bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-cost drug discovery with engineeredE. colireveals an anti-mycobacterial activity of benazepril
Authors: Bongaerts Nadine , Edoo Zainab , Abukar Ayan A. , Song Xiaohu , Sosa Carrillo Sebastián , Lindner Ariel B. , Wintermute Edwin H. 
Published: March 2021

ABSTRACTWhole-cell screening forMycobacterium tuberculosis(Mtb) inhibitors is complicated by the pathogen’s slow growth and biocontainment requirements. Here we present a synthetic biology framework for assayingMtbdrug targets in engineeredE. coli. We construct Target Essential SurrogateE. coli(TESEC) in which an essential metabolic enzyme is deleted and replaced with anMtb-derived functional analog, linking bacterial growth to the activity of the target enzyme. High throughput screening of a TESEC model forMtbalanine racemase (ALR) revealed benazepril as a targeted inhibitor. In vitro biochemical assays indicated a noncompetitive mechanism unlike that of clinical ALR inhibitors. This is the first report of an antimicrobial activity in an approved Angiotensin Converting Enzyme (ACE) inhibitor and may explain clinical data associating use of ACE inhibitors with reducedMtbinfection risk. We establish the scalability of TESEC for drug discovery by characterizing TESEC strains for four additional targets.SIGNIFICANCE STATEMENTThe challenge of discovering new antibiotics is both scientific and economic. No simple test can determine if a given molecule will be safe and effective in real human patients. Many drug candidates must therefore be advanced for each new antibiotic that reaches the market - a risky and expensive process.In this work we use synthetic biology to engineer the common laboratory model bacteriumE. colias a tool for early stage antibiotic discovery. As a proof of concept we expressed a known tuberculosis drug target and found a novel inhibitor: benazepril.Many other drug targets could be screened similarly using the system that we describe. BecauseE. colican be grown safely and cheaply, this approach may help to reduce costs and make drug discovery more accessible.
RNA chaperones Hfq and ProQ play a key role in the virulence of the plant pathogenic bacteriumDickeya dadantii
Authors: Leonard Simon , Villard Camille , Nasser William , Reverchon Sylvie , Hommais Florence 
Published: March 2021

AbstractDickeya dadantiiis an important pathogenic bacterium that infects a number of crops including potato and chicory. While extensive works have been carried out on the control of the transcription of its genes encoding the main virulence functions, little information is available on the post-transcriptional regulation of these functions. We investigated the involvement of the RNA chaperones Hfq and ProQ in the production of the mainD. dadantiivirulence functions. Phenotypic assays on thehfqandproQmutants showed that inactivation ofhfqresulted in a growth defect, a modified capacity for biofilm formation and strongly reduced motility, and in the production of degradative extracellular enzymes (proteases, cellulase and pectate lyases). Accordingly, thehfqmutant failed to cause soft rot on chicory leaves. TheproQmutant had reduced resistance to osmotic stress, reduced extracellular pectate lyase activity compared to the wild-type strain, and reduced virulence on chicory leaves. Most of the phenotypes of thehfqandproQmutants were related to the low amounts of mRNA of the corresponding virulence factors. Complementation of the double mutanthfq-proQby each individual protein and cross-complementation of each chaperone suggested that they might exert their effects via partially overlapping but different sets of targets. Overall, it clearly appeared that the two Hfq and ProQ RNA chaperones are important regulators of pathogenicity inD. dadantii. This underscores that virulence genes are regulated post transcriptionally by non-coding RNAs.
Differential viral RNA methylation contributes to pathogen blocking inWolbachia-colonized arthropods
Authors: Bhattacharya Tamanash , Yan Liewei , Zaher Hani , Newton Irene L.G. , Hardy Richard W. 
Published: March 2021

AbstractArthropod endosymbiontWolbachia pipientisis part of a global biocontrol strategy to reduce the replication of mosquito-borne RNA viruses such as alphaviruses. We previously demonstrated the importance of a host cytosine methyltransferase, DNMT2, inDrosophilaand viral RNA as a cellular target during pathogen-blocking. Here we report on the role of DNMT2 inWolbachia-induced alphavirus inhibition inAedesspecies. Expression of DNMT2 in mosquito tissues, including the salivary glands, is elevated upon virus infection. Notably, this is suppressed inWolbachia-colonizedanimals, coincident with reduced virus replication and decreased infectivity of progeny virus. Ectopic expression of DNMT2 in culturedAedescells is proviral, increasing progeny virus infectivity, and this effect of DNMT2 on virus replication and infectivity is dependent on its methyltransferase activity. Finally, examining the effects ofWolbachiaon modifications of viral RNA by LC-MS show a decrease in the amount of 5-methylcytosine modification consistent with the down-regulation of DNMT2 inWolbachiacolonized mosquito cells and animals. Collectively, our findings support the conclusion that disruption of 5-methylcytosine modification of viral RNA is a vital mechanism operative in pathogen blocking. These data also emphasize the essential role of epitranscriptomic modifications in regulating fundamental alphavirus replication and transmission processes.
Rapid response of nitrogen cycling gene transcription to labile carbon amendments in a soil microbial community
Authors: Chuckran Peter F. , Fofanov Viacheslav , Hungate Bruce A. , Morrissey Ember M , Schwartz Egbert , Walkup Jeth , Dijkstra Paul 
Published: March 2021

ABSTRACTEpisodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48 h laboratory incubation with an agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four timepoints that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased transcription of genes encoding for ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes.IMPORTANCEA large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant. However, we lack a full understanding of the short-term effects of labile carbon inputs on the metabolism of microbes living in soil. Here, we found that soil microbial communities responded to labile carbon addition by rapidly transcribing genes encoding proteins and enzymes responsible for inorganic nitrogen acquisition, including nitrogen fixation. This work demonstrates that soil microbial communities respond within hours to carbon inputs through altered gene expression. These insights are essential for improved understanding of the microbial processes governing soil organic matter production, decomposition, and nutrient cycling in natural and agricultural ecosystems.
An empirical pipeline for personalized diagnosis of Lafora disease mutations
Authors: Brewer M. Kathryn , Machio-Castello Maria , Viana Rosa , Wayne Jeremiah L. , Kuchtová Andrea , Simmons Zoe R. , Sternbach Sarah , Li Sheng , Garcia-Gimeno Maria Adelaida , Serratosa Jose , Sanz Pascual , Vander Kooi Craig W. , Gentry Matthew S. 
Published: March 2021

ABSTRACTLafora disease (LD) is a fatal, insidious metabolic disorder characterized by progressive myoclonic epilepsy manifesting in the teenage years, rapid neurological decline, and death typically within ten years of onset. Mutations in eitherEPM2A, encoding the glycogen phosphatase laforin, orEPM2B, encoding the E3 ligase malin, cause LD. Whole exome sequencing has revealed manyEPM2Avariants associated with late-onset or slower disease progression. We established an empirical pipeline for characterizing laforin missense mutationsin vitrousing complimentary biochemical approaches. Analysis of 26 mutations revealed distinct functional classes associated with different outcomes supported by multiple clinical cases. For example, F321C and G279C mutations have attenuated functional defects and are associated with slow progression. This pipeline allows rapid characterization and classification of novelEPM2Amutations, enabling clinicians and researchers to rapidly utilize genetic information to guide treatment of LD patients.
High diversity and heterogeneity define microbial communities across an active municipal landfill
Authors: Sauk Alexandra H. , Hug Laura A. 
Published: March 2021

AbstractGlobal waste production is increasing rapidly, with the majority of waste destined for landfills. Microbial communities in landfills transform waste and generate methane in an environment unique from other built and natural environments. Previous work has largely considered landfill microbial diversity only at the phylum level, identifying complex and variable communities. The extent of shared organismal diversity across landfills or over time and at more precise levels of classification remains unknown. We used 16S rRNA gene amplicon and metagenomic sequencing to examine the taxonomic and functional diversity of the microbial communities inhabiting a Southern Ontario landfill. The diversity of microbial populations in leachate and groundwater samples was correlated with geochemical conditions to determine drivers of microbial heterogeneity. Across the landfill, 25 bacterial and archaeal phyla were present at >1% relative abundance within at least one landfill sample. The Patescibacteria, Bacteroidota, Firmicutes, and Proteobacteria had the highest relative abundances, with most other phyla present at low (<5%) abundance. Below the phylum level, very few populations were identified at multiple sites, with only 121 of 8,030 populations present at five or more sites. This indicates that, although phylum-level signatures are conserved, individual landfill microbial populations vary widely. Significant differences in geochemistry occurred across the leachate and groundwater wells sampled, with calcium, iron, magnesium, boron, meta and para xylenes, ortho xylenes, and ethylbenzene concentrations contributing most strongly to observed site differences. This study illustrates that leachate microbial communities are much more complex and diverse within landfills than previously reported, with implications for waste management best practices.
Norstictic acid is a selective allosteric transcriptional regulator
Authors: Garlick Julie M. , Sturlis Steven M. , Bruno Paul A. , Yates Joel A. , Peiffer Amanda L. , Liu Yejun , Goo Laura , Bao LiWei , De Salle Samantha N. , Tamayo-Castillo Giselle , Brooks Charles L. , Merajver Sofia D. , Mapp Anna K. 
Published: March 2021

