bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing module size bias of participation coefficient
Authors: Pedersen Mangor , Omidvarnia Amir , Shine James M. , Jackson Graeme D. , Zalesky Andrew 
Published: August 2019

AbstractBoth natural and engineered networks are often modular. Whether a network node interacts with only nodes from its own module or nodes from multiple modules provides insight into its functional role. The participation coeffcient (PC) is typically used to measure this attribute although its value also depends on the size of the module it belongs to, often leading to non-intuitive identification of highly connected nodes. Here, we develop a normalized PC that overcomes the module size bias associated with the conventional PC. Using brain, C.elegans, airport and simulated networks, we show that our measure of participation alleviates the module size bias, while preserving conceptual and mathematical properties, of the classic formulation of PC. Unlike the conventional PC, we identify London and New York as high participators in the air traffic network and demonstrate stronger associations with working memory in human brain networks, yielding new insights into nodal participation across network modules.
Culture under normoxic conditions and enhanced virulence of phase IICoxiella burnetiitransformed with a RSF1010-based shuttle vector
Authors: Luo Shengdong , He Zemin , Sun Zhihui , Yu Yonghui , Jiang Yongqiang , Tong Yigang , Song Lihua 
Published: August 2019

AbstractCoxiella burnetiiis a Gram-negative, facultative intracellular microorganism that can cause acute or chronic Q fever in human. It was recognized as an obligate intracellular organism until the revolutionary design of an axenic cystine culture medium (ACCM). Present axenic culture ofC. burnetiistrictly requires a hypoxic condition (<10% oxygen). Here we investigated the normoxic growth ofC. burnetiistrains in ACCM-2 with or without tryptophan supplementation. ThreeC. burnetiistrains - Henzerling phase I, Nine Mile phase II and a Nine Mile phase II transformant, were included. The transformant contains a pMMGK plasmid that is composed of a RSF1010 ori, a repABC operon, an eGFP gene and a kanamycin resistance cassette. We found that, under normoxia if staring from an appropriate concentration of fresh age inocula, Nine Mile phase II can grow significantly in ACCM-2 with tryptophan, while the transformant can grow robustly in ACCM-2 with or without tryptophan. In contrast, long-term frozen stocks of phase II and its transformant, and Henzerling phase I of different ages had no growth capability under normoxia under any circumstances. Furthermore, frozen stocks of the transformant consistently caused large splenomegaly in SCID mice, while wild type Nine Mile phase II induced a lesser extent of splenomegaly. Taken together, our data show that normoxic cultivation of phase IIC. burnetiican be achieved under certain conditions. Our data suggests that tryptophan and an unknown temperature sensitive signal are involved in the expression of genes for normoxic growth regulated by quorum sensing inC. burnetii.
Free-ranging dogs are capable of comprehending complex human pointing cues
Authors: Bhattacharjee Debottam , Mandal Sarab , Shit Piuli , Varghese Mebin George , Vishnoi Aayushi , Bhadra Anindita 
Published: August 2019

AbstractDogs are the most common species to be found as pets and have been subjects of human curiosity leading to extensive research on their socialization with humans. One of the dominant themes in dog cognition pertains to their capacity of understanding and responding to human referential gestures. The remarkable socio-cognitive skills of pet dogs, while interacting with humans, is quite well established. However, studies regarding the free-ranging subpopulations are greatly lacking. Free-ranging dogs represent an ideal system to investigate interspecific communication with unfamiliar humans, nullifying any contribution of indirect conditioning. The interactions of these dogs with humans are quite complex and multidimensional. For the first time, we tested free-ranging dogs’ ability to understand relatively complex human referential gestures using dynamic and momentary distal pointing cues. We found that these dogs are capable of apprehending distal pointing cues from humans. However, approximately half of the population tested showed a lack of tendency to participate even after successful familiarization with the experimental set-up. A closer inspection revealed anxious behavioural states of the individuals were responsible for such an outcome. We assume that life experiences with humans probably shape personalities of free-ranging dogs, which in turn influence their responsiveness to human communicative gestures.
Bacteria- and temperature-regulated peptides modulate beta-catenin signaling inHydra
Authors: Taubenheim J , Willoweit-Ohl D , Knop M , Franzenburg S , He J , Bosch TCG , Fraune S 
Published: August 2019

