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https://www.readbyqxmd.com/read/29458070/the-epigenetic-alterations-of-endogenous-retroelements-in-aging
#1
REVIEW
Maurizio Cardelli
Endogenous retroelements, transposons that mobilize through RNA intermediates, include some of the most abundant repetitive sequences of the human genome, such as Alu and LINE-1 sequences, and human endogenous retroviruses. Recent discoveries demonstrate that these mobile genetic elements not only act as intragenomic parasites, but also exert regulatory roles in living cells. The risk of genomic instability represented by endogenous retroelements is normally counteracted by a series of epigenetic control mechanisms which include, among the most important, CpG DNA methylation...
February 16, 2018: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/29457977/single-molecule-centroid-localization-algorithm-improves-the-accuracy-of-fluorescence-binding-assays
#2
Boyang Hua, Yanbo Wang, Seongjin Park, Kyu Young Han, Digvijay Singh, Jin Hyun Kim, Wei Cheng, Taekjip Ha
Here, we demonstrate that the use of single-molecule centroid localization algorithm can improve the accuracy of fluorescence binding assays. Two major artifacts in this type of assays, i.e., non-specific binding events and optically overlapping receptors, can be detected and corrected during analysis. The effectiveness of our method was confirmed by measuring two weak biomolecular interactions, the interaction between the B1 domain of streptococcal protein G (pGB1) and immunoglobulin G (IgG), and the one between double-stranded DNA (dsDNA) and the Cas9-RNA complex with limited sequence matches...
February 19, 2018: Biochemistry
https://www.readbyqxmd.com/read/29456882/effects-of-osmolytes-and-macromolecular-crowders-on-stable-gaaa-tetraloops-and-their-preference-for-a-cg-closing-base-pair
#3
Kaethe N Leonard, Joshua M Blose
Osmolytes and macromolecular crowders have the potential to influence the stability of secondary structure motifs and alter preferences for conserved nucleic acid sequences in vivo . To further understand the cellular function of RNA we observed the effects of a model osmolyte, polyethylene glycol (PEG) 200, and a model macromolecular crowding agent, PEG 8000, on the GAAA tetraloop motif. GAAA tetraloops are conserved, stable tetraloops, and are critical participants in RNA tertiary structure. They also have a thermodynamic preference for a CG closing base pair...
2018: PeerJ
https://www.readbyqxmd.com/read/29456732/two-protein-coding-genes-act-as-a-novel-clinical-signature-to-predict-prognosis-in-patients-with-ovarian-serous-cystadenocarcinoma
#4
Jue Zhang, Meng Xu, Han Gao, Jin-Chen Guo, Yu-Lin Guo, Miao Zou, Xu-Feng Wu
Ovarian cancer is the seventh most common type of cancer and the eighth most common cause of cancer-associated mortality among women. A number of studies have hypothesized that the expression status of certain genes may be used to predict prognosis in ovarian cancer. In the present study, the RNA expression data from next-generation sequencing and the clinical information of 413 patients from The Cancer Genome Atlas dataset was downloaded to identify the association between gene-expression level and the survival time of the patients with ovarian serous cystadenocarcinoma...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29456684/capn3-dct-mlana-and-tyrp1-are-overexpressed-in-skin-of-vitiligo-vulgaris-mexican-patients
#5
Mauricio Salinas-Santander, Víctor Trevino, Eduardo De la Rosa-Moreno, Bárbara Verduzco-Garza, Celia N Sánchez-Domínguez, Cristina Cantú-Salinas, Jorge Ocampo-Garza, Armando Lagos-Rodríguez, Jorge Ocampo-Candiani, Rocio Ortiz-López
Vitiligo is a disorder causing skin depigmentation, in which several factors have been proposed for its pathogenesis: Environmental, genetic and biological aspects of melanocytes, even those of the surrounding keratinocytes. However, the lack of understanding of the mechanisms has complicated the task of predicting the development and progression. The present study used microarray analysis to characterize the transcriptional profile of skin from Vitiligo Vulgaris (VV) patients and the identified transcripts were validated using targeted high-throughput RNA sequencing in a broader set of patients...
