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https://www.readbyqxmd.com/read/28806394/smggds-is-a-transient-nucleolar-protein-that-protects-cells-from-nucleolar-stress-and-promotes-the-cell-cycle-by-regulating-dream-complex-gene-expression
#1
P Gonyo, C Bergom, A C Brandt, S-W Tsaih, Y Sun, T M Bigley, E L Lorimer, S S Terhune, H Rui, M J Flister, R M Long, C L Williams
The chaperone protein and guanine nucleotide exchange factor SmgGDS (RAP1GDS1) is a key promoter of cancer cell proliferation and tumorigenesis. SmgGDS undergoes nucleocytoplasmic shuttling, suggesting that it has both cytoplasmic and nuclear functions that promote cancer. Previous studies indicate that SmgGDS binds cytoplasmic small GTPases and promotes their trafficking to the plasma membrane. In contrast, little is known about the functions of SmgGDS in the nucleus, or how these nuclear functions might benefit cancer cells...
August 14, 2017: Oncogene
https://www.readbyqxmd.com/read/28802576/atorvastatin-and-lovastatin-but-not-pravastatin-increased-cellular-complex-formation-between-pcsk9-and-the-ldl-receptor-in-human-hepatocyte-like-c3a-cells
#2
Quantil M Melendez, Catherine J Wooten, Dayami Lopez
Statins are the first-line treatment for hypercholesterolemic patients. Herein, the effects of three statins on complex formation between proprotein convertase subtilisin-kexin 9 (PCSK9) and the low density lipoprotein receptor (LDLR), a critical step for the PCSK9-dependent degradation of LDLR in the lysosome, were examined. Human hepatocyte-like C3A cells grown in control (containing 10% fetal bovine serum) or MITO+ (supplemented with BD™ MITO + serum extender) medium were also treated with atorvastatin (Atorv), lovastatin (Lov), or pravastatin (Prav) for 24 h...
August 9, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28801509/exosome-cofactor-hmtr4-competes-with-export-adaptor-alyref-to-ensure-balanced-nuclear-rna-pools-for-degradation-and-export
#3
Jing Fan, Bin Kuai, Guifen Wu, Xudong Wu, Binkai Chi, Lantian Wang, Ke Wang, Zhubing Shi, Heng Zhang, She Chen, Zhisong He, Siyuan Wang, Zhaocai Zhou, Guohui Li, Hong Cheng
The exosome is a key RNA machine that functions in the degradation of unwanted RNAs. Here, we found that significant fractions of precursors and mature forms of mRNAs and long noncoding RNAs are degraded by the nuclear exosome in normal human cells. Exosome-mediated degradation of these RNAs requires its cofactor hMTR4. Significantly, hMTR4 plays a key role in specifically recruiting the exosome to its targets. Furthermore, we provide several lines of evidence indicating that hMTR4 executes this role by directly competing with the mRNA export adaptor ALYREF for associating with ARS2, a component of the cap-binding complex (CBC), and this competition is critical for determining whether an RNA is degraded or exported to the cytoplasm...
August 11, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28800772/endurance-training-lowers-ribosome-density-despite-increasing-ribosome-biogenesis-markers-in-rodent-skeletal-muscle
#4
Matthew A Romero, C Brooks Mobley, Melissa A Linden, Grace Margaret-Eleanor Meers, Jeffrey S Martin, Kaelin C Young, R Scott Rector, Michael D Roberts
OBJECTIVE: The purpose of this study was to examine if: (a) high sugar/high fat Western diet (WD)-feeding affects skeletal muscle ribosome biogenesis markers in hyperphagic, diabetic-prone Otsuka Long-Evans Tokushima Fatty (OLETF) rats, and (b) 12 weeks of treadmill training rescued potential detriments that WD feeding exerted on these markers. METHODS: Eight week-old male OLETF rats were fed a low-fat control diet (O-CON, n = 10) or high/sucrose/cholesterol Western diet (WD)...
August 11, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28800614/optimization-of-recombinant-bacteria-expressing-dsrna-to-enhance-insecticidal-activity-against-a-lepidopteran-insect-spodoptera-exigua
#5
Mohammad Vatanparast, Yonggyun Kim
Double-stranded RNA (dsRNA) has been applied to control insect pests due to its induction of RNA interference (RNAi) of a specific target gene expression. However, developing dsRNA-based insecticidal agent has been a great challenge especially against lepidopteran insect pests due to variations in RNAi efficiency. The objective of this study was to screen genes of chymotrypsins (SeCHYs) essential for the survival of the beet armyworm, Spodoptera exigua, to construct insecticidal dsRNA. In addition, an optimal oral delivery method was developed using recombinant bacteria...
