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https://www.readbyqxmd.com/read/29031089/17%C3%AE-estradiol-regulates-the-rna-binding-protein-nova1-which-then-regulates-the-alternative-splicing-of-estrogen-receptor-%C3%AE-in-the-aging-female-rat-brain
#1
Cody L Shults, Caitlin B Dingwall, Chun K Kim, Elena Pinceti, Yathindar S Rao, Toni R Pak
Alternative RNA splicing results in the translation of diverse protein products arising from a common nucleotide sequence. These alternative protein products are often functional and can have widely divergent actions from the canonical protein. Studies in humans and other vertebrate animals have demonstrated that alternative splicing events increase with advanced age, sometimes resulting in pathological consequences. Menopause represents a critical transition for women, where the beneficial effects of estrogens are no longer evident; therefore, factors underlying increased pathological conditions in women are confounded by the dual factors of aging and declining estrogens...
September 14, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/29031026/genome-wide-characterization-of-differential-transcript-usage-in-arabidopsis-thaliana
#2
Dries Vaneechoutte, April R Estrada, Ying-Chen Lin, Ann E Loraine, Klaas Vandepoele
Alternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express certain isoforms at a significantly higher level than others, but under specific conditions this expression dominance can change, resulting in a different set of dominant isoforms. These events of Differential Transcript Usage (DTU) have been observed for thousands of Arabidopsis thaliana, Zea mays and Vitis vinifera genes and have been linked to development and stress response...
October 14, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29029138/the-female-genital-tract-microbiome-is-associated-with-vaginal-antiretroviral-drug-concentrations-in-human-immunodeficiency-virus-infected-women-on-antiretroviral-therapy
#3
Renee Donahue Carlson, Anandi N Sheth, Timothy D Read, Michael B Frisch, C Christina Mehta, Amy Martin, Richard E Haaland, Anar S Patel, Chou-Pong Pau, Colleen S Kraft, Igho Ofotokun
Background: The female genital tract (FGT) microbiome may affect vaginal pH and other factors that influence drug movement into the vagina. We examined the relationship between the microbiome and antiretroviral concentrations in the FGT. Methods: Over one menstrual cycle, 20 human immunodeficiency virus (HIV)-infected women virologically suppressed on tenofovir (TFV) disoproxil fumarate/emtricitabine and ritonavir-boosted atazanavir (ATV) underwent serial paired cervicovaginal and plasma sampling for antiretroviral concentrations using high-performance liquid chromatography-tandem mass spectrometry...
October 5, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29029116/upregulation-of-irs1-enhances-igf1-response-in-y537s-and-d538g-esr1-mutant-breast-cancer-cells
#4
Zheqi Li, Kevin M Levine, Amir Bahreini, Peilu Wang, David Chu, Ben Ho Park, Steffi Oesterreich, Adrian V Lee
Increased evidence suggests that somatic mutations in the ligand binding domain of estrogen receptor (ERα/ESR1) are critical mediators of endocrine-resistant breast cancer progression. Insulin-like growth factor-1 (IGF1) is an essential regulator of breast development and tumorigenesis, and also has a role in endocrine resistance. A recent study showed enhanced crosstalk between IGF1 and ERα in ESR1 mutant cells, but detailed mechanisms are incompletely understood. Using genome-edited MCF-7 and T47D cell lines harboring Y537S and D538G ESR1 mutations, we characterized altered IGF1 signaling...
September 27, 2017: Endocrinology
https://www.readbyqxmd.com/read/29029115/whole-genome-next-generation-sequencing-to-study-within-host-evolution-of-chronic-norovirus-infection-among-immunocompromised-patients
#5
J van Beek, M de Graaf, S L Smits, C M E Schapendonk, G M G M Verjans, H Vennema, A A van der Eijk, M V T Phan, M L Cotten, M P G Koopmans
Background: The genus Norovirus comprises large genetic diversity and new GII.4 variants emerge every 2-3 years. It is unknown in which host these new variants originate. Here we study whether prolonged shedders within the immunocompromised population could be a reservoir for newly emerging strains. Methods: Faecal samples (n=65) from immunocompromised patients (n=16) were retrospectively selected. Isolated viral RNA was enriched by hybridization with a custom norovirus whole-genome RNA bait set and deep sequenced on the Illumina MiSeq platform...
