bluuebunny/crossref_metadata_2025_split huggingface dataset:
ABO blood group, glycosyltransferase activity and risk of Venous Thrombosis
Authors: Kosta Manal Ibrahim , Bailly Pascal , Silvy Monique , Saut Noemie , Suchon Pierre , Morange Pierre-Emmanuel , Chiaroni Jacques , Trégouët David-Alexandre , Goumidi Louisa 
Published: March 2020

AbstractIntroductionABO blood group influence the risk of venous thrombosis (VT) by modifying A and B glycosyltransferases (AGT and BGT) activities that further modulates Factor VIII (FVIII) and von Willebrand Factor (VWF) plasma levels. The aim of this work was to evaluate the association of plasma GTs activities with VWF/FVIII plasma levels and VT risk in a case-control study.Materials and Methods420 cases were matched with 420 controls for age and ABO blood group. GT activities in plasma were measured using the quantitative transfer of tritiated N-acetylgalactosamine or galactose to the 2’-fucosyl-lactose and expressed in disintegration per minute/30µL of plasma and 2 hours of reaction (dpm/30µL/2H). FVIII and VWF plasma levels were respectively measured using human FVIII-deficient plasma in a 1-stage factor assay and STA LIATEST VWF (Diagnostica Stago).ResultsA and B GT activities were significantly lower in cases than in controls (8119±4027 vs 9682±4177 dpm/30µL/2H, p=2.03 × 10−5, and 4931±2305 vs 5524±2096 dpm/30µL/2H, p=0.043 respectively). This association was observed whatever the ABO blood groups. The ABO A1 blood group was found to explain∼80% of AGT activity. After adjusting for ABO blood groups, AGT activity was not correlated to VWF/FVIII plasma levels. Conversely, there was a moderate correlation (ρ∼0.30) between BGT activity and VWF/ FVIII plasma levels in B blood group carriers.ConclusionThis work showed, for the first time, that GT activities were decreased in VT patients in comparison to controls with the same ABO blood group. The biological mechanisms responsible for this association remained to be determined.
JNK pathway restricts DENV, ZIKV and CHIKV infection by activating complement and apoptosis in mosquito salivary glands
Authors: Chowdhury Avisha , Modahl Cassandra M. , Tan Siok Thing , Xiang Benjamin Wong Wei , Missé Dorothée , Vial Thomas , Kini R. Manjunatha , Pompon Julien Francis 
Published: March 2020

AbstractArbovirus infection ofAedes aegyptisalivary glands (SGs) determines transmission. However, there is a dearth of knowledge on SG immunity. Here, we characterized SG immune response to dengue, Zika and chikungunya viruses using high-throughput transcriptomics. The three viruses regulate components of Toll, IMD and JNK pathways. However, silencing of Toll and IMD components showed variable effects on SG infection by each virus. In contrast, regulation of JNK pathway produced consistent responses. Virus infection increased with depletion of component Kayak and decreased with depletion of negative regulator Puckered. Virus-induced JNK pathway regulates complement and apoptosis in SGs via TEP20 and Dronc, respectively. Individual and co-silencing of these genes demonstrate their antiviral effects and that both may function together. Co-silencing eitherTEP20orDroncwithPuckeredannihilates JNK pathway antiviral effect. We identified and characterized the broad antiviral function of JNK pathway in SGs, expanding the immune arsenal that blocks arbovirus transmission.
Colonization with heterologous bacteria reprograms aCaenorhabditis elegansnutritional phenotype
Authors: Sun Qing , Vega Nicole M. , Cervantes Bernardo , Mancuso Christopher P. , Mao Ning , Taylor Megan , Collins James J. , Khalil Ahmad S. , Gore Jeff , Lu Timothy K. 
Published: March 2020

AbstractAnimals rely on the gut microbiome to process complex food compounds that the host cannot digest and to synthesize nutrients that the host cannot produce. New systems are needed to study how the expanded metabolic capacity provided by the gut microbiome impacts the nutritional status and health of the host. Here we colonized the nematodeCaenorhabditis elegansgut with cellulolytic bacteria that enabledC. elegansto utilize cellulose, an otherwise indigestible substrate, as a carbon source. The nutritional benefits of colonization with cellulolytic bacteria were assayed directly, by incorporation of isotopic biomass, and indirectly, as host larval yield resulting from glucose release in the gut. As a community component in the worm gut, cellulolytic bacteria can also support additional bacterial species with specialized roles, which we demonstrate by usingLactobacillusto protect againstSalmonellainfection. As a model system,C. eleganscolonized with cellulolytic bacteria can be used to study microbiome-host interactions. Engineered microbiome communities may provide host organisms with novel functions, such as the ability to use more complex nutrient sources and to fight against pathogen infections.One Sentence SummaryHeterologous bacteria colonizing an animal gut help digest complex sugars to provide nutrition for the host in a model system.
Plant and Bacterial Metaxin-like Proteins: Novel Proteins Related to Vertebrate Metaxins Involved in Uptake of Nascent Proteins into Mitochondria
Authors: Adolph Kenneth W. 
Published: March 2020

