bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chimeric MerR-Family Regulators and Logic Elements for the Design of Metal Sensitive Genetic Circuits inBacillus subtilis
Authors: Ghataora Jasdeep S. , Gebhard Susanne , Reeksting Bianca J. 
Published: October 2022

ABSTRACTWhole-cell biosensors are emerging as promising tools for monitoring environmental pollutants such as heavy metals. These sensors constitute a genetic circuit comprising a sensing module and an output module, such that a detectable signal is produced in the presence of the desired analyte. The MerR family of metal-responsive regulators offers great potential for the construction of metal sensing circuits, due to their high sensitivity, tight transcription control and large diversity in metal-specificity. However, the sensing diversity is broadest in Gram-negative systems, while chassis organisms are often selected from Gram-positive species, particularly sporulating bacilli. This can be problematic, because Gram-negative biological parts, such as promoters, are frequently observed to be non-functional in Gram-positive hosts. Herein, we combined construction of synthetic genetic circuits and chimeric MerR regulators, supported by structure-guided design, to generate metal-sensitive biosensor modules that are functional in the biotechnological work-horse speciesBacillus subtilis. These chimeras consist of a constant Gram-positive derived DNA-binding domain fused to variable metal binding domains of Gram-negative origins. To improve the specificity of the whole-cell biosensor, we developed a modular ‘AND gate’ logic system based on theB. subtilisnatively split σ-factor, SigO-RsoA, designed to maximise future use for synthetic biology applications inB. subtilis. This work provides insights into the use of modular regulators, such as the MerR family, in the design of synthetic circuits for the detection of heavy metals, with potential wider applicability of the approach to other systems and genetic backgrounds.
Inhibition of Microbial Methane Oxidation by 2-Chloro-6-Methylpyridine
Authors: O’Loughlin Edward J. , Antonopoulos Dionysios A. , Arend Kristin K. , Flynn Theodore M. , Koval Jason C. , Owens Sarah M. 
Published: October 2022

AbstractSeveral pyridine derivatives including the pesticide nitrapyrin [2-chloro-6-(trichloromethyl) pyridine] are strong inhibitors of methane monooxygenase, a key enzyme of aerobic methane (CH4) oxidation. In this study we examined the effects of 2-chloro-6-methylpyridine (2C6MP) concentration on aerobic CH4oxidation and the development of populations of putative methanotrophs in sediment from Old Woman Creek, a freshwater estuary in Huron Co., Ohio. Experimental systems were prepared in serum bottles containing minimal medium with a headspace containing 20% O2and 10% CH4. The microcosms were spiked with 2C6MP to achieve concentrations of 0, 0.1, 1, or 10 mM and inoculated with sediment. When headspace CH4concentrations decreased from 10% to < 2%, subsamples were taken for DNA extraction and sequencing of 16S rRNA gene amplicons. There was minimal effect of 2C6MP on CH4oxidation at concentrations of 0.1, and 1 mM, but complete inhibition for > 20 months was observed at 10 mM. ANOSIM of weighted UniFrac distances between groups of triplicate samples supported a primary distinction of the inoculum relative to the enrichments (R=0.999) and a secondary distinction between bottles containing 2C6MP versus those without (R=0.464 [0.1 mM]; R=0.894 [1 mM]). The inoculum was dominated by members of theProteobacteria(49.9±1.5%), and to a lesser extent byBacteroidetes(8.8±0.2%),Acidobacteria(8.9±0.4%), andVerrucomicrobia(4.4±0.3%). In enrichments with or without 2C6MP,Proteobacteriaexpanded to comprise 65–70% of the total. In the absence of inhibitor, members of theMethylococcaceaeandMethylophilaceaeincreased in relative abundance from < 0.1% of the inoculum to 8.5±1.0% and 13.4±2.3%, of the total community respectively. At both 0.1 and 1 mM concentrations of the inhibitor, theMethylococcaceaewere much less abundant, representing 3.3±0.5% and 2.8±3.3% respectively. No inhibition of theMethylophilaceaewas seen at the lower concentration of 2C6MP, but at the higher concentration this taxon was only 7.8±1.1% of the total. In contrast, members of theCrenotrichaceae, another group of methane oxidizers, increased in relative abundance with greater amounts of inhibitor, representing 8.6±3.6% of the total at 0.1 mM and 12.0±4.5% at 1 mM, compared to only 4.1±0.4% when no inhibitor was present. These results clearly show changes in the populations of putative aerobic methanotrophs relative to the amount of 2C6MP present.
PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration
Authors: Chen Jinghao , Holt Jesse R. , Evans Elizabeth L. , Lowengrub John S. , Pathak Medha M. 
Published: October 2022

