bluuebunny/crossref_metadata_2025_split huggingface dataset:
The functional differences between paralogous regulators define the control of the General Stress Response in Sphingopyxis granuli TFA
Authors: de Dios Rubén , Santero Eduardo , Reyes-Ramírez Francisca 
Published: October 2021

ABSTRACTSphingopyxis granuli TFA is a contaminant degrading alphaproteobacterium that responds to adverse conditions by inducing the General Stress Response (GSR), an adaptive response that controls the transcription of a variety of genes to overcome adverse conditions. The GSR triggered by TFA is driven by two extracytoplasmic function σ factors (ECFs), EcfG1 and EcfG2, whose functional differences have been addressed previously, being EcfG2 the main activator. Upstream in this cascade, NepR anti-σ factors directly inhibit EcfG activity under non-stress conditions, whereas PhyR response regulators sequester the NepR elements upon stress sensing to relieve EcfG inhibition. These elements, which are essential mediators of the GSR regulation, are duplicated in TFA, being NepR1 and NepR2, and PhyR1 and PhyR2. Here, based on multiple genetic, phenotypical and biochemical evidences including in vitro transcription assays, we have assigned distinct functional features to each of these paralogs and assessed their contribution to the GSR regulation, dictating its timing and the intensity. We show that different stress signals are differentially integrated into the GSR by PhyR1 and PhyR2, therefore producing different levels of GSR activation. We demonstrate in vitro that both NepR1 and NepR2 bind EcfG1 and EcfG2, although NepR1 produces a more stable interaction than NepR2. Conversely, NepR2 interacts with phosphorylated PhyR1 and PhyR2 more efficiently than NepR1. We propose an integrative model where NepR2 would play a dual negative role: it would directly inhibit the σ factors upon activation of the GSR and it would modulate the GSR activity indirectly by titrating the PhyR regulators.IMPORTANCEIn Alphaproteobacteria, the General Stress Response (GSR) aims at protecting against a variety of stresses. Needing to integrate different signals, its modulation is capital to produce a proportionate response according to the environmental conditions. Individual alphaproteobacterial species have evolved distinct GSR cascades in which the information flow is usually straightforward to ascertain due to the presence of a single copy of at least one of its main regulators (PhyR, NepR and EcfG), restricting the regulatory possibilities. However, Sphingopyxis granuli TFA encodes two paralogs of each regulator, multiplying the possible regulatory interplays. We demonstrate that functional differences between paralogous GSR regulators allow an intrinsic feedback regulation in this pathway. We provide evidence of a NepR anti-σ factor that exerts a dual negative feedback regulation on the GSR by interacting with the EcfG σ factors and with the PhyR regulators. This would attune its output to the actual needs of the cell.
Hair phenotype diversity across Indriidae lemurs
Authors: Tapanes Elizabeth , Jacobs Rachel L. , Harryman Ian , Louis Edward E. , Irwin Mitchell T. , Kamilar Jason M. , Bradley Brenda J. 
Published: October 2021

AbstractObjectivesHair (i.e., pelage/fur) is a salient feature of primate (including human) diversity and evolution— serving functions tied to thermoregulation, protection, camouflage, and signaling—but wild primate pelage evolution remains relatively understudied. Specifically, assessing multiple hypotheses across distinct phylogenetic scales is essential but is rarely conducted. We examine whole body hair color and density variation across Indriidae (Avahi, Indri, Propithecus)—a lineage that, like humans, exhibits vertical posture (i.e., their whole bodies are vertical to the sun).Materials and MethodsOur analyses consider multiple phylogenetic scales (family-level, genus-level) and hypotheses (e.g., Gloger’s rule, the body cooling hypotheses). We obtain hair color and density from museum and/or wild animals, opsin genotypes from wild animals, and climate data from WorldClim. To analyze our data, we use phylogenetic generalized linear mixed models (PGLMM) using Markov chain Monte Carlo algorithms.ResultsOur results show that across the Indriidae family, darker hair is typical in wetter regions. However, within Propithecus, dark black hair is common in colder forest regions. Results also show pelage redness increases in populations exhibiting enhanced color vision. Lastly, we find follicle density on the crown and limbs increases in dry and open environments.DiscussionThis study highlights how different selective pressures across distinct phylogenetic scales have likely acted on primate hair evolution. Specifically, our data across Propithecus may implicate thermoregulation and is the first empirical evidence of Bogert’s rule in mammals. Our study also provides rare empirical evidence supporting an early hypothesis on hominin hair evolution.
Wild-type Caenorhabditis elegans Isolates Exhibit Distinct Gene Expression Profiles in Response to Microbial Infection
Authors: Lansdon Patrick , Carlson Maci , Ackley Brian D. 
Published: October 2021

