bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of endopeptidases in peptidoglycan synthesis mediated by alternative cross-linking enzymes inEscherichia coli
Authors: Voedts Henri , Dorchêne Delphine , Lodge Adam , Vollmer Waldemar , Arthur Michel , Hugonnet Jean-Emmanuel 
Published: February 2021

ABSTRACTBacteria resist to the turgor pressure of the cytoplasm through a net-like macromolecule, the peptidoglycan, made of glycan strands connected via peptides cross-linked by penicillin-binding proteins (PBPs). We recently reported the emergence of β-lactam resistance resulting from a bypass of PBPs by the YcbB L,D-transpeptidase (LdtD), which form chemically distinct 3→3 cross-links compared to 4→3 formed by PBPs. Here we show that peptidoglycan expansion requires controlled hydrolysis of cross-links and identify amongst eight endopeptidase paralogues the minimum enzyme complements essential for bacterial growth with 4→3 (MepM) and 3→3 (MepM and MepK) cross-links. Purified Mep endopeptidases unexpectedly displayed a 4→3 and 3→3 dual specificity implying recognition of a common motif in the two cross-link types. Uncoupling of the polymerization of glycan chains from the 4→3 cross-linking reaction was found to facilitate the bypass of PBPs by YcbB. These results illustrate the plasticity of the peptidoglycan polymerization machinery in response to the selective pressure of β-lactams.
Chlorine inactivation ofEscherichia coli O157:H7in fresh produce wash process: effectiveness and modeling
Authors: Abnavi Mohammadreza Dehghan , Kothapalli Chandrasekhar R. , Munther Daniel , Srinivasan Parthasarathy 
Published: February 2021

AbstractThis study presents a modified disinfection kinetics model to evaluate the potential effect of organic content on the chlorine inactivation coefficient ofEscherichia coli O157:H7in fresh produce wash processes. Results show a significant decrease in the bactericidal efficacy of free chlorine (FC) in the presence of organic load compared to its absence. While the chlorine inactivation coefficient ofEscherichia coli O157:H7is 70.39 ± 3.19 L.mg−1.min−1in the absence of organic content, it drops by 73% in chemical oxygen demand (COD) level of 600 - 800 mg.L−1. Results also indicate that the initial chlorine concentration and bacterial load have no effect on the chlorine inactivation coefficient. A second-order chemical reaction model for FC decay, which utilizes a percentage of COD as an indicator of organic content in fresh produce wash was employed, yielding an apparent reaction rate of (9.45 ± 0.22) × 10−4μM−1.min−1. This model was validated by predicting FC concentration (R2= 0.96) in multi-run continuous wash cycles with periodic replenishment of chlorine.
TargetingGys1with AAV‐SaCas9 decreases pathogenic polyglucosan bodies and neuroinflammation in Adult Polyglucosan Body and Lafora disease mouse models
Authors: Gumusgoz Emrah , Guisso Dikran R , Kasiri Sahba , Wu Jun , Dear Matthew , Verhalen Brandy , Nitschke Silvia , Mitra Sharmistha , Nitschke Felix , Minassian Berge A. 
Published: February 2021