AbstractThe collective migration of keratinocytes during wound healing requires both the generation and transmission of mechanical forces for individual cellular locomotion and the coordination of movement across cells. Leader cells along the wound edge transmit mechanical and biochemical cues to ensuing follower cells, ensuring their coordinated direction of migration across multiple cells. Despite the observed importance of mechanical cues in leader cell formation and in controlling coordinated directionality of cell migration, the underlying biophysical mechanisms remain elusive. The mechanically-activated ion channel PIEZO1 was recently identified to play an inhibitory role during the reepithelialization of wounds. Here, through an integrative experimental and mathematical modeling approach, we elucidate PIEZO1’s contributions to collective migration. Time-lapse microscopy reveals that PIEZO1 activity inhibits leader cell formation at the wound edge. To probe the relationship between PIEZO1 activity, leader cell formation and inhibition of reepithelialization, we developed an integrative 2D continuum model of wound closure that links observations at the single cell and collective cell migration scales. Through numerical simulations and subsequent experimental validation, we found that coordinated directionality plays a key role during wound closure and is inhibited by upregulated PIEZO1 activity. We propose that PIEZO1-mediated retraction suppresses leader cell formation which inhibits coordinated directionality between cells during collective migration.Author summaryDuring the healing of a wound, cells called keratinocytes that make up the outer layer of the skin migrate collectively to close the wound gap. The mechanically activated ion channel PIEZO1 was previously found to inhibit wound closure. Here, through a combined modeling and experimental approach, we investigate the role of PIEZO1 in regulating collective migration. Specialized cells called leader cells, which typically form along the wound edge, are important for guiding the migration of neighboring cells. These leader cells dictate the coordinated directionality, or the cohesiveness of the migration direction between neighboring cells, through the transmission of mechanical and biochemical cues. We find that PIEZO1 activity inhibits the formation of these leader cells and, as a result, inhibits cell coordinated directionality causing the collective movement of cells to become disorganized and less effective in closing the wound. Our findings shed light on the complex mechanisms underlying collective migration, providing valuable insight into how mechanical cues affect the movement of cells during wound closure.
Improved Protocol for Single-Nucleus RNA-sequencing of Frozen Human Bladder Tumor Biopsies
Authors: Schmøkel Sofie S. , Nordentoft Iver , Lindskrog Sia V. , Lamy Philippe , Knudsen Michael , Jensen Jørgen Bjerggaard , Dyrskjøt Lars 
Published: October 2022

AbstractThis paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines. We tested different lysis buffers (IgePal and Nuclei EZ) and incubation times in combination with different approaches for tissue and cell dissection; sectioning, semi-automated dissociation, manual dissociation with pestles, and semi-automated dissociation combined with manual dissociation with pestles. Our results showed a combination of IgePal lysis buffer, tissue dissection by sectioning and short incubation time was the best conditions for gentle nuclei isolation applicable for snRNA-seq, and we found limited confounding transcriptomic changes based on the isolation procedure. This protocol makes it possible to analyze biobanked material from patients with well described clinical and histopathological information and known clinical outcomes with snRNA-seq.
Analysis of Skin Cancers from Xeroderma Pigmentosum Patients Reveals Heterogeneous UV-Induced Mutational Profiles Shaped by DNA Repair
Authors: Yurchenko Andrey A. , Rajabi Fatemeh , Braz-Petta Tirzah , Fassihi Hiva , Lehmann Alan , Nishigori Chikako , Padioleau Ismael , Gunbin Konstantin , Panunzi Leonardo , Morice-Picard Fanny , Laplante Pierre , Robert Caroline , Kannouche Patricia L. , Menck Carlos F. M. , Sarasin Alain , Nikolaev Sergey I. 
Published: October 2022

