bluuebunny/crossref_metadata_2025_split huggingface dataset:
Negative interplay between biofilm formation and competence in the environmental strains ofBacillus subtilis
Authors: She Qianxuan , Hunter Evan , Qin Yuxuan , Nicolau Samantha , Zalis Eliza A. , Wang Hongkai , Chen Yun , Chai Yunrong 
Published: June 2020

AbstractEnvironmental strains of the soil bacteriumBacillus subtilishave valuable applications in agriculture, industry, and biotechnology. They are capable of forming robust biofilms and demonstrate excellent biological control activities in plant protection. However, environmental strains are genetically less accessible, a sharp contrast to the laboratory strains well known for their natural competence and a limitation toward their application. In this study, we observed that robust biofilm formation of the environmental strains greatly reduces the rate of competent cells within the biofilm. By using the model strain 3610, we reveal a cross-pathway regulation that allows biofilm matrix producers and competence-developing cells to undergo mutually exclusive cell differentiation. We show that the competence activator ComK represses the key biofilm regulatory genesinIby directly binding to thesinIpromoter, thus blocking competent cells from simultaneously becoming matrix producers. In parallel, the biofilm activator SlrR represses competence through three distinct mechanisms, involving both genetic regulation and cell morphological changes. We discuss potential implications of limiting competence in a bacterial biofilm.ImportanceThe soil bacteriumBacillus subtilisis capable of forming robust biofilms, a multicellular community important for its survival in the environment.B. subtilisalso exhibits natural competence, the ability of cells to acquire genetic materials directly from the environment. By investigating competence developmentin situduringB. subtilisbiofilm formation, we reveal that robust biofilm formation, an important feature of the environmental strains ofB. subtilis, often greatly reduces the rate of competent cells within the biofilm. We characterize a cross-pathway regulation that allows cells associated with these two developmental events to undergo mutually exclusive cell differentiation during biofilm formation. Finally, we discuss potential biological implications of limiting competence in a bacterial biofilm.
A CRISPRi-dCas9 system for archaea and its use to examine gene function during nitrogen fixation byMethanosarcina acetivorans
Authors: Dhamad Ahmed E. , Lessner Daniel J. 
Published: June 2020

ABSTRACTCRISPR-based systems are emerging as the premier method to manipulate many cellular processes. In this study, a simple and efficient CRISPR interference (CRISPRi) system for targeted gene repression in archaea was developed. TheMethanosarcina acetivoransCRISPR-Cas9 system was repurposed by replacing Cas9 with the catalytically dead Cas9 (dCas9) to generate a CRISPRi-dCas9 system for targeted gene repression. To test the utility of the system, genes involved in nitrogen (N2) fixation were targeted for dCas9-mediated repression. First, thenifoperon (nifHI1I2DKEN) that encodes molybdenum nitrogenase was targeted by separate guide RNAs (gRNA), one targeting the promoter and the othernifD. Remarkably, growth ofM. acetivoranswith N2was abolished by dCas9-mediated repression of thenifoperon with each gRNA. The abundance ofniftranscripts was >90% reduced in both strains expressing the gRNAs, and NifD was not detected in cell lysate. Next, we targeted NifB, which is required for nitrogenase cofactor biogenesis. Expression of a gRNA targeting the coding sequence of NifB decreasednifBtranscript abundance >85% and impaired but did not abolish growth ofM. acetivoranswith N2. Finally, to ascertain the ability to study gene regulation using CRISPRi-dCas9,nrpR1encoding a subunit of the repressor of thenifoperon was targeted. ThenrpR1repression strain grew normally with N2but had increasednifoperon transcript abundance consistent with a NrpR1 as repressor. These results highlight the utility of the system, whereby a single gRNA when expressed with dCas9 can block transcription of targeted genes and operons inM. acetivorans.IMPORTANCEGenetic tools are needed to understand and manipulate the biology of archaea, which serve critical roles in the biosphere. Methanogenic archaea (methanogens) are essential for the biological production of methane, an intermediate in the global carbon cycle, an important greenhouse gas and a biofuel. The CRISPRi-dCas9 system in the model methanogenM. acetivoransis the first Cas9-based CRISPR interference system in archaea. Results demonstrate that the system is remarkably efficient in targeted gene repression and provide new insight into nitrogen fixation by methanogens, the only archaea with nitrogenase. Overall, the CRISPRi-dCas9 system provides a simple, yet powerful, genetic tool to control the expression of target genes and operons in methanogens.
PQS-Induced Outer Membrane Vesicles Enhance Biofilm Dispersion inPseudomonas aeruginosa
Authors: Cooke Adam C. , Florez Catalina , Dunshee Elise B. , Lieber Avery D. , Terry Michelle L. , Light Caitlin J. , Schertzer Jeffrey W. 
Published: June 2020

