bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detoxification of endogenous serine prevents cell lysis upon glucose depletion in bacteria
Authors: Kriner Michelle A. , Subramaniam Arvind R. 
Published: June 2018

AbstractThe amino acid serine, despite its diverse metabolic roles, can become toxic when present in excess. Indeed, many bacteria rapidly deaminate exogenously supplied serine into pyruvate and ammonia, even at the expense of biomass production. Here we report a surprising case in which endogenously produced serine must be detoxified in order for the bacteriumEscherichia colito survive. Specifically, we show thatE. colicells lacking thesdaCBoperon, which encodes a serine transporter and a serine deaminase, lyse upon glucose depletion when serine is absent from the growth medium. Lysis can be prevented by omission of glycine or by inhibition of the glycine cleavage system, suggesting that activation of glycine catabolism upon glucose depletion causes a transient increase in intracellular serine levels. Heterologous expression of the serine transporter SdaC is sufficient to prevent lysis, indicating a dominant role for serine export, rather than deamination, in mitigating serine toxicity. Since lysis can be modulated by altering alanine availability, we further propose that mis-incorporation of serine instead of alanine into peptidoglycan crosslinks is the cause of lysis. Together, our results reveal that SdaC-mediated detoxification of intracellularly produced serine plays a protective role during sudden shifts in nutrient availability in bacteria.Author summaryThe amino acid serine is a building block used to make many types of macromolecules, yet bacteria actively degrade serine that is provided in growth media. Serine degradation is thought to prevent toxic serine accumulation, but the biological role of this process is not fully understood. We observed that cells lacking thesdaCBoperon, which encodes a serine transporter and an enzyme that converts serine to pyruvate, suddenly lyse upon depletion of glucose from the growth medium. This surprising phenotype occurs only in media lacking serine, suggesting thatsdaCBis required to detoxify intracellularly produced serine. Expression of the serine transporter SdaC is sufficient to prevent lysis, providing the first evidence that serine export can be an essential function of this protein. Our results reveal that sudden shifts in nutrient availability can increase the intracellular concentration of useful metabolites to toxic levels and suggest that increasing intracellular serine levels by manipulating SdaC activity may be a possible antimicrobial strategy.
GLnexus: joint variant calling for large cohort sequencing
Authors: Lin Michael F. , Rodeh Ohad , Penn John , Bai Xiaodong , Reid Jeffrey G. , Krasheninina Olga , Salerno William J. 
Published: June 2018

ABSTRACTAs ever-larger cohorts of human genomes are collected in pursuit of genotype/phenotype associations, sequencing informatics must scale up to yield complete and accurate genotypes from vast raw datasets. Joint variant calling, a data processing step entailing simultaneous analysis of all participants sequenced, exhibits this scaling challenge acutely. We present GLnexus (GL, Genotype Likelihood), a system for joint variant calling designed to scale up to the largest foreseeable human cohorts. GLnexus combines scalable joint calling algorithms with a persistent database that grows efficiently as additional participants are sequenced. We validate GLnexus using 50,000 exomes to show it produces comparable or better results than existing methods, at a fraction of the computational cost with better scaling. We provide a standalone open-source version of GLnexus and a DNAnexus cloud-native deployment supporting very large projects, which has been employed for cohorts of >240,000 exomes and >22,000 whole-genomes.
Codon usage influences fitness through RNA toxicity
Authors: Mittal Pragya , Brindle James , Stephen Julie , Plotkin Joshua B. , Kudla Grzegorz 
Published: June 2018