ABSTRACTThe metaxins were originally identified as vertebrate proteins of the outer mitochondrial membrane involved in protein import into mitochondria. Metaxin proteins have also been found in diverse invertebrate phyla. The present study is concerned with examining whether metaxin-like proteins occur in plants and bacteria. Metaxin-like proteins were revealed by their homology with human metaxins and the possession of characteristic GST_Metaxin protein domains. The results demonstrate that metaxin-like proteins exist in plants that include a wide variety of angiosperms, both eudicots and monocots, and other plant groups. Metaxin-like proteins can also be detected in bacteria, particularly in the Proteobacteria phylum, but also in different bacterial phyla. Phylogenetic analysis indicates that plant metaxin-like proteins, bacterial metaxin-like proteins, and vertebrate metaxins form distinct phylogenetic groups, but are related. Metaxin-like proteins, however, are only distantly related to GSTs (glutathione S-transferase proteins). A similar degree of homology is found in aligning the amino acid sequences of plant and bacterial metaxin-like proteins with human metaxins 1, 2, and 3 and other vertebrate metaxins. The amino acid identities range from about 22%-28% for each alignment. The presence of two conserved protein domains, GST_N_Metaxin and GST_C_Metaxin, in both plant and bacterial metaxin-like proteins provides evidence that these proteins are related to the vertebrate and invertebrate metaxins. The metaxin-like proteins have predicted secondary structures that are dominated by alpha-helical segments, like the vertebrate and invertebrate metaxins.
Phosphorylation barcode-dependent signal bias of the dopamine D1 receptor
Authors: Kaya Ali I. , Perry Nicole A. , Gurevich Vsevolod V. , Iverson T.M. 
Published: March 2020

AbstractAgonist-activated G protein-coupled receptors (GPCRs) must correctly select from hundreds of potential downstream signaling cascades and effectors. To accomplish this, GPCRs first bind to an intermediary signaling protein, such as G protein or arrestin. These intermediaries initiate signaling cascades that promote the activity of different effectors, including several protein kinases. The relative roles of G proteins versus arrestins in initiating and directing signaling is hotly debated, and it remains unclear how the correct final signaling pathway is chosen given the ready availability of protein partners. Here, we begin to deconvolute the process of signal bias from the dopamine D1 receptor (D1R) by exploring factors that promote the activation of ERK1/2 or Src, the kinases that lead to cell growth and proliferation. We found that ERK1/2 activation involves both arrestin and Gαs, while Src activation depends solely on arrestin. Interestingly, we found that the phosphorylation pattern influences both arrestin and Gαs coupling, suggesting an additional way the cells regulate G protein signaling. The phosphorylation sites in the D1R intracellular loop 3 are particularly important for directing the binding of G protein versus arrestin and for selecting between the activation of ERK1/2 and Src. Collectively, these studies correlate functional outcomes with a physical basis for signaling bias and provide fundamental information on how GPCR signaling is directed.Significance StatementThe functional importance of receptor phosphorylation in GPCR regulation has been demonstrated. Over the past decade, the phospho-barcode concept was developed to explain the multi-dimensional nature of the arrestin-dependent signaling network downstream of GPCRs. Here, we used the dopamine-1 receptor (D1R) to explore the effect of receptor phosphorylation on G protein-dependent and arrestin-dependent ERK and Src activation. Our studies suggest that D1R intracellular loop-3 phosphorylation affects both G proteins and arrestins. Differential D1R phosphorylation can direct signaling toward ERK or Src activation. This implies that phosphorylation induces different conformations of receptor and/or bound arrestin to initiate or select different cellular signaling pathways.
Genome-wide targets identification by CRISPRi-Omics for high-titer production of free fatty acids inEscherichia coli
Authors: Fang Lixia , Fan Jie , Wang Congya , Cao Yingxiu , Song Hao 
Published: March 2020

