention of diseases in beneficial insects. The potential to synthesise large quantities of dsRNA by in-vitro transcription or in bacterial systems for RNA interference applications has generated significant demand for the development and application of high throughput analytical tools for the rapid extraction, purification and analysis of dsRNA...
December 21, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28087991/an-exceptionally-selective-dna-cooperatively-binding-two-ca2-ions
#14
Wenhu Zhou, Runjhun Saran, Po-Jung Jimmy Huang, Jinsong Ding, Juewen Liu
Ca2+ is a highly important metal ion in biology and in the environment, leading to extensive work in developing sensors for Ca2+ detection. While many Ca2+ binding proteins are known, few nucleic acids can selectively bind Ca2+. DNA-based biosensors are attractive for its high stability and excellent programmability. Herein, we report a RNA-cleaving DNAzyme named EtNa cooperatively binding two Ca2+ ions but only one Mg2+. Four DNAzymes with known Ca2+-dependent activity were compared, and the EtNa has the best selectivity...
January 14, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28087642/stxbp4-drives-tumor-growth-and-is-associated-with-poor-prognosis-through-pdgf-receptor-signaling-in-lung-squamous-cell-carcinoma
#15
Yukihiro Otaka, Susumu Rokudai, Kyoichi Kaira, Michiru Fujieda, Ikuko Horikoshi, Reika Kawabata, Shinji Yoshiyama, Takehiko Yokobori, Yoichi Ohtaki, Kimihiro Shimizu, Tetsunari Oyama, Jun'ichi Tamura, Carol Prives, Masahiko Nishiyama
PURPOSE: Expression of the ΔN isoform of p63 (ΔNp63) is a diagnostic marker highly specific for lung squamous cell carcinoma (SCC). We previously found that Syntaxin Binding Protein 4 (STXBP4) regulates ΔNp63 ubiquitination, suggesting that STXBP4 may also be a SCC biomarker. To address this issue, we investigated the role of STXBP4 expression in SCC biology and the impact of STXBP4 expression on SCC prognosis. EXPERIMENTAL DESIGN: We carried out a clinicopathological analysis of STXBP4 expression in 87 lung SCC patients...
January 13, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28087495/comparative-analysis-of-variation-and-selection-in-the-hcv-genome
#16
Juan Ángel Patiño-Galindo, Fernando González-Candelas
Genotype 1 of the hepatitis C virus (HCV) is the most prevalent of the variants of this virus. Its two main subtypes, HCV-1a and HCV-1b, are associated to differences in epidemic features and risk groups, despite sharing similar features in most biological properties. We have analyzed the impact of positive selection on the evolution of these variants using complete genome coding regions, and compared the levels of genetic variability and the distribution of positively selected sites. We have also compared the distributions of positively selected and conserved sites considering different factors such as RNA secondary structure, the presence of different epitopes (antibody, CD4 and CD8), and secondary protein structure...
January 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28086788/comprehensive-circrna-expression-profile-and-selection-of-key-circrnas-during-priming-phase-of-rat-liver-regeneration
#17
Lifei Li, Jianlin Guo, Yanhui Chen, Cuifang Chang, Cunshuan Xu
BACKGROUND: Rat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play important roles. The molecular mechanism of hepatocyte proliferation, energy metabolism and substance metabolism during rat LR had been elucidated. Further, the correlation of circular RNA (circRNA) abundance with proliferation has recently been clarified. However, the regulatory capacity of circRNA in rat LR remains a fascinating topic...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081541/circular-rna-0000096-affects-cell-growth-and-migration-in-gastric-cancer
#18
Peifei Li, Huilin Chen, Shengcan Chen, Xiaoyan Mo, Tianwen Li, Bingxiu Xiao, Rui Yu, Junming Guo
BACKGROUND: Circular RNAs (circRNAs) are a class of non-coding RNAs broadly expressed in cells of various species. Their role in cancers, especially in gastric cancer, is poorly understood. METHODS: Circular RNA 0000096 (hsa_circ_0000096) levels in 101 paired gastric cancer tissues and adjacent non-tumorous tissues from patients with gastric cancer were detected by real-time quantitative reverse transcription-polymerase chain reaction. A receiver operating characteristic curve was generated to evaluate the diagnostic value of hsa_circ_0000096...
January 12, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28081468/role-of-mir-15a-in-intervertebral-disc-degeneration-through-targeting-map3k9
#19
Ping Cai, Ting Yang, Xingjie Jiang, Minghui Zheng, Gang Xu, Jianlong Xia
BACKGROUND: Accumulating evidence indicates that microRNAs are involved in various cellular processes, including cell proliferation, differentiation, apoptosis and metastasis. miR-15a is an important regulator of immune responses and angiogenesis, endogenous controls as well as potential targets and hallmarks of cancer. However, the role of miR-15a in intervertebral disc degeneration (IDD) has not been elucidated. METHODS: Total RNA was extracted from degenerative nucleus pulposus (NP) tissues of 20 patients with IDD and NP cells, respectively...
January 9, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28081465/biological-function-and-mechanism-of-lncrna-meg3-in-tenon-s-capsule-fibroblasts-proliferation-by-meg3-nrf2-protein-interaction
#20
Yuan Wang, Jing Wang, Li-Juan Wei, Dong-Mei Zhu, Jin-Song Zhang
OBJECTIVE: The proliferation of Tenon's capsule fibroblasts after glaucoma filtration surgery is a harmful element for operation failure. However, the underlying mechanism remains unclear. In this study, we evaluated the role of long non-coding RNA (lncRNA)-MEG3 in the proliferation of Glaucoma Tenon's capsule fibroblasts (GTFs) with a model of transforming growth factor-β (TGF-β)-induced proliferation which has been used in previous studies to explore the mechanism underlying glaucoma surgery failure...
January 9, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
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