bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microfluidic study of effects of flow velocity and nutrient concentration on biofilm accumulation and adhesive strength in microchannels
Authors: Liu Na , Skauge Tormod , Landa-Marbán David , Hovland Beate , Thorbjørnsen Bente , Radu Florin Adrain , Vik Bartek Florczyk , Baumann Thomas , Bødtker Gunhild 
Published: July 2018

AbstractBiofilm accumulation in the porous media can cause plugging and change many physical properties of porous media. Up to now, applications of desired biofilm growth and its
subsequent bioplugging have been attempted for various practices. A deeper understanding of the relative influences of hydrodynamic conditions including flow velocity and nutrient concentration, on biofilm growth and detachment is necessary to plan and analyze bioplugging experiments and field trials. The experimental results by means of microscopic imaging over a T-shape microchannel show that flow velocity and nutrient concentrations can have significant impacts on biofilm accumulation and adhesive strength in both flowing and stagnant microchannels. Increase in fluid velocity could facilitate biofilm growth, but that above a velocity threshold, biofilm detachment and inhibition of biofilm formation due to high shear stress were observed. High nutrient concentration prompts the biofilm growth, but was accompanied by a relatively weak adhesive strength. This research provides an overview of biofilm development in a hydrodynamic environment for better predicting and modelling the bioplugging associated with porous system in petroleum industry, hydrogeology, and water purification.IMPORTANCEIn the recent decade, the use of bacteria has become more and more important in many applications. Bioplugging caused by bacteria growth in porous media has been explored as a viable technique for some applications, such as bioremediation, water purification and microbial enhanced oil recovery (MEOR). In order to control biofilms/biomasses selectively/directionally plugging in desirable places, the role of hydrodynamic conditions on biofilm growth and detachment is essential to investigate. Herein, a T-shape microchannel was prepared to study effects of flow velocity and nutrient concentration on biofilm accumulation and adhesive strength at pore scale. Our results suggest that flow velocity and nutrient concentration could control biofilm accumulation in microchannels. The finding helps explain and predict the engineering bioplugging in porous media, especially for the selective plugging strategy of a MEOR field trial.
Activation of 2,4-diaminoquinazoline in Mycobacterium tuberculosis by Rv3161c, a putative dioxygenase
Authors: Melief Eduard , Bonnett Shilah A. , Zuniga Edison S. , Parish Tanya 
Published: July 2018

AbstractThe diaminoquinazoline series has good potency against Mycobacterium tuberculosis. Resistant isolates have mutations in Rv3161c, a putative dioxygenase. We carried out metabolite analysis on wild-type and an Rv3161c mutant strain after exposure to a diaminoquinazoline. The parental compound was found in intracellular extracts from the mutant, but not the wild-type. A metabolite consistent with a mono-hydroxylated form was identified in the wild-type. These data support the hypothesis that Rv3161c metabolizes diaminoquinazolines in M. tuberculosis.
CexE Is A Virulence Factor ofCitrobacter rodentiumAnd Present In Enteric Pathogens Of Humans
Authors: Rivas Zachary , McCormack Ryan M. , Adkins Becky , Munson George P. 
Published: July 2018

AbstractCexE is a 12 kDa protein that was originally reported to be present in just three strains of enterotoxigenicEscherichia coli(ETEC); a frequent causes of diarrheal illnesses worldwide. However, an examination of recently sequenced genomes has revealed that CexE is actually present in a majority of ETEC strains. Homologs of CexE are also present in enteroaggregativeE. coli(EAEC) and other enteric pathogens includingYersinia enterocolitica, Providencia alcalifaciens, andCitrobacter rodentium. CexE and its homologs are expressed within virulence regulons of ETEC, EAEC, andC. rodentium. This, along with its distribution across several species of enteric pathogens, suggest that CexE confers a selective advantage to these pathogens. However, this hypothesis has yet to be testedin vivo. Here we demonstrate that CexE is conditionally secreted to the external leaf of the outer membrane of ETEC. Although CexE does not appear to play a role in adherencein vitro, it does facilitate colonization of murine intestinal tissues byC. rodentium in vivo. In adult mice wild-type bacteria reached significantly higher loads and were shed in higher numbers than acexE::kanmutant. A similar trend was observed in neonatal mice. In addition, all of the neonates infected with the wild-type strain succumbed to infection within 16 days of inoculation. In contrast, 45% of the neonates infected with thecexE::kanstrain survived for the 30 day duration of the experiment. These finding indicate that CexE is a conditionally secreted virulence factor that increases the colonization of hosts by enteric pathogens.
A genome-wide screen identifies genes in rhizosphere-associatedPseudomonasrequired to evade plant defenses
Authors: Liu Zhexian , Beskrovnaya Polina , Melnyk Ryan A. , Hossain Sarzana S. , Khorasani Sophie , O’Sullivan Lucy R. , Wiesmann Christina L. , Bush Jen , Richard Joël D. , Haney Cara H. 
Published: July 2018

