bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transient intracellular acidification regulates the core transcriptional heat shock response
Authors: Triandafillou Catherine G. , Katanski Christopher D. , Dinner Aaron R. , Drummond D. Allan 
Published: September 2018

AbstractHeat shock induces a conserved transcriptional program regulated by heat shock factor 1 (Hsf1) in eukaryotic cells. Activation of this heat-shock response is triggered by heat-induced misfolding of newly synthesized polypeptides, and so has been thought to depend on ongoing protein synthesis. Here, using the the budding yeastSaccharomyces cerevisiae, we report the discovery that Hsf1 can be robustly activated when protein synthesis is inhibited, so long as cells undergo cytosolic acidification. Heat shock has long been known to cause transient intracellular acidification which, for reasons which have remained unclear, is associated with increased stress resistance in eukaryotes. We demonstrate that acidification is required for heat shock response induction in translationally inhibited cells, and specifically affects Hsf1 activation. Physiological heat-triggered acidification also increases population fitness and promotes cell cycle reentry following heat shock. Our results uncover a previously unknown adaptive dimension of the well-studied eukaryotic heat shock response.
Multiple QTL underlie milk phenotypes at the CSF2RB locus
Authors: Lopdell Thomas J , Tiplady Kathryn , Couldrey Christine , Johnson Thomas JJ , Keehan Michael , Davis Stephen R , Harris Bevin L , Spelman Richard J , Snell Russell G , Littlejohn Mathew D 
Published: September 2018

AbstractBackgroundBovine milk provides an important source of nutrition in much of the Western world, forming components of many food products. Over many years, artificial selection has substantially improved milk production by cows. However, the genes underlying milk production quantitative trait loci (QTL) remain relatively poorly characterised. Here, we investigate a previously-reported QTL located at theCSF2RBlocus, for several milk production phenotypes, to better understand its underlying genetic and molecular causes.ResultsUsing a population of 29,350 taurine dairy cattle, we conducted association analyses for milk yield and composition traits, and identified highly significant QTL for milk yield, milk fat concentration, and milk protein concentration. Strikingly, protein concentration and milk yield appear to show co-located yet genetically distinct QTL. To attempt to understand the molecular mechanisms that might be mediating these effects, gene expression data were used to investigate eQTL for eleven genes in the broader interval. This analysis highlighted genetic impacts onCSF2RBandNCF4expression that share similar association signatures to those observed for lactation QTL, strongly implicating one or both of these genes as the cause of these effects. Using the same gene expression dataset representing 357 lactating cows, we also identified 38 novel RNA editing sites in the 3′UTR ofCSF2RBtranscripts. The extent to which two of these sites were edited also appears to be genetically co-regulated with lactation QTL, highlighting a further layer of regulatory complexity implicating theCSF2RBgene.ConclusionsThis chromosome 5 locus presents a diversity of molecular and lactation QTL, likely representing multiple overlapping effects that, at a minimum, highlight theCSF2RBgene as having a causal role in these processes.
Rates of increase of antibiotic resistance and ambient temperature in Europe: a cross-national analysis of 28 countries between 2000-2016
Authors: McGough Sarah F. , MacFadden Derek R. , Hattab Mohammad W. , Mølbak Kåre , Santillana Mauricio 
Published: September 2018

