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https://www.readbyqxmd.com/read/29667992/naked-eye-and-electrochemical-detection-of-isothermally-amplified-hotair-long-non-coding-rna
#1
Md Nazmul Islam, Sofia Moriam, Muhammad Umer, Hoang-Phuong Phan, Carlos Salomon, Richard Kline, Nam-Trung Nguyen, Muhammad J A Shiddiky
An inexpensive, simple and rapid sensor platform capable of detecting cancer-related long non-coding RNA (lncRNA) with high accuracy is of great interest in the field of molecular diagnostics. Herein, we report on the development of a new colorimetric and electrochemical assay platform for long non-coding HOX transcript antisense intergenic RNA (HOTAIR) detection. Isothermal reverse transcription-recombinase polymerase amplification (RT-RPA) was performed to amplify HOTAIR sequences from a RNA pool extracted from a designated number of ovarian cancer cells and a small cohort of plasma samples derived from patients with ovarian cancer...
April 18, 2018: Analyst
https://www.readbyqxmd.com/read/29667432/identification-and-characterisation-of-micrornas-and-piwi-interacting-rnas-in-cockerels-spermatozoa-by-solexa-sequencing
#2
Shengru Wu, Jiacheng Guo, Liqin Zhu, Jiantao Yang, Si Chen, Xiaojun Yang
1. There has been substantial research focused on the roles of microRNAs (miRNA) and PIWI-interacting RNAs (piRNA) delivered from mammalian spermatozoa, however comparatively little is known about the role of spermatozoa-delivered miRNAs and piRNAs within breeding cockerels' spermatozoa. 2. A small RNA library of cockerels' spermatozoa was constructed using Illumina high-throughput sequencing technology. Unique sequences with lengths of 18-26 nucleotides were mapped to miRBase 21.0 and unique sequences with lengths of 25-37 nucleotides were mapped to a piRNA database...
April 18, 2018: British Poultry Science
https://www.readbyqxmd.com/read/29667349/asb1-differential-methylation-in-ischaemic-cardiomyopathy-relationship-with-left-ventricular-performance-in-end-stage-heart-failure-patients
#3
Ana Ortega, Estefanía Tarazón, Carolina Gil-Cayuela, Luis Martínez-Dolz, Francisca Lago, José Ramón González-Juanatey, Juan Sandoval, Manuel Portolés, Esther Roselló-Lletí, Miguel Rivera
AIMS: Ischaemic cardiomyopathy (ICM) leads to impaired contraction and ventricular dysfunction, causing high rates of morbidity and mortality. Epigenomics allows the identification of epigenetic signatures in human diseases. We analyse the differential epigenetic patterns of the ASB gene family in ICM patients and relate these alterations to their haemodynamic and functional status. METHODS AND RESULTS: Epigenomic analysis was carried out using 16 left ventricular (LV) tissue samples, eight from ICM patients undergoing heart transplantation and eight from control (CNT) subjects without cardiac disease...
April 17, 2018: ESC Heart Failure
https://www.readbyqxmd.com/read/29667329/performance-of-amplicon-and-shotgun-sequencing-for-accurate-biomass-estimation-in-invertebrate-community-samples
#4
Iliana Bista, Gary R Carvalho, Min Tang, Kerry Walsh, Xin Zhou, Mehrdad Hajibabaei, Shadi Shokralla, Mathew Seymour, David Bradley, Shanlin Liu, Martin Christmas, Simon Creer
New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (3 different amplicons) and shotgun mitogenome sequencing...
April 18, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29667281/estimated-number-of-off-target-candidate-sites-for-antisense-oligonucleotides-in-human-mrna-sequences
#5
Tokuyuki Yoshida, Yuki Naito, Kiyomi Sasaki, Eriko Uchida, Yoji Sato, Mikihiko Naito, Toru Kawanishi, Satoshi Obika, Takao Inoue
Antisense oligonucleotide (ASO) therapeutics are single-stranded oligonucleotides which bind to RNA through sequence-specific Watson-Crick base pairings. A unique mechanism of toxicity for ASOs is hybridization-dependent off-target effects that can potentially occur due to the binding of ASOs to complementary regions of unintended RNAs. To reduce the off-target effects of ASOs, it would be useful to know the approximate number of complementary regions of ASOs, or off-target candidate sites of ASOs, of a given oligonucleotide length and complementarity with their target RNAs...