AbstractPseudomonas fluorescensand related plant root- (“rhizosphere”) associated species contribute to plant health by modulating defenses and facilitating nutrient uptake. To identify bacterial fitness determinants in the rhizosphere of the model plantArabidopsis thaliana, we performed a Tn-Seq screen using the biocontrol and growth-promoting strainPseudomonassp. WCS365. The screen, which was performed in parallel on wild-type and an immunocompromisedArabidopsis, identified 231 genes that positively affect fitness in the rhizosphere of wild-type plants. A subset of these genes negatively affect fitness in the rhizosphere of immunocompromised plants. We postulated that these genes might be involved in avoiding plant defenses and verified 7Pseudomonassp. WCS365 candidate genes by generating clean deletions. We found that two of these deletion strains, ΔmorA(encodes a putative diguanylate cyclase/phosphodiesterase) and ΔspuC(encodes a putrescine aminotransferase) formed enhanced biofilms and inhibited plant growth. Inhibition of plant growth by ΔspuCand ΔmorAwas the result of pattern triggered immunity (PTI) as measured by induction of anArabidopsisPTI reporter andFLS2/BAK1-dependent inhibition of plant growth. We found that MorA acts as a phosphodiesterase to inhibit biofilm formation suggesting a possible role in biofilm dispersal. We found that both putrescine and its precursor arginine promote biofilm formation that is enhanced in the ΔspuCmutant, which cannot break down putrescine suggesting that putrescine might serve as a signaling molecule in the rhizosphere. Collectively, this work identified novel bacterial factors required to evade plant defenses in the rhizosphere.ImportanceWhile rhizosphere bacteria hold the potential to improve plant health and fitness, little is known about the bacterial genes required to evade host immunity. Using a model system consisting ofArabidopsisand a beneficialPseudomonassp. isolate, we identified bacterial genes required for both rhizosphere fitness and for evading host immune responses. This work advances our understanding of how evasion of host defenses contributes to survival in the rhizosphere.
Influence of food and Nosema ceranae infection on the gut microbiota of Apis cerana workers
Authors: Huang Shao K. , Ye Kun T. , Huang Wei F. , Ying Bi H. , Su Xin , Lin Li H. , Li Jiang H. , Chen Yan P. , Li Ji L. , Bao Xiu L. , Hu Jian Z. 
Published: July 2018

AbstractBackgroundGut microbiota plays an essential role in bee’s health. To elucidate the effect of food and Nosema ceranae infection on the gut microbiota of honeybee Apis cerana, we used 16S rRNA sequencing to survey the gut microbiota of honeybee workers fed with sugar water or beebread and inoculated with or without N. ceranae.ResultsThe gut microbiota of A. cerana is dominated by Serratia, Snodgrassella, and Lactobacillus genera. The overall gut microbiota diversity was significantly differential by food type. The N. ceranae infection significantly affects the gut microbiota only at bees fed with sugar water. Higher abundance of Lactobacillus, Gluconacetobacter and Snodgrassella and lower abundance of Serratia were found in bees fed with beebread than with sugar water. N. ceranae infection led to higher abundance of Snodgrassella and lower abundance of Serratia in sugar-fed bees. Imputed bacterial KEGG pathways showed the significant metagenomics functional differences by feeding and N. ceranae infections. Furthermore, A. cerana workers fed with sugar water showed lower N. ceranae spore loads but higher mortality than those fed with beebread. The cumulative mortality was strongly positive correlated (rho=0.61) with the changes of overall microbiota dissimilarities by N. ceranae infection.ConclusionsBoth food and N. ceranae infection significantly affect the gut microbiota in A. cerana workers. Beebread feeding not only provide better nutrition but also help establish a more stabled gut microbiota therefore protect bee in response to N. ceranae infection.Abstract ImportanceGut microbiota plays an essential role in bee’s health. Scientific evidence suggests the diet and infection can affect the gut microbiota and modulate the gut health, however the interplay between those two factors and bee gut microbiota is not well known. In this study, we used high-throughput sequencing method to monitor the changes of gut microbiota by both food intake and the Nosema ceranae infection. Our result showed that the gut microbiota composition and diversity of Asia Honeybee was significantly associated with both food intake and the N. ceranae infection. More interestingly, bees fed with beebread showed higher microbiota stability and less mortality than those fed with sugar water when infected by N. ceranae. Those data suggest the potential role of beebread, not only providing better nutrition but also helping establish a more stabled gut microbiota to protect bee against N. ceranae infection.
Experimental demonstration that screening can enable the environmental recruitment of a defensive microbiome
Authors: Innocent Tabitha , Holmes Neil , Bassam Mahmoud Al , Schiøtt Morten , Scheuring István , Wilkinson Barrie , Hutchings Matthew I , Boomsma Jacobus J , Yu Douglas W 
Published: July 2018

