bluuebunny/crossref_metadata_2025_split huggingface dataset:
NickSeq for genome-wide strand-specific identification of DNA single-strand break sites with single nucleotide resolution
Authors: Elacqua Joshua J. , Ranu Navpreet , Dilorio Sarah E. , Blainey Paul C. 
Published: December 2019

ABSTRACTDNA single-strand breaks (SSBs), or ‘nicks’, are the most common form of DNA damage. Nicks occur at rates of tens of thousands per cell per day, and result from many sources including oxidative stress and endogenous enzyme activities. Accumulation of nicks, due to high rates of occurrence or defects in repair enzymes, has been implicated in multiple diseases. However, improved methods for nick analysis are needed to learn how their locations and number affect cells, disease progression, and health outcomes. In addition to natural processes including DNA repair, leading genome-editing technologies rely on nuclease activity, including nick generation, at target sites. There is currently a pressing need for methods to study unintended nicking activity genome-wide to evaluate the impact of emerging genome editing tools on cells and organisms. Here we developed a new method, NickSeq, for efficient strand-specific profiling of nicks in complex DNA samples with single nucleotide resolution and low false-positive rates. NickSeq produces deep sequence datasets enriched for reads near nick sites and establishes a readily detectable mutational signal that allows for determination of the nick site and strand. In this work, we apply NickSeq to profile off-target activity of the Nb.BsmI nicking endonuclease and an engineered spCas9 nickase. NickSeq will be useful in exploring the relevance of spontaneously occurring or repair-induced DNA breaks in human disease, DNA breaks caused by DNA damaging agents including therapeutics, and the activity of engineered nucleases in genome editing and other biotechnological applications.
Crystal structure of the membrane anchoring domain of mycobacterial Wag31: a dimer-of-dimer suggests how a Wag31 filament might self-assemble
Authors: Choukate Komal , Chaudhuri Barnali 
Published: December 2019

AbstractWag31, or DivIVA, is an essential protein and a drug target in human pathogen Mycobacterium tuberculosis that self-assembles at the negatively curved membrane surface to form a higher-order structural scaffold, maintains rod-shaped cellular morphology, and localizes key cell-wall synthesizing proteins at the pole for exclusive polar growth. We determined the crystal structure of N-terminal membrane anchoring domain of mycobacterial Wag31 at 2.3 Å resolution using molecular replacement method. Crystal packing analysis revealed a previously unseen dimer-of-dimer assembly state of N-terminal Wag31 with C2 point group symmetry, which is formed by antiparallel stacking of two coiled coil dimers. Size-exclusion column chromatography-coupled small angle solution X-ray scattering data showed a tetrameric form as a major assembly state of N-terminal Wag31 in solution, further supporting the crystal structure. Plausible models of linear self-assembling, and branching, of Wag31 filaments consistent with available data are suggested.
Cultivation and characterization of human midbrain organoids in sensor integrated microfluidic chips
Authors: Spitz Sarah , Zanetti Cristian , Bolognin Silvia , Muwanigwa Mudiwa Nathasia , Smits Lisa , Berger Emanuel , Jordan Christian , Harasek Michael , Schwamborn Jens C. , Ertl Peter 
Published: December 2019

1.ABSTRACTWith its ability to emulate microarchitectures and functional characteristics of native organs in vitro, induced pluripotent stem cell (iPSC) technology has enabled the generation of a plethora of organotypic constructs, including that of the human midbrain. However, reproducibly engineering and differentiating such human midbrain organoids (hMOs) under a biomimetic environment favorable for brain development still remains challenging. This study sets out to address this problem by combining the potential of iPSC technology with the advantages of microfluidics, namely its precise control over fluid flow combined with sensor integration. Here, we present a novel sensor-integrated platform for the long-term cultivation and non-invasive monitoring of hMOs under an interstitial flow regime. Our results show that dynamic cultivation of iPSC-derived hMOs maintains high cellular viabilities and dopaminergic neuron differentiation over prolonged cultivation periods of up to 50 days.
Analysis of co-regulated abundance of genes associated with arsenic and phosphate metabolism in Andean Microbial Ecosystems
Authors: Saona L.A. , Valenzuela-Diaz S. , Kurth D. , Contreras M. , Meneses C. , Castro-Nallar E. , Farías M.E. 
Published: December 2019