AbstractThe soil-dwelling nematode Caenorhabditis elegans serves as a model system to study innate immunity against microbial pathogens. C. elegans have been collected from around the world, where they, presumably, adapted to regional microbial ecologies. Here we use survival assays and RNA- sequencing to better understand how two isolates from disparate climates respond to pathogenic bacteria. We found that, relative to N2 (originally isolated in Bristol, UK), CB4856 (isolated in Hawaii), was more susceptible to the Gram-positive pathogen, Staphylococcus epidermidis, but equally susceptible to Staphylococcus aureus as well as two Gram-negative pathogens, Providencia rettgeri and Pseudomonas aeruginosa. We performed transcriptome analysis of infected worms and found gene- expression profiles were considerably different in an isolate-specific and pathogen-specific manner. We performed GO term analysis to categorize differential gene expression in response to S. epidermidis. In N2, genes that encoded detoxification enzymes and extracellular matrix proteins were significantly enriched, while in CB4856, genes that encoded detoxification enzymes, C-type lectins, and lipid metabolism proteins were enriched, suggesting they have different responses to these bacterial pathogens, despite being the same species. Overall, discerning gene expression signatures in an isolate by pathogen manner can help us to understand the different possibilities for the evolution of immune responses within organisms.
The quantitative contribution of different Photosystem II compartments to non-photochemical quenching in Arabidopsis
Authors: Nicol Lauren , Mascoli Vincenzo , van Amerongen Herbert , Croce Roberta 
Published: October 2021

AbstractExcess excitation energy in the light-harvesting antenna of Photosystem II (PSII) can cause irreversible damage to the photosynthetic apparatus. In periods of high light intensity, a feedback mechanism known as non-photochemical quenching (NPQ), induces the formation of quenchers which can safely dissipate excess excitation energy as heat. Although quenchers have been identified in more than one compartment of the PSII supercomplex, there is currently no quantitative description of how much NPQ is occurring at each of these locations. Here, we perform time-resolved fluorescence measurements on WT and antenna mutants lacking LHCII (NoL) and all peripheral antenna (Ch1 and Ch1lhcb5). By combining the results with those of steady-state fluorescence experiments we are able to estimate the intrinsic rate of NPQ for each plant and each PSII compartment. It is concluded that 60-70% of quenching occurs in LHCII, 15-20% in the minor antenna and 15-20% in the PSII core.
Insight in the quorum sensing-driven lifestyle of the non-pathogenic Agrobacterium tumefaciens 6N2 and the interactions with the yeast Meyerozyma guilliermondii
Authors: Bertini Elisa Violeta , Torres Mariela Analía , Léger Thibaut , Garcia Camille , Hong Kar-Wai , Chong Teik Min , de Figueroa Lucía I. Castellanos , Chan Kok-Gan , Dessaux Yves , Camadro Jean-Michel , Nieto-Peñalver Carlos Gabriel 
Published: October 2021

AbstractAgrobacterium tumefaciens is considered a prominent phytopathogen, though most isolates are nonpathogenic. Agrobacteria can inhabit plant tissues interacting with other microorganisms. Yeasts are likewise part of these communities. We analyzed the quorum sensing (QS) systems of A. tumefaciens strain 6N2, and its relevance for the interaction with the yeast Meyerozyma guilliermondii, both sugarcane endophytes. We show that strain 6N2 is nonpathogenic, produces OHC8-HSL, OHC10-HSL, OC12-HSL and OHC12-HSL as QS signals, and possesses a complex QS architecture, with one truncated, two complete systems, and three additional QS-signal receptors. A proteomic approach showed differences in QS-regulated proteins between pure (64 proteins) and dual (33 proteins) cultures. Seven proteins were consistently regulated by quorum sensing in pure and dual cultures. M. guilliermondii proteins influenced by QS activity were also evaluated. Several up- and down- regulated proteins differed depending on the bacterial QS. These results show the importance of the QS regulation in the bacteria-yeast interactions.HighlightsThe avirulent A. tumefaciens 6N2 has two replicons and a complex QS architectureThe profile of QS-regulated proteins is modified in dual cultures with Pa. laurentiiThe bacterial QS activity alters the proteome of the yeast Pa. laurentii
Supercharged Cellulases Show Reduced Non-Productive Binding, But Enhanced Activity, on Pretreated Lignocellulosic Biomass
Authors: Nemmaru Bhargava , Douglass Jenna , Yarbrough John M , De Chellis Antonio , Shankar Srivatsan , Thokkadam Alina , Wang Allan , Chundawat Shishir P. S. 
Published: October 2021

