bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery and characterisation of novel circular bacteriocin plantacyclin B21AG fromLactobacillus plantarumB21
Authors: Golneshin Aida , Gor Mian Chee , Vezina Ben , Williamson Nicholas , Van Thi Thu Hao , May Bee K. , Smith Andrew T 
Published: April 2020

AbstractLactobacillus plantarumB21 isolated from Vietnamese sausage (nem chua) has previously displayed broad antimicrobial activity against gram positive bacteria including foodborne pathogensListeria monocytogenesandClostridium perfringens. This study successfully identified the antimicrobial agent as plantacyclin B21AG, a 5668 Da circular bacteriocin demonstrating high thermostability, resistance to a wide range of pH, proteolytic resistance and temporal stability. We report a reverse genetics approach used to identify and characterise plantacyclin B21AG. The bacteriocin was purified from culture supernatant by a short process consisting of concentration, n-butanol extraction and cation exchange chromatography. Ade novopeptide sequencing using LC-MS/MS techniques identified two putative peptide fragments which were mapped to the genome ofLactobacillus plantarumB21. This revealed an ORF corresponding to a putative circular bacteriocin with a 33-amino acid leader peptide and 58-amino acid mature peptide found on native plasmid pB21AG01. The corresponding gene cluster, consisted of seven genes associated with post-translational circularisation, immunity and secretion. The robust nature of plantacyclin B21AG, its antimicrobial activity and associated machinery for cyclisation make it an interesting biotechnological target for further development, and application as a food-safe antimicrobial.
Combinatorial analysis of gene regulatory network reveals the causal genetic basis of breast cancer and gene-specific personalized drug treatments
Authors: Sharif Siam Mohammad Kawsar , Sharif Shohan Mohammad Umer , Syed Easin Uddin 
Published: April 2020

AbstractCancer is the major burden of diseases around the world. The incidence and mortality rate of cancers is mounting up with the passage of days. Breast cancer is the most demoralizing cause of death, where both diseases interlocked with each other due to some genetic, biological and behavioral motives. The molecular mechanism of breast cancer through which they crop up and manifest together remains questionable. The genetic basis of protein-protein interactions and gene networks has elucidated a group of gene regulatory systems in Breast cancer. Thus, the extraction of all genomic and proteomic data has enabled unprecedented views of gene-protein co-expression, co-regulation, and interactions in the biological system. This study explored the biological system to develop a gene-disease interaction model by implementing the extracted genomic and proteomic data of Breast cancer. The disease-specific and correlated genes were pulled out and their cabling studied by PPI, disease pathway and drug-disease interaction data to articulate their role in disease development. By analyzing mined genes that are related to breast cancer, a network model is also proposed. Exploration of all the correlated genes, Hub and common genes have given some promising pieces of evidence surrounding the genetic networking models. The result of this prospective study disclosed breast cancer mediated crosslinking or possible metastatic relation on a genetic basis. Moreover, other diseases like prostate, colorectal and ovarian cancers are at the same risk and might count into consideration. The finding provides a narrative broad approach for understanding the genetic basis of these fatal diseases by the pathway analysis with gene regulatory network evaluation.
Putative condition-dependent viability selection in wild type stocks ofDrosophila pseudoobscura
Authors: Altindag Ulku H. , Taylor Hannah N. , Shoben Chelsea , Pownall Keeley A. , Stevison Laurie S 
Published: April 2020