AbstractMany organisms are subject to selective pressure that gives rise to unequal usage of synonymous codons, known as codon bias. To experimentally dissect the mechanisms of selection on synonymous sites, we expressed several hundred synonymous variants of the GFP gene inEscherichia coli, and used quantitative growth and viability assays to estimate bacterial fitness. Unexpectedly, we found many synonymous variants whose expression was toxic toE. coli. Unlike previously studied effects of synonymous mutations, the effect that we discovered is independent of translation, but it depends on the production of toxic mRNA molecules. We identified RNA sequence determinants of toxicity, and evolved suppressor strains that can tolerate the expression of toxic GFP variants. Genome sequencing of these suppressor strains revealed a cluster of promoter mutations that prevented toxicity by reducing mRNA levels. We conclude that translation-independent RNA toxicity is a previously unrecognized obstacle in bacterial gene expression.Significance statementSynonymous mutations in genes do not change protein sequence, but they may affect gene expression and cellular function. Here we describe an unexpected toxic effect of synonymous mutations inEscherichia coli, with potentially large implications for bacterial physiology and evolution. Unlike previously studied effects of synonymous mutations, the effect that we discovered is independent of translation, but it depends on the production of toxic mRNA molecules. We hypothesize that the mechanism we identified influences the evolution of endogenous genes in bacteria, by imposing selective constraints on synonymous mutations that arise in the genome. Of interest for biotechnology and synthetic biology, we identify bacterial strains and growth conditions that alleviate RNA toxicity, thus allowing efficient overexpression of heterologous proteins.
G-quadruplex forming sequences in the genome of all known human viruses: a comprehensive guide
Authors: Lavezzo Enrico , Berselli Michele , Frasson Ilaria , Perrone Rosalba , Palù Giorgio , Brazzale Alessandra R. , Richter Sara N. , Toppo Stefano 
Published: June 2018

ABSTRACTG-quadruplexes are non-canonical nucleic acid structures that control transcription, replication, and recombination in organisms. G-quadruplexes are present in eukaryotes, prokaryotes, and viruses. In the latter, mounting evidence indicates their key biological activity. Since data on viruses are scattered, we here present a comprehensive analysis of putative G-quadruplexes in the genome of all known viruses that can infect humans. We show that the presence, distribution, and location of G-quadruplexes are features characteristic of each virus class and family. Our statistical analysis proves that their presence within the viral genome is orderly arranged, as indicated by the possibility to correctly assign up to two-thirds of viruses to their exact class based on the G-quadruplex classification. For each virus we provide: i) the list of all G-quadruplexes formed by GG-, GGG- and GGGG-islands present in the genome (positive and negative strands), ii) their position in the viral genome along with the known function of that region, iii) the degree of conservation among strains of each G-quadruplex in its genome context, iv) the statistical significance of G-quadruplex formation. This information is accessible from a database (http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=g4virus) to allow the easy and interactive navigation of the results. The availability of these data will greatly expedite research on G-quadruplex in viruses, with the possibility to accelerate finding therapeutic opportunities to numerous and some fearsome human diseases.
Rhamnolipids fromPseudomonas aeruginosaDisperse the Biofilms of Sulfate-Reducing Bacteria
Authors: Wood Thammajun L. , Zhu Lei , Miller James , Miller Daniel S. , Yin Bei , Wood Thomas K. 
Published: June 2018

ABSTRACTBiofilm formation is an important problem for many industries.Desulfovibrio vulgarisis the representative sulfate-reducing bacterium (SRB) which causes metal corrosion in oil wells and drilling equipment, and the corrosion is related to its biofilm formation. Biofilms are extremely difficult to remove since the cells are cemented in a polymer matrix. In an effort to eliminate SRB biofilms, we examined the ability of supernatants fromPseudomonas aeruginosaPA14 to disperse SRB biofilms. We found that theP. aeruginosasupernatants dispersed more than 98% of the biofilm. To determine the genetic basis of this SRB biofilm dispersal, we examined a series ofP. aeruginosamutants and found that mutantsrhlA,rhlB,rhlI, andrhlR,defective in rhamnolipids production, had significantly reduced levels of SRB biofilm dispersal. Corroborating these results, purified rhamnolipids dispersed SRB biofilms, and rhamnolipids were detected in theP. aeruginosasupernatants. Hence,P. aeruginosasupernatants disperse SRB biofilms via rhamnolipids. In addition, the supernatants ofP. aeruginosadispersed the SRB biofilms more readily than protease in M9 glucose minimum medium and were also effective against biofilms ofEscherichia coliandBacillus subtilis.
clonealign: statistical integration of independent single-cell RNA & DNA-seq from human cancers
Authors: Campbell Kieran R , Steif Adi , Laks Emma , Zahn Hans , Lai Daniel , McPherson Andrew , Farahani Hossein , Kabeer Farhia , O’Flanagan Ciara , Biele Justina , Brimhall Jazmine , Wang Beixi , Walters Pascale ,   IMAXT Consortium, Bouchard-Côté Alexandre , Aparicio Samuel , Shah Sohrab P 
Published: June 2018

