bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of biofilm dispersal approaches in Pseudomonas aeruginosa and evaluation of dispersed cells in acute infection mouse model
Authors: Ruhal Rohit , De Winter Fien , de Jonger Bart , Xavier Basil Britto , lammens Christine , Goossens Herman , Singh Samir Kumar , Malhotra-Kumar Surbhi 
Published: July 2019

ABSTRACTBiofilm dispersal is biologically significant process to fully understand its consequences during biofilm based infections. The mechanism for biofilm dispersal may involve response to environmental cues and changes in intracellular secondary messengers. Considering range of cues for biofilm dispersal, it is significant to study if dispersed cells generated by different methods have similar phenotype. In the present study, we have compared four type of biofilm dispersal in P. aeruginosa based in response to environment cues (starvation and nutrient rich), c-di-GMP knockdown and signaling molecule NO. We have determined their dispersal efficiency, susceptibility of dispersed cells for antibiotics, their transcriptomic changes compared to planktonic and biofilm. We also determined if dispersed cells can cause acute infections in mouse models. In vitro experiments showed that NO and c-di-GMP based dispersal methods had high biofilm reduction efficiency of 50 and 75% respectively, however, the nutrient induced dispersion showed low efficiency (≈30%) and more tolerance to colistin. We also showed that in vitro dispersed cells induced >10-fold transcriptomic expression of genes (at significance level of p < 0.005) related to efflux pumps (mexCD-oprJ), antibiotic resistance (arnDET) in dispersed cells induced by NO and nutrient change, while denitrification pathway and virulence (T3SS, VreI, T2SS) genes in all dispersed cells compared to planktonic and biofilm state. When the ability of the dispersed cells was tested in mouse model of lung infection, c-di-GMP and NO based dispersed cells displayed enhanced infections and haematogenous spread to liver and spleen and higher mortality. Although degree of immune response (cytokines) does not differ based on phenotypes inoculated in our experimental conditions. Based on our data most efficient dispersal methods increase murine mortality. This indicates their capability of making biofilm associated infection more complicated. Our data encourage to be more careful for studies suggesting biofilm dispersal during treatment of biofilm infections.
Modulation of RNA condensation by the DEAD-box protein eIF4A
Authors: Tauber Devin , Tauber Gabriel , Khong Anthony , Van Treeck Briana , Pelletier Jerry , Parker Roy 
Published: July 2019

SUMMARYStress granules are condensates of non-translating mRNAs and proteins involved in the stress response and neurodegenerative diseases. Stress granules form in part through intermolecular RNA-RNA interactions, although the process of RNA condensation is poorly understood. In vitro, we demonstrate that RNA is effectively recruited to the surfaces of RNA or RNP condensates. We demonstrate that the DEAD-box protein eIF4A reduces RNA condensation in vitro and limits stress granule formation in cells. This defines a purpose for eIF4A to limit intermolecular RNA-RNA interactions in cells, thereby allowing for proper RNP function. These results establish an important role for DEAD-box proteins as ATP-dependent RNA chaperones that can limit the intermolecular condensation and entanglement of RNA, analogous to the function of proteins like HSP70 in combatting protein aggregates.eTOC BlurbStress granules are formed in part by the process of RNA condensation, which is mediated by and promotes trans RNA-RNA interactions. The essential DEAD-box protein and translation initiation factor eIF4A limits stress granule formation by reducing RNA condensation through its function as an ATP-dependent RNA binding protein, behaving analogously to how protein chaperones like HSP70 combat protein aggregates.HighlightsRNA condensates promote intermolecular RNA-RNA interactions at their surfaceseIF4A limits the recruitment of RNAs to stress granules in cellseIF4A reduces the nucleation of stress granules in cellsRecombinant eIF4A1 inhibits the condensation of RNA in vitro in an ATP-dependent manner
In vitro testing of flash-frozen sublingual membranes for storage and reproducible permeability studies of macromolecular drugs from solution or nanofiber mats
Authors: Berka Pavel , Stránská Denisa , Semecký Vladimír , Berka Karel , Doležal Pavel 
Published: July 2019

