bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualizing Wnt secretion from Endoplasmic Reticulum to Filopodia
Authors: Moti Naushad , Yu Jia , Boncompain Gaelle , Perez Franck , Virshup David M 
Published: April 2018

AbstractWnts are a family of secreted palmitoleated glycoproteins that play a key role in cell to cell communications during development and regulate stem cell compartments in adults. Wnt receptors, downstream signaling cascades and target pathways have been extensively studied while less is known about how Wnts are secreted and move from producing cells to receiving cells. We used the synchronization system called Retention Using Selective Hook (RUSH) to study Wnt trafficking from endoplasmic reticulum to Golgi and then to plasma membrane and filopodia in real time. Consistent with prior studies, inhibition of porcupine (PORCN) or knockout of Wntless (WLS) blocked Wnt exit from the ER. Indeed, WLS was rate-limiting for Wnt ER exit. Wnt-containing vesicles paused at sub-cortical regions of the plasma membrane before exiting the cell. Wnt-containing vesicles were transported to adjacent cells associated with filopodia. Increasing the number of filopodia by expression of LGR5 in the producing cell increased the ability of a cell to send a Wnt signal. The RUSH system is a powerful tool to provide new insights into the Wnt secretory pathway.
Parental neural responsivity to infants’ visual attention: how mature brains scaffold immature brains during social interaction
Authors: S.V. Wass , V. Noreika , S. Georgieva , K. Clackson , L. Brightman , R. Nutbrown , L. Santamaria , V. Leong 
Published: April 2018

AbstractAlmost all attention and learning - in particular, most early learning – takes place in social settings. But little is known of how our brains support dynamic social interactions. We recorded dual-EEG from infants and parents during solo play and joint play. During solo play, fluctuations in infants’ Theta power significantly forward-predicted their subsequent attentional behaviours. But this forwards-predictiveness was lower during joint play than solo play, suggesting that infants’ endogenous neural control over attention is greater during solo play. Overall, however, infants were more attentive to the objects during joint play. To understand why, we examined how adult brain activity related to infant attention. We found that parents’ Theta power closely tracked and responded to changes in their infants’ attention. Further, instances in which parents showed greater neural responsivity were associated with longer sustained attention by infants. Our results offer new insights into how one partner influences another during social interaction.
The diversity of antibiotic resistance and virulence genes are correlated in human gut and environmental microbiomes
Authors: Escudeiro Pedro , Pothier Joël , Dionisio Francisco , Nogueira Teresa 
Published: April 2018

AbstractHuman beings have used large amounts of antibiotics, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of non-pathogenic bacterial species are affected as well. Therefore, both pathogenic and non-pathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still co-occurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes issuing from different individuals and from distinct human populations across the world. We found a great diversity of antibiotic resistance determinants (ARd) and virulence factors (VFd) in metagenomes. Importantly there is a correlation between ARd and VFd, even after correcting for protein family richness. In the human gut there are less ARd and VFd than in more diversified environments, and yet correlations between the ARd and VFd are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to non-existent in the uncontacted Amerindians. We conclude that there is co-occurrence of resistance and virulence determinants, suggesting a possible co-selective mechanism. For example, by selecting for resistant bacteria, we may be selecting for more virulent strains as a side effect of antimicrobial therapy.
RAB-35 aids apoptotic cell clearance by regulating cell corpse recognition and phagosome maturation
Authors: Haley Ryan C. , Wang Ying , Zhou Zheng 
Published: April 2018

