bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethanolamine regulates CqsR quorum-sensing signaling inVibrio cholerae
Authors: Watve Samit , Barrasso Kelsey , Jung Sarah A. , Davis Kristen J. , Hawver Lisa A. , Khataokar Atul , Palaganas Ryan G. , Neiditch Matthew B. , Perez Lark J. , Ng Wai-Leung 
Published: March 2019

ABSTRACTThe pathogen that causes cholera,Vibrio cholerae, uses the cell-cell communication process known as quorum sensing (QS) to regulate virulence factor production and biofilm formation in response to changes in population density and complexity. QS is mediated through the detection of extracellular chemical signals called autoinducers. Four histidine kinases, LuxPQ, CqsS, CqsR and VpsS, have been identified as receptors to activate the key QS regulator LuxO at low cell density. At high cell density, detection of autoinducers by these receptors leads to deactivation of LuxO, resulting in population-wide gene expression changes. While the cognate autoinducers that regulate the activity of CqsS and LuxQ are known, the signals that regulate CqsR have not been determined. Here we show that the common metabolite ethanolamine specifically interacts with the ligand-binding CACHE domain of CqsRin vitroand induces the high cell-density QS response through CqsR kinase inhibition inV. choleraecells. We also identified residues in the CqsR CACHE domain important for ethanolamine detection and signal transduction. Moreover, mutations disrupting endogenous ethanolamine production inV. choleraedelay the onset of, but do not abolish, the high cell-density QS gene expression. Finally, we demonstrate that modulation of CqsR QS response by ethanolamine occurs inside animal hosts. Our findings suggest thatV. choleraeuses CqsR as a dual-function receptor to integrate information from the self-made signals as well as exogenous ethanolamine as an environmental cue to modulate QS response.IMPORTANCEMany bacteria use quorum sensing to regulate cellular processes that are important for their survival and adaptation to different environments. Quorum sensing usually depends on the detection on chemical signals called autoinducers made endogenously by the bacteria. We show here ethanolamine, a common metabolite made by various bacteria and eukaryotes, can modulate the activity of one of the quorum-sensing receptors inVibrio cholerae, the etiological agent of the disease cholera. Our results raise the possibility thatV. choleraeor other quorum-sensing bacteria can combine environmental sensing and quorum sensing to control group behaviors.
Both galactosaminogalactan and α-1,3-glucan contribute to aggregation ofAspergillus oryzaehyphae in liquid culture
Authors: Miyazawa Ken , Yoshimi Akira , Sano Motoaki , Tabata Fuka , Sugahara Asumi , Kasahara Shin , Koizumi Ami , Yano Shigekazu , Nakajima Tasuku , Abe Keietsu 
Published: March 2019

AbstractFilamentous fungi generally form aggregated hyphal pellets in liquid culture. We previously reported that α-1,3-glucan-deficient mutants ofAspergillus nidulansdid not form hyphal pellets and their hyphae were fully dispersed, and we suggested that α-1,3-glucan functions in hyphal aggregation. Yet,Aspergillus oryzaeα-1,3-glucan-deficient (AGΔ) mutants still form small pellets; therefore, we hypothesized that another factor responsible for forming hyphal pellets remains in these mutants. Here, we identified an extracellular matrix polysaccharide galactosaminogalactan (GAG) as such a factor. To produce a double mutant ofA. oryzae(AG-GAGΔ), we disrupted the genes required for GAG biosynthesis in an AGΔ mutant. Hyphae of the double mutant were fully dispersed in liquid culture, suggesting that GAG is involved in hyphal aggregation inA. oryzae. Addition of partially purified GAG fraction to the hyphae of the AG-GAGΔ strain resulted in formation of mycelial pellets. Acetylation of the amino group in galactosamine of GAG weakened GAG aggregation, suggesting that hydrogen bond formation by this group is important for aggregation. Genome sequences suggest that α-1,3-glucan, GAG, or both are present in many filamentous fungi and thus may function in hyphal aggregation in these fungi. We also demonstrated that production of a recombinant polyesterase, CutL1, was higher in the AG-GAGΔ strain than in the wild-type and AGΔ strains. Thus, controlling hyphal aggregation factors of filamentous fungi may increase productivity in the fermentation industry.ImportanceProduction using filamentous fungi is an important part of the fermentation industry, but hyphal aggregation in these fungi in liquid culture limits productivity compared with that of yeast or bacterial cells. We found that galactosaminogalactan and α-1,3-glucan both function in hyphal aggregation inAspergillus oryzae, and that the hyphae of a double mutant deficient in both polysaccharides become fully dispersed in liquid culture. We also revealed the relative contribution of α-1,3-glucan and galactosaminogalactan to hyphal aggregation. Recombinant protein production was higher in the double mutant than in the wild-type strain. Our research provides a potential technical innovation for the fermentation industry that uses filamentous fungi, as regulation of the growth characteristics ofA.oryzaein liquid culture may increase productivity.
Shh induces symmetry breaking in the presomitic mesoderm by inducing tissue shear and orientated cell rearrangements
Authors: Yin J. , Saunders T. E. 
Published: March 2019