ABSTRACTXeroderma pigmentosum (XP) is a genetic disorder caused by mutations in genes of the Nucleotide Excision Repair (NER) pathway (groups A-G) or in Translesion Synthesis (TLS) DNA polymerase η (V). XP is associated with an increased skin cancer risk, reaching, for some groups, several thousand-fold compared to the general population. Here, we analyzed 38 skin cancer genomes from five XP groups. We found that the activity of NER determines heterogeneity of the mutation rates across skin cancer genomes and that transcription-coupled NER extends beyond the gene boundaries reducing the intergenic mutation rate. Mutational profile in XP-V tumors and experiments withPOLH-KO cell line revealed the role of polymerase η in the error-free bypass of (i) rare TpG and TpA DNA lesions, (ii) 3’ nucleotides in pyrimidine dimers, and (iii) TpT photodimers. Our study unravels the genetic basis of skin cancer risk in XP and provides insights into the mechanisms reducing UV-induced mutagenesis in the general population.
DNMT1 inhibition by pUG-fold quadruplex RNA
Authors: Jansson-Fritzberg Linnea I. , Sousa Camila I. , Smallegan Michael J. , Song Jessica J. , Gooding Anne R. , Kasinath Vignesh , Rinn John L. , Cech Thomas R. 
Published: October 2022

ABSTRACTAberrant DNA methylation is one of the earliest hallmarks of cancer. DNMT1 is responsible for methylating newly replicated DNA, but the precise regulation of DNMT1 to ensure faithful DNA methylation remains poorly understood. A link between RNA and chromatin-associated proteins has recently emerged, and several studies have shown that DNMT1 can be regulated by a variety of RNAs. In this study we have confirmed that human DNMT1 indeed interacts with multiple RNAs, including its own nuclear mRNA. Unexpectedly, we found that DNMT1 exhibits a strong and specific affinity for GU-rich RNAs that form a pUG-fold, a non-canonical G-quadruplex. We find that pUG-fold-capable RNAs inhibit DNMT1 activity by inhibiting binding of hemimethylated DNA, and additionally provide evidence for multiple RNA binding modes with DNMT1. Together, our data indicates that a human chromatin-associated protein binds to and is regulated by pUG-fold RNA.
Arts marketing during COVID-19: a critical review and theoretical integration
Authors: Fillis Ian , Lehman Kim , Rentschler Ruth , Lee Boram 
Published: October 2022

PurposeThis paper aims to provide clarity on arts marketing during COVID-19 by undertaking a critical review and theoretical integration of published cultural and creative industries (CCIs) data on the pandemic.Design/methodology/approachThe study draws on the findings from a content analysis of published refereed journal articles and research reports, between 2020 and 2022.FindingsThis study clarifies how scholars in the arts marketing field have examined the concept and identified core dimensions. It also brings together these conceptual categories into an integrative multilevel framework of relevance for arts marketing during COVID-19. The framework outlines interconnected processes as well as dualities, such as digitisation, monetisation and sustainability of the CCIs and poses a future centred on entrepreneurial actions.Originality/valueThe originality of the paper is that it provides clear-cut evidence for new frontiers for research in the field during a period of discontinuous change due to COVID-19, through a literature review that has not been undertaken previously. It links the need to be entrepreneurial as a means for the CCIs to survive and thrive during and after a global crisis.
Market competition, capital regulation and cost of financial intermediation: an empirical study on the banking sector of Bangladesh
Authors: Mia MD. Rasel 
Published: October 2022