AbstractIn metazoans, apoptotic cells are swiftly engulfed by phagocytes and degraded inside phagosomes. Multiple small GTPases in the Rab family are known to function in phagosome maturation by regulating vesicle trafficking. We discoveredrab-35as a new gene important for apoptotic cell clearance using an RNAi screen targeting putative Rab GTPases inCaenorhabditis elegans. We further identified TBC-10 as a putative GTPase-activating protein (GAP), and FLCN-1 and RME-4 as two putative Guanine Nucleotide Exchange Factors (GEFs), for RAB-35. RAB-35 function was found to be required for the incorporation of early endosomes to phagosomes and for the timely degradation of apoptotic cell corpses. More specifically, RAB-35 facilitates the switch of phagosomal membrane phosphatidylinositol species from PtdIns(4,5)P2to PtdIns(3)P and promotes the recruitment of the small GTPase RAB-5 to phagosomal surfaces, processes that are essential for phagosome maturation. Interestingly, we observed that CED-1 performs these same functions, and to a much larger extent than RAB-35. Remarkably, in addition to cell corpse degradation, RAB-35 also facilitates the recognition of cell corpses independently of the CED-1 and CED-5 pathways. RAB-35 localizes to extending pseudopods and is further enriched on nascent phagosomes, consistent with its dual roles in regulating cell corpse-recognition and phagosome maturation. Epistasis analyses indicate thatrab-35represents a novel third genetic pathway that acts in parallel to both of the canonicalced-1/6/7andced-2/5/10/12engulfment pathways. We propose that RAB-35 acts as a robustness factor, leading a pathway that aids the canonical pathways for the engulfment and degradation of apoptotic cells.
Evaluation and optimization of the protocols for measuring cytochrome P450 activity in aphids
Authors: Cao He-He , Liu Tong-Xian 
Published: April 2018

AbstractCytochrome P450 enzymes play major roles in insect detoxification of plant toxins and insecticides. However, measuring P450 activity in aphids has variable success, and a reliable method is not available yet. In this study, we evaluated and optimized the method for measuring P450 activity in aphids using the 7-ethoxycoumarin as the substrate. First, we found that nicotinamide adenine dinucleotide phosphate and protective agents are not needed in the aphid P450 activity assay, and homogenizing the green peach aphid,Myzus persicae, in the microplate resulted in significantly higher P450 activities than those in Eppendorf tube. Homogenizing aphids in Eppendorf tube could grind tissues thoroughly and released uncharacterized compounds that could inhibit aphid and pig liver P450 activities, whereas aphids in the microplate likely could not be thoroughly ground and thus released fewer such inhibitors. Then, the microplate homogenization method was optimized to follows: one or two aphids were put into one well of the microplate and ground in phosphate buffer using pipette tips for 20 cycles, followed by addition of 7-ethoxycoumarin, and then incubated for 1 h at room temperature, after which glycine buffer-ethanol mixture was added to stop the reaction. This method is also suitable for the pea aphid,Acyrthosiphon pisum, and the bird cherry □oat aphid,Rhopalosiphum padi.These results emphasize the importance of considering inhibitory effect of endogenous compounds in insects on their P450 activity and provide one possible method to reduce this inhibitory effect.
Comment on ‘Multiple Origin but Single Domestication Led to Oryza sativa’
Authors: Civáň Peter , Brown Terence A. 
Published: April 2018

AbstractIn 2015, we published an analysis of rice genomic data and showed that the japonica, indica and aus groups of cultivated rice were independently domesticated. Our conclusions were controversial as they contradicted a previous, high-profile analysis of the same dataset, which had suggested that all of cultivated rice derives from a single origin. Although there have been attempts since 2015 to bolster the single-origin hypothesis, until recently there has been no direct rebuttal of the methodology that we used to infer multiple origins. Such a rebuttal has now been published (Choi J.Y., Purugganan M.D., 2018 Multiple origin but single domestication led to Oryza sativa. G3 8:797-803), but the reanalysis that is presented only supports the single origin hypothesis if phylogenetic trees that are clearly paraphyletic are interpreted as monophyletic, and furthermore addresses only one component of the evidence that we presented for multiple domestications. We caution against accepting these analyses uncritically.
Identification of protein abundance changes in biopsy-level hepatocellular carcinoma tissues using PCT-SWATH
Authors: Zhu Yi , Zhu Jiang , Lu Cong , Sun Ping , Xie Wei , Zhang Qiushi , Yue Liang , Zhu Tiansheng , Ruan Guan , Aebersold Ruedi , Huang Shi’ang , Guo Tiannan 
Published: April 2018

