bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Rad51-Independent Pathway Promotes Single-Strand Template Repair in Gene Editing
Authors: Gallagher Danielle N. , Pham Nhung , Tsai Annie M. , Janto Abigail N. , Choi Jihyun , Ira Grzegorz , Haber James E. 
Published: February 2020

AbstractThe Rad51/RecA family of recombinases perform a critical function in typical repair of double-strand breaks (DSBs): strand invasion of a resected DSB end into a homologous double-stranded DNA (dsDNA) template sequence to facilitate repair. However, repair of a DSB using single stranded DNA (ssDNA) as a template, a common method of CRISPR/Cas9-mediated gene editing, is Rad51-independent. We have analyzed the genetic requirements for these Rad51-independent events inSaccharomyces cerevisiaein two different assays. Gene editing events were carried out either by creating a DSB with the site-specific HO endonuclease and repairing the DSB with 80-nt single-stranded oligonucleotides (ssODNs) or by using a bacterial retron system that produces ssDNA templatesin vivoin combination with DSBs created by Cas9. We show that single strand template repair (SSTR), is dependent on Rad52, Rad59, Srs2 and the Mre11-Rad50-Xrs2 (MRX) complex, but not Rad51, Rad54 or Rad55. Srs2 acts to prevent overloading of Rad51 on the ssDNA filament, whereas Rad59 appears to alleviate the inhibition of Rad51 on Rad52’s strand annealing activity; thus, deletion ofRAD51suppresses both thesrs2Δ andrad59Δ phenotypes. This same suppression byrad51Δ ofrad59Δ is found in another DSB repair pathway, single strand annealing (SSA). In contrast, gene targeting using an 80-bp dsDNA template of the same sequence is Rad51-dependent. We also examined SSTR events in which the ssODN carried several mismatches. In the absence of the mismatch repair protein, Msh2, we found that the fate of mismatches carried on the ssDNA template are very different at the 3’ end, which can anneal directly to the resected DSB end, compared to the 5’ end. We also find that DNA polymerase Polδ’s 3’ to 5’ proofreading activity frequently excises a mismatch close to the 3’ end of the template, similar to its removal of heterologies close to the 3’ invading end of the DSB. We further report that SSTR is accompanied by a 600-fold increase in mutations in a region adjacent to the sequences directly undergoing repair. These DNA polymerase ζ-dependent mutations may compromise the accuracy of gene editing.
Transcriptome analysis of somatic cell populations in theDrosophilatestis links metabolism and stemness
Authors: Hof-Michel Silvana , Bökel Christian 
Published: February 2020

AbstractDue to its simple cellular architecture and genetic tractability the fly testis was one of the first model systems in which stem cell - niche interactions were studied at the molecular level. However, to date there is no comprehensive information on the endogenous, cell type specific transcription profiles associated with either stem cell or differentiated states. Focusing on the somatic lineage we have therefore isolated CySCs, differentiated CyCs, hub cells, and stem cell-like tumour cells overexpressing Zfh1, and have mapped their transcriptomes by RNAseq.Here we report i) that the different somatic cell populations show extensive, genome wide differences in transcription levels, in particular associated with energy metabolism and innate immune signalling, ii) that differential activation of multiple signalling pathways renders Zfh1 overexpressing tumour cells unsuitable for use as a stem cell model, and iii) that the transcriptome data could be successfully used for identifying genes with stem cell specific expression patterns and for predicting aspects of stem cell physiology whose relevance for stem cell function could be validated in preliminary experiments.The present data set should therefore facilitate future research on the interaction of stem cells with their niche using the highly successful fly testis model system.
A disulfide constrains the ToxR periplasmic domain structure, altering its interactions with ToxS and bile-salts
Authors: Midgett Charles R , Swindell Rachel A , Pellegrini Maria , Kull F Jon 
Published: February 2020

AbstractToxR is a transmembrane transcription factor that, together with its integral membrane periplasmic binding partner ToxS, is conserved across theVibriofamily. In some pathogenicVibrios, includingV. parahaemolyticusandV. cholerae, ToxR is required for bile resistance and virulence, and ToxR is fully activated and protected from degradation by ToxS. ToxS achieves this in part by ensuring formation of an intra-chain disulfide bond in the C-terminal periplasmic domain of ToxR (dbToxRp). In this study, biochemical analysis showed dbToxRp to have a higher affinity for the ToxS periplasmic domain than the non-disulfide bonded conformation. Analysis of our dbToxRp crystal structure showed this is due to disulfide bond stabilization. Furthermore, dbToxRp is structurally homologous to theV. parahaemolyticusVtrA periplasmic domain. These results highlight the critical structural role of disulfide bond in ToxR and along with VtrA define a domain fold involved in environmental sensing conserved across theVibriofamily.
Dynamics as a cause for the nanoscale organization of the genome
Authors: Barth R. , Fourel G. , Shaban H. A. 
Published: February 2020

