Site Usage Research Articles

Comprehensive Analysis of APA Events and Their Association With Tumor Microenvironment in Lung Adenocarcinoma.

BackgroundAlternative polyadenylation (APA) is a pervasive posttranscriptional mechanism regulating gene expression. However, the specific dysregulation of APA events and its potential biological or clinical significance in lung adenocarcinoma (LUAD) remain unclear.MethodsHere, we collected RNA-Seq data from two independent datasets: GSE40419 (n = 146) and The Cancer Genome Atlas (TCGA) LUAD (n = 542). The DaPars algorithm was employed to characterize the APA profiles in tumor and normal samples. Spearman correlation was used to assess the effects of APA regulators on 3′ UTR changes in tumors. The Cox proportional hazard model was used to identify clinically relevant APA events and regulators. We stratified 512 patients with LUAD in the TCGA cohort through consensus clustering based on the expression of APA factors.FindingsWe identified remarkably consistent alternative 3′ UTR isoforms between the two cohorts, most of which were shortened in LUAD. Our analyses further suggested that aberrant usage of proximal polyA sites resulted in escape from miRNA binding, thus increasing gene expression. Notably, we found that the 3′ UTR lengths of the mRNA transcriptome were correlated with the expression levels of APA factors. We further identified that CPSF2 and CPEB3 may serve as key regulators in both datasets. Finally, four LUAD subtypes according to different APA factor expression patterns displayed distinct clinical results and oncogenic features related to tumor microenvironment including immune, metabolic, and hypoxic status.InterpretationOur analyses characterize the APA profiles among patients with LUAD and identify two key regulators for APA events in LUAD, CPSF2 and CPEB3, which could serve as the potential prognostic genes in LUAD.

Drivers of online social media addiction in the context of public unrest: A sense of virtual community perspective

During periods of public unrest, people tend to increase their daily usage of social media sites, such as Facebook, Instagram, or WhatsApp, to keep themselves abreast of developments and share their opinions. Over the last trimester of 2019, there were many demonstrations of public unrest in Latin-American countries, including Ecuador, Chile, and Bolivia. These events boosted the social media use. Individuals are exposed to information that is more sensitive and engaging than what is encountered in less agitated times. For instance, images of clashes between demonstrators and police, graphic violence, fake news, and accusations become more plentiful. The increased online interaction and the engaging nature of information during extended periods of public unrest may encourage the development of social media addiction. This study explores the sense of virtual community theory and uses self-assertion as moderator to capture the drivers of online social media addiction in the context of public unrest. Results reveal that immersion has a significant association with addiction, and self-assertion moderates the relationship between influence and membership.

SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

BackgroundChAdOx1 nCoV-19 is a recombinant adenovirus vaccine against SARS-CoV-2 that has passed phase III clinical trials and is now in use across the globe. Although replication-defective in normal cells, 28 kbp of adenovirus genes is delivered to the cell nucleus alongside the SARS-CoV-2 S glycoprotein gene.MethodsWe used direct RNA sequencing to analyse transcript expression from the ChAdOx1 nCoV-19 genome in human MRC-5 and A549 cell lines that are non-permissive for vector replication alongside the replication permissive cell line, HEK293. In addition, we used quantitative proteomics to study over time the proteome and phosphoproteome of A549 and MRC5 cells infected with the ChAdOx1 nCoV-19 vaccine.ResultsThe expected SARS-CoV-2 S coding transcript dominated in all cell lines. We also detected rare S transcripts with aberrant splice patterns or polyadenylation site usage. Adenovirus vector transcripts were almost absent in MRC-5 cells, but in A549 cells, there was a broader repertoire of adenoviral gene expression at very low levels. Proteomically, in addition to S glycoprotein, we detected multiple adenovirus proteins in A549 cells compared to just one in MRC5 cells.ConclusionsOverall, the ChAdOx1 nCoV-19 vaccine’s transcriptomic and proteomic repertoire in cell culture is as expected. The combined transcriptomic and proteomics approaches provide a detailed insight into the behaviour of this important class of vaccine using state-of-the-art techniques and illustrate the potential of this technique to inform future viral vaccine vector design.

Genome-wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis.