AbstractBackgroundWidely recognized as a major public health threat globally, the rapid increase of antibiotic resistance in bacteria could soon render our most effective method to combat infections obsolete. Factors influencing the burden of resistance in human populations remain poorly described, though temperature is known to play an important role in mechanisms at the bacterial level.MethodsWe performed an ecologic analysis of country level antibiotic resistance prevalence in 3 common bacterial pathogens across 28 countries in Europe, and used multivariable models to evaluate associations with minimum temperature and other predictors over a 17-year period (2000-2016). We quantified the effects of minimum temperature, population density, and antibiotic consumption on the rate of change of antibiotic resistance across geographies.FindingsFor three common bacterial pathogens and four classes of antibiotics, we found evidence of a long-term effect of ambient minimum temperature on rates of increase of antibiotic resistance across 28 countries in Europe between 2000-2016. Specifically, we show that across all antibiotic classes for the pathogensE. coliandK. pneumoniae, European countries with 10°C warmer ambient temperatures have experienced more rapid increases in antibiotic resistance over the 17-year period, ranging between 0.33%/year (95% CI 0.2, 0.5) and 1.2%/year (0.4, 1.9), even after accounting for recognized drivers of resistance including antibiotic consumption and population density. We found a decreasing relationship forS. aureusand methicillin of −0.4%/year (95% CI −0.7, 0.0), reflecting widespread declines in MRSA across Europe over the study period.InterpretationAmbient temperature may be an important modulator of the rate of change of antibiotic resistance. Our findings suggest that rising temperatures globally may hasten the spread of resistance and complicate efforts to mitigate it.FundingCanadian Institutes of Health Research Fellowship (D.R.M.).
Metagenomics Analyses of Cellulose and Volatile Fatty Acids Metabolism by Microorganisms in the Cow Rumen
Authors: Wang Lijun , Jiang Xin , Xu Hongjian , Zhang Yonggen 
Published: September 2018

ABSTRACTThe purpose of this study was to evaluate the effects of different forage-to-concentrate (F:C) ratios (7:3 high-forage, 3:7 high-concentrate) on rumen microflora and fiber degradation mechanism. Compared with the high-concentrate (HC) group, the high-forage(HF) group showed improved fiber degradation and a sustained high level of carboxymethyl cellulose (CMCase), β-glucosidase and β-xylosidase activities, but the total VFAs decreased. Among bacteria at the family level,LachnospiraceaeandSuccinivibrionaceaein HF groups were 2-fold and 4-fold more abundant than in the HC group, respectively. A KEGG analysis revealed that succinate-CoA synthetase (EC: 6.2.1.5) and propionate-CoA transferase (EC: 2.8.3.1) leading directly to propionate production were more abundant in HC group. Conversely, butyryl-CoA dehydrogenase (EC: 1.3.8.1) was directly related to butyrate production and was higher in the HF group. A gene expression analysis showed that the relative content ofFibrobacter succinogenesandButyrivibrio fibrisolvenswas higher in the HF group and contributed more to fiber degradation and VFA production.Prevotella ruminicola, Selenomonas ruminantium, andVeillonella alkalescenscontributed more to starch degradation and propionate production, which relative content was higher in the HC group. This research gave a further explanation of the fiber degradation parameters and microbiota under different F:C ration. The fiber-degrading bacteria in the roughage group have a high content level, and the corresponding cellulase activity is also high. These results supported the potential of diets for microbial manipulation, which can increase feed digestibility and explored new fibrinolytic bacteria.IMPORTANCEThe forage of the cow’s feed occupies a large proportion. The shortage of high-quality forage in cow breeding has become an important factor limiting the China’s dairy industry. The effective measure is to improve the utilization of low-quality forage. Based on traditional nutrient metabolism, the reasons for the effects of roughage on the growth and metabolism of dairy cows can be explored, but the metabolic mechanism is not well analyzed, and the further utilization of forage is also limited. Metagenomics has proven to be a powerful tool for studying rumen microbial structures and gene function. This experiment used metagenomics to study the metabolism of cellulose and volatile acids in the rumen. Our research showed that different forage-to-concentrate shifted the composition of microorganisms and the activity of enzymes, resulting in different metabolic pathways of volatile fatty acids. This work provides a background for microbial community composition and further use of forage.
Sex differences in the behavioral and synaptic consequences of a single exposure to cannabinoid at puberty and adulthood
Authors: Borsoi Milene , Manduca Antonia , Bara Anissa , Lassalle Olivier , Pelissier-Alicot Anne-Laure , Manzoni Olivier J. 
Published: September 2018

