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RNA metabolism

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https://www.readbyqxmd.com/read/29161413/nrf2-regulates-endothelial-glycolysis-and-proliferation-with-mir-93-and-mediates-the-effects-of-oxidized-phospholipids-on-endothelial-activation
#1
Suvi M Kuosmanen, Emilia Kansanen, Minna U Kaikkonen, Virve Sihvola, Kati Pulkkinen, Henna-Kaisa Jyrkkänen, Pauli Tuoresmäki, Juha Hartikainen, Mikko Hippeläinen, Hannu Kokki, Pasi Tavi, Sami Heikkinen, Anna-Liisa Levonen
Phospholipids, such as 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (PAPC), are the major components of cell membranes. Their exposure to reactive oxygen species creates oxidized phospholipids, which predispose to the development of chronic inflammatory diseases and metabolic disorders through endothelial activation and dysfunction. Although the effects of oxidized PAPC (oxPAPC) on endothelial cells have been previously studied, the underlying molecular mechanisms evoking biological responses remain largely unknown...
November 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29160173/gene-delivery-to-joints-by-intra-articular-injection
#2
Christopher H Evans, Steven Craig Ghivizzani, Paul D Robbins
Most forms of arthritis are incurable, difficult to treat and a major cause of disability in western countries. Better local treatment of arthritis is impaired by the pharmacokinetics of the joint that make it very difficult to deliver drugs to joints at sustained, therapeutic concentrations. This is especially true of biologic drugs, such as proteins and RNA, many of which show great promise in pre-clinical studies. Gene transfer provides a strategy for overcoming this limitation. The basic concept is to deliver cDNAs encoding therapeutic products by direct intra-articular injection, leading to sustained, endogenous synthesis of the gene products within the joint...
November 21, 2017: Human Gene Therapy
https://www.readbyqxmd.com/read/29158985/coral-associated-viral-communities-show-high-levels-of-diversity-and-host-auxiliary-functions
#3
Karen D Weynberg, Patrick W Laffy, Elisha M Wood-Charlson, Dmitrij Turaev, Thomas Rattei, Nicole S Webster, Madeleine J H van Oppen
Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a diverse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the Caudovirales dominate across all species examined, and ssDNA viruses, notably the Microviridae, are also prevalent...
2017: PeerJ
https://www.readbyqxmd.com/read/29158786/fh535-inhibits-proliferation-and-motility-of-colon-cancer-cells-by-targeting-wnt-%C3%AE-catenin-signaling-pathway
#4
Yanyan Chen, Xianping Rao, Kangmao Huang, Xiaoxia Jiang, Haohao Wang, Lisong Teng
Aberrant Wnt/β-catenin pathway activation is frequently observed in human colorectal cancer (CRC) and has become a promising target for CRC treatment. Our study aimed to evaluate the effect of FH535, a small molecule inhibitor of Wnt/β-catenin pathway, on two colon cancer cell lines, HT29 and SW480. We found FH535 significantly inhibited colon cancer cell proliferation in vitro and induced cell cycle arrest. Moreover, FH535 inhibited colon cancer xenograft growth in vivo. Wound-healing assay and Transwell assay revealed that FH535 notably suppressed migration and invasion of SW480 cells...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/29158586/insights-into-gene-expression-profiles-induced-by-socs3-depletion-in-keratinocytes
#5
Archana Bajpai, Takashi Ishii, Kosuke Miyauchi, Vipul Gupta, Yuka Nishio-Masaike, Yuki Shimizu-Yoshida, Masato Kubo, Hiroaki Kitano
Specific deletion of suppressor of cytokine signaling 3 (Socs3) in keratinocytes can cause severe skin inflammation with infiltration of immune cells. The molecular mechanisms and key regulatory pathways involved in these processes remain elusive. To investigate the role of Socs3 in keratinocytes, we generated and analyzed global RNA-Seq profiles from Socs3 conditional knockout (cKO) mice of two different ages (2 and 10 weeks). Over 400 genes were significantly regulated at both time points. Samples from 2-week-old mice exhibited down-regulation of genes involved in keratin-related functions and up-regulation of genes involved in lipid metabolism...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29158339/genome-wide-mapping-of-decay-factor-mrna-interactions-in-yeast-identifies-nutrient-responsive-transcripts-as-targets-of-the-deadenylase-ccr4
#6
Jason E Miller, Liye Zhang, Haoyang Jiang, Yunfei Li, B Franklin Pugh, Joseph C Reese
The Ccr4-Not complex is a major regulator of stress responses that controls gene expression at multiple levels, from transcription to mRNA decay. Ccr4, a core subunit of the complex, is the main cytoplasmic deadenylase in Saccharomyces cerevisiae, however its mRNA targets have not been mapped on a genome-wide scale. Here we describe a genome-wide approach, RNA immunoprecipitation-high throughput sequencing (RIP-seq), to identify the RNAs bound to Ccr4, and two proteins that associate with it, Dhh1 and Puf5...