AbstractChromatin ‘blobs’ were recently identified by live super-resolution imaging as pervasive, but transient and dynamic structural entities consisting of a few associating nucleosomes. The origin and functional implications of these blobs are, however, unknown. Following these findings, we explore whether causal relationships exist between parameters characterizing the chromatin blob dynamics and structure, by adapting a framework for spatio-temporal Granger-causality inference. Our analysis reveals that chromatin dynamics is a key determinant of both blob area and local density. However, such causality can only be demonstrated in small areas (10 – 20%) of the nucleus, highlighting that chromatin dynamics and structure at the nanoscale is dominated by stochasticity. Pixels for which the inter-blob distance can be effectively demonstrated to depend on chromatin dynamics appears as clump in the nucleus, and display both a higher blob density and higher local dynamics as compared with the rest of the nucleus. Furthermore, we show that the theory of active semiflexible polymers can be invoked to provide potential mechanisms leading to the organization of chromatin into blobs. Based on active motion-inducing effectors, this framework qualitatively recapitulates experimental observations and predicts that chromatin blobs might be formed stochastically by a collapse of local polymer segments consisting of a few nucleosomes. Our results represent a first step towards elucidating the mechanisms that govern the dynamic and stochastic organization of chromatin in a cell nucleus.
Data-driven polymer model for mechanistic exploration of diploid genome organization
Authors: Qi Yifeng , Reyes Alejandro , Johnstone Sarah E. , Aryee Martin J. , Bernstein Bradley E. , Zhang Bin 
Published: February 2020

AbstractChromosomes are positioned non-randomly inside the nucleus to coordinate with their transcriptional activity. The molecular mechanisms that dictate the global genome organization and the nuclear localization of individual chromosomes are not fully understood. We introduce a polymer model to study the organization of the diploid human genome: it is data-driven as all parameters can be derived from Hi-C data; it is also a mechanistic model since the energy function is explicitly written out based on a few biologically motivated hypotheses. These two features distinguish the model from existing approaches and make it useful both for reconstructing genome structures and for exploring the principles of genome organization. We carried out extensive validations to show that simulated genome structures reproduce a wide variety of experimental measurements, including chromosome radial positions and spatial distances between homologous pairs. Detailed mechanistic investigations support the importance of both specific inter-chromosomal interactions and centromere clustering for chromosome positioning. We anticipate the polymer model, when combined with Hi-C experiments, to be a powerful tool for investigating large scale rearrangements in genome structure upon cell differentiation and tumor progression.
What drives consumer demand for rice fragrance? Evidence from South and Southeast Asia
Authors: Bairagi Subir , Demont Matty , Custodio Marie Claire , Ynion Jhoanne 
Published: February 2020

PurposeThe purpose of this paper is to analyze geographic heterogeneity of consumer preferences for intrinsic quality attributes of rice in South and Southeast Asia and the drivers of demand for these attributes, with a particular focus on rice fragrance and the role of gender.Design/methodology/approachStated-preference surveys were conducted with 4,231 urban and rural consumers in 37 cities across seven countries (Bangladesh, India, Cambodia, Indonesia, the Philippines, Thailand, and Vietnam) during 2013–2014 and analyzed through a rank-ordered logistic regression with incomplete ranking choice data.FindingsPreferences for rice attributes are found to be significantly heterogeneous among consumers in South and Southeast Asia. Urban Thai consumers tend to prioritize appearance and cooking characteristics over taste and nutritional benefits, relative to all other surveyed consumers. In contrast with South Asian consumers, Southeast Asian consumers have largely adopted Thai preferences for rice texture and fragrance, a trend that was earlier coined “Jasminization.” We find that demand for rice fragrance is mainly driven by women, educated consumers, large families, families spending a lower share of their food expenditures on rice, and consumers in Southeast Asia (particularly the Philippines and Cambodia).Originality/valueLittle is known about geographic heterogeneity, drivers, and the role of gender in demand for rice fragrance. This paper fills these knowledge gaps. Our findings suggest that the more women are empowered in grocery decision-making, the more demand for aromatic rice is expected to rise. These insights can assist market-driven and gender-responsive rice breeding programs in simultaneously enhancing rice farmers' livelihoods and gender equity.
The challenge of integrating operational knowledge in building and ship design
Authors: Rasmussen Helle Lohmann 
Published: February 2020

Purpose
For optimising long-term building operations, building clients need to enable integration of operational knowledge in the design process of new buildings. This study aims to investigate and compare how operational knowledge is integrated into the design of buildings and large ships, focussing on the roles affiliation and the competences of the client’s project manager play.