AbstractBacterial biofilms are major contributors to chronic infections in humans. Because they are recalcitrant to conventional therapy, they present a particularly difficult treatment challenge. Identifying factors involved in biofilm development can help uncover novel targets and guide the development of anti-biofilm strategies.Pseudomonas aeruginosacauses surgical site, burn wound, and hospital acquired infections, and is also associated with aggressive biofilm formation in the lungs of cystic fibrosis patients. A potent but poorly understood contributor toP. aeruginosavirulence is the ability to produce outer membrane vesicles (OMVs). OMV trafficking has been associated with cell-to-cell communication, virulence factor delivery, and the transfer of antibiotic resistance genes. Because OMVs have almost exclusively been studied using planktonic cultures, little is known about their biogenesis and function in biofilms. Our group has shown that the Pseudomonas Quinolone Signal (PQS) induces OMV formation inP. aeruginosa, and in other species, through a biophysical mechanism that is also active in biofilms. Here, we demonstrate that PQS-induced OMV production is highly dynamic during biofilm development. Interestingly, PQS and OMV synthesis are significantly elevated during dispersion, compared to attachment and maturation stages. PQS biosynthetic and receptor mutant biofilms were significantly impaired in their ability to disperse, but this phenotype could be rescued by genetic complementation or exogenous addition of PQS. Finally, we show that purified OMVs can actively degrade extracellular protein, lipid, and DNA. We therefore propose that enhanced production of PQS-induced OMVs during biofilm dispersion facilitates cell escape by coordinating the controlled degradation of biofilm matrix components.ImportanceTreatments that manipulate biofilm dispersion hold the potential to convert chronic drug-tolerant biofilm infections from protected sessile communities into released populations that are orders-of-magnitude more susceptible to antimicrobial treatment. However, dispersed cells often exhibit increased acute virulence and dissemination phenotypes. A thorough understanding of the dispersion process is therefore critical before this promising strategy can be effectively employed. PQS has been implicated in early biofilm development, but we hypothesized that its function as an OMV inducer may contribute at multiple stages. Here, we demonstrate that PQS and OMVs are differentially produced duringPseudomonas aeruginosabiofilm development and that effective biofilm dispersion is dependent on production of PQS-induced OMVs, which likely act as delivery vehicles for matrix degrading enzymes. These findings lay the groundwork for understanding the roles of OMVs in biofilm development and suggest a model to explain the controlled matrix degradation that accompanies biofilm dispersion in many species.
What has been the impact of Covid-19 on Safety Culture? A case study from a large metropolitan teaching hospital
Authors: Denning Max , Goh Ee Teng , Scott Alasdair , Martin Guy , Markar Sheraz , Flott Kelsey , Mason Sam , Przybylowicz Jan , Almonte Melanie , Clarke Jonathan , Winter-Beatty Jasmine , Chidambaram Swathikan , Yalamanchili Seema , Tan Benjamin Yong-Qiang , Kanneganti Abhiram , Sounderajah Viknesh , Wells Mary , Purkayastha Sanjay , Kinross James 
Published: June 2020

ABSTRACTIntroductionCovid-19 has placed an unprecedented demand on healthcare systems worldwide. A positive safety culture is associated with improved patient safety and in turn patient outcomes. To date, no study has evaluated the impact of Covid-19 on safety culture.MethodsThe Safety Attitudes Questionnaire (SAQ) was used to investigate safety culture at a large UK teaching hospital during Covid-19. Findings were compared with baseline data from 2017. Incident reporting from the year preceding the pandemic was also examined.ResultsSignificant increased were seen in SAQ scores of doctors and ‘other clinical staff’, there was no change in the nursing group. During Covid-19, on univariate regression analysis, female gender, age 40-49 years, non-white ethnicity, and nursing job role were all associated with lower SAQ scores. Training and support for redeployment were associated with higher SAQ scores. On multivariate analysis, non-disclosed gender (−0.13), non-disclosed ethnicity (−0.11), nursing role (−0.15), and support (0.29) persisted to significance. A significant decrease (p<0.003) was seen in error reporting after the onset of the Covid-19 pandemic.DiscussionThis is the first study to report SAQ during Covid-19 and compare with baseline. Differences in SAQ scores were observed during Covid-19 between professional groups and compared to baseline. Reductions in incident reporting were also seen. These changes may reflect perception of risk, changes in volume or nature of work. High-quality support for redeployed staff may be associated with improved safety perception during future pandemics.WHAT IS ALREADY KNOWN ON THE SUBJECTSafety culture is associated with patient safety and outcomesThis is the first study to investigate safety culture during the Covid-19 pandemicThis study uses the Safety Attitudes Questionnaire (SAQ) and Datix incident reporting data to investigate determinants of safety climate during the Covid-19 pandemic.Safety climate is context specific, this study is strengthened by the availability of benchmarking data from before the onset of the Covid-19 pandemic.Significant differences in SAQ scores between professional groups were observed during Covid-19.Gender, ethnicity and job role were significant determinants of safety attitudes.Support during redeployment was associated with improved safety attitudes.The number of incidents that were reported reduced significantly during Covid-19, although the number of events leading to harm remained constant.
Thyroid function abnormalities in COVID-19 patients
Authors: Wang Weibin , Su Xingyun , Ding Yongfeng , Fan Weina , Su Junwei , Chen Zhendong , Zhao Hong , Xu Kaijin , Ni Qin , Xu Xiaowei , Qiu Yunqing , Teng Lisong 
Published: June 2020