PurposeThis study aims to examine the impact of market competition, and capital regulation on the cost of financial intermediation of banks of the Bangladesh banking industry.Design/methodology/approachThis study has used a balanced panel dataset comprised of 340 firm-year observations for 34 commercial banks in the Bangladesh banking industry from 2011 to 2020. The Prais Winsten panel estimator has been used to assess the impact of market competition and capital regulation on the cost of financial intermediation of banks.FindingsBased on the regression results, this study has documented that greater market competition results in a lower cost of financial intermediation for banks. Similarly, an increase in the regulatory capital of banks increases the cost of financial intermediation of banks. The main findings of this study are found robust by using alternative proxies for the cost of financial intermediation, market competition and capital regulation. The regression results also suggest that private commercial banks tend to have a higher cost of financial intermediation than state-owned commercial banks.Research limitations/implicationsThe regulatory reforms should aim to foster sustainable and optimal market competition for the Bangladesh banking industry to regulate the market power of banks to reduce the cost of financial intermediation. The regulatory authority of Bangladesh should find the optimal policy measures for implementing the capital regulation in the banking industry which would reduce the cost of financial intermediation margin of banks.Originality/valueUnlike previous studies which have used structural market competition measures, this study has used non-structural market competition measures to assess the relationship between market competition and cost of financial intermediation in the Bangladesh banking industry.
Thermal behavior of a conical antenna cooled with nanofluid saturated porous media: effects of the cavity’s inclination and aspect ratio
Authors: Alilat Nacim , Martin Elena B. , Sastre Francisco , Millán García Jose Antonio , Baïri Abderrahmane 
Published: October 2022

Purpose
The aim of this work is to determine the average surface temperature of a conical antenna. Its cooling is ensured by means of a nanofluid-saturated porous structure. The volume fraction of the H2O–Cu nanofluid ranges between 0% (pure water) and 5%, whereas the ratio between the thermal conductivity of the used porous materials and that of water (fluid base) varies in the wide 4–41.2 range. The antenna is contained in a coaxial conical closed cavity with a variable distance between the cones, leading to an aspect ratio varying between 0.2 and 0.6. The axis of the assembly is also inclined with respect to the gravity field by an angle varying between 0° (a vertical axis with top of the cone oriented upwards) and 180° (a vertical axis with top of the cone oriented downwards).

Design/methodology/approach
Simulations have been done by means of the volume control method based on the SIMPLE algorithm.

Findings
Results of the numerical approach show that the cavity’s aspect ratio and inclination with respect to the gravity field significantly affect the thermal behavior of the active cone. Otherwise, the work confirms that the Maxwell and Brinkman models used to determine the nanofluid’s effective thermal conductivity and viscosity, respectively, are adapted to the considered assembly.

Originality/value
A new correlation is proposed, allowing the determination of the average surface temperature of the active cone and its correct thermal sizing. This correlation could be used in various engineering fields, including electronics, examined in the present study.
Linking organizational exploitation to extra-role behaviors: a conservation of resources perspective
Authors: Cheng Xuan-Mei , Lyu Yijing , Ye Yijiao 
Published: October 2022

Purpose
Drawing on conservation of resources (COR) theory, this study aims to explore how perceived organizational exploitation affects hospitality employees’ extra-role customer service behaviors by investigating the mediating role of depressed mood at work and the moderating role of reappraisal.

Design/methodology/approach
This study tested all of the hypotheses using multilevel path analyses with a sample of 340 supervisor–subordinate dyads.

Findings
The results show that perceived organizational exploitation is indirectly associated with hospitality employees’ extra-role customer service through depressed mood at work and that employees’ reappraisal may help mitigate the negative effect of organizational exploitation.

Practical implications
First, policies and rules should be established in advance to prevent organizational exploitation. Second, we suggest that hospitality organizations should pay special attention to employees who have low levels of reappraisal, and reappraisal training could be provided to enhance their emotion regulation skills. Third, hospitality organizations could nurture a healthy and supportive emotional climate to create positive emotions in the workplace, in case that depressed mood at work contributes to employees’ extra-role behaviors.