AbstractInhibitors of transcriptional protein-protein interactions (PPIs) have high value both as tools and for therapeutic applications. The PPI network mediated by the transcriptional coactivator Med25, for example, regulates stress-response and motility pathways and dysregulation of the PPI networks contributes to oncogenesis and metastasis. The canonical transcription factor binding sites within Med25 are large (~900 Å2) and have little topology, and thus do not present an array of attractive small-molecule binding sites for inhibitor discovery. Here we demonstrate that the depsidone natural product norstictic acid functions through an alternative binding site to block Med25-transcriptional activator PPIsin vitroand in cell culture. Norstictic acid targets a binding site comprised of a highly dynamic loop flanking one canonical binding surface and in doing so, it both orthosterically and allosterically alters Med25-driven transcription in a patient-derived model of triple negative breast cancer. These results highlight the potential of Med25 as a therapeutic target as well as the inhibitor discovery opportunities presented by structurally dynamic loops within otherwise challenging proteins.
Standardized workflow for precise mid- and high-throughput proteomics of blood biofluids
Authors: Ardle Angela Mc , Binek Aleksandra , Moradian Annie , Orgel Blandine Chazarin , Rivas Alejandro , Washington Kirstin E. , Phebus Conor , Manalo Danica-Mae , Go James , Venkatraman Vidya , Johnson Casey , Fu Qin , Cheng Susan , Raedschelders Koen , Bober Justyna-Fert , Pennington Stephen R. , Murray Christopher I. , Van Eyk Jennifer E. 
Published: March 2021

AbstractBackgroundAccurate discovery assay workflows are critical for identifying authentic circulating protein biomarkers in diverse blood matrices. Maximizing the commonalities in the proteomic workflows between different biofluids simplifies the approach and increases the likelihood for reproducibility. We developed a workflow that allows flexibility for high and mid-throughput analysis for three blood-based proteomes: naive plasma, plasma depleted of the 14 most abundant proteins, and dried blood.MethodsOptimal conditions for sample preparation and DIA-MS analysis were established in plasma then automated and adapted for depleted plasma and whole blood. The MS workflow was modified to facilitate sensitive high-throughput or deep profile analysis with mid-throughput analysis. Analytical performance was evaluated from 5 complete workflows repeated over 3 days as well as a linearity analysis of a 5–6-point dilution curve.ResultUsing our high-throughput workflow, 74%, 93%, 87% of peptides displayed an inter-day CV<30% in plasma, depleted plasma and whole blood. While the mid-throughput workflow had 67%, 90%, 78% of peptides in plasma, depleted plasma and whole blood meeting the CV<30% standard. Lower limits of detection and quantitation were determined for proteins and peptides observed in each biofluid and workflow. Combining the analysis of both high-throughput plasma fractions exceeded the number of reliably identified proteins for individual biofluids in the mid-throughput workflows.ConclusionThe workflow established here allowed for reliable detection of proteins covering a broad dynamic range. We envisage that implementation of this standard workflow on a large scale will facilitate the translation of candidate markers into clinical use.
Drift as a driver of language change: An artificial language experiment
Authors: Ventura Rafael , Plotkin Joshua B. , Roberts Gareth 
Published: March 2021

AbstractOver half a century ago, George Zipf observed that more frequent words tend to be older. Corpus studies since then have confirmed this pattern, with more frequent words being replaced and regularized less often than less frequent words. Two main hypotheses have been proposed to explain this: that frequent words change less because selection against innovation is stronger at higher frequencies, or that they change less because stochastic drift is stronger at lower frequencies. Here, we report the first experimental test of these hypotheses. Participants were tasked with learning a miniature language consisting of two nouns and two plural markers. Nouns occurred at different frequencies and were subjected to treatments that varied drift and selection. Using a model that accounts for participant heterogeneity, we measured the rate of noun regularization, the strength of selection, and the strength of drift in participant responses. Results suggest that drift alone is sufficient to generate the elevated rate of regularization we observed in low-frequency nouns, adding to a growing body of evidence that drift may be a major driver of language change.
Biochemical and Immuno-Histochemical Localization of Type IIA Procollagen in Annulus Fibrosus of Mature Bovine Intervertebral Disc
Authors: McAlinden Audrey , Hudson David M. , Fernandes Aysel A. , Ravindran Soumya , Fernandes Russell J. 
Published: March 2021

