bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate predictions of coexistence in natural systems require the inclusion of facilitative interactions and environmental dependency
Authors: Bimler Malyon D. , Stouffer Daniel B. , Lai Hao Ran , Mayfield Margaret M. 
Published: August 2018

Abstract

Coexistence between plant species is well known to depend on the outcomes of species interactions within an environmental context. The incorporation of environmental variation into empirical studies of coexistence are rare, however, due to the complex experiments needed to do so and the lack of feasible modelling approaches for determining how environmental factors alter specific coexistence mechanisms.

In this article, we present a simple modelling framework for assessing how variation in species interactions across environmental gradients impact on niche overlap and fitness differences, two core determinants of coexistence. We use a novel formulation of an annual plant population dynamics model that allows for competitive and facilitative species interactions and for variation in the strength and direction of these interactions across environmental gradients. Using this framework, we examine outcomes of plant–plant interactions between four commonly co‐occurring annual plant species from Western Australian woodlands. We then determine how niche overlap and fitness differences between these species vary across three environmental gradients previously identified as important for structuring diversity patterns in this system: soil phosphorus, shade and water.

We found facilitation to be a widespread phenomenon and that interactions between most species pairs shift between competitive and facilitative across multiple environmental gradients. Environmental conditions also altered the strength, direction and relative variation of both niche overlap and fitness differences in nonlinear and unpredictable ways.

Synthesis. We provide a simple framework for incorporating environmental heterogeneity into explorations of coexistence mechanisms. Our findings highlight the importance of the environment in determining the outcome of species interactions and the potential for pairwise coexistence between species. The prevalence of facilitation in our system indicates a need to improve current theoretical frameworks of coexistence to include noncompetitive interactions and ways of translating these effects into explicit predictions of coexistence. Our study also suggests a need for further research into determining which factors result in consistent responses of niche overlap and fitness differences to environmental variation. Such information will improve our ability to predict outcomes of coexistence, invasion events and responses of whole communities to future environmental change.
Effect of insect herbivory on plant community dynamics under contrasting water availability levels
Authors: Tamburini Giovanni , Dani Elena , Bommarco Riccardo , Marini Lorenzo 
Published: August 2018

Abstract

Plant diversity is impacted by multiple global change drivers but also by altered biotic interactions with antagonist and mutualist organisms that can potentially affect species coexistence.

With a 2‐year, outdoor mesocosm experiment in realistic mesic grassland communities, we explored the role of insect herbivory in impacting plant community dynamics under contrasting levels of water availability simulating altered rainfall regimes. We selected a grasshopper species (Calliptamus italicus L.) feeding predominantly on forbs while avoiding grasses.

High water availability reduced species coexistence, boosting productivity while decreasing individual plant survival. At the community level, herbivores were not able to promote species coexistence but asymmetrically influenced grasses and forbs, reducing forb biomass under high water availability.

Herbivores shaped individual plant responses to both abiotic conditions and individual‐neighbours’ interactions. Herbivores influenced focal plant survival by altering the effect of neighbouring plants, mitigating the negative effect of high neighbour biomass at low water availability and exacerbating it at high level of water availability.

Synthesis. Altered rainfall has the capacity to change the relative strength of plant–plant interactions and also to determine the effects of herbivores on grassland communities. The complexity of the interactions between plants and herbivores and the observed context dependence indicate the need to incorporate multiple biotic and abiotic drivers to fully understand the mechanisms underlying plant dynamics and species coexistence in a changing world.
Isotopic evidence of biotrophy and unusual nitrogen nutrition in soil‐dwelling Hygrophoraceae
Authors: Halbwachs Hans , Easton Gary L. , Bol Roland , Hobbie Erik A. , Garnett Mark H , Peršoh Derek , Dixon Liz , Ostle Nick , Karasch Peter , Griffith Gareth W. 
Published: August 2018