March 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29456189/programmable-rna-cleavage-and-recognition-by-a-natural-crispr-cas9-system-from-neisseria-meningitidis
#6
Beth A Rousseau, Zhonggang Hou, Max J Gramelspacher, Yan Zhang
The microbial CRISPR systems enable adaptive defense against mobile elements and also provide formidable tools for genome engineering. The Cas9 proteins are type II CRISPR-associated, RNA-guided DNA endonucleases that identify double-stranded DNA targets by sequence complementarity and protospacer adjacent motif (PAM) recognition. Here we report that the type II-C CRISPR-Cas9 from Neisseria meningitidis (Nme) is capable of programmable, RNA-guided, site-specific cleavage and recognition of single-stranded RNA targets and that this ribonuclease activity is independent of the PAM sequence...
February 14, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29456158/autologous-ipsc-based-vaccines-elicit-anti-tumor-responses-in-vivo
#7
Nigel G Kooreman, Youngkyun Kim, Patricia E de Almeida, Vittavat Termglinchan, Sebastian Diecke, Ning-Yi Shao, Tzu-Tang Wei, Hyoju Yi, Devaveena Dey, Raman Nelakanti, Thomas P Brouwer, David T Paik, Idit Sagiv-Barfi, Arnold Han, Paul H A Quax, Jaap F Hamming, Ronald Levy, Mark M Davis, Joseph C Wu
Cancer cells and embryonic tissues share a number of cellular and molecular properties, suggesting that induced pluripotent stem cells (iPSCs) may be harnessed to elicit anti-tumor responses in cancer vaccines. RNA sequencing revealed that human and murine iPSCs express tumor-associated antigens, and we show here a proof of principle for using irradiated iPSCs in autologous anti-tumor vaccines. In a prophylactic setting, iPSC vaccines prevent tumor growth in syngeneic murine breast cancer, mesothelioma, and melanoma models...
February 8, 2018: Cell Stem Cell
https://www.readbyqxmd.com/read/29456100/the-coding-regions-of-germline-mrnas-confer-sensitivity-to-argonaute-regulation-in-c-elegans
#8
Meetu Seth, Masaki Shirayama, Wen Tang, En-Zhi Shen, Shikui Tu, Heng-Chi Lee, Zhiping Weng, Craig C Mello
Protein-coding genes undergo a wide array of regulatory interactions with factors that engage non-coding regions. Open reading frames (ORFs), in contrast, are thought to be constrained by coding function, precluding a major role in gene regulation. Here, we explore Piwi-interacting (pi)RNA-mediated transgene silencing in C. elegans and show that marked differences in the sensitivity to piRNA silencing map to the endogenous sequences within transgene ORFs. Artificially increasing piRNA targeting within the ORF of a resistant transgene can lead to a partial yet stable reduction in expression, revealing that piRNAs not only silence but can also "tune" gene expression...
February 14, 2018: Cell Reports
https://www.readbyqxmd.com/read/29454999/long-term-treatment-with-green-tea-polyphenols-modifies-the-gut-microbiome-of-female-sprague-dawley-rats
#9
Jincheng Wang, Lili Tang, Hongyuan Zhou, Jun Zhou, Travis C Glenn, Chwan-Li Shen, Jia-Sheng Wang
Green tea polyphenols (GTP) have been shown to exert a spectrum of health benefits to animals and humans. It is plausible that the beneficial effects of GTP are a result of its interaction with the gut microbiota. This study evaluated the effect of long-term treatment with GTP on the gut microbiota of experimental rats and the potential linkage between changes of the gut microbiota with the beneficial effects of GTP. Six-month-old Sprague-Dawley rats were randomly allocated into three dosing regimens (0, 0...