AbstractFor next generation tissue-engineered constructs and regenerative medicine to succeed clinically, the basic biology and extracellular matrix composition of tissues that these repair techniques seek to restore have to be fully determined. Using the latest reagents coupled with tried and tested methodologies, we continue to uncover previously undetected structural proteins in mature intervertebral disc. In this study we show that the “embryonic” type IIA procollagen isoform (containing a cysteine-rich amino propeptide) was biochemically detectable in the annulus fibrosus of both calf and mature steer intervertebral discs, but not in the nucleus pulposus where the type IIB isoform was predominantly localized. Specifically, the triple-helical type IIA procollagen isoform immunolocalized in the outer margins of the inner annulus fibrosus. Triple helical processed type II collagen exclusively localized within the interlamellae regions and with type IIA procollagen in the intra-lamellae regions. Mass spectrometry of the α1 (II) collagen chains from the region where type IIA procollagen localized showed high 3-hydroxylation of Proline-944, a post-translational modification that is correlated with thin collagen fibrils as in the nucleus pulposus. The findings implicate small diameter fibrils of type IIA procollagen in select regions of the annulus fibrosus where it likely contributes to the organization of collagen bundles and structural properties within the type I-type II collagen transition zone.
SongExplorer: A deep learning workflow for discovery and segmentation of animal acoustic communication signals
Authors: Arthur Benjamin J. , Ding Yun , Sosale Medhini , Khalif Faduma , Kim Elizabeth , Waddell Peter , Turaga Srinivas C. , Stern David L. 
Published: March 2021

AbstractMany animals produce distinct sounds or substrate-borne vibrations, but these signals have proved challenging to segment with automated algorithms. We have developedSongExplorer, a web-browser based interface wrapped around a deep-learning algorithm that supports an interactive workflow for (1) discovery of animal sounds, (2) manual annotation, (3) supervised training of a deep convolutional neural network, and (4) automated segmentation of recordings. Raw data can be explored by simultaneously examining song events, both individually and in the context of the entire recording, watching synced video, and listening to song. We provide a simple way to visualize many song events from large datasets within an interactive low-dimensional visualization, which facilitates detection and correction of incorrectly labelled song events. The machine learning model we implemented displays higher accuracy than existing heuristic algorithms and similar accuracy as two expert human annotators. We show thatSongExplorerallows rapid detection of all song types from new species and of novel song types in previously well-studied species.
Gender stereotypes in advertising have negative cross-gender effects
Authors: Åkestam Nina , Rosengren Sara , Dahlén Micael , Liljedal Karina T. , Berg Hanna 
Published: March 2021

PurposeThis paper aims to investigate cross-gender effects of gender stereotypes in advertising. More specifically, it proposes that the negative effects found in studies of women’s reactions to stereotyped female portrayals should hold across gender portrayal and target audience gender.Design/methodology/approachIn two experimental studies, the effects of stereotyped portrayals (vs non-stereotyped portrayals) across gender are compared.FindingsThe results show that advertising portrayals of women and men have a presumed negative influence on others, leading to higher levels of ad reactance, which has a negative impact on brand-related effects across model and participant gender, and for gender stereotypes in terms of physical characteristics and roles.Research limitations/implicationsWhereas previous studies have focused on reactions of women to female stereotypes, the current paper suggests that women and men alike react negatively to stereotyped portrayals of other genders.Practical implicationsThe results indicate that marketers can benefit from adapting a more mindful approach to the portrayals of gender used in advertising.Originality/valueThe addition of a cross-gender perspective to the literature on gender stereotypes in advertising is a key contribution to this literature.
“SME executives’ perceptions and the information security preparedness model”
Authors: Saban Kenneth Albert , Rau Stephen , Wood Charles A. 
Published: March 2021

Purpose
Information security has increasingly been in the headlines as data breaches continue to occur at alarming rates. This paper aims to propose an Information Security Preparedness Model that was developed to examine how SME executives’ perceptions of security importance, implementation challenges and external influences impact their awareness and commitment to security preparedness.

Design/methodology/approach
Funded by the Department of Justice, a national survey of SME executives’ perceptions of information security preparedness was conducted. Using PLS-SEM, the survey responses were used to test the proposed Information Security Preparedness Model.

Findings
The results indicate that as perceptions of security importance and external influences increase, SME executives’ awareness and commitment to information security also increases. In addition, as implementation challenges increase, awareness and commitment to information security decreases. Finally, as security importance and awareness and commitment to information security increases, executives’ perception of security preparedness also increases.

Research limitations/implications
Executive perceptions of information security were measured and not the actual level of security. Further research that examines the agreement between executive perceptions and the true state of information security within the organization is warranted.

Originality/value
Prior information security studies using Roger’s (1975, 1983) Protection Motivation Theory have produced mixed results. This paper develops and tests the Information Security Preparedness Model to more fully explain SME executive’s perceptions of information security.