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https://www.readbyqxmd.com/read/29771354/methylation-guide-rna-evolution-in-archaea-structure-function-and-genomic-organization-of-110-c-d-box-srna-families-across-six-pyrobaculum-species
#1
Lauren M Lui, Andrew V Uzilov, David L Bernick, Andrea Corredor, Todd M Lowe, Patrick P Dennis
Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29755289/decoding-the-emerging-patterns-exhibited-in-non-coding-rnas-characteristic-of-lung-cancer-with-regard-to-their-clinical-significance
#2
Laura Sonea, Mihail Buse, Diana Gulei, Anca Onaciu, Ioan Simon, Cornelia Braicu, Ioana Berindan-Neagoe
Lung cancer continues to be the leading topic concerning global mortality rate caused by can-cer; it needs to be further investigated to reduce these dramatic unfavorable statistic data. Non-coding RNAs (ncRNAs) have been shown to be important cellular regulatory factors and the alteration of their expression levels has become correlated to extensive number of pathologies. Specifically, their expres-sion profiles are correlated with development and progression of lung cancer, generating great interest for further investigation...
May 2018: Current Genomics
https://www.readbyqxmd.com/read/29706242/diagnostic-utility-of-automated-indirect-immunofluorescence-compared-to-manual-indirect-immunofluorescence-for-anti-nuclear-antibodies-in-patients-with-systemic-rheumatic-diseases-a-systematic-review-and-meta-analysis
#3
REVIEW
Jinmi Kim, Woonhyoung Lee, Geun-Tae Kim, Hyon-Suk Kim, Soyoung Ock, In-Soo Kim, Seri Jeong
OBJECTIVE: This study aimed to review and compare the analytical and clinical performance of automated indirect immunofluorescence (AIIF) and manual indirect immunofluorescence (MIIF) as anti-nuclear antibody screening assays for patients with systemic rheumatic diseases (SRDs), such as systemic lupus erythematosus (SLE) and systemic sclerosis (SSc). METHODS: A systematic literature search was performed in the Medline, Embase, Cochrane, Web of Science, and Scopus databases for studies published before August 2017...
March 27, 2018: Seminars in Arthritis and Rheumatism
https://www.readbyqxmd.com/read/29672536/development-of-a-quantitative-pachytene-chromosome-map-and-its-unification-with-somatic-chromosome-and-linkage-maps-of-rice-oryza-sativa-l
#4
Nobuko Ohmido, Aiko Iwata, Seiji Kato, Toshiyuki Wako, Kiichi Fukui
A quantitative pachytene chromosome map of rice (Oryza sativa L.) was developed using imaging methods. The map depicts not only distribution patterns of chromomeres specific to pachytene chromosomes, but also the higher order information of chromosomal structures, such as heterochromatin (condensed regions), euchromatin (decondensed regions), the primary constrictions (centromeres), and the secondary constriction (nucleolar organizing regions, NOR). These features were image analyzed and quantitatively mapped onto the map by Chromosome Image Analyzing System ver...
2018: PloS One
https://www.readbyqxmd.com/read/29529599/lncrna-snhg16-functions-as-an-oncogene-by-sponging-mir-4518-and-up-regulating-prmt5-expression-in-glioma
#5
Ye-Fen Lu, Xue-Li Cai, Zheng-Zheng Li, Jing Lv, Yi-An Xiang, Jian-Jun Chen, Wei-Jing Chen, Wei-Yan Sun, Xiu-Mei Liu, Jian-Bo Chen
BACKGROUND/AIMS: Long noncoding RNAs (lncRNAs) have recently emerged as novel and potentially promising therapeutic targets in various cancers. However, the expression pattern and biological function of lncRNAs in glioma remain largely elusive. In the present study, we investigated the functional role of an lncRNA, small nucleolar RNA host gene 16 (SNHG16), in glioma. METHODS: The expression levels of SNHG16 and miR-4518 were measured using qRT-PCR. The relationship between the levels of SNHG16 and clinicopathologic features were statically analyzed...
March 6, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29519741/hydralazine-associated-vasculitis-overlapping-features-of-drug-induced-lupus-and-vasculitis
#6
Bharat Kumar, Jennifer Strouse, Melissa Swee, Petar Lenert, Manish Suneja
INTRODUCTION: Hydralazine is an antihypertensive medication that has been associated with drug-induced lupus erythematosus (DIL) as well as ANCA-associated vasculitis (AAV). Although rare, early diagnosis is critical since drug cessation is the mainstay of therapy. This retrospective study aims to characterize the clinical, laboratory, and histopathologic features of this disease. METHODS: Once approval was obtained from the Institutional Review Board at the University of Iowa, all patients carrying a diagnosis of vasculitis (ICD9 code: 447...
