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https://www.readbyqxmd.com/read/28933157/reduced-graphene-oxide-based-solid-phase-extraction-for-the-enrichment-and-detection-of-microrna
#1
He Yan, Youchun Xu, Ying Lu, Wanli Xing
MicroRNAs (miRNAs) are endogenous molecules with regulatory functions. The purification and enrichment of miRNA are essential for its precise and sensitive detection. miRNA isolated using commercial kits contains abundant interfering RNAs, and the concentration of miRNA may not be adequate for detection. Herein, we prepared a reduced graphene oxide (rGO)-based magnetic solid-phase extraction material for the enrichment and ultrasensitive detection of miRNA from intricate nucleic acid solutions. In situ reverse transcription (RT) was developed as the most efficient approach to desorb miRNA from rGO among the methods that are compatible for the subsequent amplification reported thus far...
September 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28924259/non-coding-rna-regulatory-circles
#2
Darran Yates
No abstract text is available yet for this article.
September 19, 2017: Nature Reviews. Neuroscience
https://www.readbyqxmd.com/read/28900093/-synthesis-of-circular-dna-templates-with-t4-rna-ligase-for-rolling-circle-amplification
#3
A R Sakhabutdinova, M A Maksimova, R R Garafutdinov
Currently, isothermal methods of nucleic acid amplification have been well established; in particular, rolling circle amplification is of great interest. In this approach, circular ssDNA molecules have been used as a target that can be obtained by the intramolecular template-dependent ligation of an oligonucleotide C-probe. Here, a new method of synthesizing small circular DNA molecules via the cyclization of ssDNA based on T4 RNA ligase has been proposed. Circular ssDNA is further used as the template for the rolling circle amplification...
July 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28860313/smooth-muscle-differentiation-control-comes-full-circle-the-circular-noncoding-rna-circacta2-functions-as-a-mirna-sponge-to-fine-tune-%C3%AE-sma-expression
#4
EDITORIAL
Mary C M Weiser-Evans
No abstract text is available yet for this article.
September 1, 2017: Circulation Research
https://www.readbyqxmd.com/read/28855687/library-sirna-generating-rna-nanosponges-for-gene-silencing-by-complementary-rolling-circle-transcription
#5
Sangwoo Han, Hyejin Kim, Jong Bum Lee
Since the discovery of RNA interference (RNAi), small interfering RNA (siRNA) has been powerful tools for gene downregulation in biomedical applications. Despite the outstanding efficacy of siRNA, the development of a therapeutic delivery system remains a challenge owing to the instability of RNA. In this study, we describe a new method for the design of siRNA-generating nanosponges by using complementary rolling circle transcription (cRCT), a technique that requires two complementary circular DNA. The sequences of one of the circular DNA are designed to have complete complementarity to the target mRNA resulting in double stranded RNA (dsRNA) that can be digested to siRNA by cellular Dicer activity...
August 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28805376/discovery-and-biosensing-applications-of-diverse-rna-cleaving-dnazymes
#6
Meng Liu, Dingran Chang, Yingfu Li
DNA-based enzymes, or DNAzymes, are not known to exist in Nature but can be isolated from random-sequence DNA pools using test tube selection techniques. Since the report of the first DNAzyme in 1994, many catalytic DNA molecules for catalyzing wide-ranging chemical transformations have been isolated and studied. Our laboratory has a keen interest in searching for diverse DNAzymes capable of cleaving RNA-containing substrates, determining their sequence requirements and structural properties, and examining their potential as biosensors...
August 14, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28766295/inducible-expression-of-eukaryotic-circular-rnas-from-plasmids
#7
Deirdre C Tatomer, Dongming Liang, Jeremy E Wilusz
Thousands of eukaryotic protein-coding genes are noncanonically spliced to generate circular RNAs. Because they have covalently linked ends, circular RNAs are resistant to degradation by exonucleases and some accumulate to higher levels than their associated linear mRNAs. The functions of most circular RNAs are still unknown, but recent work has revealed key insights into how the pre-mRNA splicing machinery catalyzes backsplicing. Exons that circularize are often flanked by intronic repeat sequences that are complementary to one another, and backsplicing is triggered when these repeats base pair and bring the intervening splice sites into close proximity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28756535/foxa1-hypermethylation-link-between-parity-and-er-negative-breast-cancer-in-african-american-women
#8
Allyson C Espinal, Matthew F Buas, Dan Wang, David Ting-Yuan Cheng, Lara Sucheston-Campbell, Qiang Hu, Li Yan, Rochelle Payne-Ondracek, Eduardo Cortes, Li Tang, Zhihong Gong, Gary Zirpoli, Thaer Khoury, Song Yao, Angela Omilian, Kitaw Demissie, Elisa V Bandera, Song Liu, Christine B Ambrosone, Michael J Higgins
BACKGROUND: Reproductive factors, particularly parity, have differential effects on breast cancer risk according to estrogen receptor (ER) status, especially among African American (AA) women. One mechanism could be through DNA methylation, leading to altered expression levels of genes important in cell fate decisions. METHODS: Using the Illumina 450K BeadChip, we compared DNA methylation levels in paraffin-archived tumor samples from 383 AA and 350 European American (EA) women in the Women's Circle of Health Study (WCHS)...