SummaryMany adult and most childhood neurological diseases have a genetic basis. CRISPR/Cas9 biotechnology holds great promise in neurological therapy, pending the clearance of major delivery, efficiency and specificity hurdles. We apply CRISPR/Cas9 genome editing in its simplest modality, namely inducing gene sequence disruption, to one adult and one pediatric disease. Adult polyglucosan body disease is a neurodegenerative disease resembling amyotrophic lateral sclerosis. Lafora disease is a severe late childhood onset progressive myoclonus epilepsy. The pathogenic insult in both is formation in the brain of glycogen with overlong branches, which precipitates and accumulates into polyglucosan bodies that drive neuroinflammation and neurodegeneration. We packagedStaphylococcus aureusCas9 and a guide RNA targeting the glycogen synthase geneGys1responsible for brain glycogen branch elongation in AAV9 virus, which we delivered by neonatal intracerebroventricular injection to one mouse model of adult polyglucosan body disease and two mouse models of Lafora disease. This resulted, in all three models, in editing of approximately 17% ofGys1alleles and a similar extent of reduction ofGys1mRNA across the brain. The latter led to approximately 50% reductions of GYS1 protein, of abnormal glycogen accumulation and of polyglucosan bodies, as well as corrections of neuroinflammatory markers in all three models. Our work represents proof of principle for virally-delivered CRISPR/Cas9 neurotherapeutics in an adult-onset (adult polyglucosan body) and a childhood-onset (Lafora) neurological diseases.
slim shadyis a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201
Authors: Dash Linkan , McEwan Robert E. , Montes Christian , Mejia Ludvin , Walley Justin W. , Dilkes Brian P. , Kelley Dior R. 
Published: February 2021

ABSTRACTAuxin is a hormone that is required for hypocotyl elongation during seedling development. In response to auxin rapid changes in transcript and protein abundance occur in hypocotyls and some auxin responsive gene expression is linked to hypocotyl growth. To functionally validate proteomic studies, a reverse genetics screen was performed on mutants in auxin-regulated proteins to identify novel regulators of plant growth. This uncovered a long hypocotyl mutant, which we calledslim shady, in an annotated insertion line inIMMUNOREGULATORY RNA-BINDING PROTEIN (IRR). Overexpression of theIRRgene failed to rescue theslim shadyphenotype and characterization of a second T-DNA allele ofIRRfound that it had a wild-type hypocotyl length. Theslim shadymutant has an elevated expression of numerous genes associated with the brassinosteroid-auxin-phytochrome (BAP) regulatory module compared to wild-type, including transcription factors that regulate brassinosteroid, auxin and phytochrome pathways. Additionally,slim shadyseedlings fail to exhibit a strong transcriptional response to auxin. Using whole genome sequence and transcriptomics data for SALK_015201C we determined that a novel single nucleotide polymorphism inPHYTOCHROME Bwas responsible for theslim shadyphenotype. This is predicted to convert induce a frameshift and premature stop codon at leucine 1125, within the histidine kinase-related domain of the carboxy terminus of PHYB, which is required for phytochrome signaling and function. Genetic complementation analyses withphyb-9confirmed that slim shady is a mutant allele ofPHYB. This study advances our understanding of the molecular mechanisms in seedling development, by furthering our understanding of how light signaling is linked to auxin dependent cell elongation. Furthermore, this study highlights the importance of confirming the genetic identity of research material before attributing phenotypes to known mutations sourced from T-DNA stocks.
SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization
Authors: Hoffmann Markus , Zhang Lu , Krüger Nadine , Graichen Luise , Kleine-Weber Hannah , Hofmann-Winkler Heike , Kempf Amy , Nessler Stefan , Riggert Joachim , Winkler Martin Sebastian , Schulz Sebastian , Jäck Hans-Martin , Pöhlmann Stefan 
Published: February 2021

SUMMARYTransmission of SARS-CoV-2 from humans to farmed mink was observed in Europe and the US. In the infected animals viral variants arose that harbored mutations in the spike (S) protein, the target of neutralizing antibodies, and these variants were transmitted back to humans. This raised concerns that mink might become a constant source of human infection with SARS-CoV-2 variants associated with an increased threat to human health and resulted in mass culling of mink. Here, we report that mutations frequently found in the S proteins of SARS-CoV-2 from mink were mostly compatible with efficient entry into human cells and its inhibition by soluble ACE2. In contrast, mutation Y453F reduced neutralization by an antibody with emergency use authorization for COVID-19 therapy and by sera/plasma from COVID-19 patients. These results suggest that antibody responses induced upon infection or certain antibodies used for treatment might offer insufficient protection against SARS-CoV-2 variants from mink.
Strong trait correlation and phylogenetic signal in North American ground beetle (Carabidae) morphology
Authors: Stachewicz Jacob D. , Fountain-Jones Nicholas M. , Koontz Austin , Woolf Hillary , Pearse William D. , Gallinat Amanda S. 
Published: February 2021

