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https://www.readbyqxmd.com/read/28231639/cell-cycle-rna-regulons-coordinating-early-lymphocyte-development
#1
REVIEW
Alison Galloway, Martin Turner
Lymphocytes undergo dynamic changes in gene expression as they develop from progenitor cells lacking antigen receptors, to mature cells that are prepared to mount immune responses. While transcription factors have established roles in lymphocyte development, they act in concert with post-transcriptional and post-translational regulators to determine the proteome. Furthermore, the post-transcriptional regulation of RNA regulons consisting of mRNAs whose protein products act cooperatively allows RNA binding proteins to exert their effects at multiple points in a pathway...
February 23, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28231404/express-or-repress-the-transcriptional-dilemma-of-damaged-chromatin
#2
Ilaria Capozzo, Fabio Iannelli, Sofia Francia, Fabrizio d'Adda di Fagagna
The fine modulation of transcriptional activity around DNA lesions is essential to carefully regulate the crosstalk between transcription, the DNA damage response, and DNA repair, particularly when the lesion occurs next to, or within, actively transcribed genes. Recently, several studies have been carried out to investigate how DNA lesions have an impact on local transcription, but the emerging model remains incomplete. Transcription of genes around damaged DNA is actively down-regulated by the DNA damage response through different mechanisms, which appear specific to the chromatin context, the type of DNA damage or its complexity...
February 23, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28231394/adaptive-divergence-in-wine-yeasts-and-their-wild-relatives-suggests-a-prominent-role-for-introgressions-and-rapid-evolution-at-non-coding-sites
#3
Pedro Almeida, Raquel Barbosa, Douda Bensasson, Paula Gonçalves, José Paulo Sampaio
In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. Since genomic data is available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives...
February 23, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28231341/identification-of-the-er-resident-e3-ubiquitin-ligase-rnf145-as-a-novel-lxr-regulated-gene
#4
Emma C L Cook, Jessica K Nelson, Vincenzo Sorrentino, Duco Koenis, Martina Moeton, Saskia Scheij, Roelof Ottenhoff, Boris Bleijlevens, Anke Loregger, Noam Zelcer
Cellular cholesterol metabolism is subject to tight regulation to maintain adequate levels of this central lipid molecule. Herein, the sterol-responsive Liver X Receptors (LXRs) play an important role owing to their ability to reduce cellular cholesterol load. In this context, identifying the full set of LXR-regulated genes will contribute to our understanding of their role in cholesterol metabolism. Using global transcriptional analysis we report here the identification of RNF145 as an LXR-regulated target gene...
2017: PloS One
https://www.readbyqxmd.com/read/28231333/molecular-mechanisms-of-cooperative-binding-of-transcription-factors-runx1-cbf%C3%AE-ets1-on-the-tcr%C3%AE-gene-enhancer
#5
Kota Kasahara, Masaaki Shiina, Ikuo Fukuda, Kazuhiro Ogata, Haruki Nakamura
Ets1 is an essential transcription factor (TF) for several important physiological processes, including cell proliferation and differentiation. Its recognition of the enhancer region of the TCRα gene is enhanced by the cooperative binding of the Runx1-CBFβ heterodimer, with the cancelation of phosphorylation-dependent autoinhibition. The detailed mechanism of this interesting cooperativity between Ets1 and the Runx1-CBFβ heterodimer is still largely unclear. Here, we investigated the molecular mechanisms of this cooperativity, by using molecular dynamics simulations...
2017: PloS One
https://www.readbyqxmd.com/read/28231303/greeklex-2-a-comprehensive-lexical-database-with-part-of-speech-syllabic-phonological-and-stress-information
#6
Antonios Kyparissiadis, Walter J B van Heuven, Nicola J Pitchford, Timothy Ledgeway
Databases containing lexical properties on any given orthography are crucial for psycholinguistic research. In the last ten years, a number of lexical databases have been developed for Greek. However, these lack important part-of-speech information. Furthermore, the need for alternative procedures for calculating syllabic measurements and stress information, as well as combination of several metrics to investigate linguistic properties of the Greek language are highlighted. To address these issues, we present a new extensive lexical database of Modern Greek (GreekLex 2) with part-of-speech information for each word and accurate syllabification and orthographic information predictive of stress, as well as several measurements of word similarity and phonetic information...