SummarySeveral lines of evidence suggest that the agaricoid, non‐ectomycorrhizal members of the family Hygrophoraceae (waxcaps) are biotrophic with unusual nitrogen nutrition. However, methods for the axenic culture and lab‐based study of these organisms remain to be developed, so our current knowledge is limited to field‐based investigations. Addition of nitrogen, lime or organophosphate pesticide at an experimental field site (Sourhope) suppressed fruiting of waxcap basidiocarps. Furthermore, stable isotope natural abundance in basidiocarps were unusually high in 15N and low in 13C, the latter consistent with mycorrhizal nutritional status. Similar patterns were found in waxcap basidiocarps from diverse habitats across four continents. Additional data from 14C analysis of basidiocarps and 13C pulse label experiments suggest that these fungi are not saprotrophs but rather biotrophic endophytes and possibly mycorrhizal. The consistently high but variable δ15N values (10–20‰) of basidiocarps further indicate that N acquisition or processing differ from other fungi; we suggest that N may be derived from acquisition of N via soil fauna high in the food chain.
Thermodesulfobium sp. strain 3baa, an acidophilic sulfate reducing bacterium forming biofilms triggered by mineral precipitation
Authors: Rüffel Viola , Maar Mona , Dammbrück Markus N. , Hauröder Bärbel , Neu Thomas R. , Meier Jutta 
Published: August 2018

SummarySulfate reducing prokaryotes are promising candidates for the remediation of acidic metal‐rich waste waters. However, only few acidophilic species have been described to date. Chemolithoautotrophic strain 3baa was isolated from sediments of an acidic mine pit lake. Based on its 16S‐rRNA gene sequence it belongs to the genus Thermodesulfobium. It was identified as an acidophile growing in artificial pore water medium in the range of pH 2.6–6.6. Though the highest sulfate reduction rates were obtained at the lower end of this range, elongated cells and extended lag phases demonstrated acid stress. Sulfate reduction at low pH was accompanied by the formation of mineral precipitates strongly adhering to solid surfaces. A structural investigation by laser scanning microscopy, electron microscopy and X‐ray microanalysis revealed the formation of Al hydroxides and Fe sulfides which were densely populated by cells. Al hydroxides precipitated first, enabling initial cell attachment. Colonization of solid surfaces coincided with increased sulfate reducing activity indicating more favourable growth conditions within biofilms compared with free‐living cells. These findings point out the importance of cell–mineral interaction for biofilm formation and contribute to our understanding how sulfate reducing prokaryotes thrive in both natural and engineered systems at low pH.
A new synbiotic dairy food containing lactobionic acid and Lactobacillus casei
Authors: García Cristina , Bautista Lucía , Rendueles Manuel , Díaz Mario 
Published: August 2018

As well as its beneficial health properties, the incorporation of the prebiotic lactobionic acid (LBA) in fermented dairy products can provide a technological advantage due to its gelling capacities. This study aimed to develop a new functional dairy product containing LBA synthesised within the process itself by the bacterium Pseudomonas taetrolens. A probiotic Lactobacillus casei strain was introduced through a sequential fermentation system. After incubation, in the case of the most effective experimental procedure, a synbiotic fermented milk with 30 g/L of prebiotic LBA was obtained, together with an active L. casei population of 109 cfu/mL and <1% lactose content.
Insight into metabolic diversity of the brown‐rot basidiomycete Postia placenta responsible for sesquiterpene biosynthesis: semi‐comprehensive screening of cytochrome P450 monooxygenase involved in protoilludene metabolism
Authors: Ichinose Hirofumi , Kitaoka Takuya 
Published: August 2018