AbstractPhosphate and arsenate are very similar compounds, and there is great interest in studying their relationship and their interaction with biological systems. Despite having no apparent biological function, specific genes regulate arsenic interaction with cells and can be located in regions of the genome called arsenic islands, where phosphate metabolism genes are also present. Although they are neighboring genes, the nature of their relationship and how they have been selected is still unknown.In this work, we analyzed the metagenomes of the four microbial ecosystems inhabiting hypersaline lakes of the Argentine Puna and the Atacama salt flat in Chile and have evaluated the presence and abundance of both arsenic and phosphate metabolism genes. The samples analyzed included microbialites, biofilms and microbial mats; all of them established under high arsenic concentrations, high UV radiation and high temperature fluctuation, among others.The results show great differences in the dispersion and abundance of genes related to both phosphate and arsenic metabolism in the analyzed samples. The main difference is given in the Diamante Lake, located in the crater of the Galan volcano characterized by being one of the lakes with the highest arsenic concentration (2.34 mM). Correlating genes abundance with the physicochemical parameters of the lakes studied, our results suggest that arsenic and phosphate metabolism are intricately co-regulated in environmental conditions.
Analysis of Mammalian Succinate Dehydrogenase Kinetics and Reactive Oxygen Species Production
Authors: Manhas Neeraj , Duong Quynh V. , Lee Pilhwa , Bazil Jason N. 
Published: December 2019

AbstractSuccinate dehydrogenase is an inner mitochondrial membrane protein complex that links the tricarboxylic acid cycle to the electron transport system. It catalyzes the reaction between succinate and ubiquinone to produce fumarate and ubiquinol. In addition, it can produce significant amounts of superoxide and hydrogen peroxide under the right conditions. While the flavin adenine dinucleotide (FAD) is the putative site of reactive oxygen species production, free radical production from other sites are less certain. Herein, we developed a computational model to analyze free radical production data from complex II and identify the mechanism of superoxide and hydrogen peroxide production. The model includes the major redox centers consisting of the FAD, three iron-sulfur clusters, and a transiently catalytic bound semi quinone. The model consists of five-states that represent oxidation status of the enzyme complex. Each step in the reaction scheme is thermodynamically constrained, and transitions between each state involve either one-electron or two-electron redox reactions. The model parameters were simultaneously fit using data consisting of enzyme kinetics and free radical production rates under a range of conditions. In the absence of respiratory chain inhibitors, model analysis revealed that the 3Fe-4S iron-sulfur cluster is the primary source of superoxide production followed by the FAD radical. However, when the quinone reductase site of complex II is inhibited or the quinone pool is highly reduced, superoxide production from the FAD site dominates at low succinate concentrations. In addition, hydrogen peroxide formation from the complex is only significant when these one of these conditions is met and the fumarate concentrations is in the low micromolar range. From the model simulations, the redox state of the quinone pool was found to be the primary determinant of free radical production from complex II. This study highlights the importance of evaluating enzyme kinetics and associated side-reactions in a consistent, quantitative and biophysical detailed manner. By incorporating the results from a diverse set of experiments, this computational approach can be used to interpret and explain key differences among the observations from a single, unified perspective.
The Lon protease links nucleotide metabolism with proteotoxic stress
Authors: Zeinert Rilee D. , Baniasadi Hamid , Tu Benjamin , Chien Peter 
Published: December 2019