2017: PloS One
https://www.readbyqxmd.com/read/28798381/transcriptional-hallmarks-of-cancer-cell-lines-reveal-an-emerging-role-of-branched-chain-amino-acid-catabolism
#6
Ieva Antanavičiūtė, Valeryia Mikalayeva, Ieva Ceslevičienė, Gintarė Milašiūtė, Vytenis Arvydas Skeberdis, Sergio Bordel
A comparative analysis between cancer cell lines and healthy dividing cells was performed using data (289 microarrays and 50 RNA-seq samples) from 100 different cancer cell lines and 6 types of healthy stem cells. The analysis revealed two large-scale transcriptional events that characterize cancer cell lines. The first event was a large-scale up-regulation pattern associated to epithelial-mesenchymal transition, putatively driven by the interplay of the SP1 transcription factor and the canonical Wnt signaling pathway; the second event was the failure to overexpress a diverse set of genes coding membrane and extracellular proteins...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28795162/global-survey-of-mrna-levels-and-decay-rates-of-chlamydia-trachomatis-trachoma-and-lymphogranuloma-venereum-biovars
#7
Rita Ferreira, Vítor Borges, Maria José Borrego, João Paulo Gomes
Interpreting the intricate bacterial transcriptomics implies understanding the dynamic relationship established between de novo transcription and the degradation of transcripts. Here, we performed a comparative overview of gene expression levels and mRNA decay rates for different-biovar (trachoma and lymphogranuloma venereum) strains of the obligate intracellular bacterium Chlamydia trachomatis. By using RNA-sequencing to measure gene expression levels at mid developmental stage and mRNA decay rates upon rifampicin-based transcription blockage, we observed that: i) 60-70% of the top-50 expressed genes encode proteins with unknown function and proteins involved in "Translation, ribosomal structure and biogenesis" for all strains; ii) the expression ranking by genes' functional categories was in general concordant among different-biovar strains; iii) the median of the half-life time (t1/2) values of transcripts were 15-17 min, indicating that the degree of transcripts' stability seems to correlate with the bacterial intracellular life-style, as these values are considerably higher than the ones observed in other studies for facultative intracellular and free-living bacteria; iv) transcript decay rates were highly heterogeneous within each C...
July 2017: Heliyon
https://www.readbyqxmd.com/read/28793929/shifts-in-coastal-sediment-oxygenation-cause-pronounced-changes-in-microbial-community-composition-and-associated-metabolism
#8
Elias Broman, Johanna Sjöstedt, Jarone Pinhassi, Mark Dopson
BACKGROUND: A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability...
August 9, 2017: Microbiome
https://www.readbyqxmd.com/read/28793203/rna-extraction-from-decaying-wood-for-meta-transcriptomic-analyses
#9
Martino Adamo, Samuele Voyron, Mariangela Girlanda, Roland Marmeisse
Wood decomposition is a key step of the terrestrial carbon cycle and of economic importance. It is essentially a microbiological process performed by fungi and to an unknown extent by bacteria. To gain access to the genes expressed by the diverse microbial communities participating to wood decay we developed an RNA extraction protocol from this recalcitrant material rich in polysaccharides and phenolic compounds. This protocol was implemented on 22 wood samples representing as many tree species from 11 plant families in the Angiosperms and Gymnosperms...
August 9, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28792938/m-6-a-mrna-methylation-controls-t-cell-homeostasis-by-targeting-the-il-7-stat5-socs-pathways
#10
Hua-Bing Li, Jiyu Tong, Shu Zhu, Pedro J Batista, Erin E Duffy, Jun Zhao, Will Bailis, Guangchao Cao, Lina Kroehling, Yuanyuan Chen, Geng Wang, James P Broughton, Y Grace Chen, Yuval Kluger, Matthew D Simon, Howard Y Chang, Zhinan Yin, Richard A Flavell
N(6)-methyladenosine (m(6)A) is the most common and abundant messenger RNA modification, modulated by 'writers', 'erasers' and 'readers' of this mark. In vitro data have shown that m(6)A influences all fundamental aspects of mRNA metabolism, mainly mRNA stability, to determine stem cell fates. However, its in vivo physiological function in mammals and adult mammalian cells is still unknown. Here we show that the deletion of m(6)A 'writer' protein METTL3 in mouse T cells disrupts T cell homeostasis and differentiation...