Heterochromatin is widespread in eukaryotic genomes and has diverse impacts depending on its genomic context. Previous studies have shown that a protein complex, the ASI1-AIPP1-EDM2 (AAE) complex, participates in polyadenylation regulation of several intronic heterochromatin-containing genes. However, the genome-wide functions of AAE are still unknown. Here, we show that the ASI1 and EDM2 mostly target the common genomic regions on a genome-wide level and preferentially interacts with genetic heterochromatin. Polyadenylation (poly(A) sequencing reveals that AAE complex has a substantial influence on poly(A) site usage of heterochromatin-containing genes, including not only intronic heterochromatin-containing genes but also the genes showing overlap with heterochromatin. Intriguingly, AAE is also involved in the alternative splicing regulation of a number of heterochromatin-overlapping genes, such as the disease resistance gene RPP4. We provided evidence that genic heterochromatin is indispensable for the recruitment of AAE in polyadenylation and splicing regulation. In addition to conferring RNA processing regulation at genic heterochromatin-containing genes, AAE also targets some transposable elements (TEs) outside of genes (including TEs sandwiched by genes and island TEs) for epigenetic silencing. Our results reveal new functions of AAE in RNA processing and epigenetic silencing, and thus represent important advances in epigenetic regulation.

Why students use social networks for education: Extension of UTAUT2

Social networks sites have a considerable impact on all our life aspects, especially the educational sector. This study aims at identifying the factors affecting students’ actual usage of social networks sites for educational purposes in Jordanian universities. The proposed model consists factors of UTAUT2 theory (Effort expectancy, Performance expectancy, Social influence, Facilitating condition, Habit, Hedonic motivation). In addition to two added factors (lecturer support, and student-related factors) as an extension. The study was conducted in (6) Jordanian universities, where (381) questionnaires were returned from the study sample with a response rate of (95%) from the total questionnaires that were distributed online. The results showed that (Performance expectancy, Social influence, Effort expectancy, Habit, lecturer support, and student-related factors) have a positive impact on the actual usage of social networks sites for educational purposes in Jordanian universities, while the factors (Facilitating condition and Hedonic motivation) don’t support their hypotheses).

McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data.

MotivationAlternative splicing removes intronic sequences from pre-mRNAs in alternative ways to produce different forms (isoforms) of mature mRNA. The composition of expressed transcripts gives specific functionalities to cells in a particular condition or developmental stage. In addition, a large fraction of human disease mutations affect splicing and lead to aberrant mRNA and protein products. Current methods that interrogate the transcriptome based on RNA-seq either suffer from short-read length when trying to infer full-length transcripts, or are restricted to predefined units of alternative splicing that they quantify from local read evidence.ResultsInstead of attempting to quantify individual outcomes of the splicing process such as local splicing events or full-length transcripts, we propose to quantify alternative splicing using a simplified probabilistic model of the underlying splicing process. Our model is based on the usage of individual splice sites and can generate arbitrarily complex types of splicing patterns. In our implementation, McSplicer, we estimate the parameters of our model using all read data at once and we demonstrate in our experiments that this yields more accurate estimates compared to competing methods. Our model is able to describe multiple effects of splicing mutations using few, easy to interpret parameters, as we illustrate in an experiment on RNA-seq data from autism spectrum disorder patients.Availability and implementationMcSplicer source code is available at https://github.com/canzarlab/McSplicer and has been deposited in archived format at https://doi.org/10.5281/zenodo.4449881.Supplementary information Supplementary data are available at Bioinformatics online.

MMADHC premature termination codons in the pathogenesis of cobalamin D disorder: Potential of translational readthrough reconstitution

Mutations in the MMADHC gene cause cobalamin D disorder (cblD), an autosomal recessive inborn disease with defects in intracellular cobalamin (cbl, vitamin B12) metabolism. CblD patients present methylmalonic aciduria (MMA), homocystinuria (HC), or combined MMA/HC, and usually suffer developmental delay and cognitive deficits. The most frequent MMADHC genetic alterations associated with disease generate MMADHC truncated proteins, in many cases due to mutations that create premature termination codons (PTC). In this study, we have performed a comprehensive and global characterization of MMADHC protein variants generated by all annotated MMADHC PTC mutations in cblD patients, and analyzed the potential of inducible translational PTC readthrough to reconstitute MMADHC biosynthesis. MMADHC protein truncation caused by disease-associated PTC differentially affected the alternative usage of translation initiation sites, protein abundance, and subcellular localization of MMADHC. Aminoglycoside compounds induced translational PTC readthrough of MMADHC truncated variants, allowing the biosynthesis of full-length MMADHC in a PTC-specific manner. Our results suggest that translational PTC readthrough-based interventions could complement current therapies for cblD patients carrying specific MMADHC PTC mutations.