SummaryDuring stress all cells must maintain proteome quality while sustaining critical processes like DNA replication. In bacteria, the Lon protease is the central route for degradation of misfolded proteins. Here, we show that inCaulobacter crescentusLon controls dNTP pools during stress through degradation of the transcription factor CcrM. We find that elevated dNTP/NTP ratios in Δloncells protects them from deletion of otherwise essential dTTP-producing pathways and shields them from lethality of hydroxyurea, known to catastrophically deplete dNTPs. Increased dNTP production in Δlonresults from higher expression of ribonucleotide reductase driven by increased CcrM. We show that misfolded proteins can stabilize CcrM by competing for limiting protease and Lon-dependent control of dNTPs improves fitness during protein misfolding conditions. We propose that linking dNTP production with the availability of Lon allowsCaulobacterto maintain replication capacity when misfolded protein burden increases, such as during rapid growth or unanticipated proteotoxic stress.HighlightsdCTP deaminase (DCD) is dispensable when Lon protease is absent due to increased dNTP pools.Stabilization of the Lon substrate CcrM transcriptionally upregulates ribonucleotide reductase, affording protection against hydroxyurea.Misfolded proteins can competitively inhibit CcrM degradation by the Lon protease.Titration of protein quality control is a mechanism that allows cells to respond to stresses that lack dedicated signal response pathways.
Quantitative Real-Time PCR assays for species-specific detection and quantification of Baltic Sea spring bloom dinoflagellates
Authors: Brink A. M. , Kremp A. , Gorokhova E. 
Published: December 2019

ABSTRACTIn the Baltic Sea, the dinoflagellatesApocalathium malmogiense, Biecheleria baltica,andGymnodinium corollariumare important contributors to the spring bloom. However, their relative contribution to the bloom community cannot be unambiguously determined by conventional light microscopy due to lack of resolution of distinctive morphological features of the three species. Here, we describe a molecular approach based on a quantitative real-time polymerase chain reaction (qPCR) primer and probe system, targeting the ITS1 and ITS2 regions of the rRNA gene for all three species and enabling their quantification. The specificity of the method was demonstrated using monocultures ofA. malmogiense,B. baltica,G. corollariumas well as three other dinoflagellate species co-occurring in the Baltic Sea during spring and validated using field-collected phytoplankton samples.
Identification of regulators of poly-ADP-ribose polymerase (PARP) inhibitor response through complementary CRISPR knockout and activation screens
Authors: Clements Kristen E. , Hale Anastasia , Tolman Nathanial J. , Nicolae Claudia M. , Sharma Anchal , Thakar Tanay , Liang Xinwen , Kawasawa Yuka Imamura , Wang Hong-Gang , De Subhajyoti , Moldovan George-Lucian 
Published: December 2019

AbstractInhibitors of poly-ADP-ribose polymerase 1 (PARPi) are highly effective in killing cells deficient in the homologous recombination (HR) DNA repair pathway, such as those lacking BRCA2. In light of this, PARPi have been utilized in recent years to treat BRCA2-mutant tumors, with many patients deriving impressive clinical benefit. However, positive response to PARPi is not universal, even among patients with HR-deficient tumors. Here, we present the results of three genome-wide CRISPR knockout and activation screens which provide an unbiased look at genetic determinants of PARPi response in wildtype or BRCA2-knockout cells. Strikingly, we reveal that depletion of the histone acetyltransferase TIP60, a top hit from our screens, robustly reverses the PARPi sensitivity caused by BRCA2 deficiency. Mechanistically, we show that TIP60 depletion rewires double strand break repair in BRCA2-deficient cells by promoting 53BP1 binding to double strand breaks to suppress end resection. Our work provides a comprehensive set of putative biomarkers that serve to better understand and predict PARPi response, and identifies a novel pathway of PARPi resistance in BRCA2-deficient cells.
Deep Learning for RNA Synthetic Biology
Authors: Angenent-Mari Nicolaas M. , Garruss Alexander S. , Soenksen Luis R. , Church George , Collins James J. 
Published: December 2019