AbstractMeiotic recombination rates vary in response to intrinsic and extrinsic factors. Recently, heat stress has been shown to reveal plasticity in recombination rates inDrosophila pseudoobscura. Here, a combination of molecular genotyping and X-linked recessive phenotypic markers were used to investigate differences in recombination rates due to either heat stress or advanced maternal age. However, haplotype frequencies deviated from equal proportions for crosses using phenotypic markers, indicating viability selection. Interestingly, skews in haplotype frequency were condition-dependent, consistent with the fixation of alleles in the wild type stocks used that are unfit at high temperature. Evidence of viability selection due to heat stress in the wild type haplotypes was most apparent on days 7-9 when more mutant non-crossover haplotypes were recovered in comparison to wild type (p=2.2e-4). Despite the condition-dependent mutational load in both wild type and mutant stocks, an analysis of recombination rate plasticity revealed days 7-9 (p=0.0085) and day 9 (p=0.037) to be significantly higher due to heat stress and days 1-3 as significantly higher due to maternal age (p=0.025). Still, to confirm these findings, SNP genotyping markers were used to further investigate recombination rate. This analysis supported days 9-10 as significantly different due to heat stress in two pairs of consecutive SNP markers (p=0.018; p=0.015), suggesting this time period as when recombination rate is most sensitive to heat stress. This peak timing for recombination plasticity is consistent withD. melanogasterbased on comparison of similarly timed key meiotic events, enabling future mechanistic work of temperature stress on recombination rate.
Conditionally essential genes for survival during starvation inEnterococcus faeciumE745
Authors: de Maat Vincent , Arredondo-Alonso Sergio , Willems Rob J.L. , van Schaik Willem 
Published: April 2020

AbstractThe nosocomial pathogenEnterococcus faeciumcan survive for prolonged periods of time on surfaces in the absence of nutrients. This trait is thought to contribute to the ability ofE. faeciumto spread among patients in hospitals. Because there is currently a lack of data on the mechanisms that are responsible for the ability ofE. faeciumto survive in the absence of nutrients, we performed a high-throughput transposon mutant library screening (Tn-seq) to identify genes that have a role in long-term survival during incubation in phosphate-buffered saline (PBS) at 20°C. A total of 18 genes were identified by Tn-seq to contribute to survival in PBS, with functions associated with the general stress response, DNA repair, metabolism, and membrane homeostasis. The gene which was quantitatively most important for survival in PBS wasusp(locus tag: EfmE745_02439), which is predicted to encode a 17.4 kDa universal stress protein. After generating a targeted deletion mutant inusp, we were able to confirm thatuspsignificantly contributes to survival in PBS and this defect was restored byin transcomplementation. Asuspis present in 99% of 1644E. faeciumgenomes that span the diversity of the species, we postulate that this gene is a key determinant for the remarkable environmental robustness ofE. faecium. Further mechanistic studies intouspand other genes identified in this study may shed further light on the mechanisms by whichE. faeciumcan survive in the absence of nutrients for prolonged periods of time.
Impaired HSF1 transactivation drives proteostasis collapse and senescent phenotype of IPF lung fibroblast
Authors: Cuevas-Mora Karina , Roque Willy , Sales Dominic , Ritzenthaler Jeffrey D. , Torres-Gonzales Edilson , Halayko Andrew J , Rosas Ivan O. , Roman Jesse , Romero Freddy 
Published: April 2020

ABSTRACTLoss of proteostasis and cellular senescence are key hallmarks of aging. Recent studies suggest that lung fibroblasts from idiopathic pulmonary fibrosis (IPF) show features of cellular senescence, decline in heat shock proteins (HSPs) expression and impaired protein homeostasis (proteostasis). However, direct cause-effect relationships are still mostly unknown. In this study, we sought to investigate whether the heat shock factor 1 (HSF1), a major transcription factor that regulates the cellular HSPs network and cytoplasmic proteostasis, contributes to cellular senescence in lung fibroblasts. We found that IPF lung fibroblasts showed an upregulation in the expression of various cellular senescence markers, including β-galactosidase activity (SA-β-gal) staining, the DNA damage marker γH2Ax, the cell cycle inhibitor protein p21, and multiple senescence-associated secretory proteins (SASP), as well as upregulation of collagen 1a1, fibronectin and alpha-smooth muscle actin (α-SMA) gene expression compared with age-matched controls. These changes were associated with impaired proteostasis, as judged by an increase in levels of p-HSF1ser307and HSF1K298 sumo, downregulation of HSPs expression, and increased cellular protein aggregation. Similarly, lung fibroblasts isolated from a mouse model of bleomycin-induced lung fibrosis and mouse lung fibroblast chronically treated with H2O2showed downregulation in HSPs and increased in cellular senescence and SASP markers. Moreover, sustained pharmacologic activation of HSF1 increased the expression of HSPs, reduced cellular senescence markers and effectively reduced the expression of pro-fibrotic genes in IPF fibroblast. Our data provide evidence that the HSF1-mediated proteostasis is important for driving lung fibroblasts toward cellular senescence and a myofibroblast phenotype. We postulate that enhancing HSF1 activity could be effective in the treatment of lung fibrosis.
The RecQ DNA helicase Rqh1 promotes Rad3ATRkinase signaling in the DNA replication checkpoint pathway of fission yeast
Authors: Ahamad Nafees , Khan Saman , Xu Yong-jie 
Published: April 2020