BackgroundThe novel coronavirus COVID-19, has caused a worldwide pandemic, impairing several human organs and systems. Whether COVID-19 affects human thyroid function remains unknown.Methods84 hospitalized COVID-19 patients in the First Affiliated Hospital, Zhejiang University School of Medicine (Hangzhou, China) were respectively enrolled in this study. In addition, 91 other patients with pneumonia and 807 healthy subjects were included as controls.FindingsWe found that the levels of TT3 and TSH were lower in COVID-19 patients than control groups (p<0·001). Within the group of COVID-19 patients, 61.9% patients (52/84) presented with thyroid function abnormalities. We found a larger proportion of patients in severe condition exhibited thyroid dysfunction than mild/moderate cases (74·6% vs. 23·8%, p < 0·001). Patients with thyroid dysfunction tended to have increased interval time for negative conversion of viral nucleic acid (14·1 ± 9·4 vs. 10·6 ± 8·3 days, p = 0·088). To note, thyroid dysfunction was also associated with decreased lymphocytes (p < 0·001) and increased CRP (p = 0·002). In 7 patients with dynamic changes of thyroid function, we observed the levels of TT3 and TSH gradually increased and reached normal range without thyroid hormone replacement at Day 30 post-admission. The correlation between TT3 and TSH level seemed to be positive rather than negative in the early stage, and gradually turned to be negatively related over time.InterpretationsThyroid function abnormalities are common in COVID-19 patients, especially in severe cases. This might be caused by virus attack and damage to the thyroid-pituitary axis. Therefore, more attention should be paid to thyroid function during treatment of COVID-19, and close follow-up is also needed after discharge.FundingThis study was supported by Zhejiang Provincial Science and technology department key R & D plan emergency project (No. 2020c03123-8).
Predictive Accuracy of a Hierarchical Logistic Model of Cumulative SARS-CoV-2 Case Growth
Authors: Kriston Levente 
Published: June 2020

ABSTRACTBackgroundInfectious disease predictions models, including virtually all epidemiological models describing the spread of the SARS-CoV-2 pandemic up to June 2020, are rarely evaluated. The aim of the present study was to investigate the predictive accuracy of a prognostic model for forecasting the development of the cumulative number of reported SARS-CoV-2 cases in countries and administrative regions worldwide.MethodsThe cumulative number of reported SARS-CoV-2 cases was forecasted in 251 regions with a horizon of two weeks, one month, and two months using a previously described hierarchical logistic model at the end of March 2020. Forecasts were compared to actual observations by using a series of evaluation metrics.ResultsOn average, predictive accuracy was very high in nearly all regions at the two weeks forecast, high in most regions at the one month forecast, and notable in the majority of the regions at the two months forecast. Higher accuracy was associated with the availability of more data for estimation and with a more pronounced cumulative case growth from the first case to the date of estimation. In some strongly affected regions, cumulative case counts were considerably underestimated.ConclusionsWith keeping its limitations in mind, the investigated model can be used for the preparation and distribution of resources during the SARS-CoV-2 pandemic. Future research should primarily address the model’s assumptions and its scope of applicability. In addition, establishing a relationship with known mechanisms and traditional epidemiological models of disease transmission would be desirable.
Modelling the Occurrence of the Novel Pandemic COVID-19 Outbreak– A Box and Jenkins Approach
Authors: Nurudeen Ajadi , Adesegun Ogunsola Isqeel , Saddam Damisa Adams 
Published: June 2020