Molecular and functional diversity of the oxytocinase subfamily of M1 aminopeptidases.

The placental leucine aminopeptidase/insulin-regulated aminopeptidase, endoplasmic reticulum aminopeptidase 1 and endoplasmic reticulum aminopeptidase 2 are part of a distinct subfamily of M1 aminopeptidases termed the 'oxytocinase subfamily'. The subfamily members show molecular diversity due to differential usage of translation initiation sites, alternative splicing and multiple single nucleotide polymorphisms. It is becoming evident that, depending on their intracellular or extracellular location, members of the oxytocinase subfamily play important roles in the maintenance of homeostasis, including the regulation of blood pressure, maintenance of normal pregnancy, retention of memory and trimming of antigenic peptides presented to major histocompatibility complex class I molecules, by acting as either aminopeptidases or binding partners of specific functional proteins in the cells. Based on their molecular diversity and moonlighting protein-like properties, it is conceivable that the subfamily members exert pleiotropic effects during evolution, to become important players in the regulation of homeostasis.

McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data

McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data

Information Disclosure and Control on Online Social Network Sites among Medical Undergraduates

Introduction: Internet usage has become a big part of many people’s lives, and among the many uses SocialNetworking Sites (SNS) which became very prevalent. How privacy concerns, trust and control are affectingSNS usage and self-disclosure has become an important question for many people.Aim: Aim of the study is to assess the information disclosure and control on online social network sitesamong medical undergraduates.Methodology: The study was conducted at Saveetha medical college and hospital among medicalundergraduates. A questionnaire on usage of online social networks and information disclosures wasadministered and analysed it for reliability, social network site usage, privacy concerns, and disclosure ofautobiographical memories.Result: Almost 81.1% of the people feel that their browsing history were tracked by social networking sites.Instagram is mainly used app by medical undergraduates (40%).Conclusion: There is an excess usage of social networking sites and easy information disclosure is seen inthe population.

Link between social distancing, cognitive dissonance, and social networking site usage intensity: a country-level study during the COVID-19 outbreak

PurposeSocial distancing is an important strategy to control the spread of the COVID-19 pandemic, so it is imperative to understand the behavioral impact of social distancing on individuals. This research studied social distancing from a cognitive appraisal of voluntary social distancing compliance (CAVSD) point of view and a non-medical perspective, specifically the psychological impact (PI) of social distancing on the usage intensity of social networking sites (SNS) during the COVID-19 outbreak in India.Design/methodology/approachThe study was conducted on 477 SNS users as a full sample and groups based on age, sex and work status. The model was empirically investigated using structural equation modeling.FindingsCAVSD was negatively associated with PI although it was not a significant predictor, while CAVSD and PI were significant predictors of SNS usage intensity; moreover, SNS usage intensity differed between groups of people.Practical implicationsThese findings are significant for organizations, corporations and educational institutions in both the public and private sectors. There is a need to identify subsections of individuals in need of social support and relief from isolation and loneliness. Individuals are relying on social media to handle social distancing and the pandemic, and this shows up in an increase in social networking activity.Originality/valueThis study contributes to the existing literature by positing social networking as a basic virtual need for socialization, and social media platform assists in that. Cognitive appraisal is an important determinant of individual response.

Judicial answers to cyber intimidation and sexting

The availability and usage of social networking sites provide both possibilities and dangers for their young users, depending on their circumstances. Using the examples of (cyber)bullying and sexting, this essay examines the relevance of the existing legal framework to these two kinds of (possibly harmful) behaviour that are increasingly happening amongst peers in the social networking environment. It includes a mapping of applicable legislative provisions at the European and national levels, an analysis of the Terms of Service of the largest social networking provider, Facebook, as well as an overview and assessment of self-regulatory initiatives taken by the industry in this area in Europe, among other things. Overall, the aim is to establish a number of components for a complete plan to make certain that the dangers of (cyber)bullying and sexting are addressed in a way that empowers young users.