August 9, 2017: Nature
https://www.readbyqxmd.com/read/28783563/stimulation-of-rna-polymerase-ii-ubiquitination-and-degradation-by-yeast-mrna-3-end-processing-factors-is-a-conserved-dna-damage-response-in-eukaryotes
#11
Jason N Kuehner, James W Kaufman, Claire Moore
The quality and retrieval of genetic information is imperative to the survival and reproduction of all living cells. Ultraviolet (UV) light induces lesions that obstruct DNA access during transcription, replication, and repair. Failure to remove UV-induced lesions can abrogate gene expression and cell division, resulting in permanent DNA mutations. To defend against UV damage, cells utilize transcription-coupled nucleotide excision repair (TC-NER) to quickly target lesions within active genes. In cases of long-term genotoxic stress, a slower alternative pathway promotes degradation of RNA Polymerase II (Pol II) to allow for global genomic nucleotide excision repair (GG-NER)...
July 23, 2017: DNA Repair
https://www.readbyqxmd.com/read/28783096/c-di-amp-an-essential-molecule-in-the-signaling-pathways-that-regulate-the-viability-and-virulence-of-gram-positive-bacteria
#12
REVIEW
Tazin Fahmi, Gary C Port, Kyu Hong Cho
Signal transduction pathways enable organisms to monitor their external environment and adjust gene regulation to appropriately modify their cellular processes. Second messenger nucleotides including cyclic adenosine monophosphate (c-AMP), cyclic guanosine monophosphate (c-GMP), cyclic di-guanosine monophosphate (c-di-GMP), and cyclic di-adenosine monophosphate (c-di-AMP) play key roles in many signal transduction pathways used by prokaryotes and/or eukaryotes. Among the various second messenger nucleotides molecules, c-di-AMP was discovered recently and has since been shown to be involved in cell growth, survival, and regulation of virulence, primarily within Gram-positive bacteria...
August 7, 2017: Genes
https://www.readbyqxmd.com/read/28782933/new-insights-into-antibiofilm-effect-of-a-nano-sized-zno-coating-against-the-pathogenic-methicillin-resistant-staphylococcus-aureus
#13
Marta M Alves, Ons Bouchami, Ana Tavares, Laura Córdoba, Catarina Ferreira Santos, Maria Miragaia, Maria de Fatima Montemor
ZnO nanoparticles (NPs) are arising as promising novel antibiotics towards device-related infections. The surface functionalization of Zn, a novel resorbable biomaterial, with ZnO NPs could present an effective solution to overcome such threat. In this sense, the antibacterial and antibiofilm activity of nano and micro-sized ZnO coatings was studied against clinically relevant bacteria - methicillin resistant Staphylococcus aureus (MRSA). The bacterial viability of planktonic and biofilm cells together with the corresponding biofilms structures revealed that only the nano-sized ZnO coating had an antibiofilm effect...
August 7, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28782251/hcv-plays-with-fire-and-yet-avoids-getting-burned-a-review-for-clinicians-on-processing-bodies-and-stress-granules
#14
Carlos Fernández-Carrillo, Gemma Pérez-Vilaró, Juana Díez, Sofía Pérez-Del-Pulgar
Over the last few years, many reports have defined several types of RNA cell granules composed of proteins and messenger RNA (mRNA) that regulate gene expression on a posttranscriptional level. Processing bodies (P-bodies) and stress granules (SGs) are among the best-known RNA granules, only detectable when they accumulate into very dynamic cytosolic foci. Recently, a tight association has been found between positive-stranded RNA viruses, including hepatitis C virus (HCV), and these granules. The present article offers a comprehensive review on the complex and paradoxical relationship between HCV, P-bodies and SGs from a translational perspective...
August 7, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28781236/structural-variation-of-type-i-f-crispr-rna-guided-dna-surveillance
#15
Patrick Pausch, Hanna Müller-Esparza, Daniel Gleditzsch, Florian Altegoer, Lennart Randau, Gert Bange
CRISPR-Cas systems are prokaryotic immune systems against invading nucleic acids. Type I CRISPR-Cas systems employ highly diverse, multi-subunit surveillance Cascade complexes that facilitate duplex formation between crRNA and complementary target DNA for R-loop formation, retention, and DNA degradation by the subsequently recruited nuclease Cas3. Typically, the large subunit recognizes bona fide targets through the PAM (protospacer adjacent motif), and the small subunit guides the non-target DNA strand. Here, we present the Apo- and target-DNA-bound structures of the I-Fv (type I-F variant) Cascade lacking the small and large subunits...
