Structure-to-Function Computational Prediction of a Subset of Ribosomal Proteins for the Small Ribosome Subunit

Extra-ribosomal functions of ribosomal proteins have been widely accepted albeit an incomplete understanding of these roles. Standard experimental studies have limited usefulness in defining the complete biological significance of ribosomal proteins. An alternative strategy is via in silico analysis. Here, we sought a sequence-to-structure-to-function approach to computationally predict the extra-ribosomal functions of a subset of ribosomal proteins of the small ribosome subunit, namely RPS12, RPS19, RPS20 and RPS24. Three-dimensional structure constructed from amino acid sequence was precisely matched with structural neighbours to extrapolate possible functions. Our analysis reveals new logical roles for these ribosomal proteins, of which represent important information for planning experimental and further in silico studies to elucidate their physiological roles

Extra-Ribosomal Functions of the Ribosomal Protein, RPS3 as Predicted by In Silico Analysis

Products of ribosomal protein (RP) genes have been found to play extra-ribosomal roles that range from DNA repair to RNA splicing. Their association with congenital disorders or cancers has also been widely documented. However, the relatively large number of different RPs, each with perhaps unique biological roles, has compounded the comprehensive elucidation of the physiological functions of each RPs. Experimental functional studies on the many and variegated RPs are labour intensive, time-consuming and costly. Moreover, experimental studies unguided by theoretically insights entail inaccurate results. Therefore, knowledge on the actual roles of these proteins remains largely undefined. A valid alternative is the use of bioinformatics resources to computationally predict functional roles of these biomolecules. Findings from such in silico studies of the RPS3 are reported herein. We reveal an array of possible extra-ribosomal functions that includes regulation of transcription (including via NF-κB-mediated, POK-induced and DNA-dependent), regulation of p53 activities and its stabilisation, inflammatory immune response, modulation of nNOS activities, and anti-oxidative capabilities. Our findings provide computational prediction of de novo extra-ribosomal functions of RPS3. These results will enhance the theoretical basis for designing future experimental studies on elucidating its definitive physiological roles

Research progress of the impact of nonalcoholic fatty liver disease on chronic hepatitis B infection

Chronic hepatitis B (CHB) is an infectious disease caused by persistent infection with the hepatitis B virus (HBV) and is highly prevalent worldwide. Non-alcoholic fatty liver disease (NAFLD) is a group of liver diseases related to metabolic abnormalities, excluding those caused by alcohol consumption or other liver injury factors. In recent years, with improvement of living standards and changes in lifestyle, the incidence of NAFLD has been increasing substantially, becoming the most common type of liver diseases in China and Western countries, and the second leading cause of liver transplantation in the West. The rising prevalence of NAFLD has also led to an increase in the incidence of NAFLD in patients with chronic HBV infection. However, there is considerable controversy both domestically and internationally regarding the relationship between these two diseases, including the disease progression, pathogenesis, impact on antiviral treatment efficacy, and prognosis of these concomitant CHB and NAFLD patients. Currently, both domestic and international guidelines lack detailed descriptions of diagnostic and treatment strategies for these conditions. This article summarizes the recent research progress in concomitant CHB and NAFLD, including epidemiology, diagnostic criteria, the impact of NAFLD on the virology of HBV infection, potential mechanisms of NAFLD-induced negative regulation of HBV, the effect of NAFLD on antiviral therapy efficacy, and prognosis. This article aims to gain a deeper understanding of the diseases themselves and provide new insights for basic and clinical research as well as diagnostic and treatment approaches

In Vitro and In Silico study on the interaction between apigenin, kaempferoland 4-hydroxybenzoic acid in xanthine oxidase inhibition

Xanthine oxidase (XO) is a biological enzyme that takes part in purine catabolism. It catalyses the conversion of hypoxanthine to xanthine and eventually xanthine to uric acid. The catabolism reaction increases the level of uric acid and subsequently leads to hyperuricemia. Allopurinol is a XO inhibitor that is used clinically to prevent purine catabolism. Although it is an effective XO inhibitor, it causes some side effects. Therefore, a more effective inhibitor with fewer side effects is in an urgent need. Phenolic compounds have been identified as effective XO inhibitors in many studies. In vitro and in silico study were conducted to investigate the interaction between apigenin, kaempferol and 4-hydroxybenzoic acid in XO inhibition. Apigenin was found to be the most effective XO inhibitor among the compounds tested with the best docking score of -8.2 kcal/mol as demonstrated in the molecular docking simulation which indicated its favourable interaction with XO enzyme. Additive interactions between compounds namely apigenin-kaempferol, apigenin-4-hydroxybenzoic acid and 4-hydroxybenzoic acid-kaempferol were demonstrated in both in vitro and in silico studies. The results showed that 4-hydroxybenzoic acid- apigenin (-7.4 kcal/mol) was the most stable ligands combination docked to XO. The multiple ligands docking simulation showed independent ligands bound to the XO active site at non-interfering regional location. In conclusion, the combination of these three compounds can be explored further for their additive interaction in XO inhibition, which could be beneficial in terms of the enhanced effectiveness and lower side effects when each is used at lower dose to give the same effect