2017: PloS One
https://www.readbyqxmd.com/read/28231299/exploration-of-inhibitory-mechanisms-of-curcumin-in-lung-cancer-metastasis-using-a-mirna-transcription-factor-target-gene-network
#7
De-Min Jiao, Li Yan, Li-Shan Wang, Hui-Zhen Hu, Xia-Li Tang, Jun Chen, Jian Wang, You Li, Qing-Yong Chen
The present study was aimed to unravel the inhibitory mechanisms of curcumin for lung cancer metastasis via constructing a miRNA-transcription factor (TF)-target gene network. Differentially expressed miRNAs between human high-metastatic non-small cell lung cancer 95D cells treated with and without curcumin were identified using a TaqMan human miRNA array followed by real-time PCR, out of which, the top 6 miRNAs (miR-302b-3p, miR-335-5p, miR-338-3p, miR-34c-5p, miR-29c-3p and miR-34a-35p) with more verified target genes and TFs than other miRNAs as confirmed by a literature review were selected for further analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28231281/the-intron-in-centromeric-noncoding-rna-facilitates-rnai-mediated-formation-of-heterochromatin
#8
Masatoshi Mutazono, Misato Morita, Chihiro Tsukahara, Madoka Chinen, Shiori Nishioka, Tatsuhiro Yumikake, Kohei Dohke, Misuzu Sakamoto, Takashi Ideue, Jun-Ichi Nakayama, Kojiro Ishii, Tokio Tani
In fission yeast, the formation of centromeric heterochromatin is induced through the RNA interference (RNAi)-mediated pathway. Some pre-mRNA splicing mutants (prp) exhibit defective formation of centromeric heterochromatin, suggesting that splicing factors play roles in the formation of heterochromatin, or alternatively that the defect is caused by impaired splicing of pre-mRNAs encoding RNAi factors. Herein, we demonstrate that the splicing factor spPrp16p is enriched at the centromere, and associates with Cid12p (a factor in the RNAi pathway) and the intron-containing dg ncRNA...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28231263/uniformity-under-in-vitro-conditions-changes-in-the-phenotype-of-cancer-cell-lines-derived-from-different-medulloblastoma-subgroups
#9
Petr Chlapek, Karel Zitterbart, Leos Kren, Lenka Filipova, Jaroslav Sterba, Renata Veselska
Medulloblastoma comprises four main subgroups (WNT, SHH, Group 3 and Group 4) originally defined by transcriptional profiling. In primary medulloblastoma tissues, these groups are thought to be distinguishable using the immunohistochemical detection of β-catenin, filamin A, GAB1 and YAP1 protein markers. To investigate the utility of these markers for in vitro studies using medulloblastoma cell lines, immunoblotting and indirect immunofluorescence were employed for the detection of β-catenin, filamin A, GAB1 and YAP1 in both DAOY and D283 Med reference cell lines and the panel of six medulloblastoma cell lines derived in our laboratory from the primary tumor tissues of known molecular subgroups...
2017: PloS One
https://www.readbyqxmd.com/read/28231262/oleanolic-acid-induces-migration-in-mv1lu-and-mda-mb-231-epithelial-cells-involving-egf-receptor-and-map-kinases-activation
#10
Ángel Bernabé-García, David Armero-Barranco, Sergio Liarte, María Ruzafa-Martínez, Antonio Jesús Ramos-Morcillo, Francisco José Nicolás
During wound healing, skin function is restored by the action of several cell types that undergo differentiation, migration, proliferation and/or apoptosis. These dynamics are tightly regulated by the evolution of the extra cellular matrix (ECM) contents along the process. Pharmacologically active flavonoids have shown to exhibit useful physiological properties interesting in pathological states. Among them, oleanolic acid (OA), a pentacyclic triterpene, shows promising properties over wound healing, as increased cell migration in vitro and improved wound resolution in vivo...
2017: PloS One
https://www.readbyqxmd.com/read/28231257/targeted-sequencing-identifies-a-novel-sh2d1a-pathogenic-variant-in-a-chinese-family-carrier-screening-and-prenatal-genetic-testing
#11
Jun-Yu Zhang, Song-Chang Chen, Yi-Yao Chen, Shu-Yuan Li, Lan-Lan Zhang, Ying-Hua Shen, Chun-Xin Chang, Yu-Qian Xiang, He-Feng Huang, Chen-Ming Xu
X-linked lymphoproliferative disease type 1 (XLP1) is a rare primary immunodeficiency characterized by a clinical triad consisting of severe EBV-induced hemophagocytic lymphohistiocytosis, B-cell lymphoma, and dysgammaglobulinemia. Mutations in SH2D1A gene have been revealed as the cause of XLP1. In this study, a pregnant woman with recurrence history of birthing immunodeficiency was screened for pathogenic variant because the proband sample was unavailable. We aimed to clarify the genetic diagnosis and provide prenatal testing for the family...