January 31, 2018: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/29454938/rare-cell-detection-by-single-cell-rna-sequencing-as-guided-by-single-molecule-rna-fish
#10
Eduardo Torre, Hannah Dueck, Sydney Shaffer, Janko Gospocic, Rohit Gupte, Roberto Bonasio, Junhyong Kim, John Murray, Arjun Raj
Although single-cell RNA sequencing can reliably detect large-scale transcriptional programs, it is unclear whether it accurately captures the behavior of individual genes, especially those that express only in rare cells. Here, we use single-molecule RNA fluorescence in situ hybridization as a gold standard to assess trade-offs in single-cell RNA-sequencing data for detecting rare cell expression variability. We quantified the gene expression distribution for 26 genes that range from ubiquitous to rarely expressed and found that the correspondence between estimates across platforms improved with both transcriptome coverage and increased number of cells analyzed...
February 7, 2018: Cell Systems
https://www.readbyqxmd.com/read/29454793/p300-acetyltransferase-mediates-stiffness-induced-activation-of-hepatic-stellate-cells-into-tumor-promoting-myofibroblasts
#11
Changwei Dou, Zhikui Liu, Kangsheng Tu, Hongbin Zhang, Chen Chen, Usman Yaqoob, Yuanguo Wang, Jialing Wen, Jan van Deursen, Delphine Sicard, Daniel Tschumperlin, Hongzhi Zou, Wei-Chien Huang, Raul Urrutia, Vijay H Shah, Ningling Kang
BACKGROUND & AIMS: Hepatic stellate cells (HSCs) contribute to desmoplasia and stiffness of liver metastases by differentiating into matrix-producing myofibroblasts. We investigated whether stiffness due to the presence of tumors increases activation of HSCs into myofibroblasts and their tumor-promoting effects, as well as the role of E1A binding protein p300 (EP300 or p300), a histone acetyltransferase that regulates transcription, in these processes. METHODS: HSCs were isolated from liver tissues of patients, mice in which the p300 gene was flanked by 2 loxP sites (p300F/F mice), and p300+/+ mice (controls)...
February 15, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29454792/clinical-and-genomic-correlates-of-neutrophil-reactive-oxygen-species-production-in-pediatric-patients-with-crohn-s-disease
#12
Lee A Denson, Ingrid Jurickova, Rebekah Karns, Kelly A Shaw, David J Cutler, David Okou, Anne Dodd, Kathryn Quinn, Kajari Mondal, Bruce J Aronow, Yael Haberman, Aaron Linn, Adam Price, Ramona Bezold, Kathleen Lake, Kimberly Jackson, Thomas D Walters, Anne Griffiths, Robert N Baldassano, Joshua D Noe, Jeffrey S Hyams, Wallace V Crandall, Barbara S Kirschner, Melvin B Heyman, Scott Snapper, Stephen L Guthery, Marla C Dubinsky, Neal S Leleiko, Anthony R Otley, Ramnik J Xavier, Christine Stevens, Mark J Daly, Michael E Zwick, Subra Kugathasan
BACKGROUND & AIMS: Individuals with monogenic disorders of phagocyte function develop chronic colitis that resembles Crohn's Disease (CD). We tested for associations between mutations in genes encoding NADPH oxidases, neutrophil function, and phenotypes of CD in pediatric patients. METHODS: We performed whole-exome sequence analysis to identify mutations in genes encoding NADPH oxidases (such as CYBA, CYBB, NCF1, NCF2, NCF4, RAC1, and RAC2) using DNA from 543 pediatric patients with inflammatory bowel diseases...