July 29, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28745814/ocular-localization-of-mycobacterial-lesions-in-tank-reared-juvenile-cobia-rachycentron-canadum
#9
A C N Phillips, R Suepaul, E Soto
Severe clinical mycobacteriosis with consistent ocular lesion localization was diagnosed in a population of 800 juvenile tank-reared Cobia (Rachycentron canadum) which experienced a sudden increase in mortality approximately 5 months after arriving into Trinidad and Tobago from Florida, USA. Moderate daily mortality (15-20 animals per day) persisted for just over 1 month. Moribund fish displayed circling behaviour and had an open-mouth gape upon death. Fish consistently presented with bilateral exophthalmia, corneal cloudiness and hyphema...
July 26, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28742826/macromolecular-biosynthetic-parameters-and-metabolic-profile-in-different-life-stages-of-leishmania-braziliensis-amastigotes-as-a-functionally-less-active-stage
#10
Marlene Jara, Maya Berg, Guy Caljon, Geraldine de Muylder, Bart Cuypers, Denis Castillo, Ilse Maes, María Del Carmen Orozco, Manu Vanaerschot, Jean-Claude Dujardin, Jorge Arevalo
It was recently hypothesized that Leishmania amastigotes could constitute a semi-quiescent stage characterized by low replication and reduced metabolic activity. This concept developed with Leishmania (Leishmania) mexicana and Leishmania (Leishmania) major models might explain numerous clinical and sub-clinical features of Leishmania (Viannia) braziliensis infections, like reactivation of the disease, non-response to chemotherapy or asymptomatic infections. We compared here in vitro the proliferative capability of L...
2017: PloS One
https://www.readbyqxmd.com/read/28723946/the-mitochondrial-genome-of-the-terrestrial-carnivorous-plant-utricularia-reniformis-lentibulariaceae-structure-comparative-analysis-and-evolutionary-landmarks
#11
Saura R Silva, Danillo O Alvarenga, Yani Aranguren, Helen A Penha, Camila C Fernandes, Daniel G Pinheiro, Marcos T Oliveira, Todd P Michael, Vitor F O Miranda, Alessandro M Varani
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome...
2017: PloS One
https://www.readbyqxmd.com/read/28722430/multi-amplified-sensing-of-microrna-by-a-small-dna-fragment-driven-enzymatic-cascade-reaction
#12
Eunjung Kim, Philip D Howes, Spencer W Crowder, Molly M Stevens
Combining technological developments such as nanomaterials, DNA nanotechnology, and functional enzymes has great potential to facilitate next generation high performance molecular diagnostic systems. In this work, we describe a microRNA (miRNA) detection assay that combines target recycling and isothermal amplification in an elegantly designed enzyme-mediated cascade reaction. Target recycling is driven by the action of duplex-specific nuclease (DSN), resulting in highly amplified translation of input miRNA to short output DNA fragments...
January 27, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28689323/a-sensitive-colorimetric-assay-system-for-nucleic-acid-detection-based-on-isothermal-signal-amplification-technology
#13
Bo Hu, Jing Guo, Ying Xu, Hua Wei, Guojie Zhao, Yifu Guan
Rapid and accurate detection of microRNAs in biological systems is of great importance. Here, we report the development of a visual colorimetric assay which possesses the high amplification capabilities and high selectivity of the rolling circle amplification (RCA) method and the simplicity and convenience of gold nanoparticles used as a signal indicator. The designed padlock probe recognizes the target miRNA and is circularized, and then acts as the template to extend the target miRNA into a long single-stranded nucleotide chain of many tandem repeats of nucleotide sequences...
July 8, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28687202/aunp-ctg-based-probing-system-targeting-cag-repeat-dna-and-rna-sequences
#14
Binh Huy Le, Han Na Joo, Do Won Hwang, Kyu Wan Kim, Young Jun Seo
We have developed a AuNP-CTG based probing system that is applicable to the detection of many units of CAG repeat sequences which was synthesized by a rolling circle amplification (RCA) system with changes in fluorescence. We also demonstrate that our AuNP-CTG based probing system could transfect without using transfection reagent and detect target CAG repeat sequences in HeLa cells with dramatic changes in fluorescence. This AuNP-CTG based probing system could also be used, in conjunction with the CAG repeat RCA system, to detect target DNA...