January 12, 2018: Seminars in Arthritis and Rheumatism
https://www.readbyqxmd.com/read/29463581/a-novel-mechanism-for-activation-of-gli1-by-nuclear-smo-that-escapes-anti-smo-inhibitors
#7
Muhammad M Rahman, Allon Hazan, Joanne L Selway, Dimalee S Herath, Catherine A Harwood, Muhammad S Pirzado, Ravinder Atkar, David P Kelsell, Kenneth J Linton, Mike P Philpott, Graham W Neill
Small molecule inhibitors of the Hedgehog (HH) pathway receptor Smoothened (SMO) have been effective in treating some patients with basal cell carcinoma (BCC), where the HH pathway is often activated, but many patients are poorly responsive. In this study, we report the results of investigations on PTCH1 signalling in the HH pathway that suggest why most BCC patients respond poorly to SMO inhibitors. In immortalised human keratinocytes, PTCH1 silencing led to the generation of a compact, holoclone-like morphology with increased expression of SMO and the downstream HH pathway transcription factor GLI1...
February 20, 2018: Cancer Research
https://www.readbyqxmd.com/read/29444615/the-mysterious-polyamines-the-enigmatic-barr-body-and-lupus-comment-on-the-article-by-kim-et-al
#8
W Brooks
"Polyamine patterns in plasma of patients with systemic lupus erythematosus and fever" by Kim et al. provides insight into possible involvement of polyamines in systemic lupus erythematosus (SLE). The authors report decreases in N1-acetylspermidine, spermidine, spermine, and N1-acetylcadaverine and increased cadaverine in SLE. Polyamine involvement in many cellular processes and their unique characteristics (high charge, length, flexibility, and ubiquity) give polyamines importance in health and disease...
January 1, 2018: Lupus
https://www.readbyqxmd.com/read/29433919/gene-expression-dominance-in-allopolyploids-hypotheses-and-models
#9
REVIEW
Samuel Bottani, Nicolae Radu Zabet, Jonathan F Wendel, Reiner A Veitia
The classical example of nonadditive contributions of the two parents to allopolyploids is nucleolar dominance, which entails silencing of one parental set of ribosomal RNA genes. This has been observed for many other loci. The prevailing explanation for this genome-wide expression disparity is that the two merged genomes differ in their transposable element (TE) complement and in their level of TE-mediated repression of gene expression. Alternatively, and not exclusively, gene expression dominance may arise from mismatches between trans effectors and their targets...
May 2018: Trends in Plant Science
https://www.readbyqxmd.com/read/29405190/-the-characteristic-of-protein-biosynthesis-in-brain-neurons-with-chronic-alcohol-intoxication
#10
Yu E Morozov, P S Velenko
The objective of the present study was to evaluate the possibilities for the use of the changes in the AgNOR staining patterns in the neurons of the dorsal raphe nucleus (DRN) for the purposes of the medical differential diagnostics of the cases of death from chronic alcohol intoxication. We elucidated the characteristics of the activity of protein biosynthesis including the number and the area of the nucleoli in the nuclei of the neurons of the individuals who had died from chronic alcohol intoxication (n=20) in comparison with the subjects of the control group (n=13)...
2018: Sudebno-meditsinskaia Ekspertiza
https://www.readbyqxmd.com/read/29391709/quantitative-and-qualitative-assessment-of-argyrophilic-nucleolar-organizer-regions-in-normal-premalignant-and-malignant-oral-lesions
#11
Buddhdev P Khushbu, Monali Chalishazar, Hemant Kale, Malay Baranwal, Tapan Modi
Aim: The aim of the study was to assess the cell proliferation and biologic aggressiveness of the lesions by evaluating the significance of number and dispersal pattern of Argyrophillic Nucleolar organizing Regions (AgNORs) using silver colloid technique in normal mucosa, premalignant and malignant lesions. Settings and Design: In-vitro study, lab setting. Methods and Material: The study sample consisted of five groups each with a sample size of 10 and a control group...
