scholarly journals Structural landscape of base pairs containing post-transcriptional modifications in RNA

2017 ◽  
Author(s):  
Preethi S. P. ◽  
Purshotam Sharma ◽  
Abhijit Mitra
Keyword(s):  
Binding Energies ◽  
Rna Structures ◽  
Base Pairs ◽  
Functional Roles ◽  
Naturally Occurring ◽  
Quantum Chemical Methods ◽  
Geometrical Features ◽  
Modified Nucleobases ◽  
Functional Rnas

ABSTRACTBase pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts towards understanding the structural and functional role of naturally occurring modified base pairs by analyzing their distribution in different RNA classes, with the help of crystal structure and sequence database analyses. In addition, we quantify the variation in geometrical features of modified base pairs within RNA structures, and characterize their optimum geometries and binding energies using advanced quantum chemical methods. Further comparison of modified base pairs with their unmodified counterparts illustrates the effect of steric and electronic structure alterations due to base modifications. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding site and the three-way junctions within tRNA, which when analyzed in context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with the specific functional roles they play in context of RNA macromolecules.

scholarly journals Reverse Watson-Crick purine-purine base pairs — the Sharp-turn motif and other structural consequences in functional RNAs

2017 ◽  
Author(s):  
Abhinav Mittal ◽  
Antarip Halder ◽  
Sohini Bhattacharya ◽  
Dhananjay Bhattacharyya ◽  
Abhijit Mitra
Keyword(s):  
Structural Alignment ◽  
Bimodal Distribution ◽  
Base Pairs ◽  
Purine Base ◽  
Functional Roles ◽  
Nmr Structures ◽  
Sharp Turn ◽  
Interesting Class ◽  
Functional Rnas ◽  
Noncanonical Base Pairs

AbstractIdentification of static and/or dynamic roles of different noncanonical base pairs is essential for a comprehensive understanding of the sequence-structure-function space of RNA. In this context, reverse Watson-Crick purine-purine base pairs (A:A, G:G&A:GW:W Trans) constitute an interesting class of noncanonical base pairs in RNA due to their characteristic C1′–C1′ distance (highest among all base pairing geometries) and parallel local strand orientation. Structural alignment of the RNA stretches containing these W:W Trans base pairs with their corresponding homologous sites in a non-redundant set of RNA crystal structures show that, as expected, these base pairs are associated with specific structural folds or functional roles. Detailed analysis of these contexts further revealed a bimodal distribution in the local backbone geometry parameters associated with these base pairs. One mode, populated by both A:A and G:G W:W Trans pairs, manifests itself as a characteristic backbone fold. We call this fold a ‘Sharp-turn’ motif. The other mode is exclusively associated with A:A W:W Trans pairs involved in mediating higher order interactions. The same trend is also observed in available solution NMR structures. We have also characterized the importance of recurrent hydrogen bonding interactions between adenine and guanine in W:W Trans geometry. Quantum chemical calculations performed at M05-2X/6-31++(2d,2p) level explain how the characteristic electronic properties of these W:W Trans base pairs facilitate their occurrence in such exclusive structural folds that are important for RNA functionalities.

scholarly journals Potential Applications and Functional Roles of Exosomes in Cardiometabolic Disease

Pharmaceutics ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2056
Author(s):  
Sergio Ayala-Mar ◽  
Belén Rodríguez-Morales ◽  
Pedro Chacón-Ponce ◽  
José González-Valdez
Keyword(s):  
Cardiovascular Complications ◽  
Biological Information ◽  
Cardiometabolic Disease ◽  
Functional Roles ◽  
Naturally Occurring ◽  
Fields Of Study ◽  
Potential Applications ◽  
Innovative Biomaterials ◽  
A Cell