AbstractMeasuring gene expression of genomically defined tumour clones at single cell resolution would associate functional consequences to somatic alterations, as a prelude to elucidating pathways driving cell population growth, resistance and relapse. In the absence of scalable methods to simultaneously assay DNA and RNA from the same single cell, independent sampling of cell populations for parallel measurement of single cell DNA and single cell RNA must be computationally mapped for genome-transcriptome association. Here we presentclonealign, a robust statistical framework to assign gene expression states to cancer clones using single-cell RNA-seq and DNA-seq independently sampled from an heterogeneous cancer cell population. We applyclonealignto triple-negative breast cancer patient derived xenografts and high-grade serous ovarian cancer cell lines and discover clone-specific dysregulated biological pathways not visible using either DNA-Seq or RNA-Seq alone.
CRISPRs for strain tracking and its application to microbiota transplantation data analysis
Authors: Lam Tony J. , Ye Yuzhen 
Published: June 2018

AbstractCRISPR-Cas systems are adaptive immune systems naturally found in bacteria and archaea. Bacteria and archaea use these systems to defend against invaders, including phages, plasmids and other mobile genetic elements. Relying on integration of invader sequences (protospacers) into CRISPR loci (forming spacers flanked by repeats), CRISPR-Cas systems store genetic memory of past invasions. While CRISPR-Cas systems have evolved in response to invading mobile elements, invaders have also developed mechanisms to avoid detection. As a result of arms-race between CRISPR-Cas systems and their targets, the CRISPR arrays typically undergo rapid turnover of the spacers with removal of old spacers and acquisition of new ones. Additionally, different individuals rarely share spacers amongst their microbiome. In this paper, we developed a pipeline (called CRISPRtrack) for strain tracking based on CRISPR spacer content, and applied it to fecal transplantation microbiome data to study the retention of donor strains in recipients. Our results demonstrate the potential use of CRISPRs as a simple yet effective tool for donor strain tracking in fecal transplantation, and also as a general purpose tool for quantifying microbiome similarity.
From Cadbury to Kay: discourse, intertextuality and the evolution of UK corporate governance
Authors: Price Michael , Harvey Charles , Maclean Mairi , Campbell David 
Published: June 2018

PurposeThe purpose of this paper is to answer two main research questions. First, the authors ask the degree to which the UK corporate governance code has changed in response to both systemic perturbations and the subsequent enquiries established to recommend solutions to perceived shortcomings. Second, the authors ask how the solutions proposed in these landmark governance texts might be explained.Design/methodology/approachThe authors take a critical discourse approach to develop and apply a discourse model of corporate governance reform. The authors draw together data on popular, corporate-political and technocratic discourses on corporate governance in the UK and analyse these data using content analysis and the historical discourse approach.FindingsThe UK corporate governance code has changed little despite periodic crises and the enquiries set up to investigate and make recommendation. Institutional stasis, the authors find, is the product of discourse capture and control by elite corporate actors aided by political allies who inhabit the same elite habitus. Review group members draw intertextually on prior technocratic discourse to create new canonical texts that bear the hallmarks of their predecessors. Light touch regulation by corporate insiders thus remains the UK approach.Originality/valueThis is one of the first applications of critical discourse analysis in the accounting literature and the first to have conducted a discursive analysis of corporate governance reports in the UK. The authors present an original model of discourse transitions to explain how systemic challenges are dissipated.
Effects of blackening parameters on the formation and adhesion of oxide on AISI 4140 steel
Authors: Chandra-ambhorn Somrerk , Srihirun Sermsak , Siripongsakul Thamrongsin 
Published: June 2018

Purpose
The purpose of this study is to investigate the aesthetic blackening coating formed by a hydrothermal process, focusing on the formation of magnetite and the oxide adhesion for improving the corrosion resistance of the steel.