SummaryA wide variety of sesquiterpenoids have been isolated from basidiomycetes, and their bioactive properties have attracted significant attention in an effort to understand biosynthetic machineries. As both sesquiterpene synthases and cytochrome P450 monooxygenases play key roles in the diversification of sesquiterpenoids, it is important to widely and mutually understand their biochemical properties. In this study, we performed genome‐wide annotation and functional characterization of sesquiterpene synthases from the brown‐rot basidiomycete Postia placenta. Using RT‐PCR, we isolated 16 sesquiterpene synthases genes as full‐length cDNAs. Heterologous expression revealed that the sesquiterpene synthases could produce a series of sesquiterpene scaffolds with distinct metabolic profiles. Based on metabolic studies, we identified 25 sesquiterpene scaffolds including Δ6‐protoilludene produced by the sesquiterpene synthases. In particular, a protoilludene synthase from the brown‐rot basidiomycete was characterized for the first time. Furthermore, we conducted a semi‐comprehensive functional screening of cytochrome P450 monooxygenases from P. placenta to elucidate biosynthetic machineries involved in metabolisms of Δ6‐protoilludene. Coexpression of protoilludene synthase and 184 isoforms of cytochrome P450 monooxygenases enabled the identification of CYP5344B1, CYP5348E1 and CYP5348J3, which catalysed the hydroxylation reaction of Δ6‐protoilludene to produce Δ6‐protoilludene‐8‐ol and Δ6‐protoilludene‐5‐ol. Furthermore, structural isomers of Δ7‐protoilludene‐6‐ol were obtained from incubation of Δ6‐protoilludene‐8‐ol in acidic culture medium.
Long‐read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments
Authors: Heeger Felix , Bourne Elizabeth C. , Baschien Christiane , Yurkov Andrey , Bunk Boyke , Spröer Cathrin , Overmann Jörg , Mazzoni Camila J. , Monaghan Michael T. 
Published: August 2018

AbstractDNA metabarcoding is widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints limit most studies to marker lengths below 600 base pairs (bp). Longer sequencing reads of several thousand bp are now possible with third‐generation sequencing. Increased marker lengths provide greater taxonomic resolution and allow for phylogenetic methods of classification, but longer reads may be subject to higher rates of sequencing error and chimera formation. In addition, most bioinformatics tools for DNA metabarcoding were designed for short reads and are therefore unsuitable. Here, we used Pacific Biosciences circular consensus sequencing (CCS) to DNA‐metabarcode environmental samples using a ca. 4,500 bp marker that included most of the eukaryote SSU and LSU rRNA genes and the complete ITS region. We developed an analysis pipeline that reduced error rates to levels comparable to short‐read platforms. Validation using a mock community indicated that our pipeline detected 98% of chimeras de novo. We recovered 947 OTUs from water and sediment samples from a natural lake, 848 of which could be classified to phylum, 397 to genus and 330 to species. By allowing for the simultaneous use of three databases (Unite, SILVA and RDP LSU), long‐read DNA metabarcoding provided better taxonomic resolution than any single marker. We foresee the use of long reads enabling the cross‐validation of reference sequences and the synthesis of ribosomal rRNA gene databases. The universal nature of the rRNA operon and our recovery of >100 nonfungal OTUs indicate that long‐read DNA metabarcoding holds promise for studies of eukaryotic diversity more broadly.
Social stress‐potentiated methamphetamine seeking
Authors: Blouin Ashley M. , Pisupati Swathi , Hoffer Colton G. , Hafenbreidel Madalyn , Jamieson Sarah E. , Rumbaugh Gavin , Miller Courtney A. 
Published: August 2018

AbstractHuman studies of substance use disorder show that psychological stress and drug availability interact following rehabilitation, contributing to the high relapse potential. Social stressors trigger particularly strong motivation for drug, but how this affects neuronal function to increase relapse is unknown. Animal models, which allow for the dissection of neural mechanisms, primarily utilize physical stressors to trigger relapse. To recapitulate psychosocial post‐rehabilitation challenges in animals, we developed a model of social stress‐potentiated methamphetamine (METH) seeking. Rats receive a single social defeat (SD) session after completion of self‐administration and extinction of lever pressing. While a reminder of the SD was insufficient to reinstate METH seeking on its own, rats that received a reminder of SD followed by a METH‐priming injection displayed potentiated reinstatement over METH‐priming alone. Examination of neuronal activation patterns of the METH‐primed reinstatement session identified c‐Fos‐immunoreactivity in the basolateral amygdala (BLA) as correlated with SD score, a measure of defeat latency. Rapidly defeated rats showed potentiated METH‐primed reinstatement and elevated BLA c‐Fos compared with controls. Conversely, rats that were undefeated during the social stress did not show potentiated METH‐primed reinstatement or elevated BLA c‐Fos. Interestingly, inactivation of the BLA with baclofen/muscimol prior to the stress reminder and METH‐priming generated a potentiation of METH seeking in the undefeated rats, suggesting the BLA may mediate resilience to the stressor. This model provides a tool for the further dissection of neural mechanisms mediating social stress‐potentiated relapse and for the development of relapse‐reducing therapeutics.
Antimicrobial efficacy of 0.5% peracetic acid and EDTA with passive ultrasonic or manual agitation in an Enterococcus faecalis biofilm model
Authors: Hartmann Rafael C. , Neuvald Lilian , Barth Valdir , de Figueiredo Jose Antônio Poli , de Oliveira Sílvia Dias , Scarparo Roberta Kochenberger , Waltrick Silvana Beltrami , Rossi‐Fedele Giampiero 
Published: August 2018

