bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic characterization ofVibrio parahaemolyticusfrom Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing thePhotorhabdusinsect-related (Pir) toxin-like genes
Authors: Yan Chrystine Zou Yi , Austin Christopher M. , Ayub Qasim , Rahman Sadequr , Gan Han Ming
Published: July 2019

The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused byVibrio parahaemolyticusharboring the pVA plasmid containing thepirAVpandpirBVpgenes which code forPhotorhabdusinsect-related (Pir) toxin. The limited genomic resource forV. parahaemolyticusstrains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water)V. parahaemolyticusfrom three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages ofV. parahaemolyticusthat harbor thepirABVpgenes. The recovery of pVA plasmid backbone devoid ofpirAVporpirABVpin someV. parahaemolyticusisolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of AsianV. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.
Regulation of neuron-specific gene transcription by stress hormone signalling requires synaptic activity in zebrafish
Authors: Eachus Helen , Subramanya Dheemanth , Jackson Harriet E. , Wang Guannyu , Berntsen Kieran , Ashton John-Paul , Esposito Umberto , Seifuddin Fayaz , Pirooznia Mehdi , Elhaik Eran , Krone Nils , Baines Richard A. , Placzek Marysia , Cunliffe Vincent T.
Published: July 2019

The Glucocorticoid Receptor (GR) co-ordinates metabolic and behavioural responses to stressors. We hypothesised that GR influences behaviour by modulating specific epigenetic and transcriptional processes in the brain. Using the zebrafish as a model organism, the brain methylomes of wild-type and grs357 mutant adults were analysed and GR-sensitive, differentially methylated regions (GR-DMRs) were identified. Two genes with GR-DMRs exhibited distinct methylation and transcriptional sensitivities to GR: the widely expressed direct GR target fkbp5 and neuron-specific aplp1. In larvae, neural activity is required for GR-mediated transcription of aplp1, but not for that of fkbp5. GR regulates metabotropic glutamate receptor gene expression, the activities of which also modulated aplp1 expression, implicating synaptic neurotransmission as an effector of GR function upstream of aplp1. Our results identify two distinct routes of GR-regulated transcription in the brain, including a pathway through which GR couples endocrine signalling to synaptic activity-regulated transcription by modulating metabotropic glutamate receptor expression.
cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences
Authors: Ereful Nelzo C. , Laurena Antonio , Liu Li-Yu , Kao Shu-Min , Tsai Eric , Thomson Michael , Greenland Andy , Powell Wayne , Mackay Ian , Leung Hei
Published: July 2019

Abstract cis and/or trans regulatory divergence within or between related taxa on a genome-wide scale has been largely unexamined in crops, more so, the effect of stress on cis/trans architecture. In this study, the indica genotypes IR64, an elite drought-susceptible lowland variety, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. Evidence of cis and/or trans regulatory differences was tested between these two indica rice genotypes. By sequencing (RNA-seq) the parents and their hybrid, we are able to map genes diverging in cis and/or trans factors between the two genotypes. Under non-stress conditions, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting conditions largely affect trans and cis + trans factors. Between the two inbred lines, Apo appears to exhibit higher expression fold change of genes enriched in “response to stress” and “photosynthesis” under non- and water-stress conditions. On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response. Parent–hybrid RNA-seq has the potential to identify genes diverging in cis and/or trans factors even between intra-sub-specifically related genotypes. By comparing cis/trans landscape under stressed and unstressed conditions, this approach has the ability to assess the impact of drought on gene expression. Computational analysis and association of several drought-yield QTL markers with cis-diverging genes provide converging evidences suggestive of a potential approach to identify trait-associated candidate genes using hybrids and their parents alone.

Key Message

cis dominantly explains divergence of two indica rice genotypes, IR64 and Apo under normal conditions while trans and cis + trans regulatory factors are largely affected by drought
FLASHDeconv: Ultrafast, high-quality feature deconvolution for top-down proteomics
Authors: Jeong Kyowon , Kim Jihyung , Gaikwad Manasi , Hidayah Siti Nurul , Heikaus Laura , Schlüter Hartmut , Kohlbacher Oliver
Published: July 2019

Feature deconvolution, the determination of intact proteoform masses, is crucial for top-down proteomics, but currently suffers from long runtimes and quality issues. We present FLASHDeconv, an algorithm based on a simple transformation of mass spectra, which turns deconvolution into the search for constant patterns thus greatly accelerating the process. We show higher deconvolution quality and two to three orders of magnitude faster execution speed than existing approaches.
PyLandStats: An open-source Pythonic library to compute landscape metrics
Authors: Bosch Martí
Published: July 2019