AbstractHeavy cannabis consumption among adolescents is associated with significant and lasting neurobiological, psychological and health consequences that depend on the age of first use. Chronic exposure to cannabinoid (CB) agonists during adolescence alters social behavior and prefrontal cortex (PFC) activity in adult rats. However, sex differences on social behavior as well as PFC synaptic plasticity after acute CB activation remain poorly explored. Here, we determined the consequences of a single CB activation differently affects PFC in males and females by assessing social behavior and PFC neuronal and synaptic functions in rats during pubertal or adulthood periods, 24h after a single in-vivo cannabinoid exposure (SCE). During puberty, SCE reduced play behavior in females but not males. In contrast, SCE impaired sociability in both sexes at adulthood. General exploration and memory recognition remained normal at both ages and both sexes. At the synaptic level, SCE ablated endocannabinoid-mediated long-term depression (eCB-LTD) in the PFC of females of both ages and heightened excitability of PFC pyramidal neurons at adulthood, while males were spared. In contrast, SCE was associated to impaired long-term potentiation in adult males. Together, the data indicate behavioral and synaptic sex differences in response to a single in-vivo exposure to cannabinoid at puberty and adulthood.
Superfolder mTurquoise2oxoptimized for the bacterial periplasm allows high efficiencyin vivoFRET of cell division antibiotic targets
Authors: Meiresonne Nils Y. , Consoli Elisa , Mertens Laureen M. Y. , Chertkova Anna , Goedhart Joachim , Blaauwen Tanneke den 
Published: September 2018

AbstractFluorescent proteins (FP)s are of vital importance to biomedical research. Many of the currently available fluorescent proteins do not fluoresce when expressed in non-native environments, such as the bacterial periplasm. This strongly limits the options for applications that employ multiple FPs, such as multiplex imaging or FRET. To address this issue, we have engineered a new cyan fluorescent protein based on mTurquoise2 (mTq2). The new variant is dubbed superfolder turquoise 2 ox (sfTq2ox) and is able to withstand challenging, oxidizing environments. sfTq2oxhas improved folding capabilities and can be expressed in the periplasm at higher concentrations without toxicity. This was tied to the replacement of native cysteines that may otherwise form promiscuous disulfide-bonds. The improved sfTq2oxhas the same spectroscopic properties as mTq2, i.e. high fluorescence lifetime and quantum yield. The sfTq2ox-mNeongreen FRET pair allows the detection of periplasmic protein-protein interactions with energy transfer rates exceeding 40 %. Employing the new FRET pair, we show the direct interaction of two essential periplasmic cell division proteins FtsL and FtsB and disrupt it by mutations, paving the way forin vivoantibiotic screening.
Competing evolutionary paths in growing populations with applications to multidrug resistance
Authors: Nicholson Michael D. , Antal Tibor 
Published: September 2018

AbstractInvestigating the emergence of a particular cell type is a recurring theme in models of growing cellular populations. The evolution of resistance to therapy is a classic example. Common questions are: when does the cell type first occur, and via which sequence of steps is it most likely to emerge? For growing populations, these questions can be formulated in a general framework of branching processes spreading through a graph from a root to a target vertex. Cells have a particular fitness value on each vertex and can transition along edges at specific rates. Vertices represents cell states, say genotypes or physical locations, while possible transitions are acquiring a mutation or cell migration. We focus on the setting where cells at the root vertex have the highest fitness and transition rates are small. Simple formulas are derived for the time to reach the target vertex and for the probability that it is reached along a given path in the graph. We demonstrate our results on several scenarios relevant to the emergence of drug resistance, including: the orderings of resistance-conferring mutations in bacteria and the impact of imperfect drug penetration in cancer.
Systematic analysis of theMyxococcus xanthusdevelopmental gene regulatory network supports posttranslational regulation of FruA by C-signaling
Authors: Saha Shreya , Patra Pintu , Igoshin Oleg , Kroos Lee 
Published: September 2018