AbstractFuture boundaries of skeletal muscle segments are determined in the presomitic mesoderm (PSM). Within the PSM, future somitic cells undergo significant changes in both morphology and position. How such large-scale cellular changes are coordinated and the effect on the future border formation is unknown. We find that cellular rearrangements differ between cell populations within the PSM. In contrast to lateral somitic cells, which display less organized rearrangement, the adaxial cell layer undergoes significant tissue shearing with dorsal and ventral cells sliding posteriorly. This shear is generated by orientated intercalations of dorsally and ventrally located adaxial cells, which induces a chevron-like pattern. We find Shh signaling is required for the tissue shear and morphogenesis of adaxial cells. In particular, we observe Shh-dependent polarized recruitment of non-muscle myosin IIA drives apical constrictions, and thus the intercalations and shear. This reveals a novel role for Shh in regulating cell mechanics in the PSM.
Harmonious genetic combinations rewire regulatory networks and flip gene essentiality
Authors: New Aaron M. , Lehner Ben 
Published: March 2019

AbstractWe lack an understanding of how the full range of genetic variants that occur in individuals can interact. To address this shortcoming, here we combine diverse mutations between genes in a model regulatory network, the galactose (GAL) switch of budding yeast. The effects of thousands of pairs of mutations fall into a limited number of phenotypic classes. While these effects are mostly predictable using simple rules that capture the ‘stereotypical’ genetic interactions of the network, some double mutants have unexpected outcomes including constituting alternative functional switches. Each of these ‘harmonious’ genetic combinations exhibits altered dependency on other regulatory genes. These cases illustrate how both pairwise and higher epistasis determines gene essentiality and how combinations of mutations rewire regulatory networks. Together, our results provide an overview of how broad spectra of mutations interact, how these interactions can be predicted, and how diverse genetic solutions can achieve ‘wild-type’ phenotypic behavior.
Efficient and specific oligo-based depletion of rRNA
Authors: Kraus Amelie J. , Brink Benedikt G. , Siegel T. Nicolai 
Published: March 2019

SummaryIn most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA or other highly abundant transcripts is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences.In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects.By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available.
The FH2 domain of formin proteins is critical for platelet cytoskeletal dynamics
Authors: Green Hannah L.H. , Zuidscherwoude Malou , Thomas Steven G. 
Published: March 2019

AbstractReorganisation of the actin cytoskeleton is required for proper functioning of platelets following activation in response to vascular damage. Formins are a family of proteins which regulate actin polymerisation and cytoskeletal organisation. Several formin protein are expressed in platelets and so we used an inhibitor of formin mediated actin polymerisation (SMIFH2) to uncover the role of these proteins in platelet spreading. Pre-treatment with SMIFH2 completely blocks platelet spreading in both mouse and human platelets through effects on the organisation and dynamics of actin and microtubules. However, platelet aggregation and secretion are unaffected. SMIFH2 also caused a decrease in resting platelet size and disrupted the balance of tubulin post-translational modification. These data therefore demonstrated an important role for formin mediated actin polymerisation in platelet spreading and highlighted their importance in cross talk between the actin and tubulin cytoskeletons.Key PointsInhibition of FH2 domains blocks platelet spreading and disrupts actin and microtubule organisationInhibition of FH2 domains causes a reduction in resting platelet size but not by microtubule coil depolymerisationFH2 domains play a role in the post-translational modification of microtubulesVisual abstract
Stoichiometric constraints modulate the effects of temperature and nutrients on biomass distribution and community stability
Authors: Sentis Arnaud , Haegeman Bart , Montoya José M. 
Published: March 2019

AbstractTemperature and nutrients are two of the most important drivers of global change. Both can modify the elemental composition (i.e. stoichiometry) of primary producers and consumers. Yet their combined effect on the stoichiometry, dynamics, and stability of ecological communities remains largely unexplored. To fill this gap, we extended the Rosenzweig-MacArthur consumer-resource model by including thermal dependencies, nutrient dynamics, and stoichiometric constraints on both the primary producer and the consumer. We found that stoichiometric constraints dampen the paradox of enrichment and increased persistence at high nutrient levels. Nevertheless, they also reduced consumer persistence at extreme temperatures. Finally, we also found that stoichiometric constraints can strongly influence biomass distribution across trophic levels by modulating consumer assimilation efficiency and resource growth rates along the environmental gradients. In the Rosenzweig-MacArthur model, consumer biomass exceeded resource biomass for most parameter values whereas, in the stoichiometric model, consumer biomass was strongly reduced and sometimes lower than resource biomass. Our findings highlight the importance of accounting for stoichiometric constraints as they can mediate the temperature and nutrient impact on the dynamics and functioning of ecological communities.
Cell shape and antibiotic resistance is maintained by the activity of multiple FtsW and RodA enzymes inListeria monocytogenes
Authors: Rismondo Jeanine , Halbedel Sven , Gründling Angelika 
Published: March 2019