The important of information & communications technology in Uber services

There is a growing interest and concern towards the concept of sustainable transport due to the low functionality of public transport, unregulated taxi pricing, lack of parking space, insufficient availability of taxies and the growing number of traffic congestion during peak hour in urban and sub-urban area.Uber services appear to be cost effective and a sustainable way to travel for public user especially commuter.The study aimed to explore the relationship between information & communications technology (ICT) and the effectiveness of Uber services.The factor that had been found that influence public ridership is information & communications technology.The application of convenience sampling with the usable data from 408 respondents who at least has the intention to use for future ride has been conducted by using online survey.In this study, there is a significant relationship between monthly salary & occupation with information & communications technology.This study contributed to city planner and local planner in developing or planning in order to have a smart city

A transformed view of cyclosporine

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62591/1/397471a0.pd

Mobile Cloud-Based Blood Pressure Healthcare for Education

Mercury, pneumatic, and electronic sphygmomanometers were widely used for traditional blood pressure (BP) measurement. Cloud BP database, and mobile information and communication technology (MICT) do not integrate to these BP measurement methods. Pen and papers were employed to record BP values for nurses and physicians, and recording errors are possible to occur. In the chapter, the cloud-based BP platform solution and advanced wireless hospital BP measurement technologies were studied. These cloud-based BT measurement technologies were used as teaching aids to train students of electrical and nursing fields for mobile BP healthcare and health promotion education, and hence interdisciplinary teaching and learning were conducted. The teachers include professors of electrical and nursing fields, physicians, hospital nurses, and the engineer and health management experts of Microlife. The interdisciplinary teaching and learning of mobile BP healthcare and health promotion for smart aging were conducted in the Department of Nursing Division, Chang Cung Memorial Hospital, Keelung Branch, Department of Nursing Ching Kuo Institute of Management and Health, School of Nursing Chung Shan Medical University, and Department of Electrical Engineering, National Taiwan Ocean University. The students of electrical and nursing fields participated for joint interdisciplinary learning. The concepts of interdisciplinary mobile BP healthcare learning and teaching involve nursing and technology, healthy aging, BP health care for smart aging, telenursing, BP care for smart aging, community/home telecare, and MICT. The objective of teaching and learning is training the design and making electrical engineers to understand BP healthcare and health promotion, and nurses to understand mobile BP healthcare and health promotion system for smart aging

Allele-specific miRNA-binding analysis identifies candidate target genes for breast cancer risk

Most breast cancer (BC) risk-associated single-nucleotide polymorphisms (raSNPs) identified in genome-wide association studies (GWAS) are believed to cis-regulate the expression of genes. We hypothesise that cis-regulatory variants contributing to disease risk may be affecting microRNA (miRNA) genes and/or miRNA binding. To test this, we adapted two miRNA-binding prediction algorithms-TargetScan and miRanda-to perform allele-specific queries, and integrated differential allelic expression (DAE) and expression quantitative trait loci (eQTL) data, to query 150 genome-wide significant ( P≤5×10-8 ) raSNPs, plus proxies. We found that no raSNP mapped to a miRNA gene, suggesting that altered miRNA targeting is an unlikely mechanism involved in BC risk. Also, 11.5% (6 out of 52) raSNPs located in 3'-untranslated regions of putative miRNA target genes were predicted to alter miRNA::mRNA (messenger RNA) pair binding stability in five candidate target genes. Of these, we propose RNF115, at locus 1q21.1, as a strong novel target gene associated with BC risk, and reinforce the role of miRNA-mediated cis-regulation at locus 19p13.11. We believe that integrating allele-specific querying in miRNA-binding prediction, and data supporting cis-regulation of expression, improves the identification of candidate target genes in BC risk, as well as in other common cancers and complex diseases.Funding Agency Portuguese Foundation for Science and Technology CRESC ALGARVE 2020 European Union (EU) 303745 Maratona da Saude Award DL 57/2016/CP1361/CT0042 SFRH/BPD/99502/2014 CBMR-UID/BIM/04773/2013 POCI-01-0145-FEDER-022184info:eu-repo/semantics/publishedVersio

Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation

During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual.In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively.These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation

The Presence of the Iron-Sulfur Motif Is Important for the Conformational Stability of the Antiviral Protein, Viperin

Viperin, an antiviral protein, has been shown to contain a CX3CX2C motif, which is conserved in the radical S-adenosyl-methionine (SAM) enzyme family. A triple mutant which replaces these three cysteines with alanines has been shown to have severe deficiency in antiviral activity. Since the crystal structure of Viperin is not available, we have used a combination of computational methods including multi-template homology modeling and molecular dynamics simulation to develop a low-resolution predicted structure. The results show that Viperin is an α -β protein containing iron-sulfur cluster at the center pocket. The calculations suggest that the removal of iron-sulfur cluster would lead to collapse of the protein tertiary structure. To verify these predictions, we have prepared, expressed and purified four mutant proteins. In three mutants individual cysteine residues were replaced by alanine residues while in the fourth all the cysteines were replaced by alanines. Conformational analyses using circular dichroism and steady state fluorescence spectroscopy indicate that the mutant proteins are partially unfolded, conformationally unstable and aggregation prone. The lack of conformational stability of the mutant proteins may have direct relevance to the absence of their antiviral activity