keyword
MENU ▼
Read by QxMD icon Read
search

RNA structure

keyword
https://www.readbyqxmd.com/read/28427244/whole-genome-expression-analyses-of-type-2-diabetes-in-human-skin-reveal-altered-immune-function-and-burden-of-infection
#1
Chun Wu, Xiaopan Chen, Jing Shu, Chun-Ting Lee
Skin disorders are among most common complications associated with type 2 diabetes mellitus (T2DM). Although T2DM patients are known to have increased risk of infections and other T2DM-related skin disorders, their molecular mechanisms are largely unknown. This study aims to identify dysregulated genes and gene networks that are associated with T2DM in human skin. We compared the expression profiles of 56,318 transcribed genes on 74 T2DM cases and 148 gender- age-, and race-matched non-diabetes controls from the Genotype-Tissue Expression (GTEx) database...
March 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426973/non-linear-enhancement-of-mrna-delivery-efficiencies-by-influenza-a-derived-ns1-protein-engendering-host-gene-inhibition-property
#2
Kyle K L Phua, Yi Liu, Shun Hui Sim
Nucleic acid induced immunogenicity remains a significant impediment in biomedical therapeutics because the innate immune system is a complex network overlaid with functional redundancies. Herein we report that non-structural protein 1 (NS1), an immune evasion protein derived from influenza A virus, when co-delivered in mRNA format is a potent mRNA transfection enhancer without toxicity. Transfection enhancement is mediated by NS1's effector domain through inhibition of IRF3 and PKR, activators of early anti-viral responses as well as CPSF30, a non immunostimulating protein...
April 12, 2017: Biomaterials
https://www.readbyqxmd.com/read/28426204/parameter-optimization-for-interaction-between-c-terminal-domains-of-hiv-1-capsid-protein
#3
Hao Sha, Fangqiang Zhu
HIV-1 capsid proteins (CAs) assemble into a capsid that encloses the viral RNA. The binding between a pair of C-terminal domains (CTDs) constitutes a major interface in both the CA dimers and the large CA assemblies. Here we attempt to use a general residue-level coarse-grained model to describe the interaction between two isolated CTDs in Monte Carlo simulations. With the standard parameters that depend only on the residue types, the model predicts a much weaker binding in comparison to the experiments. Detailed analysis reveals that some Lennard-Jones parameters are not compatible with the experimental CTD dimer structure, thus resulting in an unfavorable interaction energy...
April 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28426097/landscape-of-rna-polyadenylation-in-e-coli
#4
Alexandre Maes, Céline Gracia, Nicolas Innocenti, Kaiyang Zhang, Erik Aurell, Eliane Hajnsdorf
Polyadenylation is thought to be involved in the degradation and quality control of bacterial RNAs but relatively few examples have been investigated. We used a combination of 5΄-tagRACE and RNA-seq to analyze the total RNA content from a wild-type strain and from a poly(A)polymerase deleted mutant. A total of 178 transcripts were either up- or down-regulated in the mutant when compared to the wild-type strain. Poly(A)polymerase up-regulates the expression of all genes related to the FliA regulon and several previously unknown transcripts, including numerous transporters...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28426093/biophysical-properties-thermal-stability-and-functional-impact-of-8-oxo-7-8-dihydroguanine-on-oligonucleotides-of-rna-a-study-of-duplex-hairpins-and-the-aptamer-for-preq1-as-models
#5
Yu J Choi, Krzysztof S Gibala, Tewoderos Ayele, Katherine V Deventer, Marino J E Resendiz
A better understanding of the effects that oxidative lesions have on RNA is of importance to understand their role in the development/progression of disease. 8-oxo-7,8-dihydroguanine was incorporated into RNA to understand its structural and functional impact on RNA:RNA and RNA:DNA duplexes, hairpins and pseudoknots. One to three modifications were incorporated into dodecamers of RNA [AAGA GGG AUGAC] resulting in thermal destabilization (Δ T m - 10°C per lesion). Hairpins with tetraloops c-UUCG*-g* ( ), a-ACCG-g* ( ), c-UUG*G*-g* ( ) and c-ACG*G*-g* ( ) were modified and used to determine thermal stabilities, concluding that: (i) modifying the stem leads to destabilization unless adenosine is the opposing basepair of 8-oxoGua; (ii) modification at the loop is position- and sequence-dependent and varies from slight stabilization to large destabilization, in some cases leading to formation of other secondary structures (hairpin→duplex)...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28425641/molecular-dynamics-simulations-of-early-steps-in-rna-mediated-conversion-of-prions
#6
Erik J Alred, Michael Nguyen, Maggie Martin, Ulrich Hansmann
The rate-limiting step in prion diseases is the initial transition of a prion protein from its native form into a mis-folded state in which the protein not only forms cell-toxic aggregates but also becomes infectious. Recent experiments implicate polyadenosine RNA as a possible agent for generating the initial seed. In order to understand the mechanism of RNA-mediated mis-folding and aggregation of prions, we dock polyadenosine RNA to mouse and human prion models. Changes in stability and secondary structure of the prions upon binding to polyadenosine RNA are evaluated by comparing molecular dynamics simulations of these complexes with that of the unbound prions...
