bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of RpoS results in attenuatedEscherichia colicolonization of human intestinal organoids and a competitive disadvantage within the germ-free mouse intestine
Authors: Barron Madeline R. , Cieza Roberto J. , Hill David R. , Huang Sha , Yadagiri Veda K. , Spence Jason R. , Young Vincent B. 
Published: August 2020

AbstractPluripotent stem-cell-derived human intestinal organoids (HIOs) are three-dimensional, multicellular structures that model a previously uncolonized, naïve intestinal epithelium in anin vitrosystem. We recently demonstrated that microinjection of the non-pathogenicEscherichia colistrain, ECOR2, into HIOs induced morphological and functional maturation of the HIO epithelium, including increased secretion of mucins and cationic antimicrobial peptides. In the current work, we use ECOR2 as a biological probe to investigate the bacterial response to colonization of the HIO lumen. InE. coliand other Gram-negative bacteria, adaptation to environmental stress is regulated by the general stress response sigma factor, RpoS. We generated an isogenic ∆rpoSECOR2 mutant to compare challenges faced by a bacterium during colonization of the HIO lumen relative to the germ-free mouse intestine, which is currently the best available system for studying the initial establishment of bacterial populations within the gut. We demonstrate that loss of RpoS significantly decreases the ability of ECOR2 to colonize HIOs, though it does not prevent colonization of germ-free mice. Rather, the ∆rpoSECOR2 exhibits a fitness defect in the germ-free mouse intestine only in the context of microbial competition. These results indicate that HIOs pose a differentially restrictive luminal environment toE. coliduring colonization, thus increasing our understanding of the HIO model system as it pertains to studying the establishment of intestinal host-microbe symbioses.ImportanceTechnological advancements have and will continue to drive the adoption of organoid-based systems for investigating host-microbe interactions within the human intestinal ecosystem. UsingE. colideficient in the RpoS-mediated general stress response, we demonstrate that the type or severity of microbial stressors within the HIO lumen differ from those of thein vivoenvironment of the germ-free mouse gut. This study provides important insight into the nature of the HIO microenvironment from a microbiological standpoint.
Structure-function characterization of the conserved regulatory mechanism of theEscherichia coliM48-metalloprotease BepA
Authors: Bryant Jack A. , Cadby Ian T. , Chong Zhi-Soon , Sevastsyanovich Yanina R. , Morris Faye C. , Cunningham Adam F. , Kritikos George , Meek Richard W. , Banzhaf Manuel , Chng Shu-Sin , Lovering Andrew L. , Henderson Ian R. 
Published: August 2020

AbstractThe asymmetric Gram-negative outer membrane (OM) is the first line of defence for bacteria against environmental insults and attack by antimicrobials. The key component of the OM is lipopolysaccharide, which is transported to the surface by the essential lipopolysaccharide transport (Lpt) system. Correct folding of the Lpt system component LptD is regulated by a periplasmic metalloprotease, BepA. Here we present the crystal structure of BepA fromEscherichia coli,solved to a resolution of 2.18 Å, in which the M48 protease active site is occluded by an active site plug. Informed by our structure, we demonstrate that free movement of the active site plug is essential for BepA function, suggesting that the protein is auto-regulated by the active site plug, which is conserved throughout the M48 metalloprotease family. Targeted mutagenesis of conserved residues reveals that the negative pocket and the TPR cavity are required for function and degradation of the BAM complex component BamA under conditions of stress. Lastly, we show that loss of BepA causes disruption of OM lipid asymmetry, leading to surface exposed phospholipid.ImportanceM48 metalloproteases are widely distributed in all domains of life.E. colipossesses four members of this family located in multiple cellular compartments. The functions of these proteases are not well understood. Recent investigations revealed that one family member, BepA, has an important role in the maturation of a central component of the LPS biogenesis machinery. Here we present the structure of BepA and the results of a structure guided mutagenesis strategy, which reveal the key residues required for activity.
Inhibition ofCampylobacter jejunibiofilm formation by D-amino acids
Authors: Elgamoudi Bassam A. , Taha  , Korolik Victoria 
Published: August 2020