August 15, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28685952/a-dual-discrimination-mode-for-improved-specificity-towards-let-7a-detection-via-a-single-base-mutated-padlock-probe-based-exponential-rolling-circle-amplification
#15
Ruixue Li, Yinan Wang, Pei Wang, Jianzhong Lu
MicroRNA (miRNA) family members are usually highly homologous sequences, and it is a challenging task to selectively detect one miRNA member from other family members in medical diagnosis. Here, we describe the design of a dual discrimination mode for improved specificity towards let-7a detection over the other members of the let-7 family, in which an intentional base mutation was introduced into the padlock probe of an exponential rolling circle amplification. The inherent discrimination power of the padlock probe and the introduced base mutation constituted a dual discrimination mode, which provided enhanced specificity for let-7a, even over single-base mismatched family sequences...
July 7, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
https://www.readbyqxmd.com/read/28635587/ictv-virus-taxonomy-profile-ophioviridae
#16
María Laura García, Elena Dal Bó, John V da Graça, Selma Gago-Zachert, John Hammond, Pedro Moreno, Tomohide Natsuaki, Vicente Pallás, Jose A Navarro, Carina A Reyes, Gabriel Robles Luna, Takahide Sasaya, Ioannis E Tzanetakis, Anna María Vaira, Martin Verbeek, Ictv Report Consortium
The Ophioviridae is a family of filamentous plant viruses, with single-stranded negative, and possibly ambisense, RNA genomes of 11.3-12.5 kb divided into 3-4 segments, each encapsidated separately. Virions are naked filamentous nucleocapsids, forming kinked circles of at least two different contour lengths. The sole genus, Ophiovirus, includes seven species. Four ophioviruses are soil-transmitted and their natural hosts include trees, shrubs, vegetables and bulbous or corm-forming ornamentals, both monocots and dicots...
June 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28622300/the-als-linked-e102q-mutation-in-sigma-receptor-1-leads-to-er-stress-mediated-defects-in-protein-homeostasis-and-dysregulation-of-rna-binding-proteins
#17
Alice Dreser, Jan Tilmann Vollrath, Antonio Sechi, Sonja Johann, Andreas Roos, Alfred Yamoah, Istvan Katona, Saeed Bohlega, Dominik Wiemuth, Yuemin Tian, Axel Schmidt, Jörg Vervoorts, Marc Dohmen, Cordian Beyer, Jasper Anink, Eleonora Aronica, Dirk Troost, Joachim Weis, Anand Goswami
Amyotrophic lateral sclerosis (ALS) is characterized by the selective degeneration of motor neurons (MNs) and their target muscles. Misfolded proteins which often form intracellular aggregates are a pathological hallmark of ALS. Disruption of the functional interplay between protein degradation (ubiquitin proteasome system and autophagy) and RNA-binding protein homeostasis has recently been suggested as an integrated model that merges several ALS-associated proteins into a common pathophysiological pathway...
October 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28580104/highly-specific-imaging-of-mrna-in-single-cells-by-target-rna-initiated-rolling-circle-amplification
#18
Ruijie Deng, Kaixiang Zhang, Yupeng Sun, Xiaojun Ren, Jinghong Li
Detection of single-cell gene expression with high spatial and sequence resolution is a key challenge in single cell biology. Herein, we propose a robust method for the direct detection of mRNA, termed target RNA-initiated rolling circle amplification, which enables imaging of mRNA with single-nucleotide and near-single-molecule resolution in single cells. By utilizing a Splint R ligase capable of efficiently catalyzing the ligation of a padlock probe by the target RNA, the method can enable the efficient detection of mRNA without reverse transcription (detection efficiency over 20%)...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28575409/giant-reverse-transcriptase-encoding-transposable-elements-at-telomeres
#19
Irina R Arkhipova, Irina A Yushenova, Fernando Rodriguez
Transposable elements are omnipresent in eukaryotic genomes and have a profound impact on chromosome structure, function and evolution. Their structural and functional diversity is thought to be reasonably well-understood, especially in retroelements, which transpose via an RNA intermediate copied into cDNA by the element-encoded reverse transcriptase, and are characterized by a compact structure. Here, we report a novel type of expandable eukaryotic retroelements, which we call Terminons. These elements can attach to G-rich telomeric repeat overhangs at the chromosome ends, in a process apparently facilitated by complementary C-rich repeats at the 3'-end of the RNA template immediately adjacent to a hammerhead ribozyme motif...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28525572/crosstalk-between-vertical-and-horizontal-gene-transfer-plasmid-replication-control-by-a-conjugative-relaxase
#20
Fabián Lorenzo-Díaz, Cris Fernández-López, Rudi Lurz, Alicia Bravo, Manuel Espinosa
Horizontal gene transfer is a key process in the evolution of bacteria and also represents a source of genetic variation in eukaryotes. Among elements participating in gene transfer, thousands of small (<10 kb) mobile bacterial plasmids that replicate by the rolling circle mechanism represent a driving force in the spread of antibiotic resistances. In general, these plasmids are built as genetic modules that encode a replicase, an antibiotic-resistance determinant, and a relaxase that participates in their conjugative mobilization...
July 27, 2017: Nucleic Acids Research
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