AbstractEngineered RNA elements are programmable tools capable of detecting small molecules, proteins, and nucleic acids. Predicting the behavior of these tools remains a challenge, a situation that could be addressed through enhanced pattern recognition from deep learning. Thus, we investigate Deep Neural Networks (DNN) to predict toehold switch function as a canonical riboswitch model in synthetic biology. To facilitate DNN training, we synthesized and characterizedin vivoa dataset of 91,534 toehold switches spanning 23 viral genomes and 906 human transcription factors. DNNs trained on nucleotide sequences outperformed (R2=0.43-0.70) previous state-of-the-art thermodynamic and kinetic models (R2=0.04-0.15) and allowed for human-understandable attention-visualizations (VIS4Map) to identify success and failure modes. This deep learning approach constitutes a major step forward in engineering and understanding of RNA synthetic biology.One Sentence SummaryDeep neural networks are used to improve functionality prediction and provide insights on toehold switches as a model for RNA synthetic biology tools.
Being abused, dealt unfairly, and ethically conflicting? Quitting occupation in the lap of silence
Authors: Mannan Abdul , Kashif Muhammad 
Published: December 2019

Purpose
The purpose of this paper is to investigate the integrative effects of abusive supervision (AS), perceived injustice (PI) and ethical conflict (EC) on occupational turnover intentions (OTI) among frontline employees (FLEs). Furthermore, the mediating role of quiescent silence (QS) is examined.

Design/methodology/approach
The authors collected survey-based data from 320 FLEs working in different service sector organizations of Pakistan. The snow-ball sampling technique is employed to approach respondents of this study. The collected data are analyzed through structural equation modeling (SEM) technique using SmartPLS 3.0.

Findings
The AS, PI and EC are found to collectively predict OTI among FLEs with a mediating effect of QS. The EC is the strongest predictor of OTI.

Practical implications
The results imply that service managers must ensure that employees are treated fairly. Furthermore, relevant trainings are offered to FLEs in order to maintain the required ethical standards at work to reduce EC perceptions.

Originality/value
The study is pioneer in presenting the relationship between QS and occupational turnover among FLEs. Furthermore, the study advocates the mediating role of employee quiescent silence to enrich the relationship between socio-psychological factors (i.e. AS, EC and PI) and OTI.
Industry risk taking and risk-taking strategy of born-global firms
Authors: Huang Jing , Liu Linyu , Lu Ren 
Published: December 2019

PurposeThe purpose of this paper is to study the relationship between industry risk taking and risk-taking strategy of born-global firms (BGs), and how industry-related variety moderates that relationship.Design/methodology/approachThe authors apply fixed effect model to analyze 26,499 observations on 10,508 BGs in 276 Chinese cities.FindingsThe authors find that industry risk taking positively influences risk-taking strategy of BGs, and industry-related variety positively moderates such relationship.Originality/valueThe findings reveal how BGs formulate their risk-taking strategy given the dilemma of risk nature and hurdles in firm establishment and rapid internationalization. This paper extends understanding on BGs’ strategy making, supplements the theoretical framework on BGs with an integrated viewpoint containing “regional–industry–firm” levels and contributes to the industry variety argument.
“Boss ceiling effect”: brand downgrading consumption of workplace employees
Authors: Jia Fang , Yang Zhilin , Ji Li , Xu Shen 
Published: December 2019

PurposePrevious literature suggests that people might purchase symbolic products to signal their social identity. However, in the organizational context, subordinates as customers might choose products with less brand prestige than what they want and can afford, just to make sure their choices are below the invisible “red-line” set by the brands of their supervisors. The authors term the phenomenon as “boss ceiling effect,” and term the behavior that people often downgrade their original choice to make sure the brand prestige is lower than that of the product owned by their boss as “downgrading behavior,” which have not been explored and well explained by existing literature so far. The paper aims to discuss this issue.Design/methodology/approachThe authors conduct qualitative study to explore the existence of boss ceiling effect and providing possible influential factors of brand downgrading attitude. The quantitative study empirically examines the relationships among undesired self, perceived risk, organizational culture balance, and downgrading attitude and intension.FindingsThe authors find that undesired self-congruence and perceived risk are positively related to the downgrading attitude. In addition, the culture balance directly affects the brand downgrading attitude negatively and also moderates the relationship between undesired self-congruence and downgrading attitude positively and the relationship between perceived risk and downgrading attitude negatively.Originality/valueThe authors contribute to both organizational culture research and symbolic consumption research by considering symbolic consumption behavior in organization context. It is of great practical implications for marketers of symbolic consumption to understand the downgrading behavior.
Vichy goes to Brazil: the road to success
Authors: Silva Susana C. , Lima Dayane Gôuvea , Correia Juliana Teixeira 
Published: December 2019