Despite diagnostic and therapeutic advances, cardiometabolic disease remains the leading cause of death worldwide. Extracellular vesicles (EVs), which include exosomes and microvesicles, have gained particular interest because of their role in metabolic homeostasis and cardiovascular physiology. Indeed, EVs are recognized as critical mediators of intercellular communication in the cardiovascular system. Exosomes are naturally occurring nanocarriers that transfer biological information in the setting of metabolic abnormalities and cardiac dysfunction. The study of these EVs can increase our knowledge on the pathophysiological mechanisms of metabolic disorders and their cardiovascular complications. Because of their inherent properties and composition, exosomes have been proposed as diagnostic and prognostic biomarkers and therapeutics for specific targeting and drug delivery. Emerging fields of study explore the use exosomes as tools for gene therapy and as a cell-free alternative for regenerative medicine. Furthermore, innovative biomaterials can incorporate exosomes to enhance tissue regeneration and engineering. In this work, we summarize the most recent knowledge on the role of exosomes in cardiometabolic pathophysiology while highlighting their potential therapeutic applications.

scholarly journals BDNF pro-peptide actions facilitate hippocampal LTD and are altered by the common BDNF polymorphism Val66Met

2015 ◽  
Vol 112 (23) ◽  
pp. E3067-E3074 ◽  
Author(s):  
Toshiyuki Mizui ◽  
Yasuyuki Ishikawa ◽  
Haruko Kumanogoh ◽  
Maria Lume ◽  
Tomoya Matsumoto ◽  
...  
Keyword(s):  
Memory Function ◽  
Amino Acid Position ◽  
Human Memory ◽  
Biological Role ◽  
Neurotrophin Receptor ◽  
Functional Roles ◽  
Mature Form ◽  
Naturally Occurring

Most growth factors are initially synthesized as precursor proteins and subsequently processed into their mature form by proteolytic cleavage, resulting in simultaneous removal of a pro-peptide. However, compared with that of mature form, the biological role of the pro-peptide is poorly understood. Here, we investigated the biological role of the pro-peptide of brain-derived neurotrophic factor (BDNF) and first showed that the pro-peptide is expressed and secreted in hippocampal tissues and cultures, respectively. Interestingly, we found that the BDNF pro-peptide directly facilitates hippocampal long-term depression (LTD), requiring the activation of GluN2B-containing NMDA receptors and the pan-neurotrophin receptor p75NTR. The BDNF pro-peptide also enhances NMDA-induced α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor endocytosis, a mechanism crucial for LTD expression. Thus, the BDNF pro-peptide is involved in synaptic plasticity that regulates a mechanism responsible for promoting LTD. The well-known BDNF polymorphism valine for methionine at amino acid position 66 (Val66Met) affects human memory function. Here, the BDNF pro-peptide with Met mutation completely inhibits hippocampal LTD. These findings demonstrate functional roles for the BDNF pro-peptide and a naturally occurring human BDNF polymorphism in hippocampal synaptic depression.

Fine structure and properties of defects in naturally occurring silicates and oxides

1990 ◽  
Vol 48 (4) ◽  
pp. 460-461
Author(s):  
David R. Veblen
Keyword(s):  
Chemical Reactions ◽  
High Resolution Electron Microscopy ◽  
Extended Defects ◽  
Single Chain ◽  
Naturally Occurring ◽  
Resolution Electron ◽  
Fine Structures ◽  
Image Simulations ◽  
Similar Crystal Structure

Extended defects and interfaces control many processes in rock-forming minerals, from chemical reactions to rock deformation. In many cases, it is not the average structure of a defect or interface that is most important, but rather the structure of defect terminations or offsets in an interface. One of the major thrusts of high-resolution electron microscopy in the earth sciences has been to identify the role of defect fine structures in reactions and to determine the structures of such features. This paper will review studies using HREM and image simulations to determine the structures of defects in silicate and oxide minerals and present several examples of the role of defects in mineral chemical reactions. In some cases, the geological occurrence can be used to constrain the diffusional properties of defects.The simplest reactions in minerals involve exsolution (precipitation) of one mineral from another with a similar crystal structure, and pyroxenes (single-chain silicates) provide a good example. Although conventional TEM studies have led to a basic understanding of this sort of phase separation in pyroxenes via spinodal decomposition or nucleation and growth, HREM has provided a much more detailed appreciation of the processes involved.