September 27, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29029073/clinical-genetics-and-outcome-of-left-ventricular-non-compaction-cardiomyopathy
#6
Farbod Sedaghat-Hamedani, Jan Haas, Feng Zhu, Christian Geier, Elham Kayvanpour, Martin Liss, Alan Lai, Karen Frese, Regina Pribe-Wolferts, Ali Amr, Daniel Tian Li, Omid Shirvani Samani, Avisha Carstensen, Diana Martins Bordalo, Marion Müller, Christine Fischer, Jing Shao, Jing Wang, Ming Nie, Li Yuan, Sabine Haßfeld, Christine Schwartz, Min Zhou, Zihua Zhou, Yanwen Shu, Min Wang, Kai Huang, Qiutang Zeng, Longxian Cheng, Tobias Fehlmann, Philipp Ehlermann, Andreas Keller, Christoph Dieterich, Katrin Streckfuß-Bömeke, Yuhua Liao, Michael Gotthardt, Hugo A Katus, Benjamin Meder
Aims: In this study, we aimed to clinically and genetically characterize LVNC patients and investigate the prevalence of variants in known and novel LVNC disease genes. Introduction: Left ventricular non-compaction cardiomyopathy (LVNC) is an increasingly recognized cause of heart failure, arrhythmia, thromboembolism, and sudden cardiac death. We sought here to dissect its genetic causes, phenotypic presentation and outcome. Methods and results: In our registry with follow-up of in the median 61 months, we analysed 95 LVNC patients (68 unrelated index patients and 27 affected relatives; definite familial LVNC = 23...
October 6, 2017: European Heart Journal
https://www.readbyqxmd.com/read/29028984/a-bayesian-framework-for-the-inference-of-gene-regulatory-networks-from-time-and-pseudo-time-series-data
#7
M Sanchez-Castillo, D Blanco, I M Tienda-Luna, M C Carrion, Yufei Huang
Motivation: Molecular profiling techniques have evolved to single-cell assays, where dense molecular profiles are screened simultaneously for each cell in a population. High-throughput single-cell experiments from a heterogeneous population of cells can be experimentally and computationally sorted as a sequence of samples pseudo-temporally ordered samples. The analysis of these data sets, comprising a large number of samples, has the potential to uncover the dynamics of the underlying regulatory programmes...
September 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028926/structure-based-prediction-of-protein-peptide-binding-regions-using-random-forest
#8
Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang
Motivation: Protein-peptide interactions are one of the most important biological interactions and play crucial role in many diseases including cancer. Therefore, knowledge of these interactions provides invaluable insights into all cellular processes, functional mechanisms, and drug discovery. Protein-peptide interactions can be analyzed by studying the structures of protein-peptide complexes. However, only a small portion has known complex structures and experimental determination of protein-peptide interaction is costly and inefficient...
September 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028903/comparative-analysis-of-differential-gene-expression-tools-for-rna-sequencing-time-course-data
#9
Daniel Spies, Peter F Renz, Tobias A Beyer, Constance Ciaudo
RNA sequencing (RNA-seq) has become a standard procedure to investigate transcriptional changes between conditions and is routinely used in research and clinics. While standard differential expression (DE) analysis between two conditions has been extensively studied, and improved over the past decades, RNA-seq time course (TC) DE analysis algorithms are still in their early stages. In this study, we compare, for the first time, existing TC RNA-seq tools on an extensive simulation data set and validated the best performing tools on published data...
October 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29028866/global-and-targeted-approaches-to-single-cell-transcriptome-characterization
#10
Aleksandra A Kolodziejczyk, Tapio Lönnberg
Analysing transcriptomes of cell populations is a standard molecular biology approach to understand how cells function. Recent methodological development has allowed performing similar experiments on single cells. This has opened up the possibility to examine samples with limited cell number, such as cells of the early embryo, and to obtain an understanding of heterogeneity within populations such as blood cell types or neurons. There are two major approaches for single-cell transcriptome analysis: quantitative reverse transcription PCR (RT-qPCR) on a limited number of genes of interest, or more global approaches targeting entire transcriptomes using RNA sequencing...