ABSTRACTRad3 is the orthologue of ATR and the sensor kinase of the DNA replication checkpoint inSchizosaccharomyces pombe. Under replication stress, it initiates checkpoint signaling at the forks necessary for maintaining genome stability and cell survival. To better understand the checkpoint initiation process, we have carried out a genetic screen in fission yeast by random mutation of the genome looking for mutants with defects in Rad3 kinase signaling. In addition to the previously reportedtel2-C307Ymutant (1), this screen has identified six mutations inrqh1encoding a RecQ DNA helicase. Surprisingly, theserqh1mutations except a start codon mutation are all in the helicase domain, indicating that the helicase activity of Rqh1 plays an important role in the replication checkpoint. In support of this notion, integration of two helicase-inactive mutations or deletion ofrqh1generated a similar Rad3 signaling defect and heterologous expression of human RECQ1, BLM and RECQ4 restored the Rad3 signaling and partially rescued arqh1helicase mutant. Therefore, the replication checkpoint function of Rqh1 is highly conserved and mutations in the helicase domain of these human enzymes may cause the checkpoint defect and contribute to the cancer predisposition syndromes.
DDR2 induces linear invadosome to promote angiogenesis in a fibrillar type I collagen context
Authors: Hammoud Aya Abou , Marais Sébastien , Allain Nathalie , Ezzoukhry Zakaria , Moreau Violaine , Saltel Frédéric 
Published: April 2020

AbstractTo generate new vessels, endothelial cells (ECs) form invadosomes, which are actin-based microdomains with a proteolytic activity that degrade the basement membrane. We previously demonstrated that ECs form linear invadosomes in fibrillar type I collagen context. In this study, we aim to investigate the molecular mechanisms by which ECs guides angiogenesis in a fibrillar type I collagen context. We found that Discoidin Domain Receptor 2 (DDR2) is the collagen receptor tyrosine kinase required to form linear invadosomes in ECs. We further demonstrated that it acts in synergy with VEGF to promote extracellular matrix degradation. We highlighted the involvement of an interaction between DDR2 and the matrix metalloproteinase MMP14 in this process. Finally, using in vitro andex-vivoangiogenesis assays, we demonstrated a pro-angiogenic function of DDR2 in a collagen-rich microenvironment. This study allows us to propose DDR2-dependent linear invadosomes as targets to modulate angiogenesis.
Higher-order assumed strain plane element immune to mesh distortion
Authors: Rezaiee-Pajand Mohammad , Gharaei-Moghaddam Nima , Ramezani Mohammadreza 
Published: April 2020

Purpose
This paper aims to propose a new robust membrane finite element for the analysis of plane problems. The suggested element has triangular geometry. Four nodes and 11 degrees of freedom (DOF) are considered for the element. Each of the three vertex nodes has three DOF, two displacements and one drilling. The fourth node that is located inside the element has only two translational DOF.