AbstractFunctional traits mediate species’ responses to and roles within their environment, and are constrained by evolutionary history. While we have a strong understanding of trait evolution for macro-taxa such as birds and mammals, our understanding of invertebrates is comparatively limited. Here we address this gap in North American beetles with a sample of ground beetles (Carabidae), leveraging a large-scale collection and digitization effort by the National Ecological Observatory Network (NEON). For 154 ground beetle species, we measured seven morphological traits, which we placed into a recently-developed effect-response framework that characterizes traits by how they predict species’ effects on their ecosystems or responses to environmental stressors. We then used cytochrome oxidase one sequences from the same specimens to generate a phylogeny and tested evolutionary tempo and mode of the traits. We found strong phylogenetic signal in, and correlations among, morphological ground beetle traits. These results indicate that, for these species, beetle body shape trait evolution is constrained, and phylogenetic inertia is a stronger driver of beetle traits than (recent) environmental responses. Strong correlations among effect and response traits suggest that future environmental drivers are likely to affect both ecological composition and functioning in these beetles.
Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere
Authors: Liu Yangminghao , Patko Daniel , Engelhardt Ilonka , George Timothy S , Stanley-Wall Nicola , Ladmiral Vincent , Ameduri Bruno , Daniell Tim J , Holden Nicola , MacDonald Michael P , Dupuy Lionel X 
Published: February 2021

AbstractOur understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants’ large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 μm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point “first contact”, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.
Unravelling cotton RNAseq repositories to the fiber development specific modules and their alliance with the fiber-related traits
Authors: Prasad Priti , Khatoon Uzma , Verma Rishi Kumar , Kumar Ajay , Mohapatra Debashish , Bhattacharya Parthasarthi , Bag Sumit K , Sawant Samir V 
Published: February 2021

SummaryCotton fiber development is still an intriguing question to understand the fiber commitment and development. Here, we remapped >350 publicly available cotton RNA sequencing data on recently published cotton genome with ∼400 fold coverage. The differentially expressed genes were clustered in six modules whose functions are specific to commitment, initiation, elongation and Secondary Cell Wall (SCW) fiber development stages. Gene Ontology analysis of commitment and initiation specific modules suggests enrichment of genes involved in organ development. The modules specific for elongation and SCW showed significant enrichment of hydroxyproline-rich proteins and hydrolases. Transcription factors (TFs) binding frequency of defined modules suggested that homeodomain, MYB and NAC expresses at commitment stages but their expression was governed by other TFs. We also mined the stage-specific transcriptional biomarker and Exclusively Expressed Transcripts (EETs) for fiber. These EETs were positively selected during fiber evolution and cotton domestication. The extensive expression profiling of six EETs in 100 cotton genotypes at different fiber developmental stages using nCounter assay and their correlation with eight fiber-related suggests that several EETs are correlated with different fiber quality-related traits. Thus, our study reveals several important genes and pathways that may be important for cotton fiber development and future improvement of cotton.
NGO responses to financial evaluation: auditability, purification and performance
Authors: Cazenave Bruno , Morales Jeremy 
Published: February 2021

