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https://www.readbyqxmd.com/read/29330293/differential-regulation-of-let-7-by-lin28b-isoform-specific-functions
#1
Rei Mizuno, Priya Chatterji, Sarah F Andres, Kathryn E Hamilton, Lauren Simon, Shawn W Foley, Arjun N Jeganathan, Brian D Gregory, Blair B Madison, Anil K Rustgi
The RNA binding protein LIN28B plays an important role in development, stem cell biology and tumorigenesis. LIN28B has two isoforms: the LIN28B-long and -short isoforms. Although studies have revealed the functions of the LIN28B-long isoform in tumorigenesis, the role of the LIN28B-short isoform remains unclear and represents a major gap in the field. The LIN28B-long and -short isoforms are expressed in a subset of human colorectal cancers (CRCs) and adjacent normal colonic mucosa, respectively. To elucidate the functional and mechanistic aspects of these isoforms, CRC cells (Caco-2 and LoVo) were generated to either express no LIN28B or the -short or -long isoform...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330289/brca1-through-its-e3-ligase-activity-regulates-the-transcription-factor-oct1-and-carbohydrate-metabolism
#2
Karina Vázquez-Arreguín, Jessica Maddox, Jinsuk Kang, Dongju Park, Reuben R Cano, Rachel E Factor, Thomas Ludwig, Dean Tantin
The tumor suppressor BRCA1 regulates the DNA damage response (DDR) and other processes that remain incompletely defined. Among these, BRCA1 heterodimerizes with BARD1 to ubiquitylate targets via its N-terminal E3 ligase activity. Here it is demonstrated that BRCA1 promotes oxidative metabolism by degrading Oct1 (POU2F1), a transcription factor with pro-glycolytic and tumorigenic effects. BRCA1 E3 ubiquitin ligase mutation skews cells towards a glycolytic metabolic profile while elevating Oct1 protein. CRISPR-mediated Oct1 deletion reverts the glycolytic phenotype...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29329594/modelling-the-structure-of-a-cerna-theoretical-bipartite-microrna-mrna-interaction-network-regulating-intestinal-epithelial-cellular-pathways-using-r-programming
#3
J M Robinson, W A Henderson
OBJECTIVE: We report a method using functional-molecular databases and network modelling to identify hypothetical mRNA-miRNA interaction networks regulating intestinal epithelial barrier function. The model forms a data-analysis component of our cell culture experiments, which produce RNA expression data from Nanostring Technologies nCounter® system. The epithelial tight-junction (TJ) and actin cytoskeleton interact as molecular components of the intestinal epithelial barrier. Upstream regulation of TJ-cytoskeleton interaction is effected by the Rac/Rock/Rho signaling pathway and other associated pathways which may be activated or suppressed by extracellular signaling from growth factors, hormones, and immune receptors...
January 12, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29329019/salidroside-influences-the-cellular-cross-talk-of-human-fetal-lung-diploid-fibroblasts-a-proteomic-approach
#4
Wenmin Xing, Wenyan Gao, Huili Su, Sanying Wang, Jing Zhang, Genxiang Mao, Jing Yan
Senescence is a complex multiple factor proces, which is still poorly understood. The purpose of this study was to find the proteome of cultured human fetal lung diploid fibroblasts (2BS) of different population doubling (PD), as well as the altered proteome induced by salidroside (SAL) in 2BS cells. Proteins were identified by two-dimensional electrophoresis (2-DE) combining matrix-assisted laser desorption/ionization-time and flight mass spectrometry (MAL DI-TOF/MS). As a result, we found 16 proteins with two-fold variations in senescent cells or after SAL treatment, some being reduced such as reticulocalbin-1, heat shock protein beta-6, elongation factor 1-delta, F-actin-capping protein subunit alpha-1, and chloride intracellular channel 1...
January 5, 2018: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/29327293/overexpression-of-spot-gene-in-coccoid-forms-of-clinical-helicobacter-pylori-isolates
#5
Farkhondeh Poursina, Jamshid Fagri, Nasrin Mirzaei, Hajieh Ghasemian Safaei
Helicobacter pylori (H. pylori) can convert to coccoid form in unfavorable conditions or as a result of antibiotic treatment. In order to adapt to harsh environments, H. pylori requires a stringent response which, encoded by the spoT gene, has a bifunctional enzyme possessing both (p)ppGpp synthetic and degrading activity. Our goal in this study was to compare spoT gene expression in spiral and induced coccoid forms of H. pylori with use of amoxicillin. First, clinical isolate coccoid forms were induced with amoxicillin; then, the viability test was analyzed by flow cytometer...