AbstractThe ability of bacterial pathogens to form biofilms is an important virulence mechanism in relation to its pathogenesis and transmission. Biofilms play a crucial role in survival in unfavourable environmental conditions, act as reservoirs of microbial contamination and antibiotic resistance. For intestinal pathogenCampylobacter jejuni, biofilms are considered to be a contributing factor in transmission through the food chain and currently, there are no known methods for intervention. Here we present an unconventional approach to reducing biofilm formation byC. jejuniby the application of D-amino acids (DAs), and L-amino acids (LAs). We found that DAs and not LAs, except L-alanine, reduced biofilm formation by up to 70%. The treatment ofC. jejunicells with DAs changed the biofilm architecture and reduced the appearance of amyloid-like fibrils. In addition, a mixture of DAs enhanced antimicrobial efficacy of D-Cycloserine (DCS) up to 32% as compared with DCS treatment alone. Unexpectedly, D-alanine was able to reverse the inhibitory effect of other DAs as well as that of DCS. Furthermore, L-alanine and D-tryptophan decreased transcript levels of peptidoglycan biosynthesis enzymes alanine racemase (alr) and D-alanine-D-alanine ligase (ddlA) while D-serine was only able to decrease the transcript levels ofalr. Our findings suggest that a combination of DAs could reduce biofilm formation, viability and persistence ofC. jejunithrough dysregulation ofalrandddlA.
Midcell localization of PBP4 ofEscherichia colimodulates the timing of divisome assembly
Authors: Verheul Jolanda , Lodge Adam , Yau Hamish C.L. , Liu Xiaolong , Liu Xinwei , Solovyova Alexandra S. , Typas Athanasios , Banzhaf Manuel , Vollmer Waldemar , Blaauwen Tanneke den 
Published: August 2020

ABSTRACTInsertion of new material into theEscherichia colipeptidoglycan (PG) sacculus between the cytoplasmic membrane and the outer membrane requires a well-organized balance between synthetic and hydrolytic activities to maintain cell shape and avoid lysis. The hydrolytic enzymes outnumber the enzymes that insert new PG by far and very little is known about their specific function. Here we show that the DD-carboxy/endopeptidase PBP4 localizes in a PBP1A/LpoA and FtsEX dependent fashion at midcell during septal PG synthesis. Midcell localization of PBP4 requires its non-catalytic domain 3 of unknown function, but not the activity of PBP4 or FtsE. Microscale thermophoresis with isolated proteins shows that domain 3 is needed for the interaction with NlpI, but not PBP1A or LpoA.In vivocrosslinking experiments confirm the interaction of PBP4 with PBP1A and LpoA. We propose that PBP4 functions together with the amidases AmiA and B to create denuded glycan strands to attract the initiator of septal PG synthesis, FtsN. Consistent with this model, we found that the divisome assembly at midcell was significantly affected in cells lacking PBP4.IMPORTANCEPeptidoglycan biosynthesis is a major target for antibacterials. The covalently closed peptidoglycan mesh, called sacculus, protects the bacterium from lysis due to its turgor. Sacculus growth is facilitated by the balanced activities of synthases and hydrolases, and disturbing this balance leads to cell lysis and bacterial death. Because of the large number and possible redundant functions of peptidoglycan hydrolases, it has been difficult to decipher their individual functions. In this paper we show that the DD-endopeptidase PBP4 localizes at midcell during septal peptidoglycan synthesis inEscherichia coliand is important for the timing of the assembly of the division machinery. This shows that inhibition of certain hydrolases could weaken the cells and might enhance antibiotic action.
Bi-directional encoding of context-based odor signals and behavioral states by the nucleus of the lateral olfactory tract neurons
Authors: Tanisumi Yuta , Shiotani Kazuki , Hirokawa Junya , Sakurai Yoshio , Manabe Hiroyuki 
Published: August 2020