Quantifying the spatial pattern of landscapes has become a common task of many studies in landscape ecology. Most of the existing software to compute landscape metrics is not well suited to be used in interactive environments such as Jupyter notebooks nor to be included as part of automated computational workflows. This article presents PyLandStats, an open-source Python library to compute landscape metrics within the scientific Python stack. The PyLandStats package provides a set of methods to undertake recurrent approaches to quantify landscape patterns, such as the analysis of the spatiotemporal patterns of land use/land cover change or gradient analysis. The implementation is based on the prevailing Python libraries for geospatial data analysis in a way that they can be forthwith integrated into complex computational workflows. Notably, the provided methods offer a large variety of options so that users can employ PyLandStats in the way that best supports their needs. The source code is publicly available, and is organized in a modular object-oriented structure that enhances its maintainability and extensibility.
Drug repositoning or target repositioning: a structural perspective of drug-target-indication relationship for available repurposed drugs
Authors: Parisi Daniele , Adasme Melissa F. , Sveshnikova Anastasia , Moreau Yves , Schroeder Michael
Published: July 2019

Drug repositioning aims to find new indications for existing drugs, in order to reduce drug development cost and time. Currently, numerous successful stories of drug repositioning have been reported and many drugs are already available on the market. Although many of those cases are products of serendipitous findings, repositioning opportunities can be uncovered systematically by following either a disease-centric approach, as a result of a close relation between an old and new indication, a target-centric one, which links a known target and its established drug to a new indication, or a drug-centric approach, which connects a known drug to a new target and its associated indication. The three approaches differ in their complexity, potential, and limits, and most important the necessary starting information and computational power. Which one is predominant in current drug repositioning and what does this imply for future developments? To address these questions, we systematically evaluated over 100 drugs, 200 targets structures and over 300 indications from the Drug Repositioning Database. Each of the analysed cases has been classified based on one of the three repositioning approaches, showing that the majority, more than 60%, falls within the disease-centric definition, around 30% within the target-centric, and only less than 10% within the drug-centric. We therefore concluded that so far repositioning has mainly been disease and target repositioning and not, as drug repositioning, as expected by definition. We discuss the reasons and suggest directions to exploit the full potential of techniques useful for drug-centric in order to sustain future rationale repositioning pipelines.
TLR4 mediates Il-6 production in irinotecan-induced mucositis
Authors: Khan S. , Bowen J. M. , Wardill Hannah R.
Published: July 2019

Introduction

Irinotecan is a first line chemotherapeutic agent for colorectal carcinoma and well known for debilitating diarrhoea caused by mucositis. Tlr4, a pattern recognition receptor, has been implicated in irinotecan -induced mucositis due to its activation of downstream inflammatory pathways and interaction with luminal microbes. Tlr4 deletion has been reported to attenuate mucosal injury in preclinical models of mucositis, hypothesised to occur by blockade of Il-6 production. As such, the current study aimed to determine the relationship between Tlr4 and Il-6 in the context of irinotecan induced mucositis.

Materials and methods

Archived ileum and colon tissues from BALB/c wild type (WT) and Tlr4 -/-billy (Tlr4 KO) female mice were used throughout the study. Mice had received single dose of irinotecan (i.p. 270 mg/kg) or vehicle and sacrificed at 6 and 72 hours. Il-6 mRNA and protein expression was determined by qPCR and immunofluorescence, respectively. Data was analysed by Kruskal-Wallis test (qPCR delta CT values) and one-way analysis of variance (ANOVA) (immunofluorescence % area stained).

Results

Il-6 protein expression was significantly reduced in Tlr4 KO mice as compared to WT mice at 6 h in ileum and colon. mRNA expression was not significantly different between groups.

Conclusion

These findings support the hypothesis that Tlr4 deletion protects from irinotecan-induced mucositis by ameliorating Il-6 production. The effect appears to be post-transcriptionally mediated, although further research is required to determine if it is via a direct or indirect mechanism. In the future, Il-6 may be targeted therapeutically to ameliorate symptoms of mucositis.
A Cre-amplifier to generate and detect genetic mosaicsin vivo
Authors: Trovato Francesco , Parra Riccardo , Pracucci Enrico , Landi Silvia , Cozzolino Olga , Nardi Gabriele , Cruciani Federica , Mosti Laura , Cwetsch Andrzej , Cancedda Laura , Gritti Laura , Sala Carlo , Verpelli Chiara , Maset Andrea , Lodovichi Claudia , Ratto Gian Michele
Published: July 2019

Cre-Lox manipulation is the gold standard for cell-specific expression or knockout of selected genes. However, it is not unusual to deal with conditions of low Cre expression or transient activation, which can often go undetected by conventional Cre-reporters. We designed Beatrix, a general-purpose tool specifically devised to amplify weak Cre recombinase activity, and we used it to develop a powerful approach for thein vivogeneration and detection of sparse mosaics of mutant and wild type cells.
GATA2 Expression by Intima-Infiltrating Macrophages Drives Early Atheroma Formation
Authors: Yin Charles , Vrieze Angela M. , Akingbasote James , Pawlak Emily N. , Jacob Rajesh Abraham , Hu Jonathan , Sharma Neha , Dikeakos Jimmy D. , Barra Lillian , Nagpal A. Dave , Heit Bryan
Published: July 2019