September 2017: Journal of Oral and Maxillofacial Pathology: JOMFP
https://www.readbyqxmd.com/read/29368663/developmental-dynamics-of-gene-expression-and-alternative-polyadenylation-in-the-caenorhabditis-elegans-germline
#12
Sean M West, Desirea Mecenas, Michelle Gutwein, David Aristizábal-Corrales, Fabio Piano, Kristin C Gunsalus
BACKGROUND: The 3' untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produces multiple transcript isoforms for the same gene within and across different cell types. Using LITE-Seq, a new quantitative method to capture transcript 3' ends expressed in vivo, we have characterized sex- and cell type-specific transcriptome-wide changes in gene expression and 3'UTR diversity in Caenorhabditis elegans germline cells undergoing proliferation and differentiation...
January 24, 2018: Genome Biology
https://www.readbyqxmd.com/read/29365324/expression-profiling-of-snornas-in-normal-hematopoiesis-and-aml
#13
Wayne A Warner, David H Spencer, Maria Trissal, Brian S White, Nichole Helton, Timothy J Ley, Daniel C Link
Small nucleolar RNAs (snoRNAs) are noncoding RNAs that contribute to ribosome biogenesis and RNA splicing by modifying ribosomal RNA and spliceosome RNAs, respectively. We optimized a next-generation sequencing approach and a custom analysis pipeline to identify and quantify expression of snoRNAs in acute myeloid leukemia (AML) and normal hematopoietic cell populations. We show that snoRNAs are expressed in a lineage- and development-specific fashion during hematopoiesis. The most striking examples involve snoRNAs located in 2 imprinted loci, which are highly expressed in hematopoietic progenitors and downregulated during myeloid differentiation...
January 23, 2018: Blood Advances
https://www.readbyqxmd.com/read/29300972/a-recurrent-de-novo-missense-mutation-in-ubtf-causes-developmental-neuroregression
#14
Camilo Toro, Roderick T Hori, May Christine V Malicdan, Cynthia J Tifft, Amy Goldstein, William A Gahl, David R Adams, Fauni Harper, Lynne A Wolfe, Jianfeng Xiao, Mohammad M Khan, Jun Tian, Kevin A Hope, Lawrence T Reiter, Michel G Tremblay, Tom Moss, Alexis L Franks, Chris Balak, Mark S LeDoux
UBTF (upstream binding transcription factor) exists as two isoforms; UBTF1 regulates rRNA transcription by RNA polymerase 1, whereas UBTF2 regulates mRNA transcription by RNA polymerase 2. Herein, we describe 4 patients with very similar patterns of neuroregression due to recurrent de novo mutations in UBTF (GRCh37/hg19, NC_000017.10: g.42290219C > T, NM_014233.3: c.628G > A) resulting in the same amino acid change in both UBTF1 and UBTF2 (p.Glu210Lys [p.E210K]). Disease onset in our cohort was at 2...
February 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29221119/analysis-of-npm1-splice-variants-reveals-differential-expression-patterns-of-prognostic-value-in-acute-myeloid-leukemia
#15
Malgorzata Zajac, Anna Dolnik, Grazyna Stasiak, Joanna Zaleska, Michal Kielbus, Jakub Czapinski, Matthias Schunn, Stephany C Correa, Eliza Glodkowska-Mrowka, Reddy Chakkarappan Sundaram, Olga Jankowska-Lecka, Richard F Schlenk, Hartmut Döhner, Konstanze Döhner, Andrzej Stepulak, Lars Bullinger, Krzysztof Giannopoulos
Mutations of the nucleophosmin-1 ( NPM1 ) gene in cytogenetically normal (CN) acute myeloid leukemia (AML) identify a group of patients with more favorable prognosis. NPM1 encodes three main alternatively spliced isoforms R1(B23.1), R2(B23.2), and R3(B23.3). The expression of splice variants R1, R2 and R3 were higher in AML patients compared to normal cells of healthy volunteers (HVs), although RNA-seq analysis revealed enhanced R2 expression also in less differentiated cells of HVs as well as in AML cells...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29172398/the-evaluation-of-cellular-immune-function-in-elderly-patients-with-systemic-lupus-erythematosus
#16
Kun Men, Yu Chen, Jingwei Zhang, Dianjun Wei
Background/Aims: To evaluate cellular immune function in systemic lupus erythematosus (SLE) patients over 60 years old, the association between antinuclear antibody (ANA) titers and the ratio of CD4+ /CD8+ was analyzed in this study. The distribution of ANAs and extractable nuclear antibodies (ENAs) in a healthy elderly population was also investigated. Methods: Serum ANA titers were assayed by indirect immunofluorescence (IIF) and the CD4+ /CD8+ T-cell ratio was determined by flow cytometry in 76 SLE patients and 30 healthy control individuals...