AbstractMany animals and plants recruit beneficial microbes from the environment, enhancing their defence against pathogens. However, we have only a limited understanding of the assembly mechanisms involved. A game-theoretical concept from economics, screening, potentially explains how a host selectively recruits mutualistic microbes from the environment by fomenting and biasing competition among potential symbionts in such a way that the more likely winners are antibiotic producers. The cuticular microbiomes of Acromyrmex leaf-cutting ants inspired one of the first applications of screening theory, and here we simulate this system in vitro to test screening. On agar infused with antibacterial metabolites from Acromyrmex’s vertically transmitted Pseudonocardia bacteria, we show that antibiotic-producing Streptomyces bacteria exhibit higher growth rates than do non-antibiotic-producer strains and are more likely to win in direct competition. Our results demonstrate how game-theoretical concepts can provide powerful insight into host-microbiome coevolution.
Outcome contingency selectively affects the neural coding of outcomes but not of tasks
Authors: Wisniewski David , Forstmann Birte , Brass Marcel 
Published: July 2018

AbstractValue-based decision-making is ubiquitous in every-day life, and critically depends on the contingency between choices and their outcomes. Only if outcomes are contingent on our choices can we make meaningful value-based decisions. Here, we investigate the effect of outcome contingency on the neural coding of rewards and tasks. Participants performed a reversal-learning task in which reward outcomes were contingent on trial-by-trial choices, and performed a ‘free choice’ task in which rewards were random and not contingent on choices. We hypothesized that contingent outcomes enhance the neural coding of rewards and tasks, which was tested using multivariate pattern analysis of fMRI data. Reward outcomes were encoded in a large network including the striatum, dmPFC and parietal cortex, and these representations were indeed amplified for contingent rewards. Tasks were encoded in the dmPFC at the time of decision-making, and in parietal cortex in a subsequence maintenance phase. We found no evidence for contingency-dependent modulations of task signals, demonstrating highly similar coding across contingency conditions. Our findings suggest selective effects of contingency on reward coding only, and further highlight the role of dmPFC and parietal cortex in value-based decision-making, as these were the only regions strongly involved in both reward and task coding.
Are we overestimating the utility of hair glucocorticoids? A systematic review exploring the empirical evidence supporting hair glucocorticoids as a measure of stress
Authors: Kalliokoski Otto , Jellestad Finn K. , Murison Robert 
Published: July 2018

AbstractQuantitating glucocorticoids (GCs) in hairs is a popular method for assessing chronic stress in studies of humans and animals alike. The cause-and-effect relationship between stress and elevated GC levels in hairs, sampled weeks later, is however hard to prove. This systematic review evaluated the evidence supporting hair glucocorticoids (hGCs) as a biomarker of stress.Only a relatively small number of controlled studies employing hGC analyses have been published, and the quality of the evidence is compromised by unchecked sources of bias. Subjects exposed to stress mostly demonstrate elevated levels of hGCs, and these concentrations correlate significantly with GC concentrations in serum, saliva and feces. This supports hGCs as a biomarker of stress, but the dataset provided no evidence that hGCs are a marker of historical stress. Only in cases where the stressor persisted at the time of hair sampling could a clear link between stress and hGCs be established.
Regional Collapsing of Rare Variation Implicates Specific Genic Regions in ALS
Authors: Gelfman Sahar , Dugger Sarah , Martins Moreno Cristiane de Araujo , Ren Zhong , Wolock Charles J. , Shneider Neil A. , Phatnani Hemali , Cirulli Elizabeth T. , Lasseigne Brittany N. , Harris Tim , Maniatis Tom , Rouleau Guy A. , Brown Robert H. , Gitler Aaron D. , Myers Richard M. , Petrovski Slavé , Allen Andrew , Harms Matthew B. , Goldstein David B. 
Published: July 2018

