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https://www.readbyqxmd.com/read/28812932/celebrating-wobble-decoding-half-a-century-and-still-much-is-new
#1
Paul F Agris, Emily R Eruysal, Amithi Narendran, Ville Y P Väre, Sweta Vangaveti, Srivathsan V Ranganathan
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons...
August 16, 2017: RNA Biology
https://www.readbyqxmd.com/read/28812395/current-research-on-circular-rnas-associated-with-colorectal-cancer
#2
Penghui Wang, Xiaodong He
Representing a novel type of endogenous noncoding RNAs, circular RNAs (circRNAs) have recently gained much attention for their involvement in multiple biological processes. CircRNAs are ubiquitously expressed in eukaryotic cells and modulate gene expression by acting as sponges of microRNAs (miRNAs) or other proteins, such as RNA-binding proteins (RBPs). Due to their unique structure, circRNAs are more stable than linear RNAs. Expression profiles of circRNAs are associated with clinicopathological characteristics of colorectal cancer patients, such as differentiation, TNM classification and distant metastasis...
August 16, 2017: Scandinavian Journal of Gastroenterology
https://www.readbyqxmd.com/read/28812261/backbone-and-side-chain-1-h-15-n-and-13-c-resonance-assignments-of-two-sac10b-family-members-mvo10b-and-mth10btqqa-from-archaea
#3
Jinsong Xuan, Hongwei Yao, Yingang Feng, Jinfeng Wang
The Sac10b family proteins, also named as Alba, are small, basic, nucleic acid-binding proteins widely distributed in archaea. They possess divergent physiological functions such as binding to both DNA and RNA with a high affinity and involving in genomic DNA compaction, RNA transactions and transcriptional regulations. The structures of many Sac10b family proteins from hyperthermophilic archaea have been reported, while those from thermophilic and mesophilic archaea are largely unknown. As was pointed out, the homologous members from thermophilic and mesophilic archaea may have functions different from the hyperthermophilic members...
August 16, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28812142/tcdd-administered-on-activated-carbon-eliminates-bioavailability-and-subsequent-shifts-to-a-key-murine-gut-commensal
#4
Robert D Stedtfeld, J Brett Sallach, Robert B Crawford, Tiffany M Stedtfeld, Maggie R Williams, Hassan Waseem, Cliff T Johnston, Hui Li, Brian J Teppen, Norbert E Kaminski, Stephen A Boyd, James M Tiedje, Syed A Hashsham
Activated carbon (AC) is an increasingly attractive remediation alternative for the sequestration of dioxins at contaminated sites globally. However, the potential for AC to reduce the bioavailability of dioxins in mammals and the residing gut microbiota has received less attention. This question was partially answered in a recent study examining 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced hallmark toxic responses in mice administered with TCDD sequestered by AC or freely available in corn oil by oral gavage...
August 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28812060/reolysin-and-histone-deacetylase-inhibition-in-the-treatment-of-head-and-neck-squamous-cell-carcinoma
#5
Alena C Jaime-Ramirez, Jun-Ge Yu, Enrico Caserta, Ji Young Yoo, Jianying Zhang, Tae Jin Lee, Craig Hofmeister, John H Lee, Bhavna Kumar, Quintin Pan, Pawan Kumar, Robert Baiocchi, Theodoros Teknos, Flavia Pichiorri, Balveen Kaur, Matthew Old
Oncolytic viruses (OVs) are emerging as powerful anti-cancer agents and are currently being tested for their safety and efficacy in patients. Reovirus (Reolysin), a naturally occurring non-pathogenic, double-stranded RNA virus, has natural oncolytic activity and is being tested in phase I-III clinical trials in a variety of tumor types. With its recent US Food and Drug Administration (FDA) orphan drug designation for several tumor types, Reolysin is a potential therapeutic agent for various cancers, including head and neck squamous cell carcinomas (HNSCCs), which have a 5-year survival of ∼55%...
June 16, 2017: Molecular Therapy Oncolytics
https://www.readbyqxmd.com/read/28811345/inhibitors-of-the-histone-methyltransferases-ezh2-1-induce-a-potent-antiviral-state-and-suppress-infection-by-diverse-viral-pathogens
#6
Jesse H Arbuckle, Paul J Gardina, David N Gordon, Heather D Hickman, Jonathan W Yewdell, Theodore C Pierson, Timothy G Myers, Thomas M Kristie
Epigenetic regulation is based on a network of complexes that modulate the chromatin character and structure of the genome to impact gene expression, cell fate, and development. Thus, epigenetic modulators represent novel therapeutic targets used to treat a range of diseases, including malignancies. Infectious pathogens such as herpesviruses are also regulated by cellular epigenetic machinery, and epigenetic therapeutics represent a novel approach used to control infection, persistence, and the resulting recurrent disease...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28811159/implementing-and-scaling-up-hcv-treatment-services-for-people-who-inject-drugs-and-other-high-risk-groups-in-ukraine-an-evaluation-of-programmatic-and-treatment-outcomes
#7
Alyona Mazhnaya, Anna Meteliuk, Tetiana Barnard, Alexei Zelenev, Sergii Filippovych, Frederick L Alticec
BACKGROUND: HCV prevalence estimates among people who inject drugs (PWID) in Ukraine is high (60-90%), yet barriers to HCV treatment and care remain substantial including limited access to direct acting antiviral (DAA) medications. A feasibility scale-up project implemented HCV treatment in community-based settings to improve access to DAA treatment for key populations in this context. METHODS: Using program-level data and verified medical records, we describe the development, implementation processes and outcomes for HCV treatment for PWID and other risks groups...