ABSTRACTNon-productive adsorption of cellulolytic enzymes to various plant cell wall components, such as lignin and cellulose, necessitates high enzyme loadings to achieve efficient conversion of pretreated lignocellulosic biomass to fermentable sugars. Carbohydrate-binding modules (CBMs), appended to various catalytic domains (CDs), promote lignocellulose deconstruction by increasing targeted substrate-bound CD concentration but often at the cost of increased non-productive enzyme binding. Here, we demonstrate how a computational protein design strategy can be applied to a model endocellulase enzyme (Cel5A) from Thermobifida fusca to allow fine-tuning its CBM surface charge, which led to increased hydrolytic activity towards pretreated lignocellulosic biomass (e.g., corn stover) by up to ∼330% versus the wild-type Cel5A control. We established that the mechanistic basis for this improvement arises from reduced non-productive binding of supercharged Cel5A mutants to cell wall components such as crystalline cellulose (up to 1.7-fold) and lignin (up to 1.8-fold). Interestingly, supercharged Cel5A mutants that showed improved activity on various forms of pretreated corn stover showed increased reversible binding to lignin (up to 2.2-fold) while showing no change in overall thermal stability remarkably. In general, negative supercharging led to increased hydrolytic activity towards both pretreated lignocellulosic biomass and crystalline cellulose whereas positive supercharging led to a reduction of hydrolytic activity. Overall, selective supercharging of protein surfaces was shown to be an effective strategy for improving hydrolytic performance of cellulolytic enzymes for saccharification of real-world pretreated lignocellulosic biomass substrates. Future work should address the implications of supercharging cellulases from various families on inter-enzyme interactions and synergism.
14-3-3ζ constrains insulin secretion by regulating mitochondrial function in pancreatic β-cells
Authors: Mugabo Y , Zhao C , Tan JJ , Ghosh A , Campbell SA , Fadzeyeva E , Paré F , Pan SS , Galipeau M , Ast J , Broichhagen J , Hodson DJ , Mulvihill EE , Petropoulos S , Lim GE 
Published: October 2021

AbstractWhile critical for neurotransmitter synthesis in the brain, members of the 14-3-3 protein family are often assumed to have redundant, over-lapping roles due to their high sequence homology and ubiquitous expression. Despite this assumption, various mammalian 14-3-3 isoforms have now been implicated in regulating cellular and organismal metabolism; however, these functions were primarily observed in cell lines or from systemic knockout mouse models. To date, we have begun to define the contributions of 14-3-3ζ in adipocytes, but whether 14-3-3ζ has additional metabolic roles in other cell types, such as the pancreatic β-cell, is unclear. We previously documented a pro-survival role of 14-3-3ζ in MIN6 insulinoma cells, as depletion of 14-3-3ζ induced cell death, but paradoxically, whole-body deletion of 14-3-3ζ in mice resulted in significantly enlarged β-cell area with no effects on insulin secretion. To better understand the role of 14-3-3ζ in β-cells, we generated β-cell-specific 14-3-3ζ knockout (β14-3-3ζKO) mice, and while no differences in β-cell mass were observed, β14-3-3ζKO mice displayed potentiated insulin secretion due to enhanced mitochondrial function and ATP synthesis. Deletion of 14-3-3ζ led to profound changes to the β-cell transcriptome, where pathways associated with mitochondrial respiration and oxidative phosphorylation were upregulated. Acute treatment of mouse islets and human islets with pan-14-3-3 inhibitors recapitulated the potentiation in glucose-stimulated insulin secretion (GSIS) and mitochondrial function, suggesting that 14-3-3ζ is a critical isoform in β-cells that regulates GSIS. In dysfunctional db/db islets and islets from type 2 diabetic donors, expression of Ywhaz/YWHAZ, the gene encoding 14-3-3ζ, was inversely associated with insulin secretory capacity, and pan-14-3-3 protein inhibition was capable of enhancing GSIS and mitochondrial function. Taken together, this study demonstrates important regulatory functions of 14-3-3ζ and its related isoforms in insulin secretion and mitochondrial function in β-cells. A deeper understanding of how 14-3-3ζ influences β-cell function will further advance our knowledge of how insulin secretion from β-cells is regulated.
Relationship between learning strategies and academic performance: a comparison between accreditation of prior experiential learning (APEL) and regular entry undergraduates
Authors: Tan Saw Fen , Din Eak Arathai , Ooi Li Hsien , Abdullah Anna Christina 
Published: October 2021

