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https://www.readbyqxmd.com/read/28102265/chemical-and-structural-effects-of-base-modifications-in-messenger-rna
#1
Emily M Harcourt, Anna M Kietrys, Eric T Kool
A growing number of nucleobase modifications in messenger RNA have been revealed through advances in detection and RNA sequencing. Although some of the biochemical pathways that involve modified bases have been identified, research into the world of RNA modification - the epitranscriptome - is still in an early phase. A variety of chemical tools are being used to characterize base modifications, and the structural effects of known base modifications on RNA pairing, thermodynamics and folding are being determined in relation to their putative biological roles...
January 18, 2017: Nature
https://www.readbyqxmd.com/read/28100610/the-measles-virus-receptor-slamf1-can-mediate-particle-endocytosis
#2
Daniel Gonçalves-Carneiro, Jane A McKeating, Dalan Bailey
: The signalling lymphocyte activation molecule F1 (SLAMF1) is both a microbial sensor and entry receptor for Measles virus (MeV). Herein, we describe a new role for SLAMF1 to mediate MeV endocytosis that is in contrast with the alternative, and generally accepted, model that MeV genome enters cells only after fusion at the cell surface. We demonstrated that MeV engagement of SLAMF1 induces dramatic but transient morphological changes, most prominently in the formation of membrane blebs, which were shown to co-localise with incoming viral particles, and rearrangement of the actin cytoskeleton in infected cells...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28096075/hpprna-a-snakemake-based-handy-parameter-free-pipeline-for-rna-seq-analysis-of-numerous-samples
#3
Dapeng Wang
RNA-Seq technology has been gradually becoming a routine approach for characterizing the properties of transcriptome in terms of organisms, cell types and conditions and consequently a big burden has been put on the facet of data analysis, which calls for an easy-to-learn workflow to cope with the increased demands from a large number of laboratories across the world. We report a one-in-all solution called hppRNA, composed of four scenarios such as pre-mapping, core-workflow, post-mapping and sequence variation detection, written by a series of individual Perl and R scripts, counting on well-established and preinstalled software, irrespective of single-end or paired-end, unstranded or stranded sequencing method...
January 17, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28095772/empirical-assessment-of-analysis-workflows-for-differential-expression-analysis-of-human-samples-using-rna-seq
#4
Claire R Williams, Alyssa Baccarella, Jay Z Parrish, Charles C Kim
BACKGROUND: RNA-Seq has supplanted microarrays as the preferred method of transcriptome-wide identification of differentially expressed genes. However, RNA-Seq analysis is still rapidly evolving, with a large number of tools available for each of the three major processing steps: read alignment, expression modeling, and identification of differentially expressed genes. Although some studies have benchmarked these tools against gold standard gene expression sets, few have evaluated their performance in concert with one another...
January 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28094554/impact-of-phytochemicals-and-dietary-patterns-on-epigenome-and-cancer
#5
Wissam Zam, Aziz Khadour
Cancer remains one of the leading causes of death around the world. Initially it is recognized as a genetic disease, but now it is known to involve epigenetic abnormalities along with genetic alterations. Epigenetics refers to heritable changes that are not encoded in the DNA sequence itself, but play an important role in the control of gene expression. It includes changes in DNA methylation, histone modifications, and RNA interference. Although it is heritable, environmental factors such as diet could directly influence epigenetic mechanisms in humans...
January 17, 2017: Nutrition and Cancer
https://www.readbyqxmd.com/read/28091672/a-rapid-way-to-discover-nonstandard-macrocyclic-peptide-modulators-of-drug-targets
#6
Toby Passioura, Hiroaki Suga
Studies of the fundamental nature of RNA catalysis and the potential mechanism of a shift from the "RNA world" to proteinaceous life lead us to identify a set of ribozymes (flexizymes) capable of promiscuous tRNA acylation. Whilst theoretically and mechanistically interesting in their own right, flexizymes have turned out to have immense practical value for the simple synthesis of tRNAs acylated with unusual amino acids, which in turn can be used for the ribosomal synthesis of peptides containing non-canonical residues...
January 16, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#7
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081189/global-gene-expression-analysis-of-cross-protected-phenotype-of-pectobacterium-atrosepticum
#8
Vladimir Gorshkov, Stanford Kwenda, Olga Petrova, Elena Osipova, Yuri Gogolev, Lucy N Moleleki
The ability to adapt to adverse conditions permits many bacterial species to be virtually ubiquitous and survive in a variety of ecological niches. This ability is of particular importance for many plant pathogenic bacteria that should be able to exist, except for their host plants, in different environments e.g. soil, water, insect-vectors etc. Under some of these conditions, bacteria encounter absence of nutrients and persist, acquiring new properties related to resistance to a variety of stress factors (cross-protection)...