November 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29158334/global-transcriptome-sequencing-reveals-molecular-profiles-of-summer-diapause-induction-stage-of-onion-maggot-delia-antiqua-diptera-anthomyiidae
#7
Shuang Ren, You-Jin Hao, Bin Chen, You-Ping Yin
The onion maggot, Delia antiqua, is a worldwide subterranean pest and can enter diapause during summer and winter seasons. The molecular regulation of the ontogenesis transition remains largely unknown. Here we used high-throughput RNA-Seq to identify candidate genes and processes linked to summer diapause induction by comparing the transcriptome differences between the most sensitive larval developmental stage of summer-diapause (SD) and non-diapause (ND). Nine pair-wise comparisons were performed and significantly differentially regulated transcripts were identified...
November 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29158240/novel-genes-and-regulators-that-influence-production-of-cell-surface-exopolysaccharides-in-sinorhizobium-meliloti
#8
Melanie J Barnett, Sharon R Long
Sinorhizobium meliloti is a soil-dwelling α-proteobacterium that engages in a nitrogen-fixing root nodule symbiosis with leguminous plants. Cell surface polysaccharides are important for both adapting to stresses in the soil and development of an effective symbiotic interaction. Among the polysaccharides characterized to date, the acidic exopolysaccharides EPS-I (succinoglycan) and EPS-II (galactoglucan) are particularly important for protection from abiotic stresses, biofilm formation, root colonization, and infection of plant roots...
November 20, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/29158222/trehalose-metabolism-genes-render-rice-white-tip-nematode-aphelenchoides-besseyi-nematoda-aphelenchoididae-resistant-to-anaerobic-environment
#9
Qiaoli Chen, Feng Wang, Danlei Li, Ruizhi Zhang, Yaming Ling
After experiencing anaerobic environments, Aphelenchoides besseyi will enter a state of suspended animation known as anoxybiosis, which may use trehalose for energy supply to survive. To identify the function of trehalose metabolism, two trehalose-6-phosphate synthase (TPS) genes (Ab-tps1 and Ab-tps2) encoding enzymes catalyzing trehalose synthesis and three trehalase (TRE) genes (Ab-ntre1, Ab-ntre2 and Ab-atre) encoding enzymes catalyzing the hydrolysis of trehalose were identified and investigated. Ab-tps1 and Ab-tps2 were active when A...
November 20, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29157225/identification-of-drought-responsive-mirnas-and-physiological-characterization-of-tea-plant-camellia-sinensis-l-under-drought-stress
#10
Yuqiong Guo, Shanshan Zhao, Chen Zhu, Xiaojun Chang, Chuan Yue, Zhong Wang, Yuling Lin, Zhongxiong Lai
BACKGROUND: Drought stress is one of the major natural challenges in the main tea-producing regions of China. The tea plant (Camellia sinensis) is a traditional beverage plant whose growth status directly affects tea quality. Recent studies have revealed that microRNAs (miRNAs) play key functions in plant growth and development. Although some miRNAs have been identified in C. sinensis, little is known about their roles in the drought stress response of tea plants. RESULTS: Physiological characterization of Camellia sinensis 'Tieguanyin' under drought stress showed that the malondialdehyde concentration and electrical conductivity of leaves of drought-stressed plants increased when the chlorophyll concentration decreased under severe drought stress...