Tracing Digital Fragmentation at the User Level: Gen Y & Gen Z from a European Perspective

This study compares the usage of Social Networking Sites (SNS) in two non-Anglophone settings. A longitudinal mixed-method approach was designed to gather data face-to-face with Gen Y and Gen Z participants in Lyon (France) and St Petersburg (Russia) between 2011 and 2018, by means of survey, forum and focus groups. The initial differences observed in user behaviour were no longer apparent by 2018. Noticeably similar user behaviour reflected converging SNS consumption. From the findings, we identify socio-technical changes that influence SNS usage, in order to produce a typology of user behaviours for identifying user segments.

The Mediating Effect of Bridging Social Capital Between Social Media Usage and Affective Attitude

In this work, the authors develop and test a theoretical model that investigates the mediating effect of bridging social capital between usage of a brand specific social network site and consumer attitude towards the brand. Specifically, they see how usage of online social network sites drives consumer purchase intent, using university football as a domain to test the model. They find that bridging social capital is indeed a mediating construct between the university's sports social networking site usage and affective attitude towards the team brand. As social network site usage increases, both injunctive norms (perceptions about the expectations of referent others) and descriptive norms (perceptions of the actual behavior of referent others) increase. They show that these influence emotional reward, in the form of increased bridging social capital, which in turn influences affective attitude towards the brand. The findings contribute to understanding how consumer tribes form on online forums and how subjective norms influence affective consumer attitude.

Scale Development and Validation for Usage of Social Networking Sites During Covid-19

Scale Development and Validation for Usage of Social Networking Sites During Covid-19

Profiles of Emerging Adult Online Daters and Psychosocial Cognitions about Condom Use

Online dating provides emerging adults with a way of connecting with others more frequently and efficiently than traditional courtship. Online dating sites pose opportunities for relationships and sexual encounters, which may be accompanied by engagement in sexual risk behaviors, such as lack of condom use. The present study used the theory of planned behavior to explore psychosocial cognitions (i.e. constructs) about condom use among online daters. The sample size consisted of N = 156 emerging adults (Mage = 20.6) who participated in an online survey of health behaviors and sexual risk. Using attitudes, subjective norms, and self-efficacy about condom use, latent class analysis identified four latent classes: Consistent Condom Users (17%), Inconsistent Condom Users with Low Dating Site Usage (23%), Inconsistent Condom Users with High Dating Site Usage (40%), and Consistent Condom Non-Users (20%). Consistent Condom Non-Users had the highest probability of utilizing dating sites 2+ hours per day, the highest probability of low self-efficacy and low subjective norms about condom use, and a zero probability of using a condom. Inconsistent Condom Users with Low Dating Site Usage and Inconsistent Condom Users with High Dating Site Usage varied in their attitudes and self-efficacy toward condom use. Consistent Condom Users were low on dating site usage, high on all psychosocial constructs, and had a 100% probability of using a condom. Results highlight the need to further explore interventions throughout college campuses and online within dating sites, to strengthen attitudes, subjective norms, and self-efficacy toward condom use among online dating emerging adults.

Modulation of alternative cleavage and polyadenylation events by dCas9-mediated CRISPRpas.

The CRISPR/Cas9 technology is revolutionizing genomic engineering. The high efficiency and selectivity of the system have inspired the development of various derived tools for gene regulation at different levels, such as transcriptional activation or inhibition, epigenetic modification, splicing, and base editing. Cleavage and polyadenylation (CPA) is an essential 3' end maturation step for almost all eukaryotic mRNAs. CPA is tightly coupled with transcriptional termination, and its activity impacts gene expression. Over half of all human genes display alternative polyadenylation (APA), where multiple cleavage and polyadenylation sites (PASs) lead to mRNA isoforms with variable termini. APA isoforms often have distinct metabolisms, and their relative abundance can change drastically in different cells. Here, we describe a method based on delivering a catalytically dead Cas9 (dCas9) to genomic regions nears the PAS, which alters APA site usage in 3'UTRs or introns. This method, named CRISPRpas, allows investigators to examine functional significance of APA isoforms of individual genes. We also describe using the bioinformatics program APAlyzer to examine APA events of interest with RNA-seq data.