Aberrant macrophage polarization is a major contributor to the onset and progression of atherosclerosis. Despite this, macrophage polarization during in early stages of human atherosclerotic disease is poorly understood. Using transcriptomic analysis of macrophages recovered from early-stage human atherosclerotic lesions, we have identified a unique gene expression profile dissimilar to that observed in later stages of disease that is characterized by upregulation of the hematopoietic transcription factor GATA2. GATA2 overexpressionin vitrorecapitulated defects observed in patient macrophages, including deficiencies in the uptake and processing of apoptotic cells, and in the catalysis of atherogenic protein modifications, with GATA2 knockdown abrogating these defects. Our data describe a previously unreported macrophage differentiation state present in early atheroma formation and identifies GATA2 as a driver of macrophage functional defects during the early stages of atherosclerosis in humans.
Integrated biorefinery fromArthrospira platensisbiomass as feedstock for bioethanol and lactic acid production
Authors: Esquivel-Hernández Diego A. , Pennacchio Anna , Saldivar Roberto Parra , Faraco Vincenza
Published: July 2019

An integrated biorefinery for ethanol and lactic acid production from the biomass of cyanobacteriumArthrospira platensiswas investigated. Different pretreatments consisting of supercritical fluid extraction (SFE) and microwave assisted extraction (MAE) with non-polar (MAE-NPS) and polar solvents (MAE-PS) were tested on cyanobacterial biomass to obtain bioactive metabolites and the resulting residual biomass was used as a substrate for fermentation withSaccharomyces cerevisiaeLPB-287 andLactobacillus acidophilusATCC 43121 to produce ethanol and lactic acid, respectively. The maximum concentrations achieved in our processes were 3.02±0.07 g/L of ethanol by the MAE-NPS process at 120 rpm 30 °C, and 9.67±0.05 g/L of lactic acid by the SFE process at 120 rpm 37 °C. Our results suggest that the proposed approach can be successfully applied in bioactive metabolites extraction and subsequently in the production of Ethanol and Lactic acid fromA. platensisdepleted biomass.
Extending site-based observations to predict the spatial patterns of vegetation structure and composition
Authors: McNellie Megan J , Oliver Ian , Ferrier Simon , Newell Graeme , Manion Glenn , Griffioen Peter , White Matt , Koen Terry , Somerville Michael , Gibbons Philip
Published: July 2019

Context

Conservation planning and land management are inherently spatial processes that are most effective when implemented over large areas.

Objectives

Our objectives were to (i) use existing plot data to aggregate species inventories to growth forms and derive indicators of vegetation structure and composition and ii) generate spatially-explicit, continuous, landscape scaled models of these discrete vegetation indicators, accompanied by maps of model uncertainty.

Method

Using a case study from New South Wales, Australia, we aggregated floristic observations from 7234 sites into growth forms. We trained ensembles of artificial neural networks (ANN) to predict the distribution of these indicators over a broad region covering 11.5 million hectares. Importantly, we show spatially explicit models of uncertainty so that end-users have a tangible and transparent means of assessing models.

Results

Our key findings were firstly, widely available site-based floristic records can be used to derive aggregated indicators of the structure and composition of plant growth forms. Secondly, ANNs are a powerful method to predict continuous patterns in complex, non-linear data (Pearson’s correlation coefficient 0.83 (total native vegetation cover) to 0.42 (forb cover)). Thirdly, maps of the standardised residual error give insight into model performance and provide an assessment of model uncertainty in specific locations.

Conclusions

Spatially explicit, continuous representations of vegetation composition and structural complexity can add considerable value to conventional maps of vegetation extent or community type. This application has the potential to enhance the capacity for conservation planners, landscape managers and policy-makers to make informed decisions across landscape and regional scales.
Evaluation of five cell-free DNA isolation kits for plasma
Authors: Liu Zhongzhen , Yang Xi , Chen Haixiao , Zhu Sujun , Zeng Juan , Chen Fang , Wang Wen-Jing
Published: July 2019

Cell-free DNA (cfDNA) has been widely used in prenatal test and cancer diagnosis nowadays. The cost- and time-effective isolation kits are needed especially in large-scale clinical application. Here, we compared three domestic kits: VAHTS Serum/Plasma Circulating DNA kit (VZ), MagPure Gel Pure DNA mini kit (MG) and Serum/Plasma Circulating DNA Kit (TG), together with QIAamp Circulating Nucleic Acid Kit (QC) and QIAamp DNA Blood Mini Kit (QD) in cfDNA isolation. cfDNA was isolated from the pooled samples with spike-in fragments, qPCR was conducted to quantify the spike-in fragments recovery. The results indicated that all of the five kits could isolate cfDNA with different efficiency. The VZ kit had an efficiency as high as 90 percent, which is comparable to QC kit. The libraries were constructed using the isolated cfDNAs, quantified by Qubit and analyzed by 2100 bioanalyzer. Both showed the libraries were qualified. Finally, cffDNAs were detected by qPCR targeting SRY gene using libraries from pregnant women bearing male fetuses. All five kits could isolate cffDNAs that could be detected by qPCR. Our results provided more choices in wide-scale clinical application of cfDNA-based non-invasive genetic tests.
Superior colliculus modulates cortical coding of somatosensory information
Authors: Gharaei Saba , Honnuraiah Suraj , Arabzadeh Ehsan , Stuart Greg J
Published: July 2019