November 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29157210/genome-wide-identification-of-conserved-and-novel-micrornas-in-one-bud-and-two-tender-leaves-of-tea-plant-camellia-sinensis-by-small-rna-sequencing-microarray-based-hybridization-and-genome-survey-scaffold-sequences
#11
Anburaj Jeyaraj, Xiao Zhang, Yan Hou, Mingzhu Shangguan, Prabu Gajjeraman, Yeyun Li, Chaoling Wei
BACKGROUND: MicroRNAs (miRNAs) are important for plant growth and responses to environmental stresses via post-transcriptional regulation of gene expression. Tea, which is primarily produced from one bud and two tender leaves of the tea plant (Camellia sinensis), is one of the most popular non-alcoholic beverages worldwide owing to its abundance of secondary metabolites. A large number of miRNAs have been identified in various plants, including non-model species. However, due to the lack of reference genome sequences and/or information of tea plant genome survey scaffold sequences, discovery of miRNAs has been limited in C...
November 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29156720/novel-strategies-of-raman-imaging-for-brain-tumor-research
#12
Imiela Anna, Polis Bartosz, Polis Lech, Abramczyk Halina
Raman diagnostics and imaging have been shown to be an effective tool for the analysis and discrimination of human brain tumors from normal structures. Raman spectroscopic methods have potential to be applied in clinical practice as they allow for identification of tumor margins during surgery. In this study, we investigate medulloblastoma (grade IV WHO) (n= 5), low-grade astrocytoma (grades I-II WHO) (n =4), ependymoma (n=3) and metastatic brain tumors (n= 1) and the tissue from the negative margins used as normal controls...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156692/increased-transcriptional-and-metabolic-capacity-for-lipid-metabolism-in-the-peripheral-zone-of-the-prostate-may-underpin-its-increased-susceptibility-to-cancer
#13
Omar Al Kadhi, Maria H Traka, Antonietta Melchini, Perla Troncoso-Rey, Wiktor Jurkowski, Marianne Defernez, Purnima Pachori, Robert D Mills, Richard Y Ball, Richard F Mithen
The human prostate gland comprises three distinct anatomical glandular zones, namely the peripheral, central and transitional zones. Although prostate cancer can arise throughout the prostate, it is more frequent in the peripheral zone. In contrast, hyperplasia occurs most frequently in the transitional zone. In this paper, we test the hypothesis that peripheral and transitional zones have distinct metabolic adaptations that may underlie their different inherent predispositions to cancer and hyperplasia. In order to do this, we undertook RNA sequencing and high-throughput metabolic analyses of non-cancerous tissue from the peripheral and transitional zones of patients undergoing prostatectomy...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156518/linc00152-mir-139-5p-regulates-gastric-cancer-cell-aerobic-glycolysis-by-targeting-prkaa1
#14
Keke Sun, Pingping Hu, Feng Xu
Gastric cancer is one of the most common cancers in the world and glycolysis is a major feature of gastric cancer. MicroRNAs (miRNAs) involve in gastric cancer cell proliferation, glycolysis and other cellular processes. MiR-139-5p is reported as a tumor suppressor in cancers, however, the role of miR-139-5p including glycolytic metabolism is unclear in gastric cancer. So, the purpose of the present study is to elucidate the underlying mechanism in gastric cancer metabolism mediated by miR-139-5p. Our results revealed that miR-139-5p inhibited glycolysis by regulating AMP-activated, alpha 1 catalytic subunit (PRKAA1) expression in gastric cancer cells...
November 14, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29155830/molecular-characterization-of-tsetse-s-proboscis-and-its-response-to-trypanosoma-congolense-infection
#15
Erick O Awuoche, Brian L Weiss, Aurélien Vigneron, Paul O Mireji, Emre Aksoy, Benson Nyambega, Geoffrey M Attardo, Yineng Wu, Michelle O'Neill, Grace Murilla, Serap Aksoy
Tsetse flies (Glossina spp.) transmit parasitic African trypanosomes (Trypanosoma spp.), including Trypanosoma congolense, which causes animal African trypanosomiasis (AAT). AAT detrimentally affects agricultural activities in sub-Saharan Africa and has negative impacts on the livelihood and nutrient availability for the affected communities. After tsetse ingests an infectious blood meal, T. congolense sequentially colonizes the fly's gut and proboscis (PB) organs before being transmitted to new mammalian hosts during subsequent feedings...