AbstractIn this study, we optimized the pressure-cycling technology (PCT) and SWATH mass spectrometry workflow to analyze biopsy-level tissue samples (2 mg wet weight) from 19 hepatocellular carcinoma (HCC) patients. Using OpenSWATH and pan-human spectral library, we quantified 11,787 proteotypic peptides from 2,579 SwissProt proteins in 76 HCC tissue samples within about 9 working days (from receiving tissue to SWATH data). The coefficient of variation (CV) of peptide yield using PCT was 32.9%, and the R2 of peptide quantification was 0.9729. We identified protein changes in malignant tissues compared to matched control samples in HCC patients, and further stratified patient samples into groups with high α-fetoprotein (AFP) expression or HBV infection. In aggregate, the data identified 23 upregulated pathways and 13 ones. We observed enhanced biomolecule synthesis and suppressed small molecular metabolism in liver tumor tissues. 16 proteins of high documented relevance to HCC are highlighted in our data. We also identified changes of virus-infection-related proteins including PKM, CTPS1 and ALDOB in the HBV+ HCC subcohort. In conclusion, we demonstrate the practicality of performing proteomic analysis of biopsy-level tissue samples with PCT-SWATH methodology with moderate effort and within a relatively short timeframe.
Taxa-driven functional shifts associated with stormflow in an urban stream microbial community
Authors: Chaudhary Adit , Kauser Imrose , Ray Anirban , Poretsky Rachel 
Published: April 2018

AbstractUrban streams are susceptible to stormwater and sewage inputs that can impact their ecological health and water quality. Microbial communities in streams play important functional roles and their composition and metabolic potential can help assess ecological state and water quality. Although these environments are highly heterogenous, little is known about the influence of isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, we examined the microbial community composition and diversity in an urban stream during dry and wet weather conditions with both 16S rRNA gene sequencing across multiple years and shotgun metagenomics to more deeply analyze a single stormflow event. Metagenomics was used to assess population-level dynamics as well as shifts in the microbial community taxonomic profile and functional potential before and after a substantial rainfall. Results demonstrated general trends present in the stream under stormflow vs. baseflow conditions across years and seasons and also highlighted the significant influence of increased effluent flow following rain in shifting the stream microbial community from abundant freshwater taxa to those more associated with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to changes in functional gene content, particularly for transmembrane transport and organic substance biosynthesis. We also observed an increase in relative abundance of genes encoding degradation of organic pollutants and antibiotic resistance after rain. Overall, this study provided evidence of stormflow impacts on an urban stream microbiome from an environmental and public health perspective.ImportanceUrban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and stormflow events represent one such source of complex physical, chemical and biological perturbations. Microorganisms are important components of these streams from both ecological and public-health perspectives, and analyzing the effect of such perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced stormflow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high rainfall event, with potential environment and public health implications. Previous work in this area has been limited to specific genes/organisms or has not assessed immediate stormflow impact.
Feammox Acidimicrobiaceae bacterium A6, a lithoautotrophic electrode-colonizing bacterium
Authors: Ruiz-Urigüen Melany , Shuai Weitao , Jaffé Peter R. 
Published: April 2018

ABSTRACTAn Acidimicrobiaceae bacterium A6 (A6), from the Acitnobacteria phylum was recently identified as a microorganism that can carry out anaerobic ammonium oxidation coupled to iron reduction, a process also known as Feammox. Being an iron-reducing bacterium, A6 was studied as a potential electrode-reducing bacterium that may transfer electrons extracellularly onto electrodes while gaining energy from ammonium oxidation. Actinobacteria species have been overlooked as electrogenic bacteria, and the importance of lithoautotrophic iron-reducers as electrode-reducing bacteria at anodes has not been addressed. By installing electrodes in soil of a forested riparian wetland where A6 thrives, as well as in A6 bioaugmented constructed wetland (CW) mesocosms, characteristics and performances of this organism as an electrode-reducing bacterium candidate were investigated. In this study, we show that Acidimicrobiaceae bacterium A6 is a lithoautotrophic bacterium, capable of colonizing electrodes in the field as well as in CW mesocosoms, and that it appears to be an electrode-reducing bacterium since there was a boost in current production shortly after the CWs were seeded with Acidimicrobiaceae bacterium A6.IMPORTANCEMost studies on electrogenic microorganisms have focused on the most abundant heterotrophs, while other microorganisms also commonly present in electrode microbial communities such as Actinobacteria have been overlooked. The novel Acidimicrobiaceae bacterium A6 (Actinobacteria) is an iron-reducing bacterium that can colonize the surface of anodes and is linked to electrical current production, making it an electrode-reducing candidate. Furthermore, A6 can carry out anaerobic ammonium oxidation coupled to iron reduction, therefore, findings from this study open up the possibility of using electrodes instead of iron as electron acceptors as a mean to promote A6 to treat ammonium containing wastewater more efficiently. Altogether, this study expands our knowledge on electrogenic bacteria and opens up the possibility to develop Feammox based technologies coupled to bioelectric systems for the treatment NH4+ and other contaminants in anoxic systems.
Fermentation characteristics of mead and wine generated by yeasts isolated from beehives of two Austrian regions
Authors: Gangl Helmut , Lopandic Ksenija , Tscheik Gabriele , Mandl Stefan , Leitner Gerhard , Wechselberger Katharina , Batusic Maria , Tiefenbrunner Wolfgang 
Published: April 2018