AbstractLarge-scale sequencing efforts in amyotrophic lateral sclerosis (ALS) have implicated novel genes using gene-based collapsing methods. However, pathogenic mutations may be concentrated in specific genic regions. To address this, we developed two collapsing strategies, one focuses rare variation collapsing on homology-based protein domains as the unit for collapsing and another gene-level approach that, unlike standard methods, leverages existing evidence of purifying selection against missense variation on said domains. The application of these two collapsing methods to 3,093 ALS cases and 8,186 controls of European ancestry, and also 3,239 cases and 11,808 controls of diversified populations, pinpoints risk regions of ALS genes including SOD1, NEK1, TARDBP and FUS. While not clearly implicating novel ALS genes, the new analyses not only pinpoint risk regions in known genes but also highlight candidate genes as well.
High-level expression of STING restricts susceptibility to HBV by mediating type III IFN induction
Authors: Dansako Hiromichi , Imai Hirotaka , Ueda Youki , Satoh Shinya , Shimotohno Kunitada , Kato Nobuyuki 
Published: July 2018

AbstractHepatitis B virus (HBV) is a hepatotropic DNA virus causing hepatic diseases such as chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. To study HBV, human hepatoma HepG2 cells are currently used as an HBV infectious cell culture model worldwide. HepG2 cells exhibit susceptibility to HBV by exogenously expressing sodium taurocholate cotransporting polypeptide (NTCP). We herein demonstrated that human immortalized hepatocyte NKNT-3 cells exhibited susceptibility to HBV by exogenously expressing NTCP (NKNT-3/NTCP cells). By comparing the cGAS-STING signaling pathway in several NKNT-3/NTCP cell-derived cell clones, we found that STING was highly expressed in cell clones exhibiting resistance but not susceptibility to HBV. High-level expression of STING was implicated in HBV-triggered induction of type III IFN and a pro-inflammatory cytokine, IL-6. In contrast, RNAi-mediated knockdown of STING inhibited type III IFN induction and restored the levels of HBV total transcript in an HBV-infected cell clone exhibiting resistance to HBV. These results suggest that STING regulates susceptibility to HBV by its expression levels.STING may thus be a novel target for anti-HBV strategies.
Cycling with blood flow restriction improves performance and muscle K+ handling and blunts the effect of antioxidant infusion in humans
Authors: Christiansen Danny , Eibye Kasper H. , Rasmussen Villads , Voldbye Hans M. , Thomassen Martin , Nyberg Michael , Gunnarsson Thomas G.P. , Skovgaard Casper , Lindskrog Mads S. , Bishop David J. , Hostrup Morten , Bangsbo Jens 
Published: July 2018