AbstractThe nucleus of the lateral olfactory tract (nLOT) is not only a part of the olfactory cortex that receives olfactory sensory inputs from the olfactory bulb, but also one of the cortical amygdala areas that regulates motivational behaviors. To examine how the neural ensemble activity of the nLOT is modulated by motivational processes that occur during various states of learned goal-directed behaviors, we recorded nLOT spike activities of mice performing odor-guided go/no-go tasks for obtaining a water reward. We found that the majority of the nLOT neurons exhibited sharp go-cue excitation and persistent no-go-cue inhibition responses triggered by an odor onset. The bi-directional cue encoding introduced nLOT population response dynamics and provided a high odor decoding accuracy before executing cue-odor-evoked behaviors. The go-cue preferred neurons were also activated in the reward drinking state, indicating context-based odor-outcome associations. These findings suggest that the nLOT neurons play an important role in the translation from context-based odor information to appropriate behavioral motivation.
Intestinal inflammation and altered gut microbiota associated with inflammatory bowel disease renders mice susceptible toClostridioides difficilecolonization and infection
Authors: Abernathy-Close Lisa , Barron Madeline R. , George James M. , Dieterle Michael G. , Vendrov Kimberly C. , Bergin Ingrid I. , Young Vincent B. 
Published: August 2020

ABSTRACTClostridioides difficilehas emerged as a noteworthy pathogen in patients with inflammatory bowel disease (IBD). Concurrent IBD and CDI is associated with increased morbidity and mortality compared to CDI alone. IBD is associated with alterations of the gut microbiota, an important mediator of colonization resistance toC. difficile. Here, we describe and utilize a mouse model to explore the role of intestinal inflammation in susceptibility toC. difficilecolonization and subsequent disease severity in animals with underlying IBD.Helicobacter hepaticus, a normal member of the mouse gut microbiota, was used to trigger inflammation in the distal intestine akin to human IBD in mice that lack intact IL-10 signaling. Development of IBD resulted in a distinct intestinal microbiota community compared to non-IBD controls. We demonstrate that in this murine model, IBD was sufficient to render mice susceptible toC. difficilecolonization. Mice with IBD were persistently colonized byC. difficile, while genetically identical non-IBD controls were resistant toC. difficilecolonization. Concomitant IBD and CDI was associated with significantly worse disease than unaccompanied IBD. IL-10-deficient mice maintained gut microbial diversity and colonization resistance toC. difficilein experiments utilizing an isogenic mutant ofH. hepaticusthat does not trigger intestinal inflammation. These studies in mice demonstrate that the IBD-induced microbiota is sufficient forC. difficilecolonization and that this mouse model requires intestinal inflammation for inducing susceptibility to CDI in the absence of other perturbations, such as antibiotic treatment.IMPORTANCEThe incidence of CDI continues to increase significantly among patients with IBD, independent of antibiotic use, yet the relationship between IBD and increased risk for CDI remains to be understood. However, antibiotic-induced perturbations of the gut microbiota may mask mechanisms specific to IBD-inducedC. difficilesusceptibility and infection. Our study sought to describe and utilize a mouse model to specifically explore the relationship between the IBD-induced gut microbial community and susceptibility toC. difficilecolonization and CDI development. We demonstrate that IBD is sufficient forC. difficilecolonization and infection in mice and results in significantly worse disease than IBD alone, representing a murine model that recapitulates human IBD and CDI comorbidity. Furthermore, this model requires IBD-induced inflammation to sculpt a microbiota permissible toC. difficilecolonization. Use of this model will aid in developing new clinical approaches to predict, diagnose, and treatC. difficileinfection in the IBD population.
COVID-19 case-fatality rate and demographic and socioeconomic influencers: a worldwide spatial regression analysis based on country-level data
Authors: Cao Yang , Hiyoshi Ayako , Montgomery Scott 
Published: August 2020

AbstractWe used the COVID-19 dataset obtained from the Our World in Data website and investigated the associations between COVID-19 CFR and nine country-level indices of 209 countries/territories using the Matern correlation regression model. Spatial dependence among the data was controlled using the latitude and longitude of the centroid of the countries/territories. Stratified analyses were conducted by economic level and COVID-19 testing policy. The average of country/territory-specific COVID-19 CFR is about 2-3% worldwide, which is higher than previously reported at 0.7-1.3%. Statistically significant associations were observed between COVID-19 CFR and population size and proportion of female smokers. The open testing policies are associated with decreased CFR. Strictness of anti-COVID-19 measures was not statistically significantly associated with CFR overall, but the higher stringency index was associated with higher CFR in higher income countries with active testing policies. The statistically significant association between population size and COVID-19 CRF suggests the healthcare strain and lower treatment efficiency in countries with large populations. The observed association between smoking in females and COVID-19 CFR might be due to that the proportion of female smokers reflected broadly income level of a country. When testing is warranted and healthcare resources are sufficient, strict quarantine and/or lockdown measures might result in excess deaths in underprivileged populations.
Isolation Considered Epidemiological Model for the Prediction of COVID-19 Trend in Tokyo, Japan
Authors: Utamura Motoaki , Koizumi Makoto , Kirikami Seiichi 
Published: August 2020