AbstractSublingual drug delivery allows systemic delivery of drug without difficulties connected with the gastrointestinal pathway. We developed a new simple protocol for easy-to-use processing and storage of porcine sublingual mucosal membrane for in vitro studies using “flash freezing” in liquid nitrogen. All the dextrans used as mucosal membrane integrity and permeability markers permeated only slowly through sublingual mucosa illustrating usability both the “fresh” and “flash frozen” sublingual membranes whereas conventional cold storage “frozen” membranes have shown significantly higher permeabilities for macromolecules due to the sustained damage. The permeability values were too low to expect dextrans to be potential carriers at this context. To test albumin as a drug carrier we compared FITC-albumin permeation from solutions vs. nanofiber mats donors. To increase the amounts and prolong the transport, we manufactured nanofiber mats loaded with fluorescently marked albumin using well-scalable electrospinning technology. Nanofiber mats have allowed albumin passage through the sublingual membrane in similar amounts as from the pure artificial saliva solution. Since salivary washout strictly limits the duration of liquid dosages, nanofiber mats may thus permit prolonged sublingual administration.Graphical abstract
Exploiting Heterogeneous Time Scale of Dynamics to Enhance 2D HETCOR Solid-State NMR Sensitivity
Authors: Zhang Rongchun , Nishiyama Yusuke , Ramamoorthy Ayyalusamy 
Published: July 2019

AbstractMultidimensional solid-state NMR spectroscopy plays a significant role in offering atomic-level insights into molecular systems. In particular, heteronuclear chemical shift correlation (HETCOR) experiments could provide local chemical and structural information in terms of spatial heteronuclear proximity and through-bond connectivity. In solid state, the transfer of magnetization between heteronuclei, a key step in HETCOR experiments, is usually achieved using cross-polarization (CP) or INEPT (insensitive nuclei enhanced by polarization transfer) depending on the sample characteristics and magic-angle-spinning (MAS) frequency. But, for a multiphase system constituting molecular components that differ in their time scales of mobilities, CP efficiency is pretty low for mobile components because of the averaging of heteronuclear dipolar couplings whereas INEPT is inefficient due to the short T2 of immobile components and can be non-selective due to strong proton spin diffusion for immobile components especially under moderate spinning speeds. Herein, in this study we present two 2D pulse sequences that enable the sequential acquisition of 13C/1H HETCOR NMR spectra for the rigid and mobile components by taking full advantage of the abundant proton magnetization in a single experiment with barely increasing the overall experimental time. In particular, the 13C-detected HETCOR experiment could be applied under slow MAS conditions, where a multiple-pulse sequence is typically employed to enhance 1H spectral resolution in the indirect dimension. In contrast, the 1H-detected HETCOR experiment should be applied under ultrafast MAS, where CP and transient heteronuclear nuclear Overhauser effect (NOE) polarization transfer are combined to enhance 13C signal intensities for mobile components. These pulse sequences are experimentally demonstrated on two model systems to obtain 2D 13C/1H chemical shift correlation spectra of rigid and mobile components independently and separately. These pulse sequences can be used for dynamics difference based spectral editing and resonance assignments. Therefore, we believe the proposed 2D HETCOR NMR pulse sequences will be beneficial for the structural studies of heterogeneous systems containing molecular components that differ in their time scale of motions for understanding the interplay of structures and properties.
Mutant ACTB mRNA 3′UTR Promotes Hepatocellular Carcinoma Development by Regulating miR-1 and miR-29a
Authors: Li Yong , Ma Hong-Bin , Shi Chang-Ying , Feng Fei-Ling , Yang Liang 
Published: July 2019