April 18, 2018: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/29666977/candidate-genes-of-flavonoid-biosynthesis-in-selaginella-bryopteris-l-baker-identified-by-rna-seq
#6
Ravi S Singh, Ravi Kesari, Ujjwal Kumar, Vikash Kumar Jha, Anjani Kumar, Tribhuwan Kumar, Awadhesh K Pal, Prabhash K Singh
In the present study, de novo transcriptome analysis of Selaginella bryopteris in frond and root was performed to understand the regulation of flavonoid (FL) biosynthesis. High-quality data of 5.84 and 5.86 Gb was generated for frond and root, respectively, that assembled into 94,713 and 81,567 transcripts. A total of 87,471 and 73,395 unigenes were obtained from frond and root, respectively. A total of 41,267 and 31,048 CDS of frond and root, respectively, were annotated by BLASTX, which showed maximum hits against S...
April 18, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29666912/magnetic-bead-capture-dna-glucose-loaded-nanoliposomes-for-amplifying-the-glucometer-signal-in-the-rapid-screening-of-hepatitis-c-virus-rna
#7
Haijian Tu, Kun Lin, Yongzhi Lun, Liuming Yu
A digital detection strategy based on a portable personal glucometer (PGM) was developed for the simple, rapid, and sensitive detection of hepatitis C virus (HCV) RNA, involving the release of glucose-loaded nanoliposomes due to coupling-site-specific cleavage by the endonuclease BamHI. The glucose-loaded nanoliposomes were synthesized using a reversed-phase evaporation method and provided an amplified signal at the PGM in the presence of HCV RNA. Initially, a 21-mer oligonucleotide complementary to HCV RNA was covalently conjugated to a magnetic bead through the amino group at the 5' end of the oligonucleotide, and then bound to a glucose-loaded liposome by typical carbodiimide coupling at its 3' end...
April 17, 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29666883/snp-based-pool-genotyping-and-haplotype-analysis-accelerate-fine-mapping-of-the-wheat-genomic-region-containing-stripe-rust-resistance-gene-yr26
#8
Jianhui Wu, Qingdong Zeng, Qilin Wang, Shengjie Liu, Shizhou Yu, Jingmei Mu, Shuo Huang, Hanan Sela, Assaf Distelfeld, Lili Huang, Dejun Han, Zhensheng Kang
NGS-assisted super pooling emerging as powerful tool to accelerate gene mapping and haplotype association analysis within target region uncovering specific linkage SNPs or alleles for marker-assisted gene pyramiding. Conventional gene mapping methods to identify genes associated with important agronomic traits require significant amounts of financial support and time. Here, a single nucleotide polymorphism (SNP)-based mapping approach, RNA-Seq and SNP array assisted super pooling analysis, was used for rapid mining of a candidate genomic region for stripe rust resistance gene Yr26 that has been widely used in wheat breeding programs in China...
April 17, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29666766/mirnaome-expression-profiles-in-the-gonads-of-adult-melopsittacus-undulatus
#9
Lan Jiang, Qingqing Wang, Jue Yu, Vinita Gowda, Gabriel Johnson, Jianke Yang, Xianzhao Kan, Xiaojun Yang
The budgerigar ( Melopsittacus undulatus ) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals...
2018: PeerJ
https://www.readbyqxmd.com/read/29666464/an-adolescence-onset-male-leukoencephalopathy-with-remarkable-cerebellar-atrophy-and-novel-compound-heterozygous-aars2-gene-mutations-a-case-report
#10
Qing Dong, Ling Long, Yan-Yu Chang, Yan-Jun Lin, Mei Liu, Zheng-Qi Lu
Mutations in the mitochondrial alanyl-transfer (t)RNA synthetase 2 (AARS2; OMIM 612035) have been linked to leukoencephalopathy recently. Until now, there have been only 13 cases reported in the literature. Hence, the clinical and genetic characteristics of this disease are not fully understood. Here, we reported an adolescence-onset male leukoencephalopathy patient characterized by progressive limb tremor at the age of 17 years. He had no signs of a cardiomyopathy. Magnetic resonance imaging scanning demonstrated severe cerebellar atrophy and white matter abnormalities involving descending tracts...