September 25, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29028833/merkel-cell-polyomavirus-recruits-mycl-to-the-ep400-complex-to-promote-oncogenesis
#11
Jingwei Cheng, Donglim Esther Park, Christian Berrios, Elizabeth A White, Reety Arora, Rosa Yoon, Timothy Branigan, Tengfei Xiao, Thomas Westerling, Alexander Federation, Rhamy Zeid, Benjamin Strober, Selene K Swanson, Laurence Florens, James E Bradner, Myles Brown, Peter M Howley, Megha Padi, Michael P Washburn, James A DeCaprio
Merkel cell carcinoma (MCC) frequently contains integrated copies of Merkel cell polyomavirus DNA that express a truncated form of Large T antigen (LT) and an intact Small T antigen (ST). While LT binds RB and inactivates its tumor suppressor function, it is less clear how ST contributes to MCC tumorigenesis. Here we show that ST binds specifically to the MYC homolog MYCL (L-MYC) and recruits it to the 15-component EP400 histone acetyltransferase and chromatin remodeling complex. We performed a large-scale immunoprecipitation for ST and identified co-precipitating proteins by mass spectrometry...
October 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29028450/comparing-two-approaches-of-mir-34a-target-identification-biotinylated-mirna-pulldown-vs-mirna-overexpression
#12
Hassaan Mehboob Awan, Abdullah Shah, Farooq Rashid, Shuai Wei, Liang Chen, Ge Shan
microRNAs (miRNAs) are critical regulators of gene expression. For elucidating functional roles of miRNAs, it is critical to identify their direct targets. There are debates about whether pulldown of biotinylated miRNA mimics can be used to identify miRNA targets or not. Here we show that biotin-labelled miR-34a can be loaded to AGO2, and AGO2 immunoprecipitation can pulldown biotinylated miR-34a (Bio-miR pulldown). RNA-sequencing (RNA-seq) of the Bio-miR pulldown RNAs efficiently identified miR-34a mRNA targets, which could be verified with luciferase assays...
October 13, 2017: RNA Biology
https://www.readbyqxmd.com/read/29028334/dynamic-control-of-aptamer-ligand-activity-using-strand-displacement-reactions
#13
Jonathan Lloyd, Claire H Tran, Krishen Wadhwani, Christian Cuba Samaniego, Hari K K Subramanian, Elisa Franco
Nucleic acid aptamers are an expandable toolkit of sensors and regulators. To employ aptamer regulators within non-equilibrium molecular networks, the aptamer-ligand interactions should be tunable over time, so that functions within a given system can be activated or suppressed on demand. This is accomplished through complementary sequences to aptamers, which achieve programmable aptamer-ligand dissociation by displacing the aptamer from the ligand. We demonstrate the effectiveness of our simple approach on light-up aptamers as well as on aptamers inhibiting viral RNA polymerases, dynamically controlling the functionality of the aptamer-ligand complex...
October 13, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29028266/circpro-an-integrated-tool-for-the-identification-of-circrnas-with-protein-coding-potential
#14
Xianwen Meng, Qi Chen, Peijing Zhang, Ming Chen
Summary: Circular RNAs (circRNAs), a novel class of endogenous RNAs, are widespread in eukaryotic cells. Emerging roles in diverse biological processes suggest that circRNA is a promising key player in RNA world. Most circRNAs are generated through back-splicing of pre-mRNAs, forming a covalently closed loop structure with no 5' caps or 3' polyadenylated tails. In addition, most circRNAs were not associated with translating ribosomes, therefore, circRNAs were deemed to be noncoding. However, the latest research findings revealed that some circRNAs could generate proteins in vivo, which expands the landscape of transcriptome and proteome...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028182/hypothesis-rna-and-dna-viral-sequence-integration-into-the-mammalian-host-genome-supports-long-term-b-cell-and-t-cell-adaptive-immunity
#15
Julia L Hurwitz, Bart G Jones, Emmanuelle Charpentier, David L Woodland
Viral sequence integration into the mammalian genome has long been perceived as a health risk. In some cases, integration translates to chronic viral infection, and in other instances, oncogenic gene mutations occur. However, research also shows that animal cells can benefit from integrated viral sequences (e.g., to support host cell development or to silence foreign invaders). Here we propose that, comparable with the clustered regularly interspaced short palindromic repeats that provide bacteria with adaptive immunity against invasive bacteriophages, animal cells may co-opt integrated viral sequences to support immune memory...