The cortex sends a direct projection to the superior colliculus. What is largely unknown is whether (and if so how) the superior colliculus modulates activity in the cortex. Here, we directly investigate this issue, showing that optogenetic activation of superior colliculus changes the input-output relationship of neurons in somatosensory cortex during whisker movement, enhancing responses to low amplitude whisker deflections. While there is no direct pathway from superior colliculus to somatosensory cortex, we found that activation of superior colliculus drives spiking in the posterior medial (POm) nucleus of the thalamus via a powerful monosynaptic pathway. Furthermore, POm neurons receiving input from superior colliculus provide excitatory input to somatosensory cortex. Silencing POm abolished the capacity of superior colliculus to modulate cortical whisker responses. Our findings indicate that the superior colliculus, which plays a key role in attention, modulates sensory processing in somatosensory cortex via a powerful disynaptic pathway through the thalamus.
Gradient-independent Wnt signaling instructs asymmetric neurite pruning in C. elegans
Authors: Lu Menghao , Mizumoto Kota
Published: July 2019

During development, the nervous system undergoes refinement process by which neurons initially extend an excess number of neurites, the majority of which will be eliminated by the mechanism called neurite pruning. Some neurites undergo stereotyped and developmentally regulated pruning. However, the signaling cues that instruct stereotyped neurite pruning are yet to be fully elucidated. Here we show that Wnt morphogen instructs stereotyped neurite pruning for proper neurite projection patterning of the cholinergic motor neuron called PDB in C. elegans. In the loss of lin-44/wnt and lin-17/frizzled mutant animals, the PDB neurites often failed to prune and grew towards the lin-44-expressing cells. Surprisingly, membrane-tethered lin-44 is sufficient to induce proper neurite pruning in PDB, suggesting that neurite pruning does not require Wnt gradient. LIN-17 and DSH-1/Dishevelled proteins were recruited to the pruning neurites in lin-44-dependent manners. Our results revealed the novel gradient-independent role of Wnt signaling in instructing neurite pruning.
Disease-modifying effects of natural Δ9-tetrahydrocannabinol in endometriosis-associated pain
Authors: Escudero-Lara Alejandra , Argerich Josep , Cabañero David , Maldonado Rafael
Published: July 2019

Endometriosis is a chronic painful disease highly prevalent in women that is defined by growth of endometrial tissue outside the uterine cavity and lacks adequate treatment. Medical use of cannabis derivatives is a current hot topic and it is unknown whether phytocannabinoids may modify endometriosis symptoms and development. Here we evaluate the effects of repeated exposure to Δ9-tetrahydrocannabinol (THC) in a mouse model of surgically-induced endometriosis. In this model, female mice develop pelvic mechanical hypersensitivity, anxiety-like behavior and sharp memory deficits associated to the presence of extrauterine endometrial cysts. Interestingly, chronic THC (2 mg/kg/day) provides sustained alleviation of pelvic hypersensitivity without altering the anxiogenic phenotype, modifies uterine innervation and restores cognitive function, an effect correlated with neuroinflammatory changes in prefrontal cortex. Strikingly, THC also inhibits the development of endometrial cysts. These data highlight the interest of scheduled clinical trials designed to investigate possible benefits of THC for women with endometriosis.
µbialSim: constraint-based dynamic simulation of complex microbiomes
Authors: Popp Denny , Centler Florian
Published: July 2019

Microbial communities are pervasive in the natural environment, associated with many animal hosts, and of increasing importance in biotechnological applications. The complexity of these microbial systems makes the underlying mechanisms driving their dynamics difficult to identify. While experimental meta-OMICS techniques are routinely applied to record the inventory and activity of microbiomes over time, it remains difficult to obtain quantitative predictions based on such data. Mechanistic, quantitative mathematical modeling approaches hold the promise to both provide predictive power and shed light on cause-effect relationships driving these dynamic systems. We introduceµbialSim (pronounced “microbialsim”), a dynamic Flux-Balance-Analysis-based (dFBA) numerical simulator which is able to predict the time course in terms of composition and activity of microbiomes containing 100s of species in batch or chemostat mode. Activity of individual species is simulated by using separate FBA models which have access to a common pool of compounds, allowing for metabolite exchange. A novel augmented forward Euler method ensures numerically accuracy by temporarily reducing the time step size when compound concentrations decrease rapidly due to high compound affinities and/or the presence of many consuming species. We present three exemplary applications ofµbialSim: a batch culture of a hydrogenotrophic archaeon, a syntrophic methanogenic biculture, and a 773-species human gut microbiome which exhibits a complex and dynamic pattern of metabolite exchange.