BackgroundCoronavirus Disease 2019 (COVID19) currently poses a global public health threat. Although no exception, Tokyo, Japan was affected at first by only a small epidemic. Medical collapse nevertheless nearly happened because no predictive method existed for counting patients. A standard SIR epidemiological model and its derivatives predict susceptible, infectious, and removed (recovered/deaths) cases but ignore isolation of confirmed cases. Predicting COVID19 trends with hospitalized and infectious people in field separately is important to prepare beds and develop quarantine strategies.MethodsTime-series COVID19 data from February 28 to May 23, 2020 in Tokyo were adopted for this study. A novel epidemiological model based on delay differential equation was proposed. The model can evaluate patients in hospitals and infectious cases in the field. Various data such as daily new cases, cumulative infections, patients in hospital, and PCR test positivity ratios were used to examine the model. This approach derived an alternative formulation equivalent to the standard SIR model. Its results were compared quantitatively with those of the present isolation model.ResultsThe basic reproductive number, inferred as 2.30, is a dimensionless parameter composed of modeling parameters. Effects of intervention to mitigate the epidemic spread were assessed a posteriori. An exit policy of how and when to release a statement of emergency was also assessed using the model. Furthermore, results suggest that the rapid isolation of infectious cases has a large potential to effectively mitigate the spread of infection and restores social and economic activities safely.ConclusionsA novel mathematical model was proposed and examined using COVID19 data for Tokyo. Results show that shortening the period from infection to hospitalization is effective against outbreak without rigorous public health intervention and control. Faster and precise case cluster detection and wider and quicker introduction of testing measures are strongly recommended.
Job insecurity, financial threat and mental health in the COVID-19 context: The buffer role of perceived social support
Authors: Alcover Carlos-María , Salgado Sergio , Nazar Gabriela , Ramírez-Vielma Raúl , González-Suhr Carolina 
Published: August 2020

AbstractThe social distancing, confinement and quarantine adopted since March 2020 to confront the COVID-19 pandemic have affected multiple vital areas, and specially work, business and productive activities. Prior research has highlighted the relation between perceptions of risk in employment and its concomitant financial risk with a myriad of consequences for people’s well-being and health. In order to analyze the potential negative consequences of temporary layoffs, downsizing or closure of companies and businesses, and the consequent insecurity about the continuity of employment, the aim of this study is twofold. Firstly, to analyze the relations between the perceptions of job insecurity and financial threat and overall mental health during the first month of the COVID-19 pandemic in a sample of the Chilean adult population. And secondly, to identify the potential buffer effect of perceived social support on this relation. To analyze this, we carried out a cross-sectional study on a non-probabilistic sample aimed at a general Chilean adult population. The results show that both perceptions of job insecurity and financial threat are associated with a decline in perceived mental health. Additionally, results indicate a moderate buffer effect of perceived social support relative to the size of the social network. Thus, in relation to job insecurity and financial threat, the network size mitigates the association of both with the decline in perceived mental health. The theoretical and applied scope of these findings are analyzed, and their challenges and limitations are discussed.
Detection of Toxoplasmic Encephalitis in HIV Positive Patients in Urine with Hydrogel Nanoparticles
Authors: Steinberg Hannah E. , Bowman Natalie M. , Diestra Andrea , Ferradas Cusi , Russo Paul , Clark Daniel E. , Zhu Deanna , Magni Ruben , Malaga Edith , Diaz Monica , Pinedo-Cancino Viviana , Asayag Cesar Ramal , Calderón Maritza , Carruthers Vern B , Liotta Lance A. , Gilman Robert H. , Luchini Alessandra ,   the Toxoplasmosis working group in Peru and Bolivia
Published: August 2020