AbstractMead is a traditional alcoholic beverage that is produced by fermentation of diluted honey. The mead quality is primarily influenced by the honey variety, although the yeast microflora as the main catalyst of alcoholic fermentation also plays a significant role in the organoleptic and chemical quality of the final product. The impact of the indigenous honey associated-yeasts on the mead properties has scarcely been investigated. To fill this gap the main objective of this work was to assess the metabolic properties of the yeasts isolated from honey and pollen from beehives of northeast Austria.The biodiversity was low and only two yeast species were identified,Zygosaccharomyces rouxiiandCandida apicola.The fermentation potentials of these yeasts were estimated in two media, grape juice (since yeasts isolated from honey may be useful for sweet wine production) and diluted honey of similar sugar concentration, and compared with those of the reference strainsSaccharomyces cerevisiae;S. uvarumandS. eubayanus.Depending on the fermentation substrate, yeasts differed with respect to their metabolic power, fermentation rate, sugar utilization and production of glycerol and organic acids. During mead fermentationSaccharomycesspecies showed the highest metabolic turnover, while the fermentation rate did not differ significantly. Addition of assimilable nitrogen to the diluted honey enhanced fermentation rate ofS. cerevisiae, but not of the other species. Fermentation of grape juice occurred much faster than that of diluted honey and differences between yeasts were more pronounced. TheS. cerevisiaecommercial wine strain, adapted to high alcohol concentrations, andS. eubayanusoutperformed the others,S. uvarumwas comparable withZ. rouxii, whileC. apicolahad the lowest fermentation rate. Fructophily ofZ. rouxiiand to a lesser degree ofC. apicolawas observed in both media. An increased production of glycerol was achieved byS. eubayanusin both media and byC. apicoladuring the fermentation of honey must. A commercialS. cerevisiaestrain,S. eubayanusandZ. rouxiiwere able to metabolize malic acid in wine. In mead, theS. eubayanusandS. uvarumyeasts showed the tendency of increasing the level of malic acid. Aroma profile depended profoundly on yeast species. This study demonstrates that the composition and complexity of the fermentation substrate determines the activity and the final metabolic outcomes of the studied yeasts.
The within-subject application of diffusion tensor MRI and CLARITY reveals brain structural changes inNrxn2deletion mice
Authors: Pervolaraki Eleftheria , Tyson Adam L. , Pibiri Francesca , Poulter Steven L. , Reichelt Amy C. , Rodgers R. John , Clapcote Steven J. , Lever Colin , Andreae Laura C. , Dachtler James 
Published: April 2018