AbstractRod-shaped bacteria have two modes of peptidoglycan synthesis: lateral synthesis and synthesis at the cell division site. These two processes are controlled by two macromolecular protein complexes, the elongasome and divisome. Recently, it has been shown that theBacillus subtilisRodA protein, which forms part of the elongasome, has peptidoglycan glycosyltransferase activity. The cell division specific RodA homolog FtsW fulfils a similar role at the divisome. The human pathogenListeria monocytogenesencodes up to six FtsW/RodA homologs, however their functions have not yet been investigated. Analysis of deletion and depletion strains led to the identification of the essential cell division-specific FtsW protein, FtsW1. Interestingly,L. monocytogenesencodes a second FtsW protein, FtsW2, which can compensate for the lack of FtsW1, when expressed from an inducible promoter.L. monocytogenesalso possesses three RodA homologs, RodA1, RodA2 and RodA3 and their combined absence is lethal. Cells of arodA1/rodA3double mutant are shorter and have increased antibiotic and lysozyme sensitivity, probably due to a weakened cell wall. Results from promoter activity assays revealed that expression ofrodA3andftsW2is induced in the presence of antibiotics targeting penicillin binding proteins. Consistent with this, arodA3mutant was more susceptible to the β-lactam antibiotic cefuroxime. Interestingly, overexpression of RodA3 also led to increased cefuroxime sensitivity. Our study highlights thatL. monocytogenesencodes a multitude of functional FtsW and RodA enzymes to produce its rigid cell wall and that their expression needs to be tightly regulated to maintain growth, cell division and antibiotic resistance.ImportanceThe human pathogenListeria monocytogenesis usually treated with high doses of β-lactam antibiotics, often combined with gentamicin. However, these antibiotics only act bacteriostatically onL. monocytogenesand the immune system is needed to clear the infection. Therefore, individuals with a compromised immune system are at risk to develop a severe form ofListeriainfection, which can be fatal in up to 30% of cases. The development of new strategies to treatListeriainfections is therefore necessary. Here we show that the expression of some of the FtsW and RodA enzymes ofL. monocytogenesis induced by the presence of β-lactam antibiotics and their combined absence makes bacteria more susceptible to this class of antibiotics. The development of antimicrobials that inhibit the activity or production of FtsW/RodA enzymes might therefore help to improve the treatment ofListeriainfections and thereby lead to a reduction in mortality.
Quantitative lean assessment of line of balance schedules’ quality
Authors: Ungureanu Lucian Constantin , Hartmann Timo , Serbanoiu Ion 
Published: March 2019

Purpose
The line of balance (LOB) method is a suitable scheduling technique that managers can use to support lean planning efforts for projects composed of repetitive activities such as high-rise building construction. Like any other method, LOB has certain disadvantages that create a set of practical limitations in its application. An LOB schedule gives insights about how continuous and synchronized single resources are scheduled and how uniform these resources are distributed over the project duration. However, these three characteristics have to be visually checked, which makes the evaluation and the comparison of different schedule alternatives difficult. To overcome this problem, the purpose of this paper is to present a quantitative method to calculate quality degrees for the continuity, the synchronization and the uniformity of an LOB schedule that can be applied to assess an LOB schedule globally.

Design/methodology/approach
The paper introduces a set of global indicators, termed quality degrees, which allow for a quick quantitative evaluation of LOB schedules at the global level. These quality degrees are quantitative indicators for the: degree of continuity, degree of synchronization and degree of uniformity within a specific LOB alternative. A mathematical model was developed to calculate the quality degrees for LOB schedules. This model was validated using a well-known case study extracted from literature, and its practical implementation was exemplified on two real Romanian projects.

Findings
The paper illustrates this contribution using two case studies that confirm that the proposed method can be used to evaluate different schedule alternatives. In particular, the paper shows that quality indicators can be used to analyze and control interdependencies between cost and time.

Research limitations/implications
The main limitation of the proposed method is that it cannot indicate the desired level of continuity, synchronization or uniformity to be achieved. Further studies need to explore this possibility, as well the relationship between indicators.

Practical implications
The presented quality indicators contribute to existing LOB methods as they allow for the quick analysis and assessment of schedules without an in-depth visual analysis.