August 12, 2017: International Journal on Drug Policy
https://www.readbyqxmd.com/read/28810905/omni-polya-a-method-and-tool-for-accurate-recognition-of-poly-a-signals-in-human-genomic-dna
#8
Arturo Magana-Mora, Manal Kalkatawi, Vladimir B Bajic
BACKGROUND: Polyadenylation is a critical stage of RNA processing during the formation of mature mRNA, and is present in most of the known eukaryote protein-coding transcripts and many long non-coding RNAs. The correct identification of poly(A) signals (PAS) not only helps to elucidate the 3'-end genomic boundaries of a transcribed DNA region and gene regulatory mechanisms but also gives insight into the multiple transcript isoforms resulting from alternative PAS. Although progress has been made in the in-silico prediction of genomic signals, the recognition of PAS in DNA genomic sequences remains a challenge...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28810711/whole-rna-sequencing-and-transcriptome-assembly-of-candida-albicans-and-candida-africana-under-chlamydospore-inducing-conditions
#9
Domenico Giosa, Maria Rosa Felice, Travis J Lawrence, Megha Gulati, Fabio Scordino, Letterio Giuffrè, Carla Lo Passo, Enrico D'Alessandro, Giuseppe Criseo, David H Ardell, Aaron D Hernday, Clarissa J Nobile, Orazio Romeo
Candida albicans is the most common cause of life-threatening fungal infections in humans, especially in immunocompromised individuals. Crucial to its success as an opportunistic pathogen is the considerable dynamism of its genome, which readily undergoes genetic changes generating new phenotypes and shaping the evolution of new strains. Candida africana is an intriguing C. albicans biovariant strain that exhibits remarkable genetic and phenotypic differences when compared with standard C. albicans isolates...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28810265/viral-retinopathy-in-experimental-models-of-zika-infection
#10
Zhenyang Zhao, Matthew Yang, Sasha R Azar, Lynn Soong, Scott C Weaver, Jiaren Sun, Yan Chen, Shannan L Rossi, Jiyang Cai
Purpose: Emerging evidence has shown that both congenital and adult Zika virus (ZIKV) infection can cause eye diseases. The goals of the current study were to explore mechanisms and pathophysiology of ZIKV-induced eye defects. Methods: Wild-type or A129 interferon type I receptor-deficient mice were infected by either FSS13025 or Mex1-7 strain of ZIKV. Retinal histopathology was measured at different time points after infection. The presence of viral RNA and protein in the retina was determined by in situ hybridization and immunofluorescence staining, respectively...
August 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28810078/discovery-of-key-physicochemical-structural-and-spatial-properties-of-rna-targeted-bioactive-ligands
#11
Brittany S Morgan, Jordan E Forte, Rebecca N Culver, Yuqi Zhang, Amanda E Hargrove
While myriad non-coding RNAs are known to be essential in cellular processes and misregulated in diseases, the development of RNA-targeted small molecule probes has met with limited success. To elucidate guiding principles for selective small molecule:RNA recognition, we analyzed cheminformatic and shape-based descriptors for 104 RNA-targeted ligands with demonstrated biological activity (RNA-targeted BIoactive ligaNd Database, RBIND). We then compared R-BIND to both FDA-approved small molecule drugs and RNA ligands without reported bioactivity...
August 15, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28809395/cryo-em-structures-of-the-80s-ribosomes-from-human-parasites-trichomonas-vaginalis-and-toxoplasma-gondii
#12
Zhifei Li, Qiang Guo, Lvqin Zheng, Yongsheng Ji, Yi-Ting Xie, De-Hua Lai, Zhao-Rong Lun, Xun Suo, Ning Gao
As an indispensable molecular machine universal in all living organisms, the ribosome has been selected by evolution to be the natural target of many antibiotics and small-molecule inhibitors. High-resolution structures of pathogen ribosomes are crucial for understanding the general and unique aspects of translation control in disease-causing microbes. With cryo-electron microscopy technique, we have determined structures of the cytosolic ribosomes from two human parasites, Trichomonas vaginalis and Toxoplasma gondii, at resolution of 3...