2017: PloS One
https://www.readbyqxmd.com/read/28231234/notes-from-the-field-francisella-tularensis-type-b-infection-from-a-fish-hook-injury-minnesota-2016
#12
Tory Whitten, Jenna Bjork, Dave Neitzel, Kirk Smith, Maureen Sullivan, Joni Scheftel
On June 27, 2016, the Minnesota Department of Health (MDH) Public Health Laboratory (PHL) was notified of a suspected Francisella tularensis isolate cultured at a hospital laboratory. The isolate was confirmed as F. tularensis type B at MDH PHL by reverse transcription-polymerase chain reaction, culture, and direct fluorescent antibody testing. Francisella tularensis subspecies tularensis (type A) and holarctica (type B) bacteria are the causative agents of tularemia.
February 24, 2017: MMWR. Morbidity and Mortality Weekly Report
https://www.readbyqxmd.com/read/28231055/the-role-of-extracellular-vesicle-micrornas-in-cancer-biology
#13
Ryou-U Takahashi, Marta Prieto-Vila, Ai Hironaka, Takahiro Ochiya
MicroRNAs (miRNAs) constitute a large family of small, approximately 20-22 nucleotide non-coding RNAs that regulate the expression of target genes, mainly at the post-transcriptional level. Multiple studies report that miRNAs are involved in homeostatic maintenance and that aberrant expression of miRNAs is often observed in various types of diseases, including cancer. In cancer biology, miRNAs exert functional roles in tumor initiation, drug resistance, and metastasis. MiRNAs are also secreted through small vesicles called exosomes, which are endosome-derived vesicles derived from various cell types including immune and tumor cells...
February 23, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28231034/upscaling-of-hips-cell-derived-neurons-for-high-throughput-screening
#14
Stefanie Traub, Heiko Stahl, Holger Rosenbrock, Eric Simon, Ralf Heilker
The advent of human-induced pluripotent stem (hiPS) cell-derived neurons promised to provide better model cells for drug discovery in the context of the central nervous system. This work demonstrates both the upscaling of cellular expansion and the acceleration of neuronal differentiation to accommodate the immense material needs of a high-throughput screening (HTS) approach. Using GRowth factor-driven expansion and INhibition of NotCH (GRINCH) during maturation, the derived cells are here referred to as GRINCH neurons...
March 2017: SLAS Discov
https://www.readbyqxmd.com/read/28231019/pro-inflammatory-cytokines-impair-vitamin-d-induced-host-defense-in-cultured-airway-epithelial-cells
#15
Jasmijn A Schrumpf, Gimano D Amatngalim, Joris B Veldkamp, Renate M Verhoosel, Dennis K Ninaber, Soledad R Ordonez, Anne M van der Does, Henk P Haagsman, Pieter S Hiemstra
Vitamin D is a regulator of host defense against infections and induces expression of the antimicrobial peptide hCAP18/LL-37. Vitamin D deficiency is associated with chronic inflammatory lung diseases and respiratory infections. However, it is incompletely understood if and how (chronic) airway inflammation affects vitamin D metabolism and action. We hypothesized that long-term exposure of primary bronchial epithelial cells (PBEC) to pro-inflammatory cytokines alters their vitamin D metabolism, antibacterial activity and expression of hCAP18/LL-37...
February 23, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28230975/tuning-of-recombinant-protein-expression-in-escherichia-coli-by-manipulating-transcription-translation-initiation-rates-and-incorporation-of-non-canonical-amino-acids
#16
Orr Schlesinger, Yonatan Chemla, Mathias Heltberg, Eden Ozer, Ryan Marshall, Vincent Noireaux, Mogens Hogh Jensen, Lital Alfonta
Protein synthesis in cells has been thoroughly investigated and characterized over the past 60 years. However, some fundamental issues remain unresolved, including the reasons for genetic code redundancy and codon bias. In this study, we changed the kinetics of the E. coli transcription and translation processes by mutating the promoter and ribosome binding domains and by using genetic code expansion. The results expose a counterintuitive phenomenon, whereby an increase in the initiation rates of transcription and translation lead to a decrease in protein expression...