AbstractThe corona virus disease 2019 (COVID-19) is a novel pandemic disease that spreads very fast and causes severe respiratory problem to its carrier and thereby results to death in some cases. In this research, we studied the trend, model Nigeria daily COVID-19 cases and forecast for the future occurrences in the country at large. We adopt the Box and Jenkins approach. The time plot showed that the cases of COVID-19 rises rapidly in recent time. KPSS test confirms the non-stationarity of the process (p < 0.05) before differencing. The test also confirmed the stationarity of the process (p > 0.05) after differencing. Various ARIMA (p,d,q) were examined with their respective AICs and Log-likelihood. ARIMA (1, 2, 1) was selected as the best model due to its least AIC (559.74) and highest log likelihood (−276.87). Both Shapiro-Wilk test and Box test performed confirm the fitness of the model (p > 0.05) for the series. Forecast for 30 days was then made for COVID-19 cases in Nigeria. Conclusively, the model obtained in this research can be used to model, monitor and forecast the daily occurrence of COVID-19 cases in Nigeria.
Recognition memory: familiarity signals increase selectively in the lateral entorhinal cortex following hippocampal lesions
Authors: Mahnke Liv , Atucha Erika , Kitsukawa Takashi , Sauvage Magdalena M. 
Published: June 2020

AbstractThe sense of familiarity for events is crucial for successful recognition memory. However, the neural substrate and mechanisms supporting familiarity remain unclear. Some human and animal studies suggest that the lateral entorhinal (LEC) and the perirhinal (PER) cortices might be essential for familiarity judgments while others attribute this function to the hippocampus (HIP) and it is unclear whether LEC, PER and HIP interact within this frame. Here, we especially investigate if LEC and PER’s contribution to familiarity depends on hippocampal integrity. Using a human to rat translational memory task and high resolution IEG imaging, we report that hippocampal lesions selectively enhance activity in LEC during familiarity judgments. These findings suggest that different mechanisms support familiarity in LEC and PER and, that HIP might exert a tonic inhibition on LEC during recognition memory that might be released when HIP is compromised, possibly constituting a compensatory mechanism in aging and amnesic patients.
Social signaling via bioluminescent blinks drives schooling behavior in the flashlight fishAnomalops katoptron
Authors: Jägers Peter , Wagner Louisa , Schütz Robin , Mucke Maximilian , Senen Budiono , Limmon Gino V. , Herlitze Stefan , Hellinger Jens 
Published: June 2020

AbstractThe bioluminescent flashlight fishAnomalops katoptronlive in schools of several hundred specimens. To understand how flashlight fish, integrate bioluminescent signaling into their schooling behavior, we analyzed movement profiles and blink frequencies. Isolated specimen ofA. katoptronshow a high motivation to align with fixed or moving artificial light organs. Depending on presented frequenciesA. katoptronresponds with a reduction in swimming speed and its own blink frequency. Higher presented blink frequencies reduce the nearest neighbor distance. In the natural environmentA. katoptronis changing its blink frequencies and nearest neighbor distance in a context specific manner. Blink frequencies are increased from day to night and during avoidance behavior, while nearest neighbor distance is decreased with increasing blink frequencies.A. katoptronchanges its blink frequencies by modifying light organ occlusion. Our results suggest that visually transmitted information via specific blink patterns determine intraspecific communication and group cohesion in schoolingA. katoptron.
In vivofluorescence lifetime imaging captures metabolic changes in macrophages during wound responses in zebrafish
Authors: Miskolci Veronika , Tweed Kelsey E , Lasarev Michael R , Britt Emily C , McDougal Courtney E , Walsh Alex J , Fan Jing , Sauer John-Demian , Skala Melissa C , Huttenlocher Anna 
Published: June 2020

AbstractThe effector functions of macrophages across the spectrum of activation statesin vitroare linked to profound metabolic rewiring. However, the metabolism of macrophages remains poorly characterizedin vivo. To assess changes in the intracellular metabolism of macrophages in their native inflammatory microenvironment, we employed two-photon fluorescence lifetime imaging microscopy (FLIM) of metabolic coenzymes NAD(P)H and FAD. We found that pro-inflammatory activation of macrophagesin vivowas associated with a decrease in the optical redox ratio [NAD(P)H/(NAD(P)H+FAD)] relative to a pro-resolving population during both infected and sterile inflammation. FLIM also resolved temporal changes in the optical redox ratio and lifetime variables of NAD(P)H in macrophages over the course of sterile inflammation. Collectively, we show that non-invasive and label-free imaging of autofluorescent metabolic coenzymes is sensitive to dynamic changes in macrophage activation in interstitial tissues. This imaging-based approach has broad applications in immunometabolism by probing in real time the temporal and spatial metabolic regulation of immune cell function in a live organism.SignificanceMetabolic regulation of macrophage effector functions has recently emerged as a key concept in immune cell biology. Studies rely onin vitroandex vivoapproaches to study macrophage metabolism, however the high plasticity of these cells suggest that removal from their native microenvironment may induce changes in their intracellular metabolism. Here, we show that fluorescence lifetime imaging microscopy of metabolic coenzymes captures dynamic changes in the metabolic activity of macrophages while maintaining them in their endogenous microenvironment. This approach also resolves variations on a single-cell level, in contrast to bulk measurements provided by traditional biochemical assays, making it a potentially valuable tool in the field of immunometabolism.