Learning outcomes
The learning outcomes are as follows: analyze the risks and difficulties involved in the internationalization process and the impact of cultural variables (external analysis); understand how the balance between adaptation and standardization can be worked out in building a successful international marketing strategy (adaptation vs standardization dilemma); and analyze how a restructuring of marketing mix variables can shape an assertive and effective repositioning strategy (marketing-mix program).

Case overview/synopsis
The case of Vichy presents a specific internationalization process, from a European brand in a growing segment, to Brazil, a country with extreme cultural diversity where the barriers to internationalization are large and complex. The case can be analyzed from the point of view of brand repositioning, as it discusses the strategies adopted by the brand during entry into the Brazilian market, and its subsequent repositioning, bearing in mind a better adaptation to the market in question. The goal is to encourage discussions about how cultural barriers can influence the internationalization process of a brand and how the balance between adaptation and standardization can be worked out in building an assertive and effective international marketing strategy.

Complexity academic level
Master students.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 8: Marketing.
Customers’ reactions to different organizational tactics in a service termination context
Authors: Nazifi Amin , El-Manstrly Dahlia , Gelbrich Katja 
Published: December 2019

Purpose
This study aims to examine the effects of organizational tactics (e.g. explanation and monetary compensation) on customers’ reactions to service termination. The mediating role of anger and the moderating role of termination strategy on the effectiveness of organizational tactics are examined to enhance the understanding of customers’ reactions to service termination.

Design/methodology/approach
Three experimental studies are conducted with different contexts (telecom and banking) and samples (students and consumers).

Findings
Study 1 results show that explanation and high monetary compensation reduce negative word-of-mouth and enhance corporate image and anger mediates these effects. Study 2a results show that high monetary compensation becomes ineffective when firms use a soft termination approach. Study 2b results show that an explanation is equally effective in soft and hard termination approaches. Importantly, unlike high monetary compensation, the explanation can fully eliminate the negative consequences of service termination.

Practical implications
Managers can mitigate negative customers’ reactions to service termination by offering a truthful explanation. Further, they should provide high monetary compensation only if they do not help dismissed customers find an alternative provider.

Originality/value
This paper contributes to the service termination literature by shedding more light on the effectiveness of different organizational tactics following different termination strategies. The findings challenge existing wisdom on the overrated role of monetary compensation showing that in service termination, the explanation is the most effective remedy. Further, unlike justice, anger better explains customers’ reactions to service termination.
Army wives’ consumer vulnerability and communities of coping
Authors: Bruce Helen L. , Banister Emma 
Published: December 2019

Purpose
The spouses or partners of serving members of the UK Armed Forces are often subject to similar constraints to those of enlisted personnel. This paper aims to examine the experiences and wellbeing of a group of army wives. In particular, it focuses on their shared experiences of consumer vulnerability and related challenges, exploring the extent to which membership of military wives’ communities can help them to cope.

Design/methodology/approach
Using an interpretivist approach, data were collected through four focus group discussions involving 30 army wives, and seven individual in-depth interviews.

Findings
The paper highlights shared experiences of consumer vulnerability and demonstrates how army wives’ approaches to coping incorporate both individual and community-based approaches. It proposes that communities of coping develop within the army wives community, providing women with both practical and emotional support.

Research limitations/implications
The paper acknowledges that there is a range of factors that will impact military spouses’ experiences of consumer vulnerability and strategies for coping. This heterogeneity was difficult to capture within a small exploratory study.

Practical implications
The UK Government should consider their duties towards military spouses and children. This would entail a significant cultural shift and recognition of military personnel’s caring responsibilities.

Originality/value
This research contributes to understandings regarding the potentially shared nature of both consumer vulnerability and coping strategies. The study introduces the relevance of communities of coping to consumer contexts, highlighting how members can benefit from both practical and emotional support.