AbstractWe examined if blood flow restriction (BFR) would augment training-induced improvements in muscle K+ handling and performance during intense exercise in men, and if these adaptations would be associated with an effect of muscle antioxidant function on thigh K+ release and with fibre type-dependent modulation of Na+,K+-ATPase-isoform abundance and FXYD1 phosphorylation. Ten recreationally-active men (25 ± 4 y, 49.7 ± 5.3 mL∙kg-1∙min-1) performed 6 weeks of interval cycling, where one leg trained without (control; CON-leg) and the other leg with BFR (BFR-leg, pressure: 178 mmHg). Before and after training, catheters were inserted into the femoral artery and vein, and blood flow was assessed during single-leg knee-extensions at 25% (Ex1) and 90% of leg peak aerobic power (Ex2) with intravenous infusion of N-acetylcysteine (NAC) or saline (placebo), and a resting muscle biopsy was collected. After training, performance during exhaustive exercise increased to a greater extent in BFR-leg (23%) than in CON-leg (12%, p<0.05), whereas thigh K+ release during Ex2 was attenuated in BFR-leg only (p<0.05). Before training, NAC depressed K+ release during Ex1 (p<0.05), but not during Ex2 (p>0.05). After training, this effect was blunted in BFR-leg (p<0.05), whilst the abundance of Na+,K+-ATPase-isoform α1 in type-II (51%), β1 in type-I (33%), and FXYD1 in type-I (108%) and type-II (60%) fibres was higher in BFR-leg (p<0.05; vs. CON-leg). Thus, interval training with BFR elicits greater improvements in performance and reduces muscle net K+ release during intense exercise, which may be caused by elevated ROS scavenging and fibre type-dependent increases in Na+,K+-ATPase-isoform abundance.Key pointsHere, we provide evidence that reactive oxygen species (ROS) play a role in regulating K+ homeostasis in the untrained musculature of humans, as indicated by attenuated thigh K+ efflux during exercise with concomitant antioxidant infusion.We also demonstrate that interval training with blood flow restriction (BFR) augments improvements in performance and reduces K+ release from contracting muscles during intense exerciseThe effect of training with BFR on muscle K+ handling appears to be partly mediated by increasing the protection against ROS, since the effect of antioxidant infusion was blunted after training with restricted blood flow.Further, training with BFR resulted in higher abundance of Na+,K+-ATPase-isoform α1 in type-II (51%), β1 in type-I (33%), and FXYD1 in type-I (108%) and type-II (60%) muscle fibres. This suggests fibre type-specific adaptations in Na+,K+-ATPase-isoform content are also important for improvements in muscle K+ handling by training with BFR in humans.
The Nonstructural Proteins 3 and 5 from Flavivirus Modulate Nuclear-Cytoplasmic Transport and Innate Immune Response Targeting Nuclear Proteins
Authors: Cervantes-Salazar Margot , Gutiérrez-Escolano Ana L. , Reyes-Ruiz José M. , del Angel Rosa M. 
Published: July 2018

ABSTRACTViruses hijack cellular proteins and components to be replicated in the host cell and to evade the immune response. Although flaviviruses have a cytoplasmic replicative cycle, some viral proteins such as the capsid (C) and the RNA dependent RNA polymerase, NS5, can reach the nucleus of the infected cells. Considering the important roles of NS5 in viral replication and in the control of the immune response, and its striking presence in the nucleus, the possible functions of this protein in some mechanisms orchestrated by the nucleus was analyzed. We isolated and identified nuclear proteins that interact with NS5; one of them, the DEAD-box RNA helicase DDX5 is relocated to the cytoplasm and degraded during infection with DENV, which correlates with its function in IFN dependent response. Since DDX5 and many other proteins are relocated from the nucleus to the cytoplasm during flavivirus infection, the integrity and function of the main regulator of the nuclear-cytoplasmic transport, the nuclear pore complex (NPC) was evaluated. We found that during DENV and ZIKV infection nucleoporins (NUPs) such as TPR, Nup153, Nup98, and Nup62 were cleavaged/degraded. The protease NS2B-NS3 induces NUPs degradation and it causes a dramatic inhibition of mature mRNAs export to the cytoplasm but not the export of DDX5 protein, which is dependent on NS5. Here we describe for the first time that the NS3 and NS5 proteins from flavivirus play novel functions hijacking the NPC and some nuclear proteins relevant in triggering immune response pathways, inducing a favorable environment for viral replication.IMPORTANCEViruses, as intracellular obligate parasites, hijack cellular components to enter and replicate in infected cells. Remarkably, in many cases, viruses hijack molecules with crucial functions for the cells. Here it is described how RNA viruses such as DENV and ZIKV, with a cytoplasmic replicative cycle, use NS3 and NS5, two of their unique non-structural proteins with enzymatic activity, to modulate nuclear-cytoplasmic transport. We found that NS3 disrupts the nuclear pore complex, the main regulator in nuclear-cytoplasmic transport, causing a strong reduction in the amount of mature mRNAs in the cytoplasm and an inhibition in innate immune response. Additionally, NS5 induces the relocation of nuclear proteins to the cytoplasm such as DDX5, involved in immune response, which is later degraded by NS3. These findings allow the understanding of crucial mechanisms that viruses use to deal with the control of the immune response to grant the production of new viral particles.