SummaryUpon starvationMyxococcus xanthusundergoes multicellular development. Rod-shaped cells move into mounds in which some cells differentiate into spores. Cells begin committing to sporulation at 24-30 h poststarvation, but the mechanisms governing commitment are unknown. FruA and MrpC are transcription factors that are necessary for commitment. They bind cooperatively to promoter regions and activate developmental gene transcription, including that of thedevoperon. Leading up to and during the commitment period,devmRNA increased in wild type, but not in a mutant defective in C-signaling, a short-range signaling interaction between cells that is also necessary for commitment. The C-signaling mutant exhibited ∼20-fold lessdevmRNA than wild type at 30 h poststarvation, despite a similar level of MrpC and only twofold less FruA. Boosting the FruA level twofold in the C-signaling mutant had little effect on thedevmRNA level, anddevmRNA was not less stable in the C-signaling mutant. Neither did high cooperativity of MrpC and FruA binding upstream of thedevpromoter explain the data. Rather, our systematic experimental and computational analyses support a model in which C-signaling activates FruA at least ninefold posttranslationally in order to commit a cell to spore formation.
Esterase Activity is Affected by Genetics, Age, Insecticide Exposure, and Viral Infection in the Honey Bee, Apis mellifera
Authors: Rinkevich Frank D. , Margotta Joseph W. , Simone-Finstrom Michael , de Guzman Lilia I. , Healy Kristen B. 
Published: September 2018

AbstractNon-target impacts of insecticide treatments are a major public and environmental concern, particularly in contemporary beekeeping. Therefore, it is important to understand the physiological mechanisms contributing to insecticide sensitivity in honey bees. In the present studies, we sought to evaluate the role of esterases as the source of variation in insecticide sensitivity. To address this question, the following objectives were completed: 1) Evaluated esterase activity among honey bee stocks, 2) Assessed the correlation of esterase activity with changes in insecticide sensitivity with honey bee age, 3) Established if esterases can be used as a biomarker of insecticide exposure, and 4) Examined the effects of Varroa mite infestation and viral infection on esterase activity.Results indicated that honey bees have a dynamic esterase capacity that is influenced by genetic stock and age. However, there was no consistent connection of esterase activity with insecticide sensitivity across genetic stocks or with age, suggests other factors are more critical for determining insecticide sensitivity. The trend of increased esterase activity with age in honey bees suggests this physiological transition is consistent with enhanced metabolic rate with age. The esterase inhibition with naled but not phenothrin or clothianidin indicates that reduced esterase activity levels may only be reliable for sublethal doses of organophosphate insecticides. The observation that viral infection, but not Varroa mite infestation, reduced esterase activity shows viruses have extensive physiological impacts. Taken together, these data suggest that honey bee esterase activity toward these model substrates may not correlate well with insecticide sensitivity. Future studies include identification of esterase substrates and inhibitors that are better surrogates of insecticide detoxification in honey bees as well as investigation on the usefulness of esterase activity as a biomarker of pesticide exposure, and viral infection.
Evaluating the effects of data visualisation techniques on interpretation and preference of feedback reports
Authors: Koh Harvey , Earnest Arul , Davis Ian D. , Loh Erwin , Evans Sue M 
Published: September 2018

AbstractObjectiveTo evaluate the different methods of data visualisation and how it affects preference and data interpretation.DesignA cross-sectional survey, assessing interpretation and preference for four methods of data presentation, was distributed to participants.SettingMelbourne, VictoriaParticipantsMembers of Prostate Cancer Outcome Registry-Victoria (PCOR-Vic) and senior hospital staff in three metropolitan Victorian hospitals.InterventionsDifferent methods of data visualisation. Mainly, funnel plots, league charts, risk adjusted sequential probability ratio test (RASPRT) charts and dashboard.Main Outcome MeasureInterpretation scores assessed capacity by participants to identify outliers and poor performers. Preference was based on a 9-point Likert-scale (0 – 9).ResultsIn total, 113 participants responded to the online survey (16/58 urologists and 97/297 senior hospital staff, response rate 32%). Respondents reported that funnel plots were easier to interpret compared to league charts (mean interpretability score difference of 28% (95% CI: 19.2% - 37.0%, P<0.0001). Predictors of worse interpretability of charts in the adjusted model were being a hospital executive compared to a urologist (coefficient= −2.50, 95% CI = −3.82, - 1.18, P<0.01) and having no statistical training compared to those with statistical training (coefficient = −1.71, 95% CI=-2.85, −0.58, P=0.003). Participants preferred funnel plots and dashboards compared to league charts and RASPRT charts (median score 7/9 vs 5/9), and preferred charts which were traffic-light coloured versus greyscale charts (43/60 (71.6%) vs 17/60 (28.3%)).ConclusionWhen developing reports for clinicians and hospitals, consideration should be given to preference of end-users and ability of groups to interpret the graphs.
Identification and capsular serotype sequetyping ofStreptococcus pneumoniaestrains
Authors: Gonzales-Siles Lucia , Salvà-Serra Francisco , Degerman Anna , Nordén Rickard , Lindh Magnus , Skovbjerg Susann , Moore Edward R. B. 
Published: September 2018