2017: PloS One
https://www.readbyqxmd.com/read/28070736/genome-wide-analysis-of-mirnas-and-tasi-rnas-in-zea-mays-in-response-to-phosphate-deficiency
#9
Saurabh Gupta, Manju Kumari, Himansu Kumar, Pritish Kumar Varadwaj
Globally important cereal crop maize provides important nutritions and starch in dietary foods. Low phosphate (LPi) availability in the soil frequently limits the maize quality and yield across the world. Small non-coding RNAs (Snc-RNAs) play crucial roles in growth and adaptation of plants to the environment. Snc-RNAs like microRNAs (miRs) and trans-acting small interfering RNAs (Tasi-Rs) play important functions in posttranscriptional regulation of gene expression, which controls plant development, reproduction, and biotic/abiotic stress responses...
January 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28069558/from-genome-to-proteome-looking-beyond-dna-and-rna-in-chronic-lymphocytic-leukemia
#10
Lauren A Thurgood, Karen M Lower, Bryone J Kuss, Tim K Chataway
Chronic lymphocytic leukemia (CLL) remains the most common leukemia in the Western world. Whilst its disease course is extremely heterogeneous (ranging from indolent to aggressive), current methods are unable to accurately predict the clinical journey of each patient. There is clearly a pressing need for both improved prognostication and treatment options for patients with this disease.Whilst molecular studies have analyzed both genetic mutations and gene expression profiles of these malignant B-cells, and as a result have shed light on the pathogenesis of CLL, proteomic studies have been largely overlooked to date...
January 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28068481/micrornas-and-periodontal-homeostasis
#11
X Luan, X Zhou, J Trombetta-eSilva, M Francis, A K Gaharwar, P Atsawasuwan, T G H Diekwisch
MicroRNAs (miRNAs) are a group of small RNAs that control gene expression in all aspects of eukaryotic life, primarily through RNA silencing mechanisms. The purpose of the present review is to introduce key miRNAs involved in periodontal homeostasis, summarize the mechanisms by which they affect downstream genes and tissues, and provide an introduction into the therapeutic potential of periodontal miRNAs. In general, miRNAs function synergistically to fine-tune the regulation of biological processes and to remove expression noise rather than by causing drastic changes in expression levels...
January 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28065965/lessons-from-a-seven-year-experience-of-paediatric-hiv-in-pakistan-a-single-centre-experience
#12
Ejaz Ahmed Khan
OBJECTIVE: To describe demographic, clinical and immunologic features of children with human immunodeficiency virus. METHODS: This descriptive study was conducted at the Shifa International Hospital, Islamabad, Pakistan, from 2005 to 2011, and comprised children with human immunodeficiency virus and acquired immune deficiency syndrome. Patients with detailed physical examination and appropriate investigations and those eligible for therapy were included. SPSS 21 was used for data analysis...
January 2017: JPMA. the Journal of the Pakistan Medical Association
https://www.readbyqxmd.com/read/28062212/inhibition-of-cd147-expression-promotes-chemosensitivity-in-hnscc-cells-by-deactivating-mapk-erk-signaling-pathway
#13
Chao Ma, Jianqi Wang, Longkun Fan, Yanjun Guo
Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers in the world. CD147, a transmembrane glycoprotein, has been reported to be correlated with cancer progression, metastasis, and chemoresistance in various cancers. In this study, we aimed to investigate the mechanism of CD147 in regulating drug resistance in HNSCC cells. qRT-PCR were used to evaluated the expression of CD147 in 57 HNSCC tumorous tissues and 2 cell lines. Increased expression of CD147 was found in most HNSCC samples, and the expression level of CD147 was correlated with multidrug resistance...
January 4, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28056753/role-of-ncrnas-in-development-diagnosis-and-treatment-of-human-cancer
#14
Francisco Esteban Nicolas Molina
BACKGROUND: Since the first reports of microRNAs and the advent of new sequencing technologies, a whole new world of regulatory non-conding RNAs (ncRNAs) has revolutionized our knowledge of the RNA dimension. Thousands of functional non-coding transcripts has been identified and grouped into new classes of ncRNAs attending to their origin and function. Despite of the fact that we have just started to study ncRNAs, it is now clear that these new regulatory actors play an important role in most of the regulated biological processes and in almost all species...
January 5, 2017: Recent Patents on Anti-cancer Drug Discovery
https://www.readbyqxmd.com/read/28053646/comparison-of-three-genomic-dna-extraction-methods-to-obtain-high-dna-quality-from-maize
#15
Amani Abdel-Latif, Gamal Osman
BACKGROUND: The world's top three cereals, based on their monetary value, are rice, wheat, and corn. In cereal crops, DNA extraction is difficult owing to rigid non-cellulose components in the cell wall of leaves and high starch and protein content in grains. The advanced techniques in molecular biology require pure and quick extraction of DNA. The majority of existing DNA extraction methods rely on long incubation and multiple precipitations or commercially available kits to produce contaminant-free high molecular weight DNA...