AbstractBackgroundDiagnosis of toxoplasmic encephalitis (TE) is challenging under the best clinical circumstances. The poor sensitivity of quantitative polymerase chain reaction (qPCR) forToxoplasmain blood and CSF and the limited availability of molecular diagnostics and imaging technology leaves clinicians in resource-limited settings with few options other than empiric treatment.Methology/Principle FindingsHere we describe proof of concept for a novel urine diagnostics for TE using Poly-N-isoproplyacrylamide nanoparticles dyed with Reactive Blue-221 to concentrate antigens, substantially increasing the limit of detection. After nanoparticle-concentration, a standard western blotting technique with a monoclonal antibody was used for antigen detection. Limit of detection was 7.8pg/ml and 31.3pg/ml ofT. gondiiantigens GRA1 and SAG1, respectively. To characterize this diagnostic approach, 164 hospitalized HIV-infected patients with neurological symptoms compatible with TE were tested for 1)T. gondiiserology (121/147, positive samples/total samples tested), 2) qPCR in cerebrospinal fluid (11/41), 3) qPCR in blood (10/112), and 4) urinary GRA1 (30/164) and SAG1 (12/164). GRA1 appears to be superior to SAG1 for detection of TE antigens in urine. Fifty-one HIV-infected,T. gondiiseropositive but asymptomatic persons all tested negative by nanoparticle western blot and blood qPCR, suggesting the test has good specificity for TE for both GRA1 and SAG1. In a subgroup of 44 patients, urine samples were assayed with mass spectrometry parallel-reaction-monitoring (PRM) for the presence ofT. gondiiantigens. PRM identified antigens in 8 samples, 6 of which were concordant with the urine diagnostic.Conclusion/SignificancesOur results demonstrate nanoparticle technology’s potential for a noninvasive diagnostic test for TE. Moving forward, GRA1 is a promising target for antigen based diagnostics for TE.Author SummaryToxoplasmic Encephalitis is a debilitating, yet highly treatable illness, classically seen in person living with HIV lacking treatment. Prompt diagnosis ensures the best outcome possible for patients, but remains a challenge: requiring invasive specimen collection, lacking necessary sensitivity, demanding significant technical skills and substantial infrastructure. Here we offer proof of concept of a diagnostic approach that is minimally invasive, using a urine-based approach that concentratesT. gondiiantigens with hydrogel mesh nanoparticles to improve □sensitivity for detection by western blot. □
Factors associated with accelerated resting heart rate among college freshmen : a cross-sectional study
Authors: You Qiqi , Wang Tiantian , Jiang Qingqing , Zhang Qiumei , Cao Shiyi 
Published: August 2020

AbstractObjectiveThis study aimed to investigate the prevalence of accelerated resting heart rates (RHRs) among freshmen in a university in Wuhan and to explore the influencing factors.MethodsWe conducted a cross-sectional survey and physical examinations in a university in Wuhan from 2015 to 2017, including 12428 freshmen. A binary logistic regression model was undertaken to identify the influencing factors associated with their accelerated RHRs.ResultsThe prevalence of accelerated RHRs was 47.5% among the 12428 freshmen surveyed. Accelerated RHR of freshmen was related to female (odds ratio [OR]: 1.484, 95% confidence interval [95% CI]: 1.368 - 1.610, P < 0.001) and high blood pressure (OR: 2.709, 95% CI: 2.212 - 3.318, P < 0.001). Compared with rural students, accelerated RHR was more likely to occur in urban students (OR: 1.452, 95% CI: 1.333 - 1.583, P < 0.001). Additionally, students who came from the central and the eastern regions (OR: 1.452, 95% CI: 1.254 - 1.682, P < 0.001; OR: 1.363, 95% CI: 1.149 - 1.618, P < 0.001), rather than who came from the western regions, were more likely to have accelerated RHRs.ConclusionsStudents with accelerated RHRs made up a high proportion of college freshmen entering the university in 2015 – 2017 in Wuhan. For people aged around 18 years, more attention was needed to pay to RHRs and specific measures such as blood pressure management were required in advance to prevent accelerated RHRs.Key questionsWhat is already known about this subject?Accelerated resting heart rate (RHR) could significantly increase the risk of suffering from cardiovascular diseases (CVDs). However, little research had reported the influencing factors associated with accelerated RHR among the young around 18 years old.What does this study add?We conducted a survey on freshmen to investigate the influencing factors associated with accelerated RHR, so as to provide early warning information for the occurrence of CVDs in a visual way.How might this impact on clinical practice?This study might serve as a reminder to young people to pay more attention to RHRs and provide early warning information about CVDs.