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RNA folding

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https://www.readbyqxmd.com/read/28817735/association-of-gene-expression-with-biomass-content-and-composition-in-sugarcane
#1
Nam V Hoang, Agnelo Furtado, Angela J O'Keeffe, Frederik C Botha, Robert J Henry
About 64% of the total aboveground biomass in sugarcane production is from the culm, of which ~90% is present in fiber and sugars. Understanding the transcriptome in the sugarcane culm, and the transcripts that are associated with the accumulation of the sugar and fiber components would facilitate the modification of biomass composition for enhanced biofuel and biomaterial production. The Sugarcane Iso-Seq Transcriptome (SUGIT) database was used as a reference for RNA-Seq analysis of variation in gene expression between young and mature tissues, and between 10 genotypes with varying fiber content...
2017: PloS One
https://www.readbyqxmd.com/read/28816581/novel-functions-for-chromatin-dynamics-in-mrna-biogenesis-beyond-transcription
#2
Catherine Dargemont, Anna Babour
The first step of gene expression results in the production of mRNA ribonucleoparticles (mRNPs) that are exported to the cytoplasm via the NPC for translation into the cytoplasm. During this process, the mRNA molecule synthesized by RNA polymerase II (Pol II) undergoes extensive maturation, folding and packaging events that are intimately coupled to its synthesis. All these events take place in a chromatin context and it is therefore not surprising that a growing number of studies recently reported specific contributions of chromatin dynamics to various steps of mRNP biogenesis...
August 17, 2017: Nucleus
https://www.readbyqxmd.com/read/28816269/-microrna-differential-expression-profile-in-tuberous-sclerosis-complex-cell-line-tsc2-mefs-and-normal-cell-line-tsc2-mefs
#3
Y Cai, H Guo, H Z Li, W D Wang, Y S Zhang
OBJECTIVE: Tuberous sclerosis complex (TSC) is a multisystem genetic disorder caused by mutations in the TSC1 and TSC2 genes, but the molecular events contributing to TSC are not well understood. However, little is known about the role of microRNAs in TSC. To explore the microRNA differential expression profile between tuberous sclerosis complex cell line TSC2(-/-) MEFs and normal type cell line TSC2(+/+) MEFs, and to provide new clues to study the mechanism of microRNA function in tuberous sclerosis complex...
August 18, 2017: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
https://www.readbyqxmd.com/read/28815951/physics-based-all-atom-modeling-of-rna-energetics-and-structure
#4
REVIEW
Louis G Smith, Jianbo Zhao, David H Mathews, Douglas H Turner
The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x-ray structures, but are 'unreliable' for predictions based only on sequence...
September 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28815851/basics-of-genome-editing-technology-and-its-application-in-livestock-species
#5
REVIEW
Bjoern Petersen
In the last decade, the research community has witnessed a blooming of targeted genome editing tools and applications. Novel programmable DNA nucleases such as zinc finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs) and the clustered regularly interspaced short palindromic repeats/Cas9 system (CRISPR/Cas9) possess long recognition sites and are capable of cutting DNA in a very specific manner. These DNA nucleases mediate targeted genetic alterations by enhancing the DNA mutation rate via induction of double-strand breaks at a predetermined genomic site...
August 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/28814318/annexin-a2-could-enhance-multidrug-resistance-by-regulating-nf-%C3%AE%C2%BAb-signaling-pathway-in-pediatric-neuroblastoma
#6
Yi Wang, Kai Chen, Yihong Cai, Yuanxia Cai, Xiaojun Yuan, Lifeng Wang, Zhixiang Wu, Yeming Wu
BACKGROUND: Chemotherapy is one of major therapeutic regimens for neuroblastoma (NB) in children. However, recurrence and metastasis associated with poor prognosis caused by acquired multidrug resistance remains a challenge. There is a great need to achieve new insight into the molecular mechanism of drug resistance in NB. The aim of this study is to identify novel drug sensitivity-related biomarkers as well as new therapeutic targets to overcome chemoresistance. METHODS: We proteome-wide quantitatively compared protein expression of two NB cell lines with different drug sensitivities, isolated from the same patient prior to and following chemotherapy...
August 16, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28814270/transcriptional-analysis-of-abdominal-fat-in-chickens-divergently-selected-on-bodyweight-at-two-ages-reveals-novel-mechanisms-controlling-adiposity-validating-visceral-adipose-tissue-as-a-dynamic-endocrine-and-metabolic-organ
#7
C W Resnyk, W Carré, X Wang, T E Porter, J Simon, E Le Bihan-Duval, M J Duclos, S E Aggrey, L A Cogburn
BACKGROUND: Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today's broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens...