Role of Flavonoids in Neurodegenerative Disorders with Special Emphasis on Tangeritin

2019 ◽  
Vol 18 (8) ◽  
pp. 581-597 ◽  
Author(s):  
Ambreen Fatima ◽  
Yasir Hasan Siddique
Keyword(s):  
Medicinal Plants ◽  
Mechanism Of Action ◽  
Neurodegenerative Disorders ◽  
Treatment Strategies ◽  
Dietary Supplementation ◽  
Plant Polyphenols ◽  
Promising Candidate ◽  
Naturally Occurring ◽  
The Brain

Flavonoids are naturally occurring plant polyphenols found universally in all fruits, vegetables and medicinal plants. They have emerged as a promising candidate in the formulation of treatment strategies for various neurodegenerative disorders. The use of flavonoid rich plant extracts and food in dietary supplementation have shown favourable outcomes. The present review describes the types, properties and metabolism of flavonoids. Neuroprotective role of various flavonoids and the possible mechanism of action in the brain against the neurodegeneration have been described in detail with special emphasis on the tangeritin.

Monosodium Glutamate Toxicity and the Possible Protective Role of L–Carnitine

2018 ◽  
Vol 6 (1) ◽  
pp. 45-56
Author(s):  
Lalrinzuali Sailo ◽  
◽  
Meesala Krishna Murthy ◽  
Khandayataray Pratima ◽  
Vikas Kumar Roy ◽  
...  
Keyword(s):  
Human Subjects ◽  
Monosodium Glutamate ◽  
Essential Amino Acids ◽  
Protective Role ◽  
Glutamate Toxicity ◽  
Common Salt ◽  
Genotoxic Effects ◽  
Naturally Occurring ◽  
Flavour Enhancer

Monosodium glutamate is naturally available non-essential amino acids, which found in naturally occurring foods and used as flavour enhancer worldwide. Monosodium glutamate is believed to be linked with diverse health problems. The aim of the study was toxic effects of monosodium glutamate (MSG) and the protective role of L-carnitine, light on the available literature from last 25 years about diverse toxicity studies which had been carried out on animal and human models. Google scholar, NCBI, PUBMED, EMBASE, Wangfang databases, and Web of Science databases were used to retrieve the available studies. MSG was linked with deleterious effects particularly in animals including induction of obesity, diabetes, hepatotoxic, neurotoxic and genotoxic effects showed in Literature. Few reports revealed increased hunger, food intake, and obesity in human subjects due to MSG consumption. Hepatotoxic, neurotoxic, and genotoxic effects of monosodium glutamate on humans carried out very limitedly. High consumption of monosodium glutamate may be linked with harmful health effects showed in available literatures. So, it is recommended to use common salt instead of MSG. Furthermore, intensive research is required to explore monosodium glutamate–related molecular and metabolic mechanisms. L-carnitine can protect from Hepatotoxic, neurotoxic, renal impairment and genotoxic effects functionally, biochemically and histopathologically with a corresponding reduction of oxidative stress.

How Artefacts Do Leadership: A Ventriloquial Analysis

2021 ◽  
pp. 089331892199807
Author(s):  
Jonathan Clifton ◽  
Fernando Fachin ◽  
François Cooren
Keyword(s):  
Organizational Communication ◽  
Recent Work ◽  
Distributed Leadership ◽  
Network Theory ◽  
Actor Network Theory ◽  
Fine Grained ◽  
Naturally Occurring ◽  
Human Actors

To date there has been little work that uses fine-grained interactional analyses of the in situ doing of leadership to make visible the role of non-human as well as human actants in this process. Using transcripts of naturally-occurring interaction as data, this study seeks to show how leadership is co-achieved by artefacts as an in-situ accomplishment. To do this we situate this study within recent work on distributed leadership and argue that it is not only distributed across human actors, but also across networks that include both human and non-human actors. Taking a discursive approach to leadership, we draw on Actor Network Theory and adopt a ventriloquial approach to sociomateriality as inspired by the Montreal School of organizational communication. Findings indicate that artefacts “do” leadership when a hybrid presence is made relevant to the interaction and when this presence provides authoritative grounds for influencing others to achieve the group’s goals.

scholarly journals Selenium and Dogs: A Systematic Review

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 418
Author(s):  
Viola Zentrichová ◽  
Alena Pechová ◽  
Simona Kovaříková
Keyword(s):  
Male Fertility ◽  
Clinical Signs ◽  
Complex Data ◽  
Selenium Status ◽  
Dog Food ◽  
Balanced Diet ◽  
Naturally Occurring ◽  
Correct Function ◽  
Indirect Assay