Focussing on metabolite exchange as the main interaction type,µbialSim allows for the mechanistic simulation of microbiomes at their natural complexity. Simulated trajectories can be used to contextualize experimental meta-OMICS data, and hypotheses on cause-effect relationships driving community dynamics can be derived based on scenario simulations.

µbialSim is implemented in Matlab and relies on the COBRA Toolbox or CellNetAnalyzer for FBA calculations. The source code is available under the GNU General Public License v3.0 athttps://git.ufz.de/UMBSysBio/microbialsim.
Does membrane feeding compromise the quality ofAedes aegyptimosquitoes?
Authors: Ross Perran A. , Lau Meng-Jia , Hoffmann Ary A.
Published: July 2019

ModifiedAedes aegyptimosquitoes are being mass-reared for release in disease control programs around the world. Releases involving female mosquitoes rely on them being able to seek and feed on human hosts. To facilitate the mass-production of mosquitoes for releases, females are often provided blood through artificial membrane feeders. When reared across generations there is a risk that mosquitoes will adapt to feeding on membranes and lose their ability to feed on human hosts. To test adaptation to membrane feeding, we selected replicate populations ofAe. aegyptifor feeding on either human arms or membrane feeders for at least 8 generations. Membrane-selected populations suffered fitness costs, likely due to inbreeding depression arising from bottlenecks. Membrane-selected females had higher feeding rates on membranes than human-selected ones, suggesting adaptation to membrane feeding, but they maintained their attraction to host cues and feeding ability on humans despite a lack of selection for these traits. Host-seeking ability in small laboratory cages did not differ between populations selected on the two blood sources, but membrane-selected females were compromised in a semi-field enclosure where host-seeking was tested over a longer distance. Our findings suggest thatAe. aegyptimay adapt to feeding on blood provided artificially, but this will not substantially compromise field performance or affect experimental assessments of mosquito fitness. However, large population sizes during mass rearing with membrane feeders should be maintained to avoid bottlenecks which lead to inbreeding depression.

Author summary

With modified mosquitoes being mass-reared for release in disease control programs, there is interest in understanding factors that can affect the quality of release stocks. In the laboratory, membrane feeding devices are often used to provide blood to female mosquitoes which they need to lay eggs. Over time, mosquitoes could adapt to membrane feeding and lose their preference for (or ability to feed on) natural hosts. Adaptation could affect the performance of lab-reared mosquitoes when deployed in the field, especially if the success of disease control programs relies on female reproduction such as in gene drive orWolbachia-based approaches. We tested to see ifAedes aegyptimosquitoes, the principal vectors of dengue virus, would adapt to feeding on blood provided via membranes. We found some evidence of adaptation, with membrane-selected mosquitoes having higher feeding rates on membranes, but this didn’t affect their ability to feed on humans or their attraction to host cues. Although membrane feeding alone does not substantially affect mosquito quality, it can lead to inbreeding depression if populations pass through bottlenecks as they adapt to feeding on blood provided artificially. Our results may inform mass-rearing programs involving the release of modified female mosquitoes.
New residential perennial floras reflect distinctive decisions of residential developers and new homeowners
Authors: Fuentes Tracy L.
Published: July 2019

Urban patterns reflect the people who build and manage urban space. However, most field research on residential vegetation focuses on household or neighborhood preferences, norms, or socioeconomic drivers of observed patterns and plant traits. Very few urban ecology researchers have studied residential real estate developers, who configure the space and establish the initial plant communities. How do the landscaping decisions of developers and homeowners shape residential perennial floras? To answer this question, I collected a stratified random sample of perennials at 60 newly built and sold homes in the Seattle, WA area. Through field sampling, conversations with new homeowners, and archival research, I assigned each individual perennial to one of three origins: remnant, planted by developers, or planted by homeowners. After describing landscaping decisions using plant traits (as presented in gardening literature), I evaluated whether planting decisions of developers and homeowners were heterogeneous and whether urban form or economic drivers influenced planted species richness. I also tested whether homeowner yard and plant buying preferences could be linked to planted richness. Given that developers and homeowners have different incentives, I hypothesized that they would choose different types of perennials and that urban metrics related to area and economics would increase species richness. I also predicted that homeowner preferences would be linked to species richness patterns. Developers planted most of the trees, shrubs, and graminoids. Homeowners planted fewer woody and more herbaceous perennial species. Parcel planting area, wealth related metrics, and parcel density increased species richness for some perennials. However, homeowner preferences were stronger predictors of their planting behavior than urban metrics. Because assembly of residential perennial flora communities is heterogeneous, future investigations in other urban ecosystems should incorporate preferences of developers and homeowners, site-specific constraints, and broader scale influences. More work is needed to understand developer incentives and preferences.
An alternative nisin A resistance mechanism affects virulence inStaphylococcus aureus
Authors: Kawada-Matsuo Miki , Watanabe Atsuko , Arii Kaoru , Oogai Yuichi , Noguchi Kazuyuki , Miyawaki Shouichi , Hayashi Tetsuya , Komatsuzawa Hitoshi
Published: July 2019