August 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28811565/iss-pc-identifying-splicing-sites-via-physical-chemical-properties-using-deep-sparse-auto-encoder
#8
Zhao-Chun Xu, Peng Wang, Wang-Ren Qiu, Xuan Xiao
Gene splicing is one of the most significant biological processes in eukaryotic gene expression, such as RNA splicing, which can cause a pre-mRNA to produce one or more mature messenger RNAs containing the coded information with multiple biological functions. Thus, identifying splicing sites in DNA/RNA sequences is significant for both the bio-medical research and the discovery of new drugs. However, it is expensive and time consuming based only on experimental technique, so new computational methods are needed...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811385/circulating-mir-200c-is-up-regulated-in-paediatric-patients-with-familial-hypercholesterolaemia-and-correlates-with-mir-33a-b-levels-implication-of-a-zeb1-dependent-mechanism
#9
Marco D'Agostino, Francesco Martino, Sara Sileno, Francesco Barilla, Sara Beji, Lorenza Marchetti, Fabio Maria Gangi, Luca Persico, Mario Picozza, Anna Montali, Eliana Martino, Cristina Zanoni, Daniele Avitabile, Sandro Parrotto, Maurizio C Capogrossi, Alessandra Magenta
Hypercholesterolaemia provokes reactive oxygen species (ROS) increase and is a major risk factor for cardiovascular diseases (CVD) development. We previously showed that circulating microRNA(miR)-33a/b expression levels were up-regulated in children with familial hypercholesterolaemia (FH). miR-33a/b control cholesterol homoeostasis and recently miR-33b has been demonstrated to directly target the transcription factor ZEB1. The latter acts in a negative feedback-loop with miR-200 family. Our previous studies showed that the ROS-dependent miR-200c up-regulation induces endothelial dysfunction and provokes a ZEB1-dependent apoptosis and senescence...
August 15, 2017: Clinical Science (1979-)
https://www.readbyqxmd.com/read/28809961/biochemical-characterization-of-recombinant-influenza-a-polymerase-heterotrimer-complex-endonuclease-activity-and-evaluation-of-inhibitors
#10
Weimei Xing, Ona Barauskas, Thorsten Kirschberg, Anita Niedziela-Majka, Michael Clarke, Gabriel Birkus, Perry Weissburg, Xiaohong Liu, Brian E Schultz, Roman Sakowicz, HyockJoo Kwon, Joy Y Feng
Influenza polymerase is a heterotrimer composed of polymerase acidic protein A (PA) and basic proteins 1 (PB1) and 2 (PB2). The endonuclease active site, located in the PA subunit, cleaves host mRNA to prime viral mRNA transcription, and is essential for viral replication. To date, the human influenza A endonuclease activity has only been studied on the truncated active-site containing N-terminal domain of PA (PAN) or full-length PA in the absence of PB1 or PB2. In this study, we characterized the endonuclease activity of recombinant proteins of influenza A/PR8 containing full length PA, PA/PB1 dimer, and PA/PB1/PB2 trimer, observing 8...
2017: PloS One
https://www.readbyqxmd.com/read/28809007/method-to-identify-silent-codon-mutations-that-may-alter-peptide-elongation-kinetics-and-co-translational-protein-folding
#11
Ronald Worthington, Elijah Ball, Brentsen Wolf, Gregory Takacs
Due to the redundancy of the protein genetic code, mutational changes in the second or third nucleotide of an existing codon may not change the amino acid specification of the resulting modified codon. When peptide primary sequence is unchanged by mutation, that mutation is assumed to have no functional consequences. However, for one key gene involved in drug transport, MDR-1, several silent, synonymous mutations have been shown to alter protein structure and substrate affinity (Kimchi-Sarfaty et al., Science 315:525-528, 2007)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808417/down-regulation-of-aminopeptidase-n-and-abc-transporter-subfamily-g-transcripts-in-cry1ab-and-cry1ac-resistant-asian-corn-borer-ostrinia-furnacalis-lepidoptera-crambidae
#12
Tiantao Zhang, Brad S Coates, Yueqin Wang, Yidong Wang, Shuxiong Bai, Zhenying Wang, Kanglai He
The Asian corn borer (ACB), Ostrinia furnacalis (Lepidoptera: Crambidae), is a highly destructive pest of cultivated maize throughout East Asia. Bacillus thuringiensis (Bt) crystalline protein (Cry) toxins cause mortality by a mechanism involving pore formation or signal transduction following toxin binding to receptors along the midgut lumen of susceptible insects, but this mechanism and mutations therein that lead to resistance are not fully understood. In the current study, quantitative comparisons were made among midgut expressed transcripts from O...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/28808269/delivery-of-large-transgene-cassettes-by-foamy-virus-vector
#13
Nathan Paul Sweeney, Jinhong Meng, Hayley Patterson, Jennifer E Morgan, Myra McClure
Viral vectors are effective tools in gene therapy, but their limited packaging capacity can be restrictive. Larger clinically-relevant vectors are needed. Foamy viruses have the largest genomes among mammalian retroviruses and their vectors have shown potential for gene therapy in preclinical studies. However, the effect of vector genome size on titre has not been determined. We inserted increasing lengths of the dystrophin open reading frame in a foamy virus vector and quantified packaged vector RNA and integrated DNA...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28806224/bromodomain-containing-protein-4-activates-voltage-gated-sodium-channel-1-7-transcription-in-dorsal-root-ganglia-neurons-to-mediate-thermal-hyperalgesia-in-rats
#14
Ming-Chun Hsieh, Yu-Cheng Ho, Cheng-Yuan Lai, Hsueh-Hsiao Wang, An-Sheng Lee, Jen-Kun Cheng, Yat-Pang Chau, Hsien-Yu Peng
BACKGROUND: Bromodomain-containing protein 4 binds acetylated promoter histones and promotes transcription; however, the role of bromodomain-containing protein 4 in inflammatory hyperalgesia remains unclear. METHODS: Male Sprague-Dawley rats received hind paw injections of complete Freund's adjuvant to induce hyperalgesia. The dorsal root ganglia were examined to detect changes in bromodomain-containing protein 4 expression and the activation of genes involved in the expression of voltage-gated sodium channel 1...