August 15, 2017: Cell Research
https://www.readbyqxmd.com/read/28809007/method-to-identify-silent-codon-mutations-that-may-alter-peptide-elongation-kinetics-and-co-translational-protein-folding
#13
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/28808919/backbone-and-side-chain-assignments-of-the-second-rna-binding-domain-of-musashi-1-in-its-free-form-and-in-complex-with-5-mer-rna
#14
Ryo Iwaoka, Takashi Nagata, Kengo Tsuda, Takao Imai, Hideyuki Okano, Naohiro Kobayashi, Masato Katahira
Musashi1 (Msi1) is an RNA-binding protein that is involved in cell fate determination. Here, we report the (1)H, (15)N, and (13)C resonance assignments of Msi1 second RNA-binding domain in free form and in complex with RNA. The assignments can be utilized for NMR structure and dynamics analyses of the Msi1:RNA complex, and moreover, for chemical shift perturbation analyses to evaluate the binding of potential small molecule inhibitors against Msi1:RNA interaction.
August 14, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28808384/molecular-authentication-of-the-traditional-medicinal-plant-lakshman-booti-smithia-conferta-sm-and-its-adulterants-through-dna-barcoding
#15
Suraj D Umdale, Parthraj R Kshirsagar, Manoj M Lekhak, Nikhil B Gaikwad
BACKGROUND: Smithia conferta Sm. is an annual herb widely used in Indian traditional medical practice and commonly known as "Lakshman booti" in Sanskrit. Morphological resemblance among the species of genus Smithia Aiton. leads to inaccurate identification and adulteration. This causes inconsistent therapeutic effects and also affects the quality of herbal medicine. AIM: This study aimed to generate potential barcode for authentication of S. conferta and its adulterants through DNA barcoding technique...
July 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28808065/the-punctilious-rna-polymerase-ii-core-promoter
#16
REVIEW
Long Vo Ngoc, Yuan-Liang Wang, George A Kassavetis, James T Kadonaga
The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure...
July 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28808060/the-human-rna-binding-protein-and-e3-ligase-mex-3c-binds-the-mex-3-recognition-element-mre-motif-with-high-affinity
#17
Lingna Yang, Chongyuan Wang, Fudong Li, Jiahai Zhang, Anam Nayab, Jihui Wu, Yunyu Shi, Qingguo Gong
MEX-3 is a KH domain-containing RNA-binding protein, first identified as a translational repressor in Caenorhabditis elegans, while its four orthologs (MEX-3A-D) in human and mouse were subsequently found to have E3 ubiquitin ligase activity mediated by a RING domain and critical for RNA degradation. Current evidence implicates human MEX-3C in many essential biological processes and suggests a strong connection with immune diseases and carcinogenesis. The highly conserved dual KH domains in MEX-3 proteins enable RNA binding and are essential for the recognition of the 3' UTR and posttranscriptional regulation of MEX-3 target transcripts...
August 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28808021/kinetic-and-high-throughput-profiling-of-epigenetic-interactions-by-3d-carbene-chip-based-surface-plasmon-resonance-imaging-technology
#18
Shuai Zhao, Mo Yang, Wenfei Zhou, Baichao Zhang, Zhiqiang Cheng, Jiaxin Huang, Min Zhang, Zhiyou Wang, Rui Wang, Zhonglei Chen, Jinsong Zhu, Haitao Li
Chemical modifications on histones and DNA/RNA constitute a fundamental mechanism for epigenetic regulation. These modifications often function as docking marks to recruit or stabilize cognate "reader" proteins. So far, a platform for quantitative and high-throughput profiling of the epigenetic interactome is urgently needed but still lacking. Here, we report a 3D-carbene chip-based surface plasmon resonance imaging (SPRi) technology for this purpose. The 3D-carbene chip is suitable for immobilizing versatile biomolecules (e...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28807826/structural-plasticity-of-t4-transcription-co-activator-gp33-revealed-by-a-protease-resistant-unfolded-state
#19
Radhakrishnan Mahalakshmi, Svetlana Rajkumar Maurya, Bhawna Burdak, Parini Surti, Manoj S Patel, Vikas Jain
Gene 33 protein (gp33) is a transcriptional coactivator for late genes of the T4 bacteriophage. gp33 possesses a 5-helix bundle core, with unstructured N- and C-terminal regions that account for >50% of the protein sequence. It plays a unique role of interacting with host RNA polymerase, couples transcription with DNA replication, and plays the dual function as repressor and co-activator in phage transcription. Here, we identify protein structural plasticity as the molecular basis of the dual nature in gp33...
August 12, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28807609/cspb-of-an-arctic-bacterium-polaribacter-irgensii-kopri-22228-confers-extraordinary-freeze-tolerance
#20
Youn Hong Jung, Yoo Kyung Lee, Hong Kum Lee, Kyunghee Lee, Hana Im
Freezing temperatures are a major challenge for life at the poles. Decreased membrane fluidity, uninvited secondary structure formation in nucleic acids, and protein cold-denaturation all occur at cold temperatures. Organisms adapted to polar regions possess distinct mechanisms that enable them to survive in extremely cold environments. Among the cold-induced proteins, cold shock protein (Csp) family proteins are the most prominent. A gene coding for a Csp-family protein, cspB, was cloned from an arctic bacterium, Polaribacter irgensii KOPRI 22228, and overexpression of cspB greatly increased the freeze-survival rates of Escherichia coli hosts, to a greater level than any previously reported Csp...
July 31, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
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