2017: Plant Methods
https://www.readbyqxmd.com/read/28050233/signaling-transcript-profile-of-the-asexual-intraerythrocytic-development-cycle-of-plasmodium-falciparum-induced-by-melatonin-and-camp
#16
Wânia Rezende Lima, Giulliana Tessarin-Almeida, Andrei Rozanski, Kleber S Parreira, Miriam S Moraes, David C Martins, Ronaldo F Hashimoto, Pedro A F Galante, Célia R S Garcia
According to the World Health Organization (WHO), Plasmodium falciparum is the deadliest parasite among all species. This parasite possesses the ability to sense molecules, including melatonin (MEL) and cAMP, and modulate its cell cycle accordingly. MEL synchronizes the development of this malaria parasite by activating several cascades, including the generation of the second messenger cAMP. Therefore, we performed RNA sequencing (RNA-Seq) analysis in P. falciparum erythrocytic stages (ring, trophozoite and schizont) treated with MEL and cAMP...
September 2016: Genes & Cancer
https://www.readbyqxmd.com/read/28049741/integrating-omics-and-alternative-splicing-reveals-insights-into-grape-response-to-high-temperature
#17
Jianfu Jiang, Xinna Liu, Guotian Liu, Chonghuai Liu, Shaohua Li, Lijun Wang
Heat stress is one of the primary abiotic stresses that limit crop production. Grape is a cultivated fruit with high economic value throughout the world, with its growth and development often influenced by high temperature. Alternative splicing (AS) is a widespread phenomenon increasing transcriptome and proteome diversity. We conducted high temperature treatments (35oC, 40oC and 45oC) on grapevines (Vitis vinifera), and assessed transcriptomic (especially AS) and proteomic changes in leaves. We found that nearly 70% of the genes were alternatively spliced under high temperature...
January 3, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28043628/expression-of-inflammatory-cytokine-and-inducible-nitric-oxide-synthase-genes-in-the-small-intestine-and-mesenteric-lymph-node-tissues-of-pauci-and-multibacillary-sheep-naturally-infected-with-mycobacterium-avium-ssp-paratuberculosis
#18
Ganesh G Sonawane, Bhupendra Nath Tripathi
OBJECTIVE/BACKGROUND: Paratuberculosis (Johne's disease) is a chronic infectious granulomatous enteritis, primarily affecting ruminants, and caused by Mycobacterium avium ssp. paratuberculosis (MAP). The disease is widely prevalent throughout the world with significant economic losses. MAP has also been implicated with human Crohn's disease. There exists a strong correlation between the immune response and development of various types of pathologies in ruminants. The polarization of the immune response, which is critical to clinical outcome of the paratuberculosis infection, is controlled by the differential expression of certain cytokines and inducible nitric oxide synthase (iNOS) in Johne's disease...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28043545/molecular-identification-of-mycobacterium-tuberculosis-complex-isolated-by-region-of-differentiation-rd-typing-from-tuberculosis-patients-in-khorasan-razavi
#19
Marjan Jalalimehr, Nader Mosavari, Saman Soleimanpour
OBJECTIVE/BACKGROUND: Tuberculosis has long been recognized as a zoonotic disease and remains one of the most life-threatening diseases worldwide. In spite of the successful treatment of this disease, the World Health Organization considers it as a disease with the highest priority in 1993, and it is now the second leading cause of infectious mortality. Since the identification of Mycobacterium tuberculosis complex species is of special importance, the aim of this study was to identify the species from the submitted mycobacterial isolates of tuberculars in Khorasan Razavi sent to the cell reference laboratory of Razavi Institute by the molecular method...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28030621/hiv-clinical-pathway-a-new-approach-to-combine-guidelines-and-sustainability-of-anti-retroviral-treatment-in-italy
#20
Davide Croce, Adriano Lazzarin, Giuliano Rizzardini, Nicola Gianotti, Francesca Scolari, Emanuela Foglia, Elisabetta Garagiola, Elena Ricci, Teresa Bini, Tiziana Quirino, Paolo Viganò, Tiziana Re, Antonella D'Arminio Monforte, Paolo Bonfanti
The present article describes the case study of a "real world" HIV practice within the debate concerning the strategic role of Clinical Governance (CG) tools in the management of a National Healthcare System's sustainability. The study aimed at assessing the impact of a Clinical Pathway (CP) implementation, required by the Regional Healthcare Service, in terms of effectiveness (virological and immunological conditions) and efficiency (economic resources absorption), from the budget holder perspective. Data derived from a multi-centre cohort of patients treated in 6 Hospitals that provided care to approximately 42% of the total HIV+ patients, in Lombardy Region, Italy...
2016: PloS One
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