AbstractTo construct a superior microbial cell factory for chemical synthesis, a major challenge is to fully exploit cell potential via identifying and engineering beneficial gene targets in the sophisticated metabolic networks. Here, we develop an approach that integrates CRISPR interference (CRISPRi) to readily modulate genes expression and omics analyses to identify potential targets in multiple cellular processes, enabling systematical discovery of beneficial chromosomal gene targets that can be engineered to optimize free fatty acids (FFAs) production inEscherichia coli. We identify 56 beneficial genes via synergistic CRISPRi-Omics strategy, including 46 novel targets functioning in cell structure and division, and signaling transduction that efficiently facilitate FFAs production. Upon repressingihfAand overexpressingaidBandtesA’inE. coli, the recombinant strain LihfA-OaidB results in a FFAs titer of 21.6 g L-1in fed-batch fermentation, which, to our best knowledge, is the maximum FFAs titer by the recombinantE. colireported to date.
The Recombinational Landscape inDaphnia pulex
Authors: Lynch Michael , Ye Zhiqiang , Maruki Takahiro 
Published: March 2020

AbstractThrough the analysis of linkage disequilibrium from genome-wide sequencing data for multiple individuals from eight populations, the general features of the recombinational landscape are revealed in the microcrustaceanDaphnia pulex.The data suggest an exceptionally uniform pattern of recombination across the genome, while also confirming general patterns that are inconsistent with existing population-genetic models for the relationship between linkage dis-equilibrium and physical distances between genomic sites. Patterns of linkage disequilibrium are highly consistent among populations, and average rates of recombination are quite similar for all chromosomes. There is no evidence of recombination hotspots, and although there does appear to be suppressed recombination in the vicinity of gene bodies, this effect is quite small. Although this species reproduces asexually in ∼ 80% of generations, the mean per-generation recombination rate per nucleotide site is ∼ 37× the per-nucleotide mutation rate. Contrary to expectations for models in which crossing-over is the primary mechanism of recombination, and consistent with data for other species, the gradient of linkage disequilibrium with increasing physical distance between sites is far too high at short distances and far too low at long distances, suggesting an important role for factors such as the nonindependent appearance of pairs of mutations on haplotypes and long-range gene-conversion-like processes. Combined with other observations on patterns of nucleotide variation, these results provide a strong case for the utility ofD. pulexas a model system for the study of mechanisms of evolution in natural populations.
Role of RgsA in oxidative stress resistance inPseudomonas aeruginosa
Authors: Hou Shuyi , Zhang Jiaqing , Ma Xiaobo , Hong Qiang , Fang Lili , Zheng Gangsen , Huang Jiaming , Gao Yingchun , Xu Qiaoli , Zhuang Xingguo , Song Xiuyu 
Published: March 2020

AbstractPseudomonas aeruginosais an extremely common opportunistic pathogen in clinical practice. Patients with metabolic disorders, hematologic diseases, malignancies, who have undergone surgery or who have received certain treatments are susceptible to this bacterium. In addition,P. aeruginosais a multidrug-resistant that tends to form biofilms and is refractory to treatment. Small regulatory RNAs are RNA molecules that are 40–500 nucleotides long, possess regulatory function, are ubiquitous in bacteria, and are also known as small RNA (sRNA). sRNAs play important regulatory roles in various vital life processes in diverse bacteria and their quantity and diversity of regulatory functions exceeds that of proteins. In this study, we showed that deletion of the sRNA RgsA decreases the growth rate and ability to resist different concentrations and durations of peroxide inP. aeruginosa. These decreases occur not only in the planktonic state, but also in the biofilm state. Finally, protein mass spectrometry was employed to understand changes in the entire protein spectrum. The results presented herein provide a description of the role of RgsA in the life activities ofP. aeruginosaat the molecular, phenotypic, and protein levels.
Business ethics disclosure and corporate governance in Sub-Saharan Africa (SSA)
Authors: Waweru Nelson 
Published: March 2020

PurposeThe purpose of this paper is to examine the relationship between business ethics practices disclosure and corporate governance characteristics in Sub-Saharan Africa.Design/methodology/approachThe study uses multiple regression to investigate the association between business ethics disclosure (BED) and corporate governance characteristics in SAA. The study sample is based on 573 non-financial corporations listed on the national stock exchanges of Ghana, Kenya, Nigeria, South Africa and Zimbabwe as of 31 December 2015.FindingsThe findings show that corporate governance characteristics (including the proportion of government ownership, board independence and board gender diversity) are positively and significantly related to BED.Originality/valueThe study contributes to the limited literature by analyzing the relationship between BED practices and corporate governance characteristics in the sub-Sahara African context, which is significantly different from the Anglo-Saxon world.
Residential adaptations as users' tacit means of communicating spatial needs in housing design
Authors: Agyefi-Mensah Stephen , Kpamma Zoya Evans , Hagan Daniel Ebo 
Published: March 2020

Purpose
Knowing and understanding the spatial needs of users is imperative for the design of livable and sustainable houses. However, the practical and theoretical difficulties associated with this, especially in social housing, create a shortfall in design knowledge known as user needs gap. To bridge this gap, design researchers over the years, have sought to provide feedback for design decision-making through post-occupancy evaluation studies using preferences and residential satisfaction as constructs. In view of their limitations, this study aims to explore residential adaptations as residents’ tacit means of communicating their spatial needs, and a pathway to understanding residents’ housing requirements.