February 23, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28230862/inactivation-of-lsd1-triggers-senescence-in-trophoblast-stem-cells-by-induction-of-sirt4
#17
Josefina Castex, Dominica Willmann, Toufike Kanouni, Laura Arrigoni, Yan Li, Marcel Friedrich, Michael Schleicher, Simon Wöhrle, Mark Pearson, Norbert Kraut, Michaël Méret, Thomas Manke, Eric Metzger, Roland Schüle, Thomas Günther
Coordination of energy metabolism is essential for homeostasis of stem cells, whereas an imbalance in energy homeostasis causes disease and accelerated aging. Here we show that deletion or enzymatic inactivation of lysine-specific demethylase 1 (Lsd1) triggers senescence in trophoblast stem cells (TSCs). Genome-wide transcriptional profiling of TSCs following Lsd1 inhibition shows gene set enrichment of aging and metabolic pathways. Consistently, global metabolomic and phenotypic analyses disclose an unbalanced redox status, decreased glutamine anaplerosis and mitochondrial function...
February 23, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28230860/carma2sh-and-ulk2-control-pathogen-associated-molecular-patterns-recognition-in-human-keratinocytes-psoriasis-linked-carma2sh-mutants-escape-ulk2-censorship
#18
Ivan Scudiero, Pellegrino Mazzone, Luca E D'Andrea, Angela Ferravante, Tiziana Zotti, Gianluca Telesio, Gabriele De Rubis, Carla Reale, Maddalena Pizzulo, Shanmugakonar Muralitharan, Pasquale Vito, Romania Stilo
The molecular complexes formed by specific members of the family of CARMA proteins, the CARD domain-containing adapter molecule BCL10 and MALT1 (CBM complex) represent a central hub in regulating activation of the pleiotropic transcription factor NF-κB. Recently, missense mutations in CARMA2sh have been shown to cause psoriasis in a dominant manner and with high penetrancy. Here, we demonstrate that in human keratinocytes CARMA2sh plays an essential role in the signal transduction pathway that connects pathogen-associated molecular patterns recognition to NF-κB activation...
February 23, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28230855/simvastatin-induced-cell-cycle-arrest-through-inhibition-of-stat3-skp2-axis-and-activation-of-ampk-to-promote-p27-and-p21-accumulation-in-hepatocellular-carcinoma-cells
#19
Sin-Ting Wang, Hsiu J Ho, Jaw-Town Lin, Jeng-Jer Shieh, Chun-Ying Wu
Hepatocellular carcinoma (HCC) is characterized by a poor prognosis and is one of the leading causes of cancer-related death worldwide. Simvastatin, an HMG-CoA reductase inhibitor, which decreases cholesterol synthesis by inhibiting mevalonate pathways and is widely used to treat cardiovascular diseases. Simvastatin exhibits anticancer effects against several malignancies. However, the molecular mechanisms underlying the anticancer effects of simvastatin on HCC are still not well understood. In this study, we demonstrated simvastatin-induced G0/G1 arrest by inducing p21 and p27 accumulation in HepG2 and Hep3B cells...
February 23, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28230854/opposite-effects-of-hdac5-and-p300-on-mrtf-a-related-neuronal-apoptosis-during-ischemia-reperfusion-injury-in-rats
#20
Na Li, Qiong Yuan, Xiao-Lu Cao, Ying Zhang, Zhen-Li Min, Shi-Qiang Xu, Zhi-Jun Yu, Jing Cheng, Chunxiang Zhang, Xia-Min Hu
Our recent study has revealed that the myocardin-related transcription factor-A (MRTF-A) is involved in the apoptosis of cortical neurons induced by ischemia/reperfusion (I/R). Histone deacetylase 5 (HDAC5) and histone acetyltransferase p300 (P300) are two well-known regulators for transcription factors; however, their roles in MRTF-A-related effect on neuronal injuries during I/R are still unclear. In this study, in a model rat cerebral I/R injury via middle cerebral artery occlusion and reperfusion, we found that the expression and activity of HDAC5 was upregulated, whereas p300 and MRTF-A were downregulated both in expression and activity during I/R...
February 23, 2017: Cell Death & Disease
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