Design/methodology/approach
The aesthetic black coating was applied on AISI 4140 steel using a hydrothermal process with a non-toxic solution consisted of ferrous sulphate hydrate (FeSO4·7H2O), sodium hydroxide (NaOH) and hydrazine hydrate (N2H4·H2O). Upon process parameters temperature and time, the morphology of the coatings and oxidation kinetics were investigated by using scanning electron microscopy and X-ray diffraction (XRD) analysis. Furthermore, the samples with coatings were subjected to the adhesion test using a tensile testing machine equipped with a charge-coupled device (CCD) camera.

Findings
From the formation parameters due to temperature and time for the conversion coatings, it was found that the oxidation kinetics had special characteristics which were in accordance with a linear rate law and Arrhenius relation. For the samples blackened, the XRD analysis results revealed that the magnetite was successfully formed on the surface of the steel. On the other hand, increasing the blackening temperature worsened the scale adhesion as observed by the lower strain provoking the first spallation and the higher sensitivity of the oxide to spall out with the imposed strain.

Originality/value
The effects of parameters of the formation of conversion coatings were investigated to understand the kinetics of the coatings. Furthermore, a tensile adhesion test using a CCD camera was applied to evaluate the adhesion between the native oxide formed by conversion coating.
The role of spirituality in alcohol abstinence self-efficacy amongst alcoholics anonymous members
Authors: Bluma Liene 
Published: June 2018

Purpose
Previous research indicates that Alcoholics Anonymous (AA) can play an effective role in alcohol use disorder recovery (Kelly, Stout, Magill, Tonigan and Pagano, 2011). Acceptance of a “Higher Power” and experiencing a “spiritual awakening” are essential components of AA recovery programme (Alcoholics Anonymous World Service, 2014). The purpose of this paper is to identify if there are high associations in levels of spirituality and alcohol abstinence self-efficacy (AASE) measures amongst AA members.

Design/methodology/approach
Self-reported measures were collected from members of AA of their spiritual and religious beliefs and their everyday experiences of alcohol abstinence. Demographic information of participant’s ethnical background, age and length of AA membership was also obtained.

Findings
The analysis revealed high levels of spirituality amongst participants with a mean of 70.14 (2dp). There was no difference in participant high or low spiritual beliefs and their attitude towards alcohol abstinence. The frequency measures of spiritual activities showed that 73.7 per cent of participants engage in private spiritual or religious activities more than once a week.

Originality/value
Overall the study supports previously conduced researches in the field of spirituality and AASE amongst AA members when considering other variables associated with sustained sobriety. The implications of the results of this study are discussed and suggestions have been made for further investigation.
Respecting the language: digitizing Native American language materials
Authors: Wise Mary , Kostelecky Sarah R. 
Published: June 2018

Purpose
Many academic libraries use digital humanities projects to disseminate unique materials in their collections; during project planning, librarians will consider platforms, scanning rates and project sustainability. Rarely, though, will academic librarians consider how members from the communities that created the materials can contribute to digitization projects. The purpose of this study is to explain how collaboration with Zuni Pueblo (a Native American tribe in the southwest) community members improved a digital humanities project to disseminate Zuni language learning materials.

Design/methodology/approach
Methodologically relying on critical making, which involved community member feedback throughout the process, the Zuni Language Materials Collection will provide digital access to 35 language learning items.

Findings
The authors argue that collaboration with members of the community of creation dramatically improved item description, collection discoverability and collection interactivity. This study historicizes CONTENTdm and describes how the team modified this content management system to meet user needs. This project produced a prototype digital collection, collaboratively authored metadata and an interactive portal that invites users to engage with the collection.