PurposeLiterature has widely studied the financial accountability pressures on NGOs but rarely analysed how NGOs respond to them. This paper studies one large humanitarian NGO to address this question. It investigates the NGO's responses to understand the extent to which NGOs are able to regain control over their own work and turn the frames of evaluation and accountability to their own advantage.Design/methodology/approachThis article draws on a case study of one of the largest French humanitarian NGOs. Interviews and observation (both participant and non-participant) were conducted in the financial department of the NGO. These data are supplemented with field-level contextual interviews.FindingsIn the NGO studied, institutional pressure is largely mediated by compliance audits. The paper thus traces the consequences of compliance audits for the NGO's central finance teams and describes how they respond. The findings detail three responses to evaluation. First, to respond to the burden of evaluation, the organisation makes itself auditable and develops preparedness. Second, to respond to the anxiety of evaluation, the organisation engages in a process of purification and succumbs to the allure of the single figure. Third, building on its newly acquired auditability and purity, the organisation performs itself as a “corporatised NGO”. Together, these three responses constitute the NGO as an “entrepreneur” competing for eligibility, and financial literacy and managerialism become crucial to respond to pressure from institutional funders.Originality/valueThis paper extends the understanding of organisational responses to evaluation. The authors show the influence of evaluation systems on NGOs, but also how NGOs can react to regain control over their work and turn the frames of evaluation and accountability to their own advantage. However, despite several decades of calls for broader conceptions of NGO accountability, the case NGO prefers to promote a very narrow view of its performance, based solely on accounting compliance. It takes some pride in its ability to comply with funders' and auditors' demands. Turning a simple matter of compliance into a display of good performance, it builds a strategy and competitive advantage on its ability to respond competently to evaluation.
Thought favorability: mediating role in fit and brand advocacy
Authors: Vashisht Devika , Mohan HFO Surindar , Chauhan Abhishek , Vashisht Raveesh 
Published: February 2021

PurposeThe purpose of this study is to investigate the effect of game-product fit on brand advocacy and mediating role of thought favorability in fit and brand advocacy relationship in the context of in-game advertising (IGA) using congruity theory and heuristic systematic model. This expounds the conditions under which in-game brand placements form favorable or unfavorable thoughts about the game and the advertised brand, and following brand advocacy.Design/methodology/approachA total of 144 student-gamers participated in the study. One-way ANOVA and a path analysis were used for hypotheses testing.FindingsResults showed that the high-fit game resulted in higher thought favorability and greater levels of brand advocacy than the low-fit game. Furthermore, results also revealed that thought favorability mediated the relationship of game-product fit and brand advocacy among players.Research limitations/implicationsResearch on IGA is still in its relative infancy, and how gamers respond to brand placements in games has yet to be fully established. This paper’s theoretical implications are primarily in the context of in-game advertising and explain the role played by game-product fit as an originator to thought favorability that further adds value to thought favorability and brand advocacy relationship.Practical implicationsThe study offers important implications for marketers, advertisers, policy-makers in terms of effective game-designing and IGA execution.OriginalitySince very little research has been done focusing on mediating role of thought favorability in game-product fit and brand advocacy relationship in the context of IGA from attention and elaboration perspectives, this paper scores as a pioneering study of its kind in India.
A probabilistic-based analysis for wind distribution determination of a runway
Authors: Suzer Ahmet Esat , Kaba Aziz 
Published: February 2021

Purpose
The purpose of this study is to describe precisely the wind speed regime and characteristics of a runway of an International Airport, the north-western part of Turkey.

Design methodology approach
Three different probability distributions, namely, Inverse Gaussian (IG), widely used two-parameter Weibull and Rayleigh distributions in the literature, are used to represent wind regime and characteristics of the runway. The parameters of each distribution are estimated by the pattern search (PS)-based heuristic algorithm. The results are compared with the other three methods-based numerical computation, including maximum-likelihood method, moment method (MoM) and power density method, respectively. To evaluate the fitting performance of the proposed method, several statistical goodness tests including the mostly used root mean square error (RMSE) and chi-squared (X2) are conducted.