AbstractBackgroundOf the many genetic mutations known to increase the risk of autism spectrum disorder, a large proportion cluster upon synaptic proteins. One such family of presynaptic proteins are the neurexins (NRXN), and recent genetic and mouse evidence has suggested a causative role forNRXN2in generating altered social behaviours. Autism has been conceptualised as a disorder of atypical connectivity, yet how single-gene mutations affect such connectivity remains under-explored. To attempt to address this, we have developed a quantitative analysis of microstructure and structural connectivity leveraging diffusion tensor MRI (DTI) with high-resolution 3D imaging in optically cleared (CLARITY) brain tissue in the same mouse, applied here to theNrxn2αknockout (KO) model.MethodsFixed brains ofNrxn2αKO mice underwent DTI using 9.4T MRI, and diffusion properties of socially-relevant brain regions were quantified. The same tissue was then subjected to CLARITY to immunolabel axons and cell bodies, which were also quantified.ResultsDTI revealed decreases in fractional anisotropy and increases in apparent diffusion coefficient in the amygdala (including the basolateral nuclei), the anterior cingulate cortex, the orbitofrontal cortex and the hippocampus. Radial diffusivity of the anterior cingulate cortex and orbitofrontal cortex was significantly increased inNrxn2αKO mice, as were tracts between the amygdala and the orbitofrontal cortex. Using CLARITY, we find significantly altered axonal orientation in the amygdala, orbitofrontal cortex and the anterior cingulate cortex, which was unrelated to cell density.ConclusionsOur findings demonstrate that deleting a single neurexin gene (Nrxn2α) induces atypical structural connectivity within socially-relevant brain regions. More generally, our combined within-subject DTI and CLARITY approach presents a new, more sensitive method of revealing hitherto undetectable differences in the autistic brain.
Dynamic modeling ofStreptococcus pneumoniaecompetence provides regulatory mechanistic insights
Authors: Weyder Mathias , Prudhomme Marc , Bergé Mathieu , Polard Patrice , Fichant Gwennaele 
Published: April 2018

AbstractIn the human pathogenStreptococcus pneumoniae, the gene regulatory circuit leading to the transient state of competence for natural transformation is based on production of an auto-inducer that activates a positive feedback loop. About one hundred genes are activated in two successive waves linked by a central alternative sigma factor ComX. This mechanism appears to be fundamental to the biological fitness ofS. pneumoniae.We have developed a knowledge-based model of the competence cycle that describes average cell behavior. It reveals that the expression rates of the two competence operon,comABandcomCDE, involved in the positive feedback loop must be coordinated to elicit spontaneous competence. Simulations revealed the requirement for an unknown latecomgene product that shuts of competence by impairing ComX activity. Further simulations led to the predictions that the membrane protein ComD bound to CSP reacts directly to pH change of the medium and that blindness to CSP during the post-competence phase is controlled by late DprA protein. Both predictions were confirmed experimentally.
Investigating the neuroprotective effect of AAV-mediated β-synuclein overexpression in a transgenic model of synucleinopathy
Authors: Sargent Dorian , Bétemps Dominique , Drouyer Matthieu , Verchere Jérémy , Gaillard Damien , Arsac Jean-Noël , Lakhdar Latifa , Salvetti Anna , Baron Thierry 
Published: April 2018

ABSTRACTParkinson’s disease (PD) and multiple system atrophy (MSA) are neurodegenerative diseases characterized by inclusions mainly composed of α-synuclein (α-syn) aggregates. The objective of this study was to investigate if β-synuclein (β-syn) overexpression could have beneficial effects by inhibiting the aggregation of α-syn. The M83 transgenic mouse is a model of synucleinopathy, which develops severe motor symptoms associated with aggregation of α-syn. M83 neonate or adult mice were injected with adeno-associated virus vectors carrying the human β-syn gene (AAVβ-syn) or green fluorescent protein gene (AAVGFP) using different injection sites. One or two months later, M83 disease was accelerated or not using brain M83 extracts from mouse (M83) or human (MSA) origins. AAV mediated β-syn overexpression detected by ELISA did not delay the disease onset, regardless of the AAV injection route and of the inoculation of brain extracts. Accordingly, phosphorylated α-syn levels detected by ELISA in sick mice were similar after injecting AAVβ-syn or AAVGFP. Instead, immunohistochemistry analysis of β-syn indicated the presence of proteinase-K resistant β-syn staining specifically in sick M83 mice inoculated with AAVβ-syn. This study indicated for the first time that β-syn could form aggregates in a model of synucleinopathy when it is expressed by a viral vector.