April 17, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29666403/intact-interleukin-10-receptor-signaling-protects-from-hippocampal-damage-elicited-by-experimental-neurotropic-virus-infection-of-sjl-mice
#11
Ann-Kathrin Uhde, Malgorzata Ciurkiewicz, Vanessa Herder, Muhammad Akram Khan, Niko Hensel, Peter Claus, Michael Beckstette, René Teich, Stefan Floess, Wolfgang Baumgärtner, Klaus Jung, Jochen Huehn, Andreas Beineke
Theiler's murine encephalomyelitis virus (TMEV) infection represents an experimental mouse model to study hippocampal damage induced by neurotropic viruses. IL-10 is a pleiotropic cytokine with profound anti-inflammatory properties, which critically controls immune homeostasis. In order to analyze IL-10R signaling following virus-induced polioencephalitis, SJL mice were intracerebrally infected with TMEV. RNA-based next generation sequencing revealed an up-regulation of Il10, Il10rα and further genes involved in IL-10 downstream signaling, including Jak1, Socs3 and Stat3 in the brain upon infection...
April 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29666243/-o-6-methylguanine-induced-transcriptional-mutagenesis-reduces-p53-tumor-suppressor-function
#12
Monika Ezerskyte, João A Paredes, Stefano Malvezzi, John A Burns, Geoffrey P Margison, Magnus Olsson, David A Scicchitano, Kristian Dreij
Altered protein function due to mutagenesis plays an important role in disease development. This is perhaps most evident in tumorigenesis and the associated loss or gain of function of tumor-suppressor genes and oncogenes. The extent to which lesion-induced transcriptional mutagenesis (TM) influences protein function and its contribution to the development of disease is not well understood. In this study, the impact of O 6 -methylguanine on the transcription fidelity of p53 and the subsequent effects on the protein's function as a regulator of cell death and cell-cycle arrest were examined in human cells...
April 17, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29666160/most-human-introns-are-recognized-via-multiple-and-tissue-specific-branchpoints
#13
Jose Mario Bello Pineda, Robert K Bradley
Although branchpoint recognition is an essential component of intron excision during the RNA splicing process, the branchpoint itself is frequently assumed to be a basal, rather than regulatory, sequence feature. However, this assumption has not been systematically tested due to the technical difficulty of identifying branchpoints and quantifying their usage. Here, we analyzed ∼1.31 trillion reads from 17,164 RNA sequencing data sets to demonstrate that almost all human introns contain multiple branchpoints...
April 17, 2018: Genes & Development
https://www.readbyqxmd.com/read/29666005/unexpected-favorable-outcome-in-a-patient-with-high-grade-b-cell-lymphoma-with-abnormalities-of-myc-bcl6-and-bcl2-loci
#14
Thomas Adams, Deborah Fuchs, Patricia K Shadoan, Laurel Johnstone, Branden M Lau, Lee McGhan, Faiz Anwer, Hussam Al-Kateb
High grade B-cell lymphoma (HGBCL) by WHO 2016 classification requires rearrangements of MYC and BCL2 and/or BCL6, practically covering the so called "double-hit" or "triple hit" lymphomas. We report a case of HGBCL "triple-hit" lymphoma in a 64-year old female. Cytogenetic and fluorescence in situ hybridization (FISH) studies revealed complex karyotype including rearrangement of MYC to a novel, non-IG partner on chromosome 18, and rearrangement of BCL2, BCL6 and IGH as well as ins(3)(q21q27...
April 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29665790/the-oncogenic-effects-of-hes1-on-salivary-adenoid-cystic-carcinoma-cell-growth-and-metastasis
#15
Xiao-Yu Huang, Rui-Huan Gan, Jian Xie, Lin She, Yong Zhao, Lin-Can Ding, Bo-Hua Su, Da-Li Zheng, You-Guang Lu
BACKGROUND: Our previous study demonstrated a close relationship between NOTCH signaling pathway and salivary adenoid cystic carcinoma (SACC). HES1 is a well-known target gene of NOTCH signaling pathway. The purpose of the present study was to further explore the molecular mechanism of HES1 in SACC. METHODS: Comparative transcriptome analyses by RNA-Sequencing (RNA-Seq) were employed to reveal NOTCH1 downstream gene in SACC cells. Immunohistochemical staining was used to detect the expression of HES1 in clinical samples...