ABSTRACTCorrect identification ofStreptococcus pneumoniae(pneumococcus) and differentiation from the closely related species of the Mitis group of the genusStreptococcus, as well as serotype identification, is important for monitoring disease epidemiology and assessing the impacts of pneumococcal vaccines. In this study, we assessed the taxonomic identifications of 422 publicly available genome sequences ofS. pneumoniae, S. pseudopneumoniaeandS. mitis, using different methods. Identification ofS. pneumoniae, by comparative analysis of thegroELpartial sequence, was possible and accurate, whereasS. pseudopneumoniaeandS. mitiscould be misclassified asS. pneumoniae, suggesting thatgroELis unreliable as a biomarker for differentiatingS. pneumoniaefrom its closest related species. The genome sequences ofS. pneumoniaeandS. pseudopneumoniaefulfilled the suggested thresholds of average nucleotide identity (ANI), i.e., > 95% genome sequence similarity to the sequence of respective type strains for identification of species, whereas none of theS. mitisgenome sequences fulfilled this criterion. However, ANI analyses of all sequencesversusall sequences allowed discrimination of the different species by clustering, with respect to species type strains. Thein silicoDNA-DNA distance method was also inconclusive for identification ofS. mitisgenome sequences, whereas presence of the “Xisco” gene proved to be a reliable biomarker forS. pneumoniaeidentification. Furthermore, we present an improved sequetyping protocol including two newly-designed internal sequencing primers with two PCRs, as well as an improved workflow for differentiation of serogroup 6 types. The proposed sequetyping protocol generates a more specific product by generating the whole gene PCR-product for sequencing, which increases the resolution for identification of serotypes. Validations of both protocols were performed with publicly availableS. pneumoniaegenome sequences, reference strains at the Culture Collection University of Gothenburg (CCUG), as well as with clinical isolates. The results were compared with serotype identifications, using real-time Q-PCR analysis, as well as the Quellung reaction or antiserum panel gel-precipitation. Our protocols provide a reliable diagnostic tool for taxonomic identification as well as serotype identification ofS. pneumoniae.
Growth of Sphagnum riparium is strongly rhythmic: Contribution of the seasonal, circalunar and third rhythmic components
Authors: Mironov Victor L. , Kondratev Aleksei Y. , Shkurko Anna V. 
Published: September 2018

AbstractContinuous high-resolution monitoring of Sphagnum growth can provide insights into the biological rhythms of moss growth. Moss Sphagnum riparium is a convenient model for growth monitoring. Application of the method of geotropic curvatures has enabled a three-year monitoring with two to five-day intervals. We measured the increment in ca. 85000 shoots and produced ca. 3500 growth rate estimates, making this study a champion in precision compared to previous efforts. The zeitgeber for seasonal growth rhythms is the temperature seasonal cycle (R2=0.21–0.52). When the temperature changes by 10°C, moss growth rate is modified by 0.10–0.17cm/day according to the linear model, and 1.47–2.06-fold in the exponential model. The zeitgeber for circalunar rhythms is the lunar synodic cycle (R2=0.14–0.26). The average amplitude of the fluctuations it induces in the growth rate is 0.0425– 0.0572cm/day, which is equivalent to the effect of a 3.43–4.53°C change in temperature. The third rhythm can be distinguished in periodograms. Its period ranges from 10 to 16 days, but we did not detect the zeitgeber.In total, three rhythms explain 51–78% of the growth rate. We believe that the strong rhythmicity in Sphagnum growth is associated with shoot growth synchronization.