AbstractWe compared the antimicrobial efficacy of EDTA and 0.5% peracetic acid (PAA), with manual agitation (MA) or passive ultrasonic irrigation (PUI) in an Enterococcus faecalis biofilm model. Fifty‐five single‐rooted human premolar teeth were chemo‐mechanically prepared and inoculated with E. faecalis for biofilm formation. These were divided into five groups (n = 11): saline solution, PAA+MA, PAA+PUI, EDTA+MA and EDTA+PUI. Root canal sampling and scanning electron microscopy of the canal lumen and dentinal tubule areas at the different root thirds were performed. The images were ranked based on contamination level. Only the PAA groups presented with no bacterial growth, with the remaining groups not presenting significant differences among them. PAA+PUI presented with the highest median position rankings in every third and location, whereas EDTA+MA performed similarly to the saline control. No differences were found when comparing MA and PUI within the same solution, however, PUI was associated with lower contamination levels mean rankings.
Insulin resistance and β‐cell dysfunction and the relationship with cardio‐metabolic disorders among women with polycystic ovary syndrome
Authors: Mu Liangshan , Zhao Yue , Lai Yuchen , Li Rong , Qiao Jie 
Published: August 2018

SummaryObjectiveTo investigate both independent and combined effects of insulin resistance and β‐cell dysfunction on cardio‐metabolic abnormalities in polycystic ovary syndrome (PCOS).DesignA national epidemiologic survey was performed in reproductive aged females in China from October 2007 to September 2011.MethodsA total of 824 PCOS and 2715 non‐PCOS were included. The Rotterdam Criteria were applied for PCOS diagnosis. We used the homeostasis model assessment of insulin resistance (HOMA‐IR) and HOMA of β‐cell function (HOMA‐β) to evaluate insulin resistance and β‐cell dysfunction, respectively.ResultsCompared with non‐PCOS, PCOS showed a higher index of HOMA‐IR and HOMA‐β, and a higher prevalence of obesity, central obesity, and dyslipidaemia. High HOMA‐IR was independently related to a high prevalence of obesity, central obesity, dyslipidaemia, and high blood glucose in PCOS. In contrast, a low index of HOMA‐β index was independently correlated with a low prevalence of obesity, and central obesity, but negatively correlated with an elevated prevalence of high blood glucose in PCOS. In addition, proportion of insulin resistance was higher than that of β‐cell dysfunction in PCOS with cardio‐metabolic disorders. β‐cell dysfunction was negatively correlated with the prevalence of central obesity and obesity.ConclusionsInsulin resistance and β‐cell dysfunction independently affected cardio‐metabolic abnormalities in PCOS, while insulin resistance was correlated with a higher prevalence of cardio‐metabolic abnormalities than that of β‐cell dysfunction. Moreover, β‐cell dysfunction and insulin resistance showed divergent correlations with obesity in PCOS.
Bi‐directional modulation of cellular interactions in an in vitro co‐culture model of tendon‐to‐bone interface
Authors: Calejo I. , Costa‐Almeida Raquel , Gonçalves Ana Isabel , Berdecka Dominika , Reis Rui Luis , Gomes Manuela Estima 
Published: August 2018