Practical implications
Libraries continue to struggle to reach and reflect their diverse users. This study describes a process that others may use and modify to engage nearby Native American communities.

Originality/value
This piece shares a unique strategy of partnering with Native American community members on all aspects of digital humanities project development and design. This case study attempts to fill a gap in the literature as the first study to describe a digitization process using CONTENTdm with a Native American community.
Factors inhibiting the internet adoption by base of the pyramid in India
Authors: Chauhan Sumedha , Gupta Parul , Jaiswal Mahadeo 
Published: June 2018

Purpose
This paper aims to explore the factors inhibiting the internet adoption among base of pyramid (BoP) and to develop further insights of such factors.

Design/methodology/approach
Researchers used a mixed-method study with QUAL/QUAN sequence in this research. Given the dearth of research on the internet usage by the BoP segment in India, the authors began with the exploratory qualitative study. Semi-structured interviews in local language were carried out with the people belonging to the BoP segment in India using common interview protocol. Face-to-face interviews were conducted for 20-30 min with ten people. Thematic analysis (Braun and Clarke, 2006) was conducted on the interview transcripts which lead to five themes. These themes were identified as the potential inhibitors to the internet adoption by the BoP segment in India. This step was further followed by a confirmatory quantitative study.

Findings
The results confirm that the factors such as lack of digital literacy, complexity and language barrier play a significant role in inhibiting the internet adoption by the BoP segment. However, there is no impact of perceived risk and cost on the internet adoption. The significant relationship between lack of digital literacy and intention to use implies that if the BoP segment is capable to locate, evaluate and use digital information, it is more likely to use the internet. Similarly, the relationship between complexity and the intention to use suggests that if the BoP segment finds it easy to use and understand the internet, it is more likely to use it.

Practical implications
This research has the implications for government departments and policymakers that are responsible for promoting use of the internet. Therefore, such departments and policymakers are advised to channelize their effort on resting the digital literacy, especially in terms of internet adoption. Findings of this study show that digital literacy, complexity and language barriers are major inhabitants in the internet adoption. Directed and focused government policies and initiatives such as subsidized seminars and training programmes specially designed for the BoP segment can help in increasing internet adoption.

Social implications
The adoption and use of the internet services by BoP have major implications for digital equality. Therefore, it would be important to explore the factors inhibiting the internet adoption among BoP.

Originality/value
This paper not only explores the factors inhibiting internet adoption among BoP in developing countries such as India but also provides deeper insights to these factors by collecting first-hand information from target segment. The finding of this research provides meaningful inputs to policymakers and also to industry to remove digital divide in the target population. This is how this research adds value to the existing knowledge available in this domain and it also provides agenda for future research.
The effect of perceived security and grievance redressal on continuance intention to use M-wallets in a developing country
Authors: Kumar Anup , Adlakaha Amit , Mukherjee Kampan 
Published: June 2018

Purpose
Many developing countries, including India, are committed to curbing black money from the economy. Therefore, these countries are focusing on a transparent online transaction facility. M-wallets are one online option facilitated by various companies using a mobile application. The purpose of this paper is to investigate the impact of perceived usefulness, perceived security, perceived ease of use, trust, grievance redressal and satisfaction on young users’ intention to continually use M-wallet in India.

Design/methodology/approach
A research framework based on the expectation–confirmation theory has been formulated and tested empirically using data from M-wallets young users in India using structural equation modeling.

Findings
The analysis reveals that perceived usefulness and perceived ease of use significantly affect user satisfaction and intention to continually use M-wallets. The effect of perceived security on user satisfaction is significant, and grievance redressal mediates the effect of perceived security on intention to continually use M-wallets.

Practical implications
The outcome of the research will help M-wallet service providers and policy makers in planning the service and increasing customer’ continuance intention.

Originality/value
The uniqueness of this research is that it adds two important constructs for mobile payment systems (grievance redressal and perceived security) that were missing in the earlier model proposed by Zhou (2013). The addition of the two constructs helped in formulating a better model.