Design/methodology/approach
The suggested formulation is based on the assumed strain method and satisfies both compatibility and equilibrium conditions within each element. This establishment results in higher insensitivity to the mesh distortion. Enforcement of the equilibrium condition to the assumed strain field leads to considerably high accuracy of the developed formulation.

Findings
To show the merits of the suggested plane element, its different properties, including insensitivity to mesh distortion, particularly under transverse shear forces, immunities to the various locking phenomena and convergence of the element are studied. The obtained results demonstrate the superiority of the suggested element compared with many of the available robust membrane elements.

Originality/value
According to the attained results, the proposed element performs better than the well-known displacement-based elements such as linear strain triangular element, Q4 and Q8 and even is comparable with robust modified membrane elements.
The relationship between perceived dissimilarity and feedback avoidance behaviour
Authors: Song Meng , Gok Kubilay , Moss Sherry , Borkowski Nancy 
Published: April 2020

PurposeThe purpose of this study is to understand the conditions in which subordinates, after making a mistake, are more likely to engage in feedback avoidance behaviour (FAB), a set of behaviours that could ultimately jeopardise patient safety in a health care context.Design/methodology/approachThis study used a sample of 183 independent leader-subordinate dyads in the health care service sector. For this study, a multiple mediator model in which three types of conflict (task conflict, relationship conflict and process conflict) were tested and acted as mediating mechanisms that transmitted the effects of perceived dissimilarity to FAB.FindingsThe results supported the mediating role of two of the three forms of conflict and highlighted the consequences of dissimilarity between supervisors and subordinates in the healthcare setting.Research limitations/implicationsOne of the noteworthy limitations of this study was that this study used cross-sectional time-lagged data. Future research should use a more rigorous longitudinal approach such as a cross-lagged design (Whitmanet al., 2012) to explore the dynamic nature of dyadic relationships over time.Practical implicationsAn important implication of our study results suggests that health care leadership development training should provide opportunities to increase awareness of the tendency of leaders to treat subordinates perceived as dissimilar more negatively.Originality/valueThese results contribute to our understanding of the interpersonal processes between subordinates and their supervisors, which could have a significant impact on organisational outcomes in the health care setting.
Exploring the spectrum of fashion rental
Authors: Mukendi Amira , Henninger Claudia Elisabeth 
Published: April 2020

PurposeCurrently, fashion rental is suggested as being a way to bring about sustainability in the fashion industry. Although there has been some success for brands in this space, as of yet fashion rental remains a niche form of consumption. This study aims to uncover consumer perspectives of fashion rental to identify opportunities for developing a fashion rental business that meets the needs of current consumers.Design/methodology/approachThis is a qualitative study utilising semi-structured interviews combined with brainstorming and drawing exercises. Interviews were conducted with 17 women and three men.FindingsFindings indicate that considerations around fashion rentals are utilitarian in nature focussing on functional benefits rather than more hedonistic ones. A spectrum of products that people would be most interested in renting is given.Research limitations/implicationsAlthough the study invited male and female participants, the sample is more female-heavy, which may reflect the fact that women tend to be more open to alternative modes of consumption.Practical implicationsAn important implication is that asking consumers to rent clothing requires a significant change in mindset. Brands need to ensure that their services “make sense” for the consumer to consider it as a viable alternative to purchasing new clothing.Originality/valueThis paper proposes a spectrum of fashion items that consumers may be interested in renting; this aims to help brands develop services that meet consumer needs.
Challenges in economic evaluations in obstetric care: a scoping review and expert opinion
Authors: Hulst SM , Brouwer WBF , Mol BW , van den Akker‐van Marle ME 
Published: April 2020