Originality/value
First, the authors go beyond previous studies to focus on a new behavioral outcome of perceived organizational exploitation, i.e. extra-role customer service. Second, it applies a new perspective of COR theory to determine the underlying mechanism of perceived organizational exploitation. Third, to the best of the authors’ knowledge, this study is one of the first to explore the boundary conditions under which the destructive effects of perceived organizational exploitation can be mitigated.
Coordinating multi-level collective action: how intermediaries and digital governance can help supply chains tackle grand challenges
Authors: Rosca Eugenia , Tate Wendy L. , Bals Lydia , Huang Feigao , Ciulli Francesca 
Published: October 2022

PurposeDriven by increasing concerns for sustainable development and digitalization, intermediaries have emerged as relevant actors who can help supply chains tackle grand societal challenges. They can also trigger significant changes in structure, shape and governance models of supply chains. The goal of this research is to advance the understanding of supply chain intermediation and digital governance as coordinating mechanisms for enabling multi-level collective action to address the world's grand challenges.Design/methodology/approachThis is a conceptual research paper that uses a vignette approach, where real examples are described to help question and expand theoretical insights and provide a basis for future research. The examples are drawn from past and ongoing extensive primary and secondary data collection efforts in diverse types of supply chains.FindingsThree contexts are proposed to illustrate how intermediaries and digital governance can play a key role in helping supply chains tackle grand challenges. The first and second context highlight the differences between material and support flow intermediaries in a triadic supply chain relationship. The third context illustrates intermediation within a multi-level network which can be industry-specific or span across industries. The three contexts are evaluated on the level of intervention, the focus on material or support flows, and traditional or digital governance. The specific Sustainable Development Goals which can be tackled through intermediary intervention are also indicated.Originality/valueIntermediaries are often hidden actors in global supply chains and have received limited attention in the academic literature. The conceptual foundation provided in this manuscript serves as the basis for future research opportunities. Three main avenues for further research in this domain are proposed: (1) novel forms of intermediation beyond economic and transactional arrangements; (2) novel forms of digital governance; and (3) translating multi-level collective action into sustainable development outcomes. Research on intermediation driven by sustainable development and digitalization trends can spur empirical advances in sustainable supply chain and operations management with important societal impact.
Advance selling of uncertain demand in low-carbon supply chain
Authors: Jia Haicheng , Li Jing , Liang Ling , Peng Weicai , Xie Jiqing , Xie Jiaping 
Published: October 2022

PurposeThe development of low-carbon production is impeded by the investment costs of green technology research and development (R&D) and carbon emission reduction while facing the uncertain risk of emission reduction investment. With the government's carbon emission constraints, green manufacturers implement the advance selling strategy to increase both profit and reduction level. However, few studies consider the consumer's green preference and emission constraints in advance selling market and spot market independently. The authors' paper investigates the optimal strategies of advance selling pricing and reduction effort for green manufacturers to maximize profits.Design/methodology/approachThe authors' paper designs a stochastic model and investigates the manufacturer's optimal strategies of advance selling price and emission reduction efforts by categorizing different purchasing periods of low-carbon consumers. With the challenges of uncertain demand and government's emission constraints, the authors' develop the non-linear optimization model to investigate the manufacturer's profit-oriented decisions.FindingsThe results show the government's carbon constraints cannot influence the manufacturer's profit, but the consumer's low-carbon preference in the advance selling period can. Interestingly, the manufacturer will make fewer reduction efforts even when the consumers have stronger environmental awareness. In addition, the increasing consumer price sensitivity will exacerbate the profit loss from mandatory emissions reduction. Overall, for achieving a win–win situation between emission reduction and profit growth, green manufacturers should not only consider the sales strategies, market demand, and government constraints in a low-carbon market, but also pay attention to the uncertainty of green technology innovation.Originality/valueWith the consideration of the government's carbon emission constraints, uncertain demand, and low-carbon consumer's preferences, the authors' study innovatively incorporates the joint impacts of advance selling strategy and emission reduction effort strategy and then differentiates between two cases that pertain to the diverse carbon emission regulations.