August 2, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28780758/investigation-of-metabolites-for-estimating-blood-deposition-time
#16
Karolina Lech, Fan Liu, Sarah K Davies, Katrin Ackermann, Joo Ern Ang, Benita Middleton, Victoria L Revell, Florence J Raynaud, Igor Hoveijn, Roelof A Hut, Debra J Skene, Manfred Kayser
Trace deposition timing reflects a novel concept in forensic molecular biology involving the use of rhythmic biomarkers for estimating the time within a 24-h day/night cycle a human biological sample was left at the crime scene, which in principle allows verifying a sample donor's alibi. Previously, we introduced two circadian hormones for trace deposition timing and recently demonstrated that messenger RNA (mRNA) biomarkers significantly improve time prediction accuracy. Here, we investigate the suitability of metabolites measured using a targeted metabolomics approach, for trace deposition timing...
August 5, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28777253/mir-30e-attenuates-isoproterenol-induced-cardiac-fibrosis-through-suppressing-snai1-tgf%C3%AE-signaling
#17
Zhang Wenqi, Chang Hong, Zhang Hexun, Zhang Lei
BACKGROUND: MicroRNAs (miRNAs) are a class of small RNA molecules that inhibit protein expression through either degradation of mRNA or interference with protein translation. Our previous work suggested an involvement of miR-30e in myocardial fibrosis; however, the exact role of miR-30e in the pathogenesis of cardiac fibrosis and the underlying mechanisms are not known. METHODS: Male Sprague Dawley rats were treated with isoproterenol to induce cardiac remodeling and fibrosis and treated with either miR-30e agomir (AG) or antagomir and respective controls...
August 4, 2017: Journal of Cardiovascular Pharmacology
https://www.readbyqxmd.com/read/28774263/evaluation-of-high-throughput-isomir-identification-tools-illuminating-the-early-isomirome-of-tribolium-castaneum
#18
Daniel Amsel, Andreas Vilcinskas, André Billion
BACKGROUND: MicroRNAs carry out post-transcriptional gene regulation in animals by binding to the 3' untranslated regions of mRNAs, causing their degradation or translational repression. MicroRNAs influence many biological functions, and dysregulation can therefore disrupt development or even cause death. High-throughput sequencing and the mining of animal small RNA data has shown that microRNA genes can yield differentially expressed isoforms, known as isomiRs. Such isoforms are particularly relevant during early development, and the extension or truncation of the 5' end can change the profile of mRNA targets compared to the original mature sequence...
August 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28772071/systemic-delivery-of-folate-peg-sirna-lipopolyplexes-with-enhanced-intracellular-stability-for-in-vivo-gene-silencing-in-leukemia
#19
Dian-Jang Lee, Eva Kessel, Taavi Lehto, Xueying Liu, Naoto Yoshinaga, Kärt Padari, Ying-Chen Chen, Susanne Kempter, Satoshi Uchida, Joachim O Rädler, Margus Pooga, Ming-Thau Sheu, Kazunori Kataoka, Ernst Wagner
Protection of small interfering RNA (siRNA) against degradation and targeted delivery across the plasma and endosomal membranes to the final site of RNA interference are major aims for the development of siRNA therapeutics. Targeting for folate receptor (FR)-expressing tumors, we optimized siRNA polyplexes by co-formulating a folate-PEG-oligoaminoamide (for surface shielding and targeting) with one of three lipo-oligoaminoamides (optionally tyrosine-modified, for optimizing stability and size) to generate ~ 100 nm targeted lipopolyplexes (TLPs), which self-stabilize by cysteine disulfide crosslinks...
August 3, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28771467/comprehensive-analysis-of-nucleocytoplasmic-dynamics-of-mrna-in-drosophila-cells
#20
Tao Chen, Bas van Steensel
Eukaryotic mRNAs undergo a cycle of transcription, nuclear export, and degradation. A major challenge is to obtain a global, quantitative view of these processes. Here we measured the genome-wide nucleocytoplasmic dynamics of mRNA in Drosophila cells by metabolic labeling in combination with cellular fractionation. By mathematical modeling of these data we determined rates of transcription, export and cytoplasmic decay for 5420 genes. We characterized these kinetic rates and investigated links with mRNA features, RNA-binding proteins (RBPs) and chromatin states...
August 3, 2017: PLoS Genetics
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