PurposeThe purpose of this study aims to compare the academic performance and types of learning strategies used by APEL and regular entry undergraduates. It also explored the relationship between the academic performance and the types of learning strategies utilised by these two groups of undergraduate.Design/methodology/approachThis quantitative study involved 400 undergraduates from an open distance learning (ODL) institution. A correlational research design was used in this study. Data were collected through archival data and questionnaire. Independent t-test and Pearson’s correlation analyses were performed using SPSS.FindingsRegular entrants were found to perform slightly better than APEL entrants. There is no significant difference between the types of learning strategies used by APEL and regular entrants. For both groups, the higher performers adopted time and study environment management as well as effort regulation strategies. Besides this, there was no correlation between cognitive skills and peer learning with their academic performance. Meta-cognitive self-regulation and help-seeking which were found to affect the regular entrants’ academic performance did not correlate with those of APEL entrants.Research limitations/implicationsThis study was conducted within only one institution. The generalisation of findings may therefore be limited. Future studies could be conducted to include students from several institutions.Practical implicationsTime management training could be provided to students. Additional support, like foundation courses and supplementary readings, could be provided to APEL entrants to support their learning.Originality/valueThe findings would be beneficial to ODL institutions who offer APEL entry to understand the academic performance and learning strategies used by APEL entrants relative to regular entrants.
An investigation on cutting of the MWCNTs doped composite plates by CO2 laser beam
Authors: Ceritbinmez Ferhat , Yapici Ahmet 
Published: October 2021

Purpose
The purpose of this study is to obtain strong materials with multiwall carbon nanotubes (MWCNTs) doped and investigate laser cut of MWCNTs also find the effect of the laser cutting parameters on composite materials.

Design/methodology/approach
The laminated composite plates were manufactured by using a vacuum infusion process. The mechanical properties of the composite materials produced were determined according to American Society for Testing and Materials (ASTM) D3039M, ASTM D3171, ASTM D 792 and ASTM D2583. A 130 Watts carbondioxide (CO2) laser cutting machine was used for drilling the two different composite plates with a thickness of 1.6–1.5 mm. Three variables were considered as process parameters including laser power (in three levels of 84.50, 104.00 and 127.40 W), cutting speed (in three levels of 4, 6, 8 mm/s) and 14 mm fixed focal position.

Findings
The fibers could not be cut due to insufficient melting in the experiments performed using 84.50 and 104.00 W laser power but the cutting was successfully completed when the laser power was 127.40 W. However, as the cutting speed increased, the contact time of the laser beam with the material decreased, so the kerf decreased, but the increased laser power created a thermal effect, causing an increase in hardness around the cutting surface. This increase was lower in MWCNTs doped composites compared to pure composites. It has been found that the addition of nanoparticles to layered glass fiber composite materials played an effective role in the strength of the material and affected the CO2 laser cutting quality.

Originality/value
This study is a unique study in which the CO2 laser cutting method of MWCNT-doped composite materials was investigated and the machinability without cutting errors, such as delamination, splitting, distortion and burring using the most suitable laser cutting parameters was revealed.
The role of boundary management in open innovation: towards a 3D perspective
Authors: Capurro Rosita , Fiorentino Raffaele , Garzella Stefano , Lombardi Rosa 
Published: October 2021

PurposeThe aim of this paper is to investigate the role of boundary management when firms should implement open innovation.Design/methodology/approachThe relevant literature on strategic management, firm boundaries and open innovation fields is revised and critically assessed. An interpretive-qualitative methodology is applied to analyse empirical data obtained from a questionnaire and subsequent interviews of a sample of Italian listed firms. By critically integrating literature review and empirical analysis, a framework is provided with the objective of supporting open innovation implementation.FindingsThe study shows that on the one hand, open innovation and many modern paths of growth are connected to a firm's boundaries and that on the other hand, boundary management plays a key role in the implementation of open innovation.Practical implicationsThe paper has implications for practitioners by driving them to shift the focus of open innovation implementation towards the management of boundaries, in which boundary capabilities and activities play a key role.Originality/valueThis paper sheds light on the advantages and risks that can jeopardize a successful opening up innovation processes without the effective management of boundary studies. Thus, the authors identify and propose causes for reflection and tools maximizing potentiality and reducing risks in the implementation of such processes.
Boosting innovative business ideas through hackathons. The “Hack for Travel” case study
Authors: Franco Stefano , Presenza Angelo , Petruzzelli Antonio Messeni 
Published: October 2021

PurposeTechnological platforms encourage the exchange of knowledge and creation of new ideas that create new value for participating members who pool and combine their knowledge, facilities, tools and skills, thus contributing to the development of innovative solutions. This paper focuses on hackathon platforms, working as open innovation intermediaries, investigating their role and functions and exploring how they encourage the collaboration and the innovativeness among participants in order to boost their innovative new ideas.Design/methodology/approachThe research method is a qualitative design that includes in-depth interviews of ten stakeholders that play different roles in “Hack for Travel,” the case under analysis. It is a hackathon organized entirely online, as a response to the crisis generated by coronavirus disease 2019 (COVID-19).FindingsFindings revealed six processes developed by the hackathon platform used to effectively organize the event and facilitate participants to cooperate and share knowledge in order to boost the spread of innovative ideas. Results identify how hackathons should be organized and through which processes they work as innovation platforms.Originality/valueThis is one of the first attempts to study the increasing phenomenon of hackathons, providing theoretical contribution and practical implications about their role in developing innovation.