Nisin A is a bacteriocin produced byLactococcus lactisand is widely used as a food preservative.Staphylococcus aureushas the BraRS-VraDE system providing resistance against low concentrations of nisin A. The BraRS is one of a two-component system that senses nisin A by BraS and finally induces the expression of ABC transporter VraDE by phosphorylated BraR. Previously, we isolated a highly nisin A resistant strain with increased VraDE expression due to a mutation ofbraRS. In this study, we isolated a BraRS-VraDE-independent, nisin A resistant mutant fromS. aureusMW2. These mutants, designated SAN2 (S.aureusnisin resistant) and SAN469, had a mutation inpmtR(MW1875) which encodes a transcriptional regulator responsible for the expression of thepmtA-Doperon. As a result, this mutant exhibited a high level of constitutive production of PmtA-D, a transporter responsible for the export of phenol soluble modulin (PSM). We also obtained twopmtA-Doverexpressing, nisin A resistant mutants which contained a point mutation inpmtRfrom otherS. aureusstrains.

Characterization of the mutants revealed that they have a decreased susceptibility to human beta defensin-3 and LL37, which are innate immune factors. Additionally, these mutants showed higher hemolytic activity than the MW2 original strain. Furthermore, in a mouse bacteremia model, the SAN2 strain exhibited a lower survival rate than the MW2 original strain. These results indicate that the over expression ofpmtA-Ddue to thepmtRmutation is an alternative nisin A resistance, which also affects virulence inS. aureus.

Author Summary

Recently, the emergence of antibiotic resistant bacteria such as MRSA, MDRP and CRE have brought serious problems for chemotherapy in the world. In addition, many antibacterial agents such as disinfectants and food additives are widely used. Therefore, it raises the possibility that bacteria are becoming resistant to all antibacterial agents. In this study, we investigated whetherS. aureusbecome resistant against nisin A, one of the food additives. Finally, we isolated nisin A highly resistantS. aureusstrains. Among these strains, we identified that one strain designated as SAN2 showed nisin A resistance by the overproduction of Pmts which were involved in the secretion of virulence factors called PSMs. We identified a mutation ofpmtRgene encoding a regulator forpmtgenes. SAN2 strain showed the decreased susceptibility to human antimicrobial peptides and the increased hemolytic activity. Finally, SAN2 showed higher lethal activity in mouse bacteremia model. Our study provides new insights into thatS. aureusmay cause resistance against various antibacterial food additives, together with the altering the virulence.
Small-angle neutron scattering (SANS) and spin-echo SANS measurements reveal the logarithmic fractal structure of the large-scale chromatin organization in HeLa nuclei
Authors: Iashina Ekaterina G. , Filatov Mikhail V. , Pantina Rimma A. , Varfolomeeva Elena Yu. , Bouwman Wim G. , Duif Chris P. , Honecker Dirk , Pipich Vitaliy , Grigoriev Sergey V.
Published: July 2019

This paper reports on the two-scale fractal structure of chromatin organization in the nucleus of the HeLa cell. Two neutron scattering methods, small-angle neutron scattering (SANS) and spin-echo SANS, are used to unambiguously identify the large-scale structure as being a logarithmic fractal with the correlation function γ(r) ∼ ln(r/ξ). The smaller-scale structural level is shown to be a volume fractal with dimension D
F = 2.41. By definition, the volume fractal is self-similar at different scales, while the logarithmic fractal is hierarchically changed upon scaling. As a result, the logarithmic fractal is more compact than the volume fractal but still has a rather high surface area, which provides accessibility at all length scales. Apparently such bi-fractal chromatin organization is the result of an evolutionary process of optimizing the compactness and accessibility of gene packing. As they are in a water solution, the HeLa nuclei tend to agglomerate over time. The large-scale logarithmic fractal structure of chromatin provides the HeLa nucleus with the possibility of penetrating deeply into the adjacent nucleus during the agglomeration process. The interpenetration phenomenon of the HeLa nuclei shows that the chromatin-free space of one nucleus is not negligible but is as large as the volume occupied by chromatin itself. It is speculated that it is the logarithmic fractal architecture of chromatin that provides a comfortable compartment for this most important function of the cell.
Synthesis, crystal structures and anti-inflammatory activity of fluorine-substituted 1,4,5,6-tetrahydrobenzo[h]quinazolin-2-amine derivatives
Authors: Sun Yue , Gao Zhongfei , Wang Chunhua , Hou Guige
Published: July 2019