January 11, 2018: Folia Microbiologica
https://www.readbyqxmd.com/read/29327101/fundamentals-of-sirna-and-mirna-therapeutics-and-a-review-of-targeted-nanoparticle-delivery-systems-in-breast-cancer
#6
REVIEW
Tamkin Ahmadzada, Glen Reid, David R McKenzie
Gene silencing via RNA interference (RNAi) is rapidly evolving as a personalized approach to cancer treatment. The effector molecules-small interfering RNAs (siRNAs) and microRNAs (miRNAs)-can be used to silence or "switch off" specific cancer genes. Currently, the main barrier to implementing siRNA- and miRNA-based therapies in clinical practice is the lack of an effective delivery system that can protect the RNA molecules from nuclease degradation, deliver to them to tumor tissue, and release them into the cytoplasm of the target cancer cells, all without inducing adverse effects...
January 11, 2018: Biophysical Reviews
https://www.readbyqxmd.com/read/29325107/2-o-2-methoxyethyl-nucleosides-are-not-phosphorylated-or-incorporated-into-the-genome-of-human-lymphoblastoid-tk6-cells
#7
Amer F Saleh, Martin Bachman, Catherine C Priestley, Nigel J Gooderham, Patrik Andersson, Scott P Henry, Nick Edmunds, Mick D Fellows
Nucleoside analogues with 2'-modified sugar moieties are often used to improve the RNA target affinity and nuclease resistance of therapeutic oligonucleotides in preclinical and clinical development. Despite their enhanced nuclease resistance, oligonucleotides could slowly degrade releasing nucleoside analogues that have the potential to become phosphorylated and incorporated into cellular DNA and RNA. For the first time, the phosphorylation and DNA and RNA incorporation of 2'-O-(2-methoxyethyl) (2'-O-MOE) nucleoside analogues have been investigated...
January 9, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29324748/trans10-cis12-conjugated-linoleic-acid-inhibits-proliferation-and-migration-of-ovarian-cancer-cells-by-inducing-er-stress-autophagy-and-modulation-of-src
#8
Mian M K Shahzad, Mildred Felder, Kai Ludwig, Hannah R Van Galder, Matthew L Anderson, Jong Kim, Mark E Cook, Arvinder K Kapur, Manish S Patankar
The goal of this study was to investigate the anti-cancer effects of Trans10,cis12 conjugated linoleic acid (t10,c12 CLA). MTT assays and QCM™ chemotaxis 96-wells were used to test the effect of t10,c12 CLA on the proliferation and migration and invasion of cancer cells. qPCR and Western Blotting were used to determine the expression of specific factors. RNA sequencing was conducted using the Illumina platform and apoptosis was measured using a flow cytometry assay. t10,c12 CLA (IC50, 7 μM) inhibited proliferation of ovarian cancer cell lines SKOV-3 and A2780...
2018: PloS One
https://www.readbyqxmd.com/read/29322304/causative-genes-in-amyotrophic-lateral-sclerosis-and-protein-degradation-pathways-a-link-to-neurodegeneration
#9
REVIEW
C Maurel, A Dangoumau, S Marouillat, C Brulard, A Chami, R Hergesheimer, P Corcia, H Blasco, C R Andres, P Vourc'h
Amyotrophic lateral sclerosis (ALS) is a disease caused by the degeneration of motor neurons (MNs) leading to progressive muscle weakness and atrophy. Several molecular pathways have been implicated, such as glutamate-mediated excitotoxicity, defects in cytoskeletal dynamics and axonal transport, disruption of RNA metabolism, and impairments in proteostasis. ALS is associated with protein accumulation in the cytoplasm of cells undergoing neurodegeneration, which is a hallmark of the disease. In this review, we focus on mechanisms of proteostasis, particularly protein degradation, and discuss how they are related to the genetics of ALS...
January 10, 2018: Molecular Neurobiology
https://www.readbyqxmd.com/read/29321445/negative-regulation-of-b-cell-responses-and-self-tolerance-to-rna-related-lupus-self-antigen
#10
Takeshi Tsubata
The antibody response to RNA-related antigens such as Sm/RNP requires the endosomal RNA sensor TLR7, and this process is crucial in the development of systemic lupus erythematosus at least in animal models. The inhibitory B cell receptor CD72 is unique because it recognizes Sm/RNP and specifically inhibits the activation of Sm/RNP-reactive B cells by activating SH2-containing protein tyrosine phosphatase 1 (SHP-1). In the normal immune system, Sm/RNP-reactive B cells are tolerized by a unique mechanism that probably involves SHP-1...