Originality/value
The paper proposes an innovative method, mathematically formulated, to quantitatively assess the quality aspects of continuity, synchronization and uniformity for LOB schedules.
Work integrated learning internships in transnational education
Authors: Bilsland Christine , Carter Leanne , Wood Leigh N. 
Published: March 2019

Purpose
Research into employability initiatives such as work integrated learning (WIL) in transnational education (TNE) is scarce, and the alumni voice in TNE is largely unreported. The purpose of this paper is to contribute to TNE research by investigating the value of internship electives in the TNE campus location.

Design/methodology/approach
A grounded theory approach employed semi-structured interviews with local business undergraduate alumni in Vietnam.

Findings
Internships were instrumental to local graduate employment transitions. University support of WIL internships was a valuable differentiator in the Vietnamese university context, where internships lack formal support mechanisms. Alumni regarded internships as transformational learning journeys, rather than simply as pathways to post-graduate jobs.

Research limitations/implications
The scope of the study was Vietnam. Findings imply the importance of incorporating local stakeholder perspectives into TNE, particularly regarding WIL.

Practical implications
Universities that operate in transnational environments must meet local stakeholder needs by providing authentic, industry-related learning activities. The findings support the integration of WIL internships into TNE programmes in Vietnam and further research relevant to other TNE contexts.

Originality/value
The study contributes to underdeveloped TNE research around employability in general, and more specifically about the particular value of internships in TNE campus locations. Alumni stakeholders constitute uniquely valuable feedback sources based on their shared experience as TNE students, interns and graduate employees in local work environments. Their insights enable universities to facilitate locally relevant learning outcomes.
Project manager’s role in safety performance of Saudi construction
Authors: Khawam Abdullah A. , Bostain Nancy S. 
Published: March 2019

Purpose
The purpose of this paper is to address the primary research question, which is what is the relationship between the project manager’s (PM) possession of the Project Management Professional (PMP) certification and the level of the safety culture present in the construction project the PM manages.

Design/methodology/approach
The research was based on a survey of a purposive sample, 109 engineers and first-line supervisors worked in 23 construction projects of which ten were led by PMP-certified PMs and 13 were led by PMs lacking PMP certification. Each PM completed a demographic questionnaire for the predictor variables of PMP certification controlled for age and experience. To assess the criterion variable of safety culture total score, engineers and first-line supervisors working in the same project completed the questionnaire of safety culture values and practices.

Findings
Results of this study indicated the level of safety culture was significantly different, and improved, for engineers and first-line supervisors who work under PMs with PMP certification compared to the level of safety culture in projects managed by PMs with no PMP certification. Although alignment of safety culture perceptions among different levels in the organization helps to achieve a positive safety culture, the role of the PM in transferring, implementing and maintaining the safety culture in the construction project is fundamental, particularly in small-to-medium sized enterprises (SMEs).

Originality/value
This study addressed the role of the PMs managerial skills in the safety performance of Saudi Arabian SMEs. The principal finding was that PMs with managerial skills perform better regarding safety performance in SME construction projects than PMs lacking managerial skills. The primary recommendation is that leaders in construction projects must carefully evaluate engineers’ managerial skills before hiring the individuals as PMs. A PM’s promotion model developed in this study provides a suitable framework and business process component for construction leaders seeking to maintain safety performance successfully.
Segmenting elder German grocery shoppers based on shopping motivations
Authors: Oeser Gerald , Aygün Tanju , Balan Claudia-Livia , Paffrath Rainer , Schuckel Marcus Thomas 
Published: March 2019

Purpose
Elder German grocery shoppers are a growing, heterogeneous, and highly relevant and attractive, but under-researched market segment. In order to understand them and their grocery shopping motivations better and target them efficiently and effectively, the purpose of this paper is to identify dimensions of their shopping motivations and segment them based on these dimensions.

Design/methodology/approach
In total, 26 grocery store-choice criteria were identified in a thorough literature review and focus-group interviews with 36 elder German consumers aged 65 and older. In a subsequent survey, the importance of these criteria was rated by 1,288 German shoppers of the same age group. A principal component and cluster analysis were performed to identify dimensions of store-choice criteria and segments of elder German grocery shoppers. Multivariate analysis of variance, analysis of variance and discriminant analysis were used to test for statistically significant differences between the clusters.

Findings
Basic quality considerations, shopping experience and social interaction, service and assistance, price consciousness, product orientation, convenient location and quick service and packaging requirements influence the grocery store choice of elder German consumers in decreasing order of variance explained. The cluster analysis revealed indifferent, leisure, convenience, assistance-oriented, no frills, product-oriented and service-oriented elder German shoppers, which differ in their shopping motivations statistically and significantly. These clusters are described and contrasted in detail to derive managerial implications.

Originality/value
This research provides the first store-choice component analysis and cluster analysis for elder German grocery shoppers. This can help food retail to reach this attractive target group more efficiently and effectively and improve the food supply of elder German consumers.