Two fluorine-substituted 1,4,5,6-tetrahydrobenzo[h]quinazolin-2-amine (BQA) derivatives, namely 2-amino-4-(2-fluorophenyl)-9-methoxy-1,4,5,6-tetrahydrobenzo[h]quinazolin-3-ium chloride, (8), and 2-amino-4-(4-fluorophenyl)-9-methoxy-1,4,5,6-tetrahydrobenzo[h]quinazolin-3-ium chloride, (9), both C19H19FN3O+·Cl−, were generated by Michael addition reactions between guanidine hydrochloride and the α,β-unsaturated ketones (E)-2-(2-fluorobenzylidene)-7-methoxy-3,4-dihydronaphthalen-1(2H)-one, C18H15FO2, (6), and (E)-2-(4-fluorobenzylidene)-7-methoxy-3,4-dihydronaphthalen-1(2H)-one, (7). Because both sides of α,β-unsaturated ketones (6) or (7) can be attacked by guanidine, we obtained a pair of isomers in (8) and (9). Single-crystal X-ray diffraction indicates that each isomer has a chiral C atom and both (8) and (9) crystallize in the achiral space group P21/c. The chloride ion, as a hydrogen-bond acceptor, plays an important role in the formation of multiple hydrogen bonds. Thus, adjacent molecules are connected through intermolecular hydrogen bonds to generate a banded structure. Furthermore, these bands are linked into an interesting 3D network via hydrogen bonds and π–π interactions. Fortunately, the solubilities of (8) and (9) were distinctly improved and can exceed 50 mg ml−1 in water or PBS buffer system (pH 7.4) at room temperature. In addition, the results of an investigation of anti-inflammatory activity show that (8) and (9), with o- and p-fluoro substituents, respectively, display more potential for inhibitory effects on LPS-induced NO secretion than starting ketones (6) and (7).
A molybdenum tris(dithiolene) complex coordinates to three bound cobalt centers in three different ways
Authors: Nguyen Neilson , Lough Alan J. , Fekl Ulrich
Published: July 2019

The synthesis and structural characterization of the molecular compound (μ3-benzene-1,2-dithiolato)hexacarbonylbis(μ3-1,1,1,4,4,4-hexafluorobut-2-ene-2,3-dithiolato)tricobaltmolybdenum, [Co3Mo(C4F6S2)2(C6H4S2)(CO)6] or Mo(tfd)2(bdt)(Co(CO)2)3 (tfd is 1,1,1,4,4,4-hexafluorobut-2-ene-2,3-dithiolate and bdt is benzene-1,2-dithiolate), are reported. The structure of the molecule contains the molybdenum tris(dithiolene) complex Mo(tfd)2(bdt) coordinated as a multidentate ligand to three cobalt dicarbonyl units. Each of the three cobalt centers is relatively close to molybdenum, with Co...Mo distances of 2.7224 (7), 2.8058 (7), and 2.6320 (6) Å. Additionally, each of the cobalt centers is bound via main-group donor atoms, but each one in a different way: the first cobalt atom is coordinated by two sulfur atoms from different dithiolenes (bdt and tfd). The second cobalt atom is coordinated by one sulfur from one tfd and two olefinic carbons from another tfd. The third cobalt is coordinated by one sulfur from bdt and two sulfurs from tfd. This is, to the best of our knowledge, the first structurally characterized example of a molybdenum (tris)dithiolene complex that coordinates to cobalt. The F atoms of two of the –CF3 groups were refined as disordered over two sets of sites with ratios of refined occupancies of 0.703 (7):0.297 (7) and 0.72 (2):0.28 (2).
Implementing a new procurement strategy: the case of social housing associations
Authors: van Zoest Simon , Volker Leentje , Hermans Marleen
Published: July 2019

Purpose

The purpose of this paper is to address the barriers that Dutch housing associations encounter in implementing new procurement strategies.

Design/methodology/approach

Several aspects of purchasing, portfolio management, project delivery and supply management are discussed in relation to the changing role of housing associations as semi-public commissioning bodies in the Dutch construction industry, based on data derived from workshops with six Dutch housing associations.

Findings

Housing associations are adapting their procurement strategy towards a more integrative and performance-based approach to supply management. Due to the complexity of implementing this process, housing associations struggle especially with moving beyond pilot projects, increasing the maturity levels throughout the organisation and aligning new policies with daily practices at a tactical and an operational level.

Practical implications

Increased knowledge of change processes and seeing the potential of maturity models will be valuable for practitioners who are dealing with changes on the work floor.

Social implications

Client organisations are considered one of the key drivers of change in the construction industry. Insights into these particular organisational change processes contribute to the potential of industry reform.

Originality/value

Most studies on collaboration and integration in the supply chain focus on the inter-organisational level or on the supply side, rather than the internal organisation of the client.
Measurement of financial efficiency and productivity of Turkish Public Universities by using non-parametric methods
Authors: Günay Aslı , Dulupçu Murat Ali
Published: July 2019

Purpose

The purpose of this paper is to measure the financial efficiency and productivity of 23 public universities founded in 1992 in Turkey over the period between 2004 and 2013. The results obtained will provide managerial information and act as a guide to public universities’ administrations, in using their resources more effectively.

Design/methodology/approach

Data envelopment analysis is applied to assess the relative financial efficiency of these universities, while Malmquist total factor productivity index is used to measure the total factor productivity change concerning financial inputs of the universities.

Findings

The number of financially efficient universities and the number of universities showing an increase in their productivity according to their financial inputs change annually and both of them display a rough trend over the years. A decrease of about 5 percent in the financial productivity of the universities is observed which stems from a technological recession. Therefore, public universities in Turkey are not able to develop effective policies to diversify, increase and use their financial resources.