April 17, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29665782/a-direct-regulatory-link-between-microrna-137-and-shank2-implications-for-neuropsychiatric-disorders
#16
Ana de Sena Cortabitarte, Simone Berkel, Flavia-Bianca Cristian, Christine Fischer, Gudrun A Rappold
BACKGROUND: Mutations in the SHANK genes, which encode postsynaptic scaffolding proteins, have been linked to a spectrum of neurodevelopmental disorders. The SHANK genes and the schizophrenia-associated microRNA-137 show convergence on several levels, as they are both expressed at the synapse, influence neuronal development, and have a strong link to neurodevelopmental and neuropsychiatric disorders like intellectual disability, autism, and schizophrenia. This compiled evidence raised the question if the SHANKs might be targets of miR-137...
April 17, 2018: Journal of Neurodevelopmental Disorders
https://www.readbyqxmd.com/read/29665451/tgf-%C3%AE-1-resulting-in-differential-microrna-expression-in-bovine-granulosa-cells
#17
Yefen Xu, Jiaqiang Niu, Guangying Xi, Xuezhi Niu, Yuheng Wang, Ming Guo, Qiangba Yangzong, Yilong Yao, Suolang Sizhu, Jianhui Tian
To explore the expression profile of the cellular miRNAs in bovine ovarian granulosa cells responding to transforming growth factor-β1 (TGF-β1), the effect of TGF-β1 on cell proliferation was firstly investigated by CCK-8 method and the results showed that there was a significant inhibitory effect on bovine granulosa cell proliferation treated with 5/10 ng/mL human recombinant TGF-β1 for 24 h compared to the control (P < 0.05). Then, we performed high-throughput sequencing of two small RNA libraries prepared from cultured bovine granulosa cells stimulated with or without 10 ng/mL human recombinant TGF-β1...
April 14, 2018: Gene
https://www.readbyqxmd.com/read/29665369/defective-rna-particles-derived-from-tomato-black-ring-virus-genome-interfere-with-the-replication-of-parental-virus
#18
Beata Hasiów-Jaroszewska, Julia Minicka, Aleksandra Zarzyńska-Nowak, Daria Budzyńska, Santiago F Elena
Tomato black ring virus (TBRV) is the only member of the Nepovirus genus that is known to form defective RNA particles (D RNAs) during replication. Here, de novo generation of D RNAs was observed during prolonged passages of TBRV isolates originated from Solanum lycopersicum and Lactuca sativa in Chenopodium quinoa plants. D RNAs of about 500 nt derived by a single deletion in the RNA1 molecule and contained a portion of the 5' untranslated region and viral replicase, and almost the entire 3' non-coding region...
April 14, 2018: Virus Research
https://www.readbyqxmd.com/read/29665239/fbxw7-regulates-a-mitochondrial-transcription-program-by-modulating-mitf
#19
Franco Abbate, Brateil Badal, Karen Mendelson, Iraz Toprak Aydin, Madhavika N Serasinghe, Ramiz Iqbal, Jarvier Mohammed, Alexander Solovyov, Benjamin D Greenbaum, Jerry E Chipuk, Julide Tok Celebi
FBXW7 is well characterized as a tumor suppressor in many human cancers including melanoma; however, the mechanisms of tumor suppressive function have not been fully elucidated. We leveraged two distinct RNA sequencing datasets: human melanoma cell lines (n=10) with control versus silenced FBXW7 and a cohort of human melanoma tumor samples (n=51) in order to define the transcriptomic fingerprint regulated by FBXW7. Here, we report that loss of FBXW7 enhances a mitochondrial gene transcriptional program that is dependent on MITF in human melanoma and confers poor patient outcomes...
April 17, 2018: Pigment Cell & Melanoma Research
https://www.readbyqxmd.com/read/29665235/genome-wide-identification-of-long-non-coding-rnas-suggests-a-potential-association-with-effector-gene-transcription-in-phytophthora-sojae
#20
Yang Wang, Wenwu Ye, Yuanchao Wang
Numerous long non-coding RNAs (lncRNAs) identified and characterized in mammals, plants, and fungi have been found to play critical regulatory roles in biological processes. However, little is known about the role of lncRNAs in oomycete plant pathogens, which cause devastating damage to the economy and ecosystems. We used strand-specific RNA sequencing (RNA-seq) to generate a computational pipeline to identify lncRNAs in Phytophthora sojae, a model oomycete plant pathogen. In total, 940 lncRNAs with 1,010 isoforms were identified from RNA-seq data obtained from four representative stages of P...
April 17, 2018: Molecular Plant Pathology
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