February 15, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29454790/increased-expression-of-the-long-non-coding-rna-linc01503-regulated-by-tp63-in-squamous-cell-carcinoma-and-effects-on-oncogenic-activities-of-cancer-cell-lines
#13
Jian-Jun Xie, Yan-Yi Jiang, Yuan Jiang, Chun-Quan Li, Lim-Mei Chee, Omer An, Anand Mayakonda, Ling-Wen Ding, Lin Long, Chun Sun, Le-Hang Lin, Li Chen, Jian-Yi Wu, Zhi-Yong Wu, Qi Cao, Wang-Kai Fang, Wei Yang, Stephen J Meltzer, Henry Yang, Melissa Fullwood, Li-Yan Xu, En-Min Li, De-Chen Lin, H Phillip Koeffler
BACKGROUND & AIMS: Long non-coding RNAs (lncRNAs) are expressed in tissue-specific pattern, but it is not clear how these are regulated. We aimed to identify squamous cell carcinoma (SCC)-specific lncRNAs and investigate mechanisms that control their expression and function. METHODS: We studied expression patterns and functions of 4 SCC-specific lncRNAs. We obtained 113 esophageal SCC (ESCC) and matched non-tumor esophageal tissues from a hospital in Shantou City, China, and performed quantitative reverse transcription PCR assays to measure expression levels of LINC01503...
February 15, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29454370/isolation-of-a-novel-rhabdovirus-from-an-insectivorous-bat-pipistrellus-kuhlii-in-italy
#14
Davide Lelli, Alice Prosperi, Ana Moreno, Chiara Chiapponi, Anna Maria Gibellini, Paola De Benedictis, Stefania Leopardi, Enrica Sozzi, Antonio Lavazza
BACKGROUND: Rhabdoviridae is one of the most ecologically diverse families of RNA viruses which can infect a wide range of vertebrates and invertebrates. Bats, among mammals, are pointed to harbor a significantly higher proportion of unknown or emerging viruses with zoonotic potential. Herein, we report the isolation of a novel rhabdovirus, detected in the framework of a virological survey on bats implemented in North Italy. METHODS: Virus isolation and identification were performed on samples of 635 bats by using cell cultures, negative staining electron microscopy and PCRs for different viruses...
February 17, 2018: Virology Journal
https://www.readbyqxmd.com/read/29454313/structrnafinder-an-automated-pipeline-and-web-server-for-rna-families-prediction
#15
Raúl Arias-Carrasco, Yessenia Vásquez-Morán, Helder I Nakaya, Vinicius Maracaja-Coutinho
BACKGROUND: The function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been developed to predict such structures or to use them to functionally annotate RNAs into RNA families. However, to fully perform this analysis, researchers should utilize multiple tools, which require the constant parsing and processing of several intermediate files. This makes the large-scale prediction and annotation of RNAs a daunting task even to researchers with good computational or bioinformatics skills...
February 17, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29454312/effects-of-a-wide-range-of-dietary-forage-to-concentrate-ratios-on-nutrient-utilization-and-hepatic-transcriptional-profiles-in-limit-fed-holstein-heifers
#16
Haitao Shi, Jun Zhang, Shengli Li, Shoukun Ji, Zhijun Cao, Hongtao Zhang, Yajing Wang
BACKGROUND: Improving the efficiency of animal production is a relentless pursuit of ruminant producers. Energy utilization and partition can be affected by dietary composition and nutrient availability. Furthermore, the liver is the central metabolic intersection in cattle. However, the specific metabolic changes in the liver under conditions of limit-feeding remain unclear and require further study. The present study aimed to elucidate the effects of a wide range of dietary forage:concentrate ratios (F:C) on energy utilization, and identify potential changes in molecular metabolism by analyzing hepatic transcriptional profiles...