2018: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/29321318/viperin-restricts-zika-virus-and-tick-borne-encephalitis-virus-replication-by-targeting-ns3-for-proteasomal-degradation
#11
Christakis Panayiotou, Richard Lindqvist, Chaitanya Kurhade, Kirstin Vonderstein, Jenny Pasto, Karin Edlund, Arunkumar S Upadhyay, Anna K Överby
Flaviviruses are arthropod-borne viruses that constitute a major global health problem, with millions of human infections annually. Their pathogenesis ranges from mild illness to severe manifestations such as hemorrhagic fever and fatal encephalitis. Type I interferons (IFNs) are induced in response to viral infection, and stimulate the expression of interferon-stimulated genes (ISGs), including that encoding viperin (virus-inhibitory protein, endoplasmic reticulum-associated, IFN-inducible), which shows antiviral activity against a broad spectrum of viruses including several flaviviruses...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29320527/transcriptome-analysis-during-ripening-of-table-grape-berry-cv-thompson-seedless
#12
Iván Balic, Paula Vizoso, Ricardo Nilo-Poyanco, Dayan Sanhueza, Patricio Olmedo, Pablo Sepúlveda, Cesar Arriagada, Bruno G Defilippi, Claudio Meneses, Reinaldo Campos-Vargas
Ripening is one of the key processes associated with the development of major organoleptic characteristics of the fruit. This process has been extensively characterized in climacteric fruit, in contrast with non-climacteric fruit such as grape, where the process is less understood. With the aim of studying changes in gene expression during ripening of non-climacteric fruit, an Illumina based RNA-Seq transcriptome analysis was performed on four developmental stages, between veraison and harvest, on table grapes berries cv Thompson Seedless...
2018: PloS One
https://www.readbyqxmd.com/read/29319934/identification-and-functional-characterization-of-type-ii-toxin-antitoxin-systems-in-aggregatibacter-actinomycetemcomitans
#13
Blair Schneider, Whitney Weigel, Maryta Sztukowska, Donald R Demuth
Type II toxin/antitoxin (TA) systems contribute to the formation of persister cells and biofilm formation for many organisms. A. actinomycetemcomitans thrives in the complex oral microbial community subjected to continual environmental flux. Little is known regarding the presence and function of type II TA systems in this organism or their contribution to adaptation and persistence in the biofilm. We identified 11 TA systems that are conserved across all seven serotypes of A. actinomycetemcomitans and represent the RelBE, MazEF and HipAB families of type II TA systems...
January 10, 2018: Molecular Oral Microbiology
https://www.readbyqxmd.com/read/29315565/the-role-of-extracellular-matrix-metalloproteinase-inducer-glycosylation-in-regulating-matrix-metalloproteinases-in-periodontitis
#14
Z Zhang, X Yang, H Zhang, X Liu, S Pan, C Li
BACKGROUND AND OBJECTIVE: Extracellular matrix metalloproteinase inducer (EMMPRIN) is a transmembrane glycoprotein that may induce activation of matrix metalloproteinases (MMPs) and lead to the destruction of periodontal tissue. The level of EMMPRIN glycosylation might be involved in this process. This study aims to investigate the role of EMMPRIN glycosylation in regulating MMP-2 and MMP-9 during the progression of periodontitis. MATERIAL AND METHODS: Gingival tissues were collected from patients with chronic periodontitis and from patients undergoing crown-lengthening procedures (healthy gingival tissue)...
January 5, 2018: Journal of Periodontal Research
https://www.readbyqxmd.com/read/29315404/interplay-between-rnaseh2-and-mov10-controls-line-1-retrotransposition
#15
Jongsu Choi, Sung-Yeon Hwang, Kwangseog Ahn
Long interspersed nuclear element 1 is an autonomous non-long terminal repeat retrotransposon that comprises ∼17% of the human genome. Its spontaneous retrotransposition and the accumulation of heritable L1 insertions can potentially result in genome instability and sporadic disorders. Moloney leukemia virus 10 homolog (MOV10), a putative RNA helicase, has been implicated in inhibiting L1 replication, although its underlying mechanism of action remains obscure. Moreover, the physiological relevance of MOV10-mediated L1 regulation in human disease has not yet been examined...