The intent of this review is to summarize the knowledge about selenium and its function in a dog’s body. For this purpose, systematic literature search was conducted. For mammals, including dogs, a balanced diet and sufficient intake of selenium are important for correct function of metabolism. As for selenium poisoning, there are no naturally occurring cases known. Nowadays, we do not encounter clinical signs of its deficiency either, but it can be subclinical. For now, the most reliable method of assessing selenium status of a dog is measuring serum or plasma levels. Levels in full blood can be measured too, but there are no reference values. The use of glutathione peroxidase as an indirect assay is questionable in canines. Commercial dog food manufactures follow recommendations for minimal and maximal selenium levels and so dogs fed commercial diets should have balanced intake of selenium. For dogs fed home-made diets, complex data are missing. However, subclinical deficiency seems to affect, for example, male fertility or recovery from parasitical diseases. Very interesting is the role of selenium in prevention and treatment of cancer.

scholarly journals Arabidopsis Disulfide Reductase, Trx-h2, Functions as an RNA Chaperone under Cold Stress

2021 ◽  
Vol 11 (15) ◽  
pp. 6865
Author(s):  
Eun Seon Lee ◽  
Joung Hun Park ◽  
Seong Dong Wi ◽  
Ho Byoung Chae ◽  
Seol Ki Paeng ◽  
...  
Keyword(s):  
Cold Stress ◽  
Wild Type ◽  
Rna Chaperone ◽  
E Coli ◽  
Cold Sensitive ◽  
Thioredoxin H ◽  
Functional Rnas

The thioredoxin-h (Trx-h) family of Arabidopsis thaliana comprises cytosolic disulfide reductases. However, the physiological function of Trx-h2, which contains an additional 19 amino acids at its N-terminus, remains unclear. In this study, we investigated the molecular function of Trx-h2 both in vitro and in vivo and found that Arabidopsis Trx-h2 overexpression (Trx-h2OE) lines showed significantly longer roots than wild-type plants under cold stress. Therefore, we further investigated the role of Trx-h2 under cold stress. Our results revealed that Trx-h2 functions as an RNA chaperone by melting misfolded and non-functional RNAs, and by facilitating their correct folding into active forms with native conformation. We showed that Trx-h2 binds to and efficiently melts nucleic acids (ssDNA, dsDNA, and RNA), and facilitates the export of mRNAs from the nucleus to the cytoplasm under cold stress. Moreover, overexpression of Trx-h2 increased the survival rate of the cold-sensitive E. coli BX04 cells under low temperature. Thus, our data show that Trx-h2 performs function as an RNA chaperone under cold stress, thus increasing plant cold tolerance.

scholarly journals The Pleiotropic Function of Human Sirtuins as Modulators of Metabolic Pathways and Viral Infections

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 460
Author(s):  
Mohammed Hamed Alqarni ◽  
Ahmed Ibrahim Foudah ◽  
Magdy Mohamed Muharram ◽  
Nikolaos E. Labrou
Keyword(s):  
Metabolic Pathways ◽  
Histone Deacetylases ◽  
Viral Infections ◽  
Cell Physiology ◽  
Functional Roles ◽  
Regulatory Processes ◽  
Complex Functions ◽  
Natural Polyphenol ◽  
Antiviral Targets

Sirtuins (SIRTs) are nicotinamide adenine dinucleotide-dependent histone deacetylases that incorporate complex functions in the mechanisms of cell physiology. Mammals have seven distinct members of the SIRT family (SIRT1-7), which play an important role in a well-maintained network of metabolic pathways that control and adapt the cell to the environment, energy availability and cellular stress. Until recently, very few studies investigated the role of SIRTs in modulating viral infection and progeny. Recent studies have demonstrated that SIRT1 and SIRT2 are promising antiviral targets because of their specific connection to numerous metabolic and regulatory processes affected during infection. In the present review, we summarize some of the recent progress in SIRTs biochemistry and their emerging function as antiviral targets. We also discuss the potential of natural polyphenol-based SIRT modulators to control their functional roles in several diseases including viral infections.

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