February 17, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29454090/characterization-of-vasa-homolog-in-a-neotropical-catfish-jundi%C3%A3-rhamdia-quelen-molecular-cloning-and-expression-analysis-during-embryonic-and-larval-development
#17
Juliana M B Ricci, Emanuel R M Martinez, Arno J Butzge, Lucas B Doretto, Marcos A Oliveira, Robie Allan Bombardelli, Jan Bogerd, Rafael H Nóbrega
We have characterized the full-length vasa cDNA from Jundiá, Rhamdia quelen (Heptapteridae, Siluriformes). vasa encodes a member of the DEAD-box protein family of ATP-dependent RNA helicases. This protein is highly conserved among different organisms and its role is associated with RNA metabolism. In the majority of the investigated species, vasa is restricted to the germ cell lineage and its expression has been used to study germline development in many organisms, including fish. The deduced R. quelen vasa amino acid sequence displayed high similarity with Vasa protein sequences from other organisms, and did not cluster with PL10 or P68 DEAD-box protein subfamilies...
February 14, 2018: Gene
https://www.readbyqxmd.com/read/29453967/discovery-of-anti-viral-molecules-and-their-vital-functions-in-bombyx-mori
#18
REVIEW
Peng Lü, Ye Pan, Yanhua Yang, Feifei Zhu, Chengjun Li, Qin Yao, Keping Chen
The silkworm Bombyx mori (B. mori), a lepidopteran model organism, has become an important model for molecular biology researches with its genome completely sequenced. Silkworms confront different types of virus diseases, mainly including those caused by Bombyx mori nucleopolyhedrovirus (BmNPV), Bombyx mori densovirus type 1 (BmDNV-1), Bombyx mori bidesovirus (BmBDV) which was termed as Bombyx mori densovirus type 2 (BmDNV-2) or Bombyx mori parvo-like virus (BmPLV) before in sericulture. B. mori offers excellent models to study the molecular mechanisms of insect innate immune responses to viruses...
February 14, 2018: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/29453856/defective-rna-sensing-by-rig-i-in-severe-influenza-virus-infection
#19
Sofie Eg Jørgensen, Mette Christiansen, Laura Barrett Ryø, Hans Henrik Gad, Jakob Gjedsted, Peter Staeheli, Jacob Giehm Mikkelsen, Merete Storgaard, Rune Hartmann, Trine Hyrup Mogensen
Influenza virus infection causes worldwide seasonal epidemics. Although influenza usually is a mild disease, a minority of patients experience very severe fulminating disease courses. Previous studies have demonstrated a role for type I interferon (IFN) in antiviral responses during influenza. However, IFN regulatory factor (IRF)7 deficiency is so far the only genetic cause of severe influenza described in humans. In this study we present a patient with severe influenza A virus (IAV) H1N1 infection during the 2009 Swine Flu pandemic...
February 17, 2018: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/29453410/molecular-characterization-of-colorectal-adenomas-with-and-without-malignancy-reveals-distinguishing-genome-transcriptome-and-methylome-alterations
#20
Brooke R Druliner, Panwen Wang, Taejeong Bae, Saurabh Baheti, Seth Slettedahl, Douglas Mahoney, Nikolaos Vasmatzis, Hang Xu, Minsoo Kim, Matthew Bockol, Daniel O'Brien, Diane Grill, Nathaniel Warner, Miguel Munoz-Gomez, Kimberlee Kossick, Ruth Johnson, Mohamad Mouchli, Donna Felmlee-Devine, Jill Washechek-Aletto, Thomas Smyrk, Ann Oberg, Junwen Wang, Nicholas Chia, Alexej Abyzov, David Ahlquist, Lisa A Boardman
The majority of colorectal cancer (CRC) arises from precursor lesions known as polyps. The molecular determinants that distinguish benign from malignant polyps remain unclear. To molecularly characterize polyps, we utilized Cancer Adjacent Polyp (CAP) and Cancer Free Polyp (CFP) patients. CAPs had tissues from the residual polyp of origin and contiguous cancer; CFPs had polyp tissues matched to CAPs based on polyp size, histology and dysplasia. To determine whether molecular features distinguish CAPs and CFPs, we conducted Whole Genome Sequencing, RNA-seq, and RRBS on over 90 tissues from 31 patients...
February 16, 2018: Scientific Reports
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