Modifying splice site usage with ModCon: Maintaining the genetic code while changing the underlying mRNP code

Codon degeneracy of amino acid sequences permits an additional “mRNP code” layer underlying the genetic code that is related to RNA processing. In pre-mRNA splicing, splice site usage is determined by both intrinsic strength and sequence context providing RNA binding sites for splicing regulatory proteins. In this study, we systematically examined modification of splicing regulatory properties in the neighborhood of a GT site, i.e. potential splice site, without altering the encoded amino acids.We quantified the splicing regulatory properties of the neighborhood around a potential splice site by its Splice Site HEXplorer Weight (SSHW) based on the HEXplorer score algorithm. To systematically modify GT site neighborhoods, either minimizing or maximizing their SSHW, we designed the novel stochastic optimization algorithm ModCon that applies a genetic algorithm with stochastic crossover, insertion and random mutation elements supplemented by a heuristic sliding window approach.To assess the achievable range in SSHW in human splice donors without altering the encoded amino acids, we applied ModCon to a set of 1000 randomly selected Ensembl annotated human splice donor sites, achieving substantial and accurate changes in SSHW. Using ModCon optimization, we successfully switched splice donor usage in a splice site competition reporter containing coding sequences from FANCA, FANCB or BRCA2, while retaining their amino acid coding information.The ModCon algorithm and its R package implementation can assist in reporter design by either introducing novel splice sites, silencing accidental, undesired splice sites, and by generally modifying the entire mRNP code while maintaining the genetic code.

Placemaking Based on Site Experience—Landscape Design of Parkhill Commons in Shenzhen

Placemaking of public open spaces, such as community parks and streetscapes that are foundational to residents’ daily social and recreational life, can significantly influence their site experience. Scholars have explored the influence of such kind of experience on users’ behavioral, physical, and mental conditions from multiple perspectives including attention restoration and stress reduction. However, the findings are seldom applied in practice to convey certain design concepts. This article introduces the landscape design project of Parkhill Commons in Shenzhen. The project team reviewed relevant research findings, and characterized the health-promoting restorative environment and social-capital-friendly communities. Accordingly, strategies for activity zones, planting design, service facilities, and slow-traffic neighborhoods were proposed to enhance site experience and serve nearby residents by creating vital and pleasant community-level public open spaces, and to maximize the social benefits and reinforce community cohesion. After completion, the project team has investigated the site usage and the public’s evaluation, in order to stimulate reflections on design strategies. Results from the questionnaire survey and field observation show the effect of placemaking strategies on users’ site experience. This article provides references for placemaking practice of community-level public open spaces and is expected to help bridge the gap between theoretical research and design practice.

HuD regulates SOD1 expression during oxidative stress in differentiated neuroblastoma cells and sporadic ALS motor cortex

The neuronal RNA-binding protein (RBP) HuD plays an important role in brain development, synaptic plasticity and neurodegenerative diseases such as Parkinson's (PD) and Alzheimer's (AD). Bioinformatics analysis of the human SOD1 mRNA 3′ untranslated region (3′UTR) demonstrated the presence of HuD binding adenine-uridine (AU)-rich instability-conferring elements (AREs). Using differentiated SH-SY5Y cells along with brain tissues from sporadic amyotrophic lateral sclerosis (sALS) patients, we assessed HuD-dependent regulation of SOD1 mRNA. In vitro binding and mRNA decay assays demonstrate that HuD specifically binds to SOD1 ARE motifs promoting mRNA stabilization. In SH-SY5Y cells, overexpression of full-length HuD increased SOD1 mRNA and protein levels while a dominant negative form of the RBP downregulated its expression. HuD regulation of SOD1 mRNA was also found to be oxidative stress (OS)-dependent, as shown by the increased HuD binding and upregulation of this mRNA after H2O2 exposure. This treatment also induced a shift in alternative polyadenylation (APA) site usage in SOD1 3'UTR, increasing the levels of a long variant bearing HuD binding sites. The requirement of HuD for SOD1 upregulation during oxidative damage was validated using a specific siRNA that downregulated HuD protein levels to 36% and prevented upregulation of SOD1 and 91 additional genes. In the motor cortex from sALS patients, we found increases in SOD1 and HuD mRNAs and proteins, accompanied by greater HuD binding to this mRNA as confirmed by RNA-immunoprecipitation (RIP) assays. Altogether, our results suggest a role of HuD in the post-transcriptional regulation of SOD1 expression during ALS pathogenesis.