April 20, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28425179/resilience-of-the-prokaryotic-microbial-community-of-acropora-digitifera-to-elevated-temperature
#7
Andrian P Gajigan, Leomir A Diaz, Cecilia Conaco
The coral is a holobiont formed by the close interaction between the coral animal and a diverse community of microorganisms, including dinoflagellates, bacteria, archaea, fungi, and viruses. The prokaryotic symbionts of corals are important for host fitness but are also highly sensitive to changes in the environment. In this study, we used 16S ribosomal RNA (rRNA) sequencing to examine the response of the microbial community associated with the coral, Acropora digitifera, to elevated temperature. The A. digitifera microbial community is dominated by operational taxonomic unit (OTUs) affiliated with classes Alphaproteobacteria and Gammaproteobacteria...
April 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28425012/a-study-of-the-damage-of-the-intestinal-mucosa-barrier-structure-and-function-of-ctenopharyngodon-idella-with-aeromonas-hydrophila
#8
Wei-Guang Kong, Si-Si Li, Xiao-Xuan Chen, Yu-Qing Huang, Ying Tang, Zhi-Xin Wu
The aim of this study is to explore the effect of Aeromonas hydrophila on the intestinal mucosal barrier structure and intestinal permeability in grass carp (Ctenopharyngodon idella). Histopathological examinations showed that A. hydrophila induced severe intestinal lesions, including inflammatory cell infiltration and intestinal villus fusion and swelling. Messenger RNA (mRNA) expression of the inflammatory cytokines TNF-α, IL-1β, IL-8, IL-10 and MyD88 was significantly increased after infection with A. hydrophila...
April 19, 2017: Fish Physiology and Biochemistry
https://www.readbyqxmd.com/read/28424513/super-multiplex-vibrational-imaging
#9
Lu Wei, Zhixing Chen, Lixue Shi, Rong Long, Andrew V Anzalone, Luyuan Zhang, Fanghao Hu, Rafael Yuste, Virginia W Cornish, Wei Min
The ability to visualize directly a large number of distinct molecular species inside cells is increasingly essential for understanding complex systems and processes. Even though existing methods have successfully been used to explore structure-function relationships in nervous systems, to profile RNA in situ, to reveal the heterogeneity of tumour microenvironments and to study dynamic macromolecular assembly, it remains challenging to image many species with high selectivity and sensitivity under biological conditions...
April 19, 2017: Nature
https://www.readbyqxmd.com/read/28424303/distribution-of-genotype-network-sizes-in-sequence-to-structure-genotype-phenotype-maps
#10
Susanna Manrubia, José A Cuesta
An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences...