Findings
In the light of the statistical goodness tests, the results of the IG-based PS attain better performance than the classical Weibull and Rayleigh functions. Both the RMSE and X2 values achieved by the IG-based PS method lower than that of Weibull and Rayleigh distributions. It exhibits a better fitting performance with 0.0074 for RMSE and 0.58 × 10−4 for X2 for probability density function (PDF) in 2012 and with RMSE of 0.0084 and X2 of 0.74 × 10−4 for PDF in 2013. As regard the cumulative density function of the measured wind data, the best results are found to be Weibull-based PS with RMSE of 0.0175 and X2 of 3.25 × 10−4 in 2012. However, Weibull-based MoM shows more excellent ability in 2013, with RMSE of 0.0166 and X2 of 2.94 × 10−4. Consequently, it is considered that the results of this study confirm that IG-based PS with the lowest error value can a good choice to model more accurately and characterize the wind speed profile of the airport.

Practical implications
This paper presents a realistic point of view regarding the wind regime and characteristics of an airport. This study may cast the light on researchers, policymakers, policy analysts and airport designers intending to investigate the wind profile of a runway at the airport in the world and also provide a significant pathway on how to determine the wind distribution of the runway.

Originality value
Instead of the well-known Weibull distribution for the representing of wind distribution in the literature, in this paper, IG distribution is used. Furthermore, the suitability of IG to represent the wind distribution is validated when compared with two-parameter Weibull and Rayleigh distributions. Besides, the performance and efficiency of PS have been evaluated by comparing it with other methods.
Budgeting as practice and knowing in action: experimenting with Bourdieu's theory of practice: an empirical evidence from a public university
Authors: Seneviratne Chaturika Priyadarshani , Martino Ashan Lester 
Published: February 2021

PurposeThe present study aims to explore how various doings, strategic actions and power relations stemming from internal agents are instrumental in (re)constituting the different forms and meanings of budgeting in a specific field.Design/methodology/approachThe paper uses a single-case study method based on a Sri Lankan public university. Data are collected using interviews, documentary evidence and observations.FindingsThe empirical evidence suggested that internal agents are crucial, and they are the producers of budgetary practice as they possess practical knowledge and power relations in the field where they operate. The case data demonstrate that organisational agents do have real essence as active and acting to produce effects in budgeting practices, and the significance of exploring the singularity of multiple agents in terms of their viewpoints, trajectories, dispositions and power relations, who may form, sustain or interrupt budgetary practices in a given setting.Research limitations/implicationsAs the research is directed towards the selection of in-depth enquiry of specific setting infused with culture, values, perception and ideology, it might cause to diminish the researcher's analytical objectivity and independence of the research.Practical implicationsAs budgetary practices are product of human interaction, it is important to note that practitioners should be concerned with what agents do in actual practice and their inactions, influences and power relations in budgeting practices, which might not align with the structural forces enlisted in the budgeting. It would be of interest for future empirical research to explore the interplay between the diverse interests of organisational agents and agents beyond the individual organisations.Originality/valueThis study contributes to the literature on management control practices by documenting the importance of understanding the “practice” through relational thinking of all three concepts is emphasised, such interrelated theoretical insights are seldom used to understand accounting practices. This research emphasises the importance of bringing out the microprocessual facets of management control to open up its non-conscious, non-strategic and non-rationalist forms.
Fixed point theorems for Geraghty-type mappings applied to solving nonlinear Volterra-Fredholm integral equations in modularG-metric spaces
Authors: Okeke Godwin Amechi , Francis Daniel 
Published: February 2021

PurposeThe authors prove the existence and uniqueness of fixed point of mappings satisfying Geraghty-type contractions in the setting of preordered modularG-metric spaces. The authors apply the results in solving nonlinear Volterra-Fredholm-type integral equations. The results extend generalize compliment and include several known results as special cases.Design/methodology/approachThe results of this paper are theoretical and analytical in nature.FindingsThe authors prove the existence and uniqueness of fixed point of mappings satisfying Geraghty-type contractions in the setting of preordered modularG-metric spaces. apply the results in solving nonlinear Volterra-Fredholm-type integral equations. The results extend, generalize, compliment and include several known results as special cases.Research limitations/implicationsThe results are theoretical and analytical.Practical implicationsThe results were applied to solving nonlinear integral equations.Social implicationsThe results has several social applications.Originality/valueThe results of this paper are new.