Design/methodology/approach
The study was exploratory in nature and a case study by design using a convergent parallel design within the mixed methods tradition. Activity Theory as used as a conceptual framework. The study involved three strands of research as follows: estimation of the floor areas of the rooms and spaces of the case study designs using the International Standards Organisation intramuros method; a survey of households and their activities using questionnaires; and observation of residents’ adaptations captured photographs and drawings. In all, 43 households out of the 66 apartments in the two case designs were surveyed.

Findings
The study found that while the units were theoretically large, they were practically inadequate when average household sizes were taken into account in a space per person analysis. In response, particularly to sleeping requirements of children, residents make different forms of adaptations – normative, such as house sharing, compositional and organizational, as well as add-ins and add-ons including and illegal alterations.

Originality/value
The paper presents residential adaptations as an empirically grounded, contextually embedded and practically useful means of exploring and understanding users’ spatial needs in housing design. Residential adaptations provide a means through which residents communicate their housing needs, albeit tacitly – a means for self-expression, self-extension and self-determination. To theory, the study shows that residential adaptations can be useful as a construct for understanding residents’ spatial needs, though fuzzy. It also helps understand how the tensions in an activity system, may result from contradictions produced by the lurking effect of contextual factors. This makes contextual knowledge, particularly cultural knowledge, critical to the design.
The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here?
Authors: Harrison Joshua G. , Griffin Eric A. 
Published: March 2020

SummaryThe interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from ~600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the 17 biomes encompassed by our survey, 7 were understudied and together composed only 7% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above‐ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.
Bacterial community diversity in the rhizosphere of nickel hyperaccumulator plant species from Borneo Island (Malaysia)
Authors: Lopez Séverine , van der Ent Antony , Sumail Sukaibin , Sugau John B. , Buang Matsain Mohd , Amin Zarina , Echevarria Guillaume , Morel Jean Louis , Benizri Emile 
Published: March 2020

SummaryThe Island of Borneo is a major biodiversity hotspot, and in the Malaysian state of Sabah, ultramafic soils are extensive and home to more than 31 endemic nickel hyperaccumulator plants. The aim of this study was to characterize the structure and the diversity of the rhizosphere bacterial communities of several of these nickel hyperaccumulator plants and factors that affect these bacterial communities in Sabah. The most abundant phyla were Proteobacteria, Acidobacteria and Actinobacteria. At family level, Burkholderiaceae and Xanthobacteraceae (Proteobacteria phylum) were the most abundant families in the hyperaccumulator rhizospheres. Redundancy analysis based on soil chemical analyses and relative abundances of the major bacterial phyla showed that abiotic factors of the studied sites drove the bacterial diversity. For all R. aff. bengalensis rhizosphere soil samples, irrespective of studied site, the bacterial diversity was similar. Moreover, the Saprospiraceae family showed a high representativeness in the R. aff. bengalensis rhizosphere soils and was linked with the nickel availability in soils. The ability of R. aff. bengalensis to concentrate nickel in its rhizosphere appears to be the major factor driving the rhizobacterial community diversity unlike for other hyperaccumulator species.
Exploring the influence of course elements and emotional connection to content on students’ approaches to learning in an introductory food science and human nutrition course
Authors: Schmidt Shelly J. 
Published: March 2020

AbstractResearchers have identified three approaches to learning—surface, strategic, and deep. These approaches are influenced by various contextual and student factors, including teaching methods, assessments, and relevance to future career. The global objective of this study was to explore the influence of course elements and students’ emotional connection to section content on students’ approaches to learning in an introductory Food Science and Human Nutrition course. Students completed two questionnaires for the Nutrition and Health (NH) and Composition and Chemistry (CC) course sections: (a) Entwistle's ASSIST Inventory and (b) a questionnaire developed to assess students’ perceived usefulness of assignments, learning resources, and emotional connection to section content. Students’ approaches to learning did not significantly differ between NH and CC sections, with the majority reporting use of strategic or deep approaches. Generally, positive correlations were obtained for learners who used the deep and strategic approaches and their perceived usefulness of assignments and learning resources. In stark contrast, negative correlations were identified for learners who used the surface approach and their perceived usefulness of learning resources and assignments. Regarding emotional connection to section content, compared to learners who used the deep and strategic approaches, learners who used the surface approach did not enjoy and felt anxious about learning the content in both sections. Furthermore, based on regression analysis, the surface learning approach was a predictor for low exam scores in both sections. Based on these findings, instructors should implement practices in course design, instructional methods, and assessment strategies that help students choose deep and strategic approaches to learning, while minimizing surface approaches.