October 13, 2017: Viral Immunology
https://www.readbyqxmd.com/read/29027980/the-plasticizer-bisphenol-a-perturbs-the-hepatic-epigenome-a-systems-level-analysis-of-the-mirnome
#16
Ludivine Renaud, Willian A da Silveira, E Starr Hazard, Jonathan Simpson, Silvia Falcinelli, Dongjun Chung, Oliana Carnevali, Gary Hardiman
Ubiquitous exposure to bisphenol A (BPA), an endocrine disruptor (ED), has raised concerns for both human and ecosystem health. Epigenetic factors, including microRNAs (miRNAs), are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops a disease that resembles human cancer. Using zebrafish as a systems toxicology model, we hypothesized that chronic BPA-exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development...
October 13, 2017: Genes
https://www.readbyqxmd.com/read/29027916/a-next-generation-sequencing-approach-uncovers-viral-transcripts-incorporated-in-poxvirus-virions
#17
Marica Grossegesse, Joerg Doellinger, Berit Haldemann, Lars Schaade, Andreas Nitsche
Transcripts are known to be incorporated in particles of DNA viruses belonging to the families of Herpesviridae and Mimiviridae, but the presence of transcripts in other DNA viruses, such as poxviruses, has not been analyzed yet. Therefore, we first established a next-generation-sequencing (NGS)-based protocol, enabling the unbiased identification of transcripts in virus particles. Subsequently, we applied our protocol to analyze RNA in an emerging zoonotic member of the Poxviridae family, namely Cowpox virus...
October 13, 2017: Viruses
https://www.readbyqxmd.com/read/29027668/decreased-sorbitol-synthesis-leads-to-abnormal-stamen-development-and-reduced-pollen-tube-growth-via-an-myb-transcription-factor-mdmyb39l-in-apple-malus-domestica
#18
Dong Meng, Mingyang He, Yang Bai, Hongxia Xu, Abhaya M Dandekar, Zhangjun Fei, Lailiang Cheng
Sugars produced by photosynthesis not only fuel plant growth and development, but may also act as signals to regulate plant growth and development. This work focuses on the role of sorbitol, a sugar alcohol, in flower development and pollen tube growth of apple (Malus domestica). Transgenic 'Greensleeves' apple trees with decreased sorbitol synthesis had abnormal stamen development, a decreased pollen germination rate and reduced pollen tube growth, which were all closely related to lower sorbitol concentrations in stamens...
October 13, 2017: New Phytologist
https://www.readbyqxmd.com/read/29027592/a-novel-citrus-viroid-found-in-australia-tentatively-named-citrus-viroid-vii
#19
G A Chambers, N J Donovan, S Bodaghi, S M Jelinek, G Vidalakis
A novel citrus viroid was discovered in a non-symptomatic Lisbon lemon (Citrus x limon L. Burm.f.) tree in New South Wales, Australia. Bioindexing, molecular detection and characterization involving sequencing combined with in silico analysis for the identification of the viroid-RNA hallmark properties of transmissibility and autonomous replication as well as specific sequence and structural motifs suggest that this viroid is a member of a new species in the genus Apscaviroid, family Pospiviroidae, which we have tentatively named "citrus viroid VII" (CVd-VII)...
October 13, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29026999/identification-of-a-novel-vitivirus-from-grapevines-in-new-zealand
#20
Arnaud G Blouin, Sandi Keenan, Kathryn R Napier, Roberto A Barrero, Robin M MacDiarmid
We report a sequence of a novel vitivirus from Vitis vinifera obtained using two high-throughput sequencing (HTS) strategies on RNA. The initial discovery from small-RNA sequencing was confirmed by HTS of the total RNA and Sanger sequencing. The new virus has a genome structure similar to the one reported for other vitiviruses, with five open reading frames (ORFs) coding for the conserved domains described for members of that genus. Phylogenetic analysis of the complete genome sequence confirmed its affiliation to the genus Vitivirus, with the closest described viruses being grapevine virus E (GVE) and Agave tequilana leaf virus (ATLV)...
October 12, 2017: Archives of Virology
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