January 5, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29314657/molecular-and-genetic-interactions-of-the-rna-degradation-machineries-in-firmicute-bacteria
#16
REVIEW
Peter Redder
Correct balance between bacterial RNA degradation and synthesis is essential for controlling expression level of all RNAs. The RNA polymerase, which performs the RNA synthesis, is highly conserved across the bacterial domain. However, this is surprisingly not the case for the RNA degradation machinery, which is composed of different subunits and performs different enzymatic reactions, depending on the organism. In Escherichia coli, the RNA decay is performed by the degradosome complex, which forms around the membrane-associated endoribonuclease RNase E, and is stable enough to be purified without falling apart...
January 5, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29311576/structural-analysis-of-mtexo-mitochondrial-rna-degradosome-reveals-tight-coupling-of-nuclease-and-helicase-components
#17
Michal Razew, Zbigniew Warkocki, Michal Taube, Adam Kolondra, Mariusz Czarnocki-Cieciura, Elzbieta Nowak, Karolina Labedzka-Dmoch, Aleksandra Kawinska, Jakub Piatkowski, Pawel Golik, Maciej Kozak, Andrzej Dziembowski, Marcin Nowotny
Nuclease and helicase activities play pivotal roles in various aspects of RNA processing and degradation. These two activities are often present in multi-subunit complexes from nucleic acid metabolism. In the mitochondrial exoribonuclease complex (mtEXO) both enzymatic activities are tightly coupled making it an excellent minimal system to study helicase-exoribonuclease coordination. mtEXO is composed of Dss1 3'-to-5' exoribonuclease and Suv3 helicase. It is the master regulator of mitochondrial gene expression in yeast...
January 8, 2018: Nature Communications
https://www.readbyqxmd.com/read/29311158/long-noncoding-rna-pancets-1-promotes-neuroblastoma-progression-through-hnrnpk-mediated-%C3%AE-catenin-stabilization
#18
Dan Li, Xiaojing Wang, Hong Mei, Erhu Fang, Lin Ye, Huajie Song, Feng Yang, Huanhuan Li, Kai Huang, Liduan Zheng, Qiangsong Tong
Long noncoding RNAs (lncRNAs) play essential roles in tumor progression. However, the functions of lncRNAs in the tumorigenesis and aggressiveness of neuroblastoma (NB) still remain to be determined. Here, we report the identification of lncRNA pancEts-1 as a novel driver of NB progression by using a public microarray dataset. LncRNA pancEts-1 promoted the growth, invasion, and metastasis of NB cells in vitro and in vivo. Mechanistically, pancEts-1 bound to hnRNPK to facilitate its physical interaction with β-catenin, while hnRNPK stabilized the β-catenin by inhibiting proteasome-mediated degradation, resulting in transcriptional alteration of target genes associated with NB progression...
January 8, 2018: Cancer Research
https://www.readbyqxmd.com/read/29310260/luminescent-quantum-dots-for-mirna-detection
#19
REVIEW
O A Goryacheva, P K Mishra, I Yu Goryacheva
MicroRNAs (miRNAs) are a class of small non-coding RNAs that are involved in nearly all developmental processes and human pathologies. MiRNAs are considered to be promising biomarkers, since their dysregulation correlates with the development and progress of many diseases. Short length, sequence homology among family members, susceptibility to degradation, and low abundance in total RNA samples make miRNA analysis a challenging task. Photoluminescent semiconductor nanoparticles (quantum dots, QDs) possess unique properties such as bright photoluminescence, photostability and narrow emission peaks, wide possibilities for surface modification and bioconjugation, which serve as the basis for the development of different analytical methods for variety of analytes...
March 1, 2018: Talanta
https://www.readbyqxmd.com/read/29305974/circular-rna-atp9b-a-competing-endogenous-rna-regulates-the-progression-of-osteoarthritis-by-targeting-mir-138-5p
#20
Zhi-Bin Zhou, Di Du, Gao-Xiang Huang, Aimin Chen, Lei Zhu
Osteoarthritis (OA) is the most common joint disease and is mainly characterized by degradation of the articular cartilage. Recently, circular RNAs (circRNAs), novel noncoding RNAs with different biological functions and pathological implications, have been reported to be closely associated with various diseases. Growing evidence indicates that circRNAs act as competing endogenous RNAs (ceRNAs) that bind with microRNAs (miRNAs) and regulate their downstream functions. Here, we identified a new circRNA, circRNA_Atp9b, and further investigated its function in OA using a well-established mouse chondrocyte model...
January 3, 2018: Gene
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