April 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28423656/effect-of-y6-an-epigallocatechingallate-derivative-on-reversing-doxorubicin-drug-resistance-in-human-hepatocellular-carcinoma-cells
#11
Yan Wen, Rui-Qiang Zhao, Yun-Kai Zhang, Pranav Gupta, Li-Xiang Fu, An-Zhou Tang, Bu-Ming Liu, Zhe-Sheng Chen, Dong-Hua Yang, Gang Liang
Cancer cells can acquire resistance to a wide variety of diverse and unrelated drugs, this phenomenon is termed multidrug resistance (MDR). Multidrug resistance has been an obstacle to the success of cancer chemotherapy. The present study investigated the reversal effect of Y6, a new compound obtained by chemically modifying the structure of epigallocatechin-3-gallate (EGCG) extracted from green tea. Y6 was proven to be effective in inhibiting cell proliferation and reversing drug resistance in doxorubicin (DOX) resistant human hepatocellular carcinoma cells (BEL-7404/DOX)...
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423032/complete-study-demonstrating-the-absence-of-rhabdovirus-in-a-distinct-sf9-cell-line
#12
Yoshifumi Hashimoto, Daniel Macri, Indresh Srivastava, Clifton McPherson, Rachael Felberbaum, Penny Post, Manon Cox
A putative novel rhabdovirus (SfRV) was previously identified in a Spodoptera frugiperda cell line (Sf9 cells [ATCC CRL-1711 lot 58078522]) by next generation sequencing and extensive bioinformatic analysis. We performed an extensive analysis of our Sf9 cell bank (ATCC CRL-1711 lot 5814 [Sf9L5814]) to determine whether this virus was already present in cells obtained from ATCC in 1987. Inverse PCR of DNA isolated from Sf9 L5814 cellular DNA revealed integration of SfRV sequences in the cellular genome. RT-PCR of total RNA showed a deletion of 320 nucleotides in the SfRV RNA that includes the transcriptional motifs for genes X and L...
2017: PloS One
https://www.readbyqxmd.com/read/28422997/promoter-hypermethylation-as-a-mechanism-for-lamin-a-c-silencing-in-a-subset-of-neuroblastoma-cells
#13
Ines Rauschert, Fabian Aldunate, Jens Preussner, Miguel Arocena-Sutz, Vanina Peraza, Mario Looso, Juan C Benech, Ruben Agrelo
Nuclear lamins support the nuclear envelope and provide anchorage sites for chromatin. They are involved in DNA synthesis, transcription, and replication. It has previously been reported that the lack of Lamin A/C expression in lymphoma and leukaemia is due to CpG island promoter hypermethylation. Here, we provide evidence that Lamin A/C is silenced via this mechanism in a subset of neuroblastoma cells. Moreover, Lamin A/C expression can be restored with a demethylating agent. Importantly, Lamin A/C reintroduction reduced cell growth kinetics and impaired migration, invasion, and anchorage-independent cell growth...
2017: PloS One
https://www.readbyqxmd.com/read/28421099/progress-in-high-amylose-cereal-crops-through-inactivation-of-starch-branching-enzymes
#14
REVIEW
Juan Wang, Pan Hu, Zichun Chen, Qiaoquan Liu, Cunxu Wei
High-amylose cereal starches provide many health benefits for humans. The inhibition or mutation of starch branching enzyme (SBE) genes is an effective method to develop high-amylose cereal crops. This review summarizes the development of high-amylose cereal crops through the inactivation of one or more SBE isoforms or combination with other genes. This review also reveals the causes of increase in amylose content in high-amylose crops. A series of changes, including amylopectin structure, crystalline structure, thermal properties, and hydrolysis properties, occurs as amylose content increases...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28421090/comparative-genomics-and-phylogenomics-of-east-asian-tulips-amana-liliaceae
#15
Pan Li, Rui-Sen Lu, Wu-Qin Xu, Tetsuo Ohi-Toma, Min-Qi Cai, Ying-Xiong Qiu, Kenneth M Cameron, Cheng-Xin Fu
The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629-25,859 bp) separated by the large single-copy (81,482-82,218 bp) and small single-copy (17,366-17,465 bp) regions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28421048/functional-information-stored-in-the-conserved-structural-rna-domains-of-flavivirus-genomes
#16
REVIEW
Alba Fernández-Sanlés, Pablo Ríos-Marco, Cristina Romero-López, Alfredo Berzal-Herranz