November 29, 2017: Korean Journal of Internal Medicine
https://www.readbyqxmd.com/read/29169375/synaptic-configuration-of-quadrivalents-and-their-association-with-the-xy-bivalent-in-spermatocytes-of-robertsonian-heterozygotes-of-mus-domesticus
#17
Soledad Berríos, Raúl Fernández-Donoso, Eliana Ayarza
BACKGROUND: The nuclear architecture of meiotic prophase spermatocytes is based on higher-order patterns of spatial associations among chromosomal domains and consequently is prone to modification by chromosomal rearrangements. We have shown that nuclear architecture is modified in spermatocytes of Robertsonian (Rb) homozygotes of Mus domesticus. In this study we analyse the synaptic configuration of the quadrivalents formed in the meiotic prophase of spermatocytes of mice double heterozygotes for the dependent Rb chromosomes: Rbs 11...
November 23, 2017: Biological Research
https://www.readbyqxmd.com/read/29127023/interobserver-variation-among-pathologists-and-refinement-of-criteria-in-distinguishing-separate-primary-tumors-from-intrapulmonary-metastases-in-lung
#18
Andrew G Nicholson, Kathleen Torkko, Patrizia Viola, Edwina Duhig, Kim Geisinger, Alain C Borczuk, Kenzo Hiroshima, Ming S Tsao, Arne Warth, Sylvie Lantuejoul, Prudence A Russell, Erik Thunnissen, Alberto Marchevsky, Mari Mino-Kenudson, Mary Beth Beasley, Johan Botling, Sanja Dacic, Yasushi Yatabe, Masayuki Noguchi, William D Travis, Keith Kerr, Fred R Hirsch, Lucian R Chirieac, Ignacio I Wistuba, Andre Moreira, Jin-Haeng Chung, Teh Ying Chou, Lukas Bubendorf, Gang Chen, Giuseppe Pelosi, Claudia Poleri, Frank C Detterbeck, Wilbur A Franklin
Multiple tumor nodules are seen with increasing frequency in clinical practice. On the basis of the 2015 WHO classification of lung tumors, we assessed the reproducibility of the comprehensive histologic assessment to distinguish second primary lung cancers (SPLCs) from intrapulmonary metastases (IPMs), looking for the most distinctive histologic features. An international panel of lung pathologists reviewed a scanned sequential cohort of 126 tumors from 48 patients and recorded an agreed set of histologic features, including tumor typing and predominant pattern of adenocarcinoma, thereby opining whether the case was SPLC, IPM, or a combination thereof...
February 2018: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/29031033/an-arabidopsis-divergent-pumilio-protein-apum24-is-essential-for-embryogenesis-and-required-for-faithful-pre-rrna-processing
#19
Thiruvenkadam Shanmugam, Nazia Abbasi, Hyung-Sae Kim, Ho Bang Kim, Nam-Il Park, Guen Tae Park, Sung Aeong Oh, Soon Ki Park, Douglas G Muench, Yeonhee Choi, Youn-Il Park, Sang-Bong Choi
Pumilio RNA-binding proteins are largely involved in mRNA degradation and translation repression. However, a few evolutionarily divergent Pumilios are also responsible for proper pre-rRNA processing in human and yeast. Here, we describe an essential Arabidopsis nucleolar Pumilio, APUM24, that is expressed in tissues undergoing rapid proliferation and cell division. A T-DNA insertion for APUM24 did not affect the male and female gametogenesis, but instead resulted in a negative female gametophytic effect on zygotic cell division immediately after fertilization...
December 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28900032/nucleolar-and-spindle-associated-protein-1-nusap1-interacts-with-a-sumo-e3-ligase-complex-during-chromosome-segregation
#20
Christine A Mills, Aussie Suzuki, Anthony Arceci, Jin Yao Mo, Alex Duncan, Edward D Salmon, Michael J Emanuele
The mitotic spindle is composed of dynamic microtubules and associated proteins that together direct chromosome movement during mitosis. The spindle plays a vital role in accurate chromosome segregation fidelity and is a therapeutic target in cancer. Nevertheless, the molecular mechanisms by which many spindle-associated proteins function remains unknown. The<u>nu</u>cleolar and<u>s</u>pindle-<u>a</u>ssociated<u>p</u>rotein NUSAP1 is a microtubule-binding protein implicated in spindle stability and chromosome segregation...
October 20, 2017: Journal of Biological Chemistry
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