ObjectiveThe aim of this study is to identify items of economic evaluation guidelines that are frequently not complied within obstetric economic evaluations and to search for reasons for non‐adherence.DesignScoping review and qualitative study.SettingLiterature on economic evaluations in obstetric care and interviews with experts.Population or sampleThe sample included 229 scientific articles and five experts.MethodsA systematic literature search was performed. All types of literature about economic evaluations in obstetric care were included. The adherence to guidelines was assessed and articles were qualitatively analysed on additional information about reasons for non‐adherence. Issues that arose from the scoping review were discussed with experts.Main outcome measuresAdherence to guideline items of the included economic evaluations studies. Analytical themes describing reasons for non‐adherence, resulting from qualitative analysis of articles and interviews with experts.ResultsA total of 184 economic evaluations and 45 other type of articles were included. Guideline items frequently not complied with were time horizon, type of economic evaluation and effect measure. Reasons for non‐adherence had to do with paucity of long‐term health data and assessing and combining outcomes for mother and child resulting from obstetric interventions.ConclusionsThis study identified items of guidelines that are frequently not complied with and the reasons behind this. The results are a starting point for a broad consensus building on how to deal with these challenges that can result in special guidance for the conduct of economic evaluations in obstetric care.Tweetable abstractNon‐adherence to guidelines in obstetric economic evaluation studies: the difficulties in detail.
Methionine as a methyl donor regulates caste differentiation in the European honey bee (Apis mellifera)
Authors: Chen Wen‐Feng , Wang Ying , Zhang Wei‐Xing , Liu Zhen‐Guo , Xu Bao‐Hua , Wang Hong‐Fang 
Published: April 2020

AbstractNutrition contributes to honey bee caste differentiation, but the role of individual nutrients is still unclear. Most essential amino acid contents, except that of methionine (Met), are greater in royal jelly than worker jelly. After ∼3.5 d, the Met content in the latter was slightly greater than in the former. Met is the major raw material used in the synthesis of S‐adenosyl‐L‐methionine, an active methyl donor for DNA methylation, which is an epigenetic driver of caste differentiation. Here, we tested whether Met regulates caste differentiation in honey bees by determining its effects on the caste development of bees receiving four diets: the basic, basic + 0.2% Met, basic + 0.2% Met + 20 mg/kg 5‐azacytidine, and basic + 20 mg/kg 5‐azacytidine. The presence of Met decreased the adult bee body length and the numbers of ovarioles, indicating that Met may direct the development of female larvae toward worker bees. The upregulated expression of SAMS, Dnmt1, and Dnmt3 caused by Met exposure in 4‐d‐old larvae indicated that the worker‐inductive effects of Met may occur through the promotion of DNA methylation. We investigated the co‐effects of Met and glucose on bee development, and found that the effects of an increased glucose level on the number of ovarioles and body length did not strengthen the worker‐inductive effects caused by Met. Our results contribute to caste development theory and suggest that Met—as a methyl donor—plays a regulatory, but not decisive, role in caste differentiation.
An optimized method for the extraction of ancient eukaryote DNA from marine sediments
Authors: Armbrecht Linda , Herrando‐Pérez Salvador , Eisenhofer Raphael , Hallegraeff Gustaaf M. , Bolch Christopher J. S. , Cooper Alan 
Published: April 2020

AbstractMarine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo‐communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead‐beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica‐solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size‐selection of low molecular‐weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead‐beating, DNA binding in silica‐solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post‐library LMW size‐selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data‐processing protocol should improve quantitative paleo‐monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.
Changes in marginal tax rates over the past three decades in the United States
Authors: Chen Xikai , Lu Meiting , Shan Yaowen 
Published: April 2020

AbstractThis paper investigates changes in corporate marginal tax rates (MTRs) in the United States over the past three decades. Similar to effective tax rate, MTR exhibits a significant but much more modest decline over time, even after accounting for tax‐related firm characteristics and industry variations. In contrast to Dyreng et al., we find that MTR declines more rapidly for purely domestic firms than for multinationals. Our findings highlight the puzzling evidence in Dyreng et al. and call for future research to study possible drivers that explain the sustained and differential decline in corporate tax rate over time between domestic and multinational firms.