August 11, 2017: Anesthesiology
https://www.readbyqxmd.com/read/28805284/interaction-of-the-n-terminal-tandem-domains-of-hnrnp-ll-with-the-bcl2-promoter-i-motif-dna-sequence
#15
Harald Schwalbe, Lauris Lannes, Phoebe Young, Christian Richter, Nina Morgner
The human genome contains GC-rich sequences able to form tetraplex secondary structures known as G-quadruplex and i-motif. Such sequences are notably present in the promoter region of oncogenes and are proposed to function as regulatory elements of the gene expression. The P1 promoter of BCL2 contains a 39-mer C-rich sequence (Py39wt) which can fold into a hairpin or an i-motif in a pH-dependent manner in vitro. The protein hnRNP LL was identified to recognise the i-motif over the hairpin conformation and act as an activating transcription factor...
August 14, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28804485/transcriptional-profiling-of-midguts-prepared-from-trypanosoma-t-congolense-positive-glossina-palpalis-palpalis-collected-from-two-distinct-cameroonian-foci-coordinated-signatures-of-the-midguts-remodeling-as-t-congolense-supportive-niches
#16
Jean M Tsagmo Ngoune, Flobert Njiokou, Béatrice Loriod, Ginette Kame-Ngasse, Nicolas Fernandez-Nunez, Claire Rioualen, Jacques van Helden, Anne Geiger
Our previous transcriptomic analysis of Glossina palpalis gambiensis experimentally infected or not with Trypanosoma brucei gambiense aimed to detect differentially expressed genes (DEGs) associated with infection. Specifically, we selected candidate genes governing tsetse fly vector competence that could be used in the context of an anti-vector strategy, to control human and/or animal trypanosomiasis. The present study aimed to verify whether gene expression in field tsetse flies (G. p. palpalis) is modified in response to natural infection by trypanosomes (T...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28803142/identification-and-characterization-of-a-long-non-coding-rna-up-regulated-during-hiv-1-infection
#17
Thomas S Postler, Shara N Pantry, Ronald C Desrosiers, Sankar Ghosh
Long non-coding RNAs (lncRNAs) are rapidly emerging as important regulators of a diverse array of cellular functions. Here, we describe a meta-analysis of two independent RNA-seq studies to identify lncRNAs that are differentially expressed upon HIV-1 infection. Only three lncRNA genes exhibited altered expression of ≥ 2-fold in HIV-1-infected cells. Of these, the uncharacterized lncRNA LINC00173 was chosen for further study. Both transcript variants of LINC00173 (lnc173 TSV1 and 2) could be detected by qPCR, localized predominantly to the nucleus and were reproducibly up-regulated during infection...
August 10, 2017: Virology
https://www.readbyqxmd.com/read/28801581/bpifcl-modulates-kiss2-expression-under-the-influence-of-11-ketotestosterone-in-female-zebrafish
#18
Shogo Moriya, Nabila Tahsin, Ishwar S Parhar
The bactericidal/permeability-increasing (BPI) fold-containing (BPIF) superfamily of genes expressed in the brain are purportedly involved in modulating brain function in response to stress, such as inflammation. Kisspeptin, encoded by kiss, is affected by inflammation in the brain; therefore, BPIF family genes might be involved in the modulation of kisspeptin in the brain. In this study, we investigated the expression of BPIF family C, like (bpifcl) in zebrafish brain and its involvement in kiss2 regulation...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800772/endurance-training-lowers-ribosome-density-despite-increasing-ribosome-biogenesis-markers-in-rodent-skeletal-muscle
#19
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/28800637/biologically-active-recombinant-human-erythropoietin-expressed-in-hairy-root-cultures-and-regenerated-plantlets-of-nicotiana-tabacum-l
#20
Poornima Devi Gurusamy, Holger Schäfer, Siva Ramamoorthy, Michael Wink
Hairy root culture is a potential alternative to conventional mammalian cell culture to produce recombinant proteins due to its ease in protein recovery, low costs and absence of potentially human pathogenic contaminants. The current study focussed to develop a new platform of a hairy root culture system from Nicotiana tabacum for the production of recombinant human EPO (rhEPO), which is regularly produced in mammalian cells. The human EPO construct was amplified with C-terminal hexahistidine tag from a cDNA of Caco-2 cells...
2017: PloS One
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