AbstractIn recent years, mounting studies have shown that ACTB is closely related to various tumors. Although ACTB is dysregulated in numerous cancer types, limited data are available on the potential function and mechanism of ACTB in hepatocellular carcinoma (HCC). This study evaluated the expression and biological roles of mutant ACTB mRNA 3′UTR in HCC. Transcriptome sequence and qRT-PCR analysis determined that mutant ACTB mRNA 3′UTR was high expression in HCC tissues. Luciferase reporter assay showed that the ACTB mRNA 3′UTR mutations made it easier to interact with miR-1 and miR-29a. Moreover, mutant ACTB mRNA 3′UTR regulated miR-1 and miR-29a degradation via AGO2. Furthermore, mutant ACTB mRNA 3′UTR promoted hepatocellular carcinoma cells migration and invasionin vitroandin vivoby up-regulating miR-1 target gene MET and miR-29a target gene MCL1. In a word, our study demonstrates that 3′UTR of ACTB plays a key role in the tumor growth of hepatocellular carcinoma (HCC) and highlights the molecular mechanisms of ACTB-involved cancer growth and development.
Phenotypic plasticity, but not genetic adaptation, underlies seasonal variation in the cold hardening response ofDrosophila melanogaster
Authors: Stone Helen M. , Erickson Priscilla A. , Bergland Alan O. 
Published: July 2019

AbstractIn temperate regions, an organism’s ability to rapidly adapt to seasonally varying environments is essential for its survival. In response to seasonal changes in selection pressure caused by variation in temperature, humidity, and food availability, some organisms exhibit plastic changes in phenotype. In other cases, seasonal variation in selection pressure can rapidly increase the frequency of genotypes that offer survival or reproductive advantages under the current conditions. Little is known about the relative influences of plastic and genetic changes in short lived organisms experiencing seasonal environmental fluctuations. Cold hardening is a seasonally relevant plastic response in which exposure to cool, but nonlethal, temperatures significantly increases the organism’s ability to later survive at freezing temperatures. In the present study, we demonstrate seasonal variation in cold hardening inDrosophila melanogasterand test the extent to which plasticity and adaptive tracking underlie that seasonal variation. We measured the cold hardening response of flies from outdoor mesocosms over the summer, fall, and winter. We bred outdoor mesocosm-caught flies for two generations in the lab and matched each outdoor cohort to an indoor control cohort of similar genetic background. We measured the cold hardening response of indoor and field-caught flies and their laboratory-reared F1 and F2 progeny to determine the roles of seasonal environmental plasticity, parental effects, and genetic changes on cold hardening. We also tested the relationship between cold hardening and other factors, including age, developmental density, food substrate, presence of antimicrobials, and supplementation with live yeast. We found strong plastic responses to a variety of field- and lab-based environmental effects, but no evidence of seasonally varying parental or genetic effects on cold hardening. We therefore conclude that seasonal variation in the cold hardening response results from environmental influences and not genetic changes.
Metformin inhibits high glucose‐induced mesangial cell proliferation, inflammation and ECM expression through the SIRT1‐FOXO1‐autophagy axis
Authors: Xu Jiang , Chen Yan , Xing Yan , Ye Shandong 
Published: July 2019

AbstractThe aim of this study was to investigate the role of metformin in high glucose‐induced mesangial cell proliferation, inflammation and extracellular matrix (ECM) accumulation and to elucidate the underlying mechanism of metformin function. An MTT assay was used to examine rat mesangial cell (RMC) proliferation. The levels of TNF‐α, IL‐6 and TGF‐β in RMCs were determined by ELISA. The protein expression of fibronectin, collagen IV and autophagy‐related proteins (Beclin‐1, LC3‐I and LC3‐II) in RMCs was detected using western blot. Fluorescence microscopy analysis was carried out to evaluate RMC autophagy. Our results showed that high glucose‐induced RMC proliferation, inflammation and ECM expression, but these effects were markedly reduced by metformin. We confirmed that metformin suppressed high glucose‐induced RMC proliferation, inflammation and ECM expression via induction of autophagy. Mechanistic investigation demonstrated an axis of SIRT1‐FOXO1 in RMC autophagy. Our data indicated that metformin inhibits high glucose‐induced mesangial cell proliferation, inflammation and ECM expression through a SIRT1‐FOXO1‐autophagy axis.
Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy
Authors: Taubert Martin , Grob Carolina , Crombie Andrew , Howat Alexandra M. , Burns Oliver J. , Weber Miriam , Lott Christian , Kaster Anne‐Kristin , Vollmers John , Jehmlich Nico , von Bergen Martin , Chen Yin , Murrell John Colin 
Published: July 2019