Originality/value

When the lack of studies within the literature measuring the financial efficiency of higher education institutions is taken into account, this study can fill a gap in this area. The analyses conducted here distinguish from existing studies on this subject with regards to the extent and diversity of financial data set and the measurement of both efficiency and productivity change of universities considering financial inputs concurrently.
Clarifying the brand personality construct in Malaysia
Authors: Mohtar Mozard , Rudd John M. , Evanschitzky Heiner
Published: July 2019

Purpose

This paper aims to investigate the variations in brand personality trait items to describe both global and local brands in Malaysia.

Design/methodology/approach

The authors adopted both factor analytic and experimental methods to investigate the internal and external validity of Malaysia brand personality (MBP) scale. They followed a stringent scale development process that ensures the scale conform to psychometric properties.

Findings

In seven studies, the results show that the 22-item four-factor Malaysian brand personality scale adheres to strong psychometric properties of scale development process. The findings further indicate that there are seven indigenous traits, while most traits emerge from factor analyses originate from studies of Aaker (1997) and colleagues (2001). This confirms universality of some brand personality traits and dimensions.

Research limitations/implications

Within the limits of the study, we did not examine the MBP facet level, and were confined to those respondents in Klang Valley only.

Practical implications

The MBP scale enables marketing managers in Malaysia to focus on brand personality dimensions that their customers can relate to. In other words, marketing communications can be more efficient when managers can identify brand personality traits that enhance customers’ behaviors and profitability.

Originality/value

Malaysia is a multicultural and multiethnic country which is increasingly becoming the focus of international brand expansion. The authors view that the development of the MBP scale is timely and should provide managers further insights into the brand personality structure that is relevant in Malaysia.
Sharing of branded viral advertisements by young consumers: the interplay between personality traits and ad appeal
Authors: Kulkarni Kalpak K. , Kalro Arti D. , Sharma Dinesh
Published: July 2019

Purpose

This study aims to investigate the influence of Big Five Personality traits (i.e. openness to experience, conscientiousness, extraversion, agreeableness and neuroticism) on young consumers’ intentions to share branded viral video advertisements. Further, this study also demonstrates that the advertising appeal (informational versus emotional) used in the viral advertisement moderates the effects of specific personality traits on the sharing of viral ads.

Design/methodology/approach

A conceptual framework is proposed based on the Five-Factor Model of Personality (McCrae and John, 1992) and advertising effectiveness literature. Using experiments, responses from young consumers were collected and hypotheses were tested using hierarchical regression and ANOVA.

Findings

Results reveal that the two personality traits, extraversion and openness to experiences, are positively associated with consumers’ viral ad sharing intentions, whereas conscientiousness, agreeableness and neuroticism are not. Moreover, individuals scoring high on openness and extraversion prefer sharing branded viral ads containing informational appeal vis-ã-vis those containing emotional appeals.

Originality/value

Studies decoding the factors behind the success of viral advertisements have more often focussed on the ad content rather than on personality dimensions of the ad sharers. This study bridges this gap by investigating the influence of Big Five Personality traits on young consumers’ intention to forward viral ads, in interaction with ad appeal. Young consumers represent key audience segments consuming and sharing viral content online, and hence, it is important to have a deeper understanding of this market segment.
Operator exposure to spray deposits using various application techniques in paddy fields
Authors: Punyawattoe Pruetthichat
Published: July 2019

Purpose

The safety of operators handling pesticides is still one of the main problems facing Thai agricultural workers. The purpose of this paper is to study the safety of farmers and the techniques recommended to farmers by the Department of Agriculture in Thailand, i.e. spraying to achieve optimum spray volume with consideration for wind direction – henceforth referred to as officer techniques.

Design/methodology/approach

Operator exposure was detected by verifying the deposition of dye tracer on the coveralls worn by ten spray service team leaders, for all applications between May and June 2017. For each technique, a total of 15 patches were attached at the lower legs, thigh, chest, forearms, upper arms, hands, face, forehead and back. Each individual technique was performed four times in the area of 1,800 m2.

Findings

The results showed that the deposits with the farmers’ techniques was much higher than with officers’ techniques ranging from 2.32 to 23.91 times at the tillering stage and 9.90 to 56.79 times at the booting stage, respectively. These results indicate that the spray application technique has a considerable potential for reducing the contamination of spray operators by 56.96–98.23 percent. Operator safety can be considerably improved by the spray application technique employed. Without any investment and changing equipment, only by considering wind direction, officers’ techniques could avoid much deposition, which is the most practical operation in the field. The boom sprayer as a novel recommended technique is an alternative giving a positive result and it can be a substitute for the conventional method. Furthermore, the authors must pay attention to personal protective equipment (PPE) because depositions were discovered on the whole of the bodies of those tested. PPE is the best way to protect an operator from pesticide contamination.

Originality/value

Operator exposure data can be helpful in further development of exposure models and databases for risk assessment and pesticide registration in Thailand.