AbstractObjectivesThis work aimed at studying in vitro interactions between human tendon‐derived cells (hTDCs) and pre‐osteoblasts (pre‐OBs) that may trigger a cascade of events involved in enthesis regeneration.Materials and methodsThe effect of 5 osteogenic medium (OM) conditions over the modulation of hTDCs and pre‐OBs towards the tenogenic and osteogenic phenotypes, respectively, was studied. Three different medium conditions were chosen for subsequently establishing a direct co‐culture system in order to study the expression of bone, tendon and interface‐related markers.ResultsA higher matrix mineralization and ALP activity was observed in co‐cultures in the presence of OM. Higher transcription levels of bone‐ (ALPL, RUNX2, SPP1) and interface‐related genes (ACAN, COMP) were found in co‐cultures. The expression of aggrecan was influenced by the presence of OM and cell‐cell interactions occurring in co‐culture.ConclusionsThe present work assessed both the influence of OM on cell phenotype modulation and the importance of co‐culture models while promoting cell‐cell interactions and the exchange of soluble factors in triggering an interface‐like phenotype to potentially modulate enthesis regeneration.
MiR‐139‐5p is associated with poor prognosis and regulates glycolysis by repressing PKM2 in gallbladder carcinoma
Authors: Chen Jianan , Yu Yan , Chen Xiaolong , He Yuting , Hu Qiuyue , Li Hongqiang , Han Qicai , Ren Fang , Li Juan , Li Chao , Bao Jie , Ren Zhigang , Duan Zhenfeng , Cui Guangying , Sun Ranran 
Published: August 2018

AbstractObjectivesGallbladder carcinoma (GBC) is the most highly aggressive cancer of biliary tract, but effective therapeutics are lacking. Emerging evidence has unveiled that miR‐139‐5p is aberrantly downregulated in cancers, including GBC. However, the functions and mechanisms of miR‐139‐5p in GBC remain unclear.Materials and methodsMiR‐139‐5p‐overexpression was established in GBC cell lines, after which cell proliferation, migration, invasion, colony formation, and glucose metabolism were assayed in vitro. Subsequently, bioinformatics prediction and dual‐luciferase reporter were performed to confirm that pyruvate kinase M2 (PKM2) was a direct target of miRNA‐139‐5p. Xenograft mouse models were applied to investigate the role of miR‐139‐5p in GBC tumourigenicity in vivo. In situ hybridization and immunohistochemical assays were performed to determine the relationships among miR‐139‐5p, PKM2 expression and clinical malignancies in GBC samples.ResultsWe found that miR‐139‐5p was substantially downregulated in GBC tissues. Low expression of miR‐139‐5p was significantly associated with poor clinical outcomes. GBC cell proliferation, migration, and invasion could be inhibited by overexpression of miR‐139‐5p either in vitro or in vivo. In addition, miR‐139‐5p overexpression could directly inhibit PKM2 expression and lead to suppression of glucose consumption, lactate production, and cellular ATP levels. Moreover, PKM2 was frequently upregulated in GBC and correlated with poor prognosis. Mechanistically, miRNA‐139‐5p inhibited cell proliferation, migration, and glycolysis in GBC, at least in part, by repressing PKM2.ConclusionsThese results demonstrated a novel role for miR‐139‐5p/PKM2 in GBC progression and provided potential prognostic predictors for GBC patients.
Multisensory stimulation modulates perceptual and post perceptual face representations: Evidence from event‐related potentials
Authors: Estudillo Alejandro J. , Kaufmann Jürgen M. , Bindemann Markus , Schweinberger Stefan R. 
Published: August 2018

AbstractSeeing a face being touched in spatial and temporal synchrony with the own face produces a bias in self‐recognition, whereby the other face becomes more likely to be perceived as the self. The present study employed event‐related potentials to explore whether this enfacement effect reflects initial face encoding, enhanced distinctiveness of the enfaced face, modified self‐identity representations, or even later processing stages that are associated with the emotional processing of faces. Participants were stroked in synchrony or asynchrony with an unfamiliar face they observed on a monitor in front of them, in a situation approximating a mirror image. Subsequently, event‐related potentials were recorded during the presentation of (a) a previously synchronously stimulated face, (b) an asynchronously stimulated face, (c) observers’ own face, (d) filler faces, and (e) a to‐be‐detected target face, which required a response. Observers reported a consistent enfacement illusion after synchronous stimulation. Importantly, the synchronously stimulated face elicited more prominent N170 and P200 responses than the asynchronously stimulated face. By contrast, similar N250 and P300 responses were observed in these conditions. These results suggest that enfacement modulates early neural correlates of face encoding and facial prototypicality, rather than identity self‐representations and associated emotional processes.