SummaryThe release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the sediment–water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with 13C‐methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalysing the first reaction step to methanol. We observed a transfer of carbon to methanol‐oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment per day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment–water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane‐oxidizing community supported a complex trophic network. Our results provide valuable eco‐physiological insights into this specialized microbial community performing an ecosystem function of global relevance.
Combining Cupuassu (Theobroma grandiflorum) Puree, Pectin, and Chitosan Nanoparticles into Novel Edible Films for Food Packaging Applications
Authors: Melo Pamela Thais S. , Nunes Juliana C. , Otoni Caio G. , Aouada Fauze A. , de Moura Marcia R. 
Published: July 2019

AbstractEvery year, the residues generated by the disposal of packaging materials produced from fossil fuels have been growing, denoting a major environmental problem that can be mitigated by the development of biodegradable materials from natural polymers, particularly edible films. This work aimed at the development of pectin films added by cupuassu puree and chitosan nanoparticles and to evaluate the improvement of the physical–mechanical performance of the composite films. The nanostructures displayed an average size of 110 nm and a zeta potential of approximately +40 mV. The films were produced by casting, and they exhibited manageability, homogeneity, and continuity. Based upon the mechanical analysis of maximum stress and elongation, it was concluded that the nanoparticles functioned as fillers, increasing the toughness of the pectin films. Water vapor permeability assays demonstrated that the nanostructured films containing cupuassu exhibited improved barrier properties. The glass transition temperature of the films was not strongly affected by the addition of nanoparticles. Conversely, the initial degradation temperature decreased with the addition of nanoparticles and cupuassu puree. The outcomes of this research pave a new route for the development of nonconventional food packaging materials.
The impact of different voxels and exposure parameters of CBCT for the assessment of external root resorptions: A phantom study
Authors: Goller Bulut Duygu , Uğur Aydın Zeliha 
Published: July 2019

AbstractThis study aimed to compare the effectiveness of the different voxel sizes and imaging parameters of cone beam computed tomography (CBCT) on the determination of external root resorption (ERR). ERRs were created in coronal, middle and apical regions. Depths (0.62–0.73 mm) and diameters (0.68–0.81 mm) of ERRs were measured using a digital calliper. Images were obtained in 0.125, 0.2, 0.25, 0.3 and 0.4 mm3 voxel sizes and at different currents. Data were analysed using Friedman and Wilcoxon signed‐rank tests at a level of P < 0.05. There was a difference between the parameters in determining the size of the ERR in coronal and middle regions (P < 0.05), but there was no difference in the apical region (P > 0.05). The change in current and exposure time did not make a difference in determining the dimensions of the ERRs (P > 0.05). Some voxel dimensions were more reliable in determining the depth and diameter of ERR in the coronal and middle region.
Impact of reduced P‐glycoprotein function on digoxin concentrations in patients with dementia
Authors: Ali Izna , Guidone Daniel , Nicolazzo Joseph A. , Brouwer Kim L.R. 
Published: July 2019