The genus Flavivirus comprises a large number of small, positive-sense single-stranded, RNA viruses able to replicate in the cytoplasm of certain arthropod and/or vertebrate host cells. The genus, which has some 70 member species, includes a number of emerging and re-emerging pathogens responsible for outbreaks of human disease around the world, such as the West Nile, dengue, Zika, yellow fever, Japanese encephalitis, St. Louis encephalitis, and tick-borne encephalitis viruses. Like other RNA viruses, flaviviruses have a compact RNA genome that efficiently stores all the information required for the completion of the infectious cycle...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28420731/distinct-modulatory-role-of-rna-in-the-aggregation-of-the-tumor-suppressor-protein-p53-core-domain
#17
Petar Stefanov Kovachev, Debapriya Banerjee, Luciana Pereira Rangel, Jonny Eriksson, Murilo M Pedrote, Mafalda Maria D C Martins-Dinis, Katarina Edwards, Yraima Cordeiro, Jerson L Silva, Suparna Sanyal
Inactivation of the tumor suppressor protein p53 by mutagenesis, chemical modification, protein-protein interaction or aggregation has been associated with different human cancers. Although DNA is the typical substrate of p53, numerous studies have reported p53 interactions with RNA. Here, we have examined the effects of RNA of varied sequence, length and origin on the mechanism of aggregation of the core domain of p53 (p53C) using light scattering, intrinsic fluorescence, transmission electron microscopy, thioflavin-T binding, seeding and immunoblot assays...
April 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28420692/an-improved-assembly-and-annotation-of-the-allohexaploid-wheat-genome-identifies-complete-families-of-agronomic-genes-and-provides-genomic-evidence-for-chromosomal-translocations
#18
Bernardo J Clavijo, Luca Venturini, Christian Schudoma, Gonzalo Garcia Accinelli, Gemy Kaithakottil, Jonathan Wright, Philippa Borrill, George Kettleborough, Darren Heavens, Helen Chapman, James Lipscombe, Tom Barker, Fu-Hao Lu, Neil McKenzie, Dina Raats, Ricardo H Ramirez-Gonzalez, Aurore Coince, Ned Peel, Lawrence Percival-Alwyn, Owen Duncan, Josua Trösch, Guotai Yu, Dan M Bolser, Guy Namaati, Arnaud Kerhornou, Manuel Spannagl, Heidrun Gundlach, Georg Haberer, Robert P Davey, Christine Fosker, Federica Di Palma, Andrew Phillips, A Harvey Millar, Paul J Kersey, Cristobal Uauy, Ksenia V Krasileva, David Swarbreck, Michael W Bevan, Matthew D Clark
Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data...
April 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28420615/the-mechanism-and-clinical-significance-of-long-noncoding-rna-mediated-gene-expression-via-nuclear-architecture
#19
Shi Jian, Li Yanming, Fang Xiangdong
Long noncoding RNAs (lncRNAs) are a class of non-protein coding transcripts exceeding 200 nucleotides in length. Accumulating evidence achieved by several sophisticated techniques such as chromatin conformation capture and RNA-seq has led to new questions concerning correlations between lncRNAs and chromatin structures. Many studies have revealed that lncRNAs exert great influences on gene expression through regulating chromatin 3D structures. In addition, lncRNAs play a crucial role in tumorigenesis and therefore hold great promises in disease diagnosis and prognosis...
March 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28420141/coordinated-actions-of-micrornas-with-other-epigenetic-factors-regulate-skeletal-muscle-development-and-adaptation
#20
REVIEW
Marzia Bianchi, Alessandra Renzini, Sergio Adamo, Viviana Moresi
Epigenetics plays a pivotal role in regulating gene expression in development, in response to cellular stress or in disease states, in virtually all cell types. MicroRNAs (miRNAs) are short, non-coding RNA molecules that mediate RNA silencing and regulate gene expression. miRNAs were discovered in 1993 and have been extensively studied ever since. They can be expressed in a tissue-specific manner and play a crucial role in tissue development and many biological processes. miRNAs are responsible for changes in the cell epigenome because of their ability to modulate gene expression post-transcriptionally...
April 15, 2017: International Journal of Molecular Sciences
keyword
keyword
79100
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"