Design/methodology/approach
A cross-sectional qualitative methodology with multiple case studies (five cases) was used. In addition, ten expert interviews and two validation focus group interviews were conducted. Case studies included in-depth interviews, document analysis and observations.

Findings
The study showed that organisational affiliation, focus and competences of the client’s project management play an important role in how much effort and resources go into ensuring integration of operational knowledge in the design process. In the ship cases, projects managers’ highest concerns were operations. Yet, the fewest procedures and tools to integrate operational knowledge in design were found implemented in these cases. Contrastingly, in the building cases, where operations were not the main matter of concern of project management, a large number of procedures and tools to integrate operational knowledge in design were implemented.

Originality/value
To the best of the author’s knowledge, this research is the first to compare how integration of operational knowledge is taking place in the design process of buildings and large ships and identifying what these industries can learn from each other. Furthermore, it adds to the limited research on operations in large ship design.
Innovative work behavior through high-quality leadership
Authors: Miller Linda , Miller Andrew Foster 
Published: February 2020

Purpose
The purpose of this study was to understand how innovative work behavior (IWB) was affected by leaders’ relationships with their employees to enhance engagement/job commitment in the grocery retail industry. The general business problem is some organizations in the grocery retail industry lack IWB to generate innovative solutions to remain competitive.

Design/methodology/approach
This study used a qualitative method and a single case study design because the literature identified a need to understand how the leader–member relationships, employee engagement/job commitment and employee idea generation and implementation affect organizational innovation in the grocery retail industry. Using this method and design provided the appropriate approach to explore a single organization business process model for innovation. The three data sources for this study were semistructured one-on-one individual interviews, a single focus group and relevant organizational documentation.

Findings
The findings showed high-quality relationships between knowledge workers and their leaders can positively affect their engagement/job commitment and ability to generate and implement useful ideas. A fundamental catalyst for IWB is when all four critical forces are in alignment including high-quality relationships between the knowledge workers and their leadership, the employee is fully engaged and the organization promotes risk-taking behavior to create new ideas with its commitment to innovation through resources and prioritization. The millennial participants indicated their leaders should be more transformational leaders coaching and mentoring them rather than transactional task-oriented disciplinarians. The Generation X and baby boomer participants were seeking more autonomy and resources to explore ideas.

Research limitations/implications
Future researchers could consider exploring a deeper understanding of the multigenerational knowledge workers’ needs to help leaders stimulate employee engagement/job commitment and increase IWB.

Practical implications
Organizations are able to meet the market demand for innovation and remain competitive.

Social implications
Higher quality leader–member relationships lead to employee engagement/job commitment that can increase innovation.

Originality/value
The findings were the trends and preferences revealed within generational groupings. The needs and wants expressed by the millennial participants indicated that their leaders should be more of a coach and mentor. The Generation X and baby boomer participants were seeking more autonomy and resources to explore ideas.
Voice behavior of Indian IT employees: a moderated mediation model
Authors: Prince R. , Rao M. Kameshwar 
Published: February 2020

PurposeThe purpose of this study is to explore how promotive and prohibitive voice behaviors of Indian information technology (IT) employees vary in their relationship with other factors. This study investigates a moderated mediation model involving different factors like managerial openness, voice self-efficacy, turnover intentions and promotive and prohibitive voice behaviors.Design/methodology/approachThis study uses a cross-sectional design to collect data from 254 executives working in the IT companies located in India. This study uses IBM SPSS 22 along with the Hayes’ PROCESS module to investigate the moderation and mediation effects.FindingsThe results reveal that both promotive and prohibitive voice behaviors fully mediate the negative relationship between managerial openness and employee turnover intentions. The results also support that voice self-efficacy strengthens the relationship between managerial openness and promotive voice behavior but not prohibitive voice behavior.Originality/valueThis is one of the very few studies to explore voice behavior from the Indian context and thus heeds to the call made by researchers to explore voice in a non-Western context. The treatment of voice as a combination of promotive and prohibitive voice rather than as a unitary concept enhances the voice literature and invites further research.
Emirati women’s professional legitimacy
Authors: Goby Valerie Priscilla 
Published: February 2020

Purpose
This paper reports an exploration of changing the legitimacy judgments of Emirati women employees in the UAE’s public sector. This paper aims to fill the research gap on gender at employee, rather than managerial level, a topic that has already generated considerable research.