AimsPatients with Alzheimer's disease (AD), the most common form of dementia, have reduced P‐glycoprotein (P‐gp) function at the blood–brain barrier. However, the effect of AD on P‐gp function in peripheral organs, and the impact on medication efficacy and toxicity is unknown. In this study, clinical chart review and physiologically based pharmacokinetic (PBPK) modelling were employed to determine whether disease‐associated changes in P‐gp could be assessed from clinically measured digoxin concentrations in patients without and with dementia.MethodsA retrospective chart review was conducted to compare digoxin dose and concentrations between cohorts. A PBPK model was developed to simulate changes in digoxin concentrations at single and multiple 62.5 and 125 μg/d doses due to reduced P‐gp function in peripheral organs.ResultsDigoxin concentrations were similar between the nondementia (n = 75) and dementia (n = 72) cohorts (mean ± standard deviation; 0.64 ± 0.31 and 0.60 ± 0.34 ng/mL, respectively; −0.06 to 0.15, 95% confidence interval of difference). PBPK simulations showed that reduced P‐gp function resulted in a significant increase in digoxin exposure (AUC), but not in Cmax. For example, when a 2‐fold reduction in P‐gp function was simulated in older people following multiple 125 μg/d digoxin doses, the AUC over the last dosing interval was increased compared to baseline (24.29 ± 3.94 vs 17.04 ± 3.46 ng/mL*h; 4.52 to 9.98); however, Cmax was similar (1.38 ± 0.20 vs 0.99 ± 0.18 ng/mL; −2.33 to 3.13).ConclusionClinically measured digoxin concentrations were not statistically different in patients with dementia. Based on PBPK simulations, digoxin AUC may need to be evaluated to adequately assess the impact of reduced P‐gp function in peripheral organs.
The impact of the guideline for pain management in Japanese neonatal intensive care units: A 5‐year follow‐up
Authors: Ozawa Mio 
Published: July 2019

AbstractBackgroundThis study presented the guidelines for the prevention and management of procedural pain management in Japan and investigated the impact of these guidelines on Japanese neonatal intensive care units (NICUs). The aim of this study was to investigate whether the published national guidelines influenced organizational factors that could lead to improved pain management and, if so, whether the number of units that perform pain assessments, the administration of local guidelines and collaboration among health care professionals had improved in the 5‐year period from 2012 to 2017.MethodAn anonymous questionnaire was sent to 106 Level 3 NICUs across Japan.ResultsThe response rate was 78% (81 units). In almost all cases, the implementation of organizational factors had increased. Forty‐seven units (47%) reported that health care professionals collaborated in pain management, compared with 11 units (17.7%) in 2012. In addition, compliance with the guidelines for pain assessment improved over the 5‐year period. Twenty‐four units (30%) reported that they used a structured scale for pain measurement, compared with nine units (15%) in 2012.ConclusionThe current study suggested that the national guidelines published in 2014 influenced the organizational factors that could lead to improved pain management in Japanese NICUs. The number of units that used a structured scale for pain measurement, the development of local guidelines, and collaboration among health care professionals increased over the 5‐year period from 2012 to 2017.
A network approach to prioritize conservation efforts for migratory birds
Authors: Xu Yanjie , Si Yali , Takekawa John , Liu Qiang , Prins Herbert H. T. , Yin Shenglai , Prosser Diann J. , Gong Peng , de Boer Willem F. 
Published: July 2019

AbstractHabitat loss can trigger migration network collapse by isolating migratory bird breeding grounds from nonbreeding grounds. Theoretically, habitat loss can have vastly different impacts depending on the site's importance within the migratory corridor. However, migration‐network connectivity and the impacts of site loss are not completely understood. We used GPS tracking data on 4 bird species in the Asian flyways to construct migration networks and proposed a framework for assessing network connectivity for migratory species. We used a node‐removal process to identify stopover sites with the highest impact on connectivity. In general, migration networks with fewer stopover sites were more vulnerable to habitat loss. Node removal in order from the highest to lowest degree of habitat loss yielded an increase of network resistance similar to random removal. In contrast, resistance increased more rapidly when removing nodes in order from the highest to lowest betweenness value (quantified by the number of shortest paths passing through the specific node). We quantified the risk of migration network collapse and identified crucial sites by first selecting sites with large contributions to network connectivity and then identifying which of those sites were likely to be removed from the network (i.e., sites with habitat loss). Among these crucial sites, 42% were not designated as protected areas. Setting priorities for site protection should account for a site's position in the migration network, rather than only site‐specific characteristics. Our framework for assessing migration‐network connectivity enables site prioritization for conservation of migratory species.