November 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29155178/induction-of-immune-related-gene-expression-by-seminal-exosomes-in-the-porcine-endometrium
#16
Rulan Bai, Zeinab Latifi, Kazuya Kusama, Keigo Nakamura, Masayuki Shimada, Kazuhiko Imakawa
Seminal plasma (SP) is considered as a vehicle to carry sperm into female reproductive tract, of which functions have not been completely understood. This study aimed to identify the function of seminal exosomes on porcine endometrium. Exosomes were isolated from the sperm-rich fraction of boar semen and were confirmed by the expression of exosome marker HSP70 and size distribution using nano-sight tracking analysis. Porcine endometrial epithelial cells (EECs) were then treated with seminal exosomes, and RNA extracted were subjected to global expression analysis...
November 16, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29155091/dynamic-molecular-events-associated-to-plasmodium-berghei-gametogenesis-through-proteomic-approach
#17
Carlos H S Garcia, Delphine Depoix, Rayner M L Queiroz, Jaques M F Souza, Wagner Fontes, Marcelo V de Sousa, Marlon D M Santos, Paulo C Carvalho, Philippe Grellier, Sébastien Charneau
Plasmodium mature sexual cycle occurs in the vector mosquitoes and ensures the transmission to a new host. Gametogenesis takes place within minutes in the vector midgut. Gametocytes have to complete a deep nuclear reorganization, quick differentiation, and in the case of male gametocytes, intracytoplasmic flagellum assembly that results in free-swimming microgametes required for macrogamete fertilization. In efforts to improve our knowledge of molecular mechanisms involved in gamete morphogenesis, we carried out a nanoLC/MSMS based quantitative proteomic analysis throughout the xanthurenic acid-induced gametogenesis of the rodent parasite P...
November 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29154927/integrative-transcriptome-and-proteome-analyses-define-marked-differences-between-neospora-caninum-isolates-throughout-the-tachyzoite-lytic-cycle
#18
P Horcajo, D Xia, N Randle, E Collantes-Fernández, J Wastling, L M Ortega-Mora, J Regidor-Cerrillo
Neospora caninum is one of the main causes of transmissible abortion in cattle. Intraspecific variations in virulence have been widely shown among N. caninum isolates. However, the molecular basis governing such variability have not been elucidated to date. In this study label free LC-MS/MS was used to investigate proteome differences between the high virulence isolate Nc-Spain7 and the low virulence isolate Nc-Spain1H throughout the tachyzoite lytic cycle. The results showed greater differences in the abundance of proteins at invasion and egress with 77 and 62 proteins, respectively...
November 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29154757/macrophage-polarization-and-meta-inflammation
#19
REVIEW
Chuan Li, Maria M Xu, Kepeng Wang, Adam J Adler, Anthony T Vella, Beiyan Zhou
Chronic overnutrition and obesity induces low-grade inflammation throughout the body. Termed "meta-inflammation," this chronic state of inflammation is mediated by macrophages located within the colon, liver, muscle, and adipose tissue. A sentinel orchestrator of immune activity and homeostasis, macrophages adopt variable states of activation as a function of time and environmental cues. Meta-inflammation phenotypically skews these polarization states and has been linked to numerous metabolic disorders. The past decade has revealed several key regulators of macrophage polarization, including the signal transducer and activator of transcription family, the peroxisome proliferator-activated receptor gamma, the CCAAT-enhancer-binding proteins (C/EBP) family, and the interferon regulatory factors...
November 3, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/29154441/root-type-and-soil-phosphate-determine-the-taxonomic-landscape-of-colonizing-fungi-and-the-transcriptome-of-field-grown-maize-roots
#20
Peng Yu, Chao Wang, Jutta A Baldauf, Huanhuan Tai, Caroline Gutjahr, Frank Hochholdinger, Chunjian Li
Different root types of plants are colonized by a myriad of soil microorganisms, including fungi, which influence plant health and performance. The distinct functional and metabolic characteristics of these root types may influence root type-inhabiting fungal communities. We performed internal transcribed spacer (ITS) DNA profiling to determine the composition of fungal communities in field-grown axial and lateral roots of maize (Zea mays) and in response to two different soil phosphate (P) regimes. In parallel, these root types were subjected to transcriptome profiling by RNA sequencing (RNA-Seq)...
November 20, 2017: New Phytologist
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