Design/methodology/approach
Data derived from semi-structured interviews with 29 Emirati women working in the public sector is analyzed using NVivo 12 to identify their attitudes to, and experience of, participating in the workforce.

Findings
Interview narratives reveal that women not only consider that they have the right to enhanced professional status but also view this as exerting a positive impact on their personal lives.

Research limitations/implications
It is suggested that this emerging sense of entitlement to work may be traced to the early political endorsement of women in the UAE workforce, underscoring the value of political and judicial agendas that contribute to female legitimacy and their rigorous implementation.

Originality/value
This study highlights the imperative of political goodwill and equitable legislation, as well as the need to assess Islamic values versus patriarchal biases in relation to women in the workforce.
Evaluating the motives of child labourers in the informal economy
Authors: Ilyas Aamar , Shahid Muhammad Shehryar , Ali Hassan Ramraini 
Published: February 2020

PurposeConventionally, the marginalised population was considered to engage in child labour due to poverty, education or lack of other options, but indeed, a few children work voluntarily. However, a growing number of scholars, in recent years, have drawn their attention to the valuable question, “why children are engaged in child labour in the informal economy”. Even though a few studies have explored the motives of informal workers, to our knowledge not a single paper has explored the motives of child labourers working in the informal economy. The purpose of this study is to fill this gap by evaluating the motives of child labourers, through three competing theorisations of the informal economy.Design/methodology/approachIn this study, face-to-face structured interviews of 45 child labourers were conducted, who worked in different automobile workshops in the city of Lahore, Pakistan. Respondents were selected using the snowball sampling technique as this strategy is suitable for researching sensitive issues and is feasible for small sample sizes.FindingsThe main finding is that no single explanation is universally applicable to all child labourers. Some (27 per cent) justify their participation in the informal sector as driven by necessity (structuralist perspective), majority (40 per cent) explain their participation in the informal economy as a rational economic choice (neo-liberal perspective) and finally, more than a quarter of respondents (31 per cent) engaged in child labour due to their own free will or voluntarily to work for their family (post-structuralist perspective). This study also revealed that entrepreneurial spawning is a key determinant of child labour as the majority of children, in our study, working in automobile workshops intended to start their own workshop business in the future.Research limitations/implicationsThis article shows that children early engaged in work with entrepreneurial intention/spawning. Entrepreneurial education is very important in a child’s life. Entrepreneurial education will be a ticket to fulfill their dreams and learn new things with entrepreneurial attitude.Practical implicationsGovernment should develop the vocational training institutes for children who left the schools.Originality/valueThis study contributes to the body of literature by providing a better understanding of why children work in informal employment, an occupation generally perceived as constituting exploitative working conditions. This study also contributes to the wider literature of entrepreneurship by exploring “entrepreneurial spawning” as one of the major reasons underlying the participation of children in informal work.
Alternative models of activation policies: the experience of public oriented services
Authors: Scarano Gianluca 
Published: February 2020

PurposeThe purpose of this paper is to understand the impact of activation policies in contexts of public-oriented employment services.Design/methodology/approachThe fieldwork was conducted in Italy, using the regional case of Emilia-Romagna as a representation of public-oriented models. The empirical research relies primarily on quantitative research methods by means of impact evaluations based on very rich and recent administrative data that includes 20,014 observations. These are integrated with some interesting insights from qualitative research tools by means of semi-structured interviews with stakeholders in the fieldwork.FindingsThe overall level of effectiveness of activation policies does not seem to be particularly high. However, the results show that, to some extent, there are more advantages for job seekers furthest from the labor market. The stronger efforts made to assist those disadvantaged groups are probably related to a loss in the overall effectiveness of the system.Research limitations/implicationsThis analysis has focused on a substantially homogeneous and economically developed region. Indeed, Italian activation policy reforms have been implemented differently in different areas of the country. Similar to other Southern European countries, they are characterized by regional fragmentation and implementation gaps in activation policies.Practical implicationsThe findings of the present study are relevant to policymakers who deal with activation policies and to both public and nonpublic organizations involved in this field. It seems plausible to support the possibility that public-oriented models could represent a proficient alternative to proposals relying heavily on market-based interventions. Such evidence becomes particularly interesting in the aftermath of the Great Recession when this model is confronted with the consequences of the economic crisis.Originality/valueThe paper adds to the literature on public-oriented models, while overcoming some of the limitations of earlier research, which has been restricted mainly to cases with early traditions of marketized services.