AbstractAnimal development has traditionally been viewed as an autonomous process directed by the host genome. But in many animals biotic and abiotic cues, like temperature and bacterial colonizers, provide signals for multiple developmental steps.Hydraoffers unique features to encode these complex interactions of developmental processes with biotic and abiotic factors. Here, we used the model animalHydrato investigate the impact of bacterial colonizers and temperature on the pattern formation process. InHydra, formation of the head organizer involves the canonical Wnt pathway. Treatment with alsterpaullone (ALP) results in acquiring characteristics of the head organizer in the body column. Intriguingly, germ-freeHydrapolyps are significantly more sensitive to ALP compared to control polyps. In addition to microbes, β-catenin dependent pattern formation is also affected by temperature. Gene expression analyses led to the identification of two small secreted peptides, named Eco1 and Eco2, being upregulated in the response to both,Curvibactersp, the main bacterial colonizer ofHydra, and low temperatures. Loss-of function experiments revealed that Eco peptides are involved in the regulation of pattern formation and have an antagonistic function to Wnt signaling inHydra.
Extracellular electron uptake inMethanosarcinalesis independent of multihemec-type cytochromes
Authors: Yee Mon Oo , Rotaru Amelia-Elena 
Published: August 2019

AbstractThe co-occurrence ofGeobacterandMethanosarcinalesis often used as a proxy for the manifestation of direct interspecies electron transfer (DIET) in man-made and natural aquatic environments. We previously reported that not allGeobacterare capable of DIET withMethanosarcina. Here we tested 15 new artificial co-culture combinations with methanogens and electrogenic bacteria, including an electrogen outside of theGeobacterclade –Rhodoferax ferrireducens.Consistently, highly effective electrogenic bacteria (G. metallireducens, G. hydrogenophilusandR. ferrireducens) formed successful associations withMethanosarcinales. Highly effective electrogens could not sustain the growth of H2-utilizing methanogens of the generaMethanococcus,Methanobacterium, Methanospirillum, MethanolaciniaorMethanoculleus.Methanosarcinales, including strict non-hydrogenotrophic methanogens of the genusMethanothrix (Mtx. harundinaceaandMtx. shoeghenii) andMethanosarcina horonobensis, conserved their ability to interact with electrogens.Methanosarcinaleswere classified as the only methanogens containingc-type cytochromes, unlike strict hydrogenotrophic methanogens. It was then hypothesized that multiheme c-type cytochromes giveMethanosarcinalestheir ability to retrieve extracellular electrons. However, multiheme c-type cytochromes are neither unique to this group of methanogens nor universal. Only two of the sevenMethanosarcinalestested had multiheme c-type cytochromes (MCH). In one of these two species -M. mazeia deletion mutant for its MCH was readily available. Here we tested if the absence of this MHC impacts extracellular electron uptake. Deletion of the MHC inM. mazeidid not impact the ability of this methanogens to retrieve extracellular electrons fromG. metallireducensor a poised cathode. SinceMethanosarcinadid not require multiheme c-type cytochromes for direct electron uptake we proposed an alternative strategy for extracellular electron uptake.
Dormancy-to-death transition in yeast spores occurs due to gradual loss of gene-expressing ability
Authors: Maire Théo , Allertz Tim , Betjes Max A. , Youk Hyun 
Published: August 2019

ABSTRACTDormancy is colloquially considered as extending lifespan by being still. Starved yeasts form dormant spores that wake-up (germinate) when nutrients reappear but cannot germinate (die) after some time. What sets their lifespans and how they age are open questions because what processes occur - and by how much - within each dormant spore remains unclear. With single-cell-level measurements, we discovered how dormant yeast spores age and die: spores have a quantifiable gene-expressing ability during dormancy that decreases over days to months until it vanishes, causing death. Specifically, each spore has a different probability of germinating that decreases because its ability to - without nutrients - express genes decreases, as revealed by a synthetic circuit that forces GFP expression during dormancy. Decreasing amounts of molecules required for gene expression - including RNA polymerases - decreases gene-expressing ability which then decreases chances of germinating. Spores gradually lose these molecules because they are produced too slowly compared to their degradations, causing gene-expressing ability to eventually vanish and, thus, death. Our work provides a systems-level view of dormancy-to-death transition.Short summaryThis study identifies systems-level quantities that decay during dormancy in Saccharomyces cerevisiae spores and thereby reveals the meaning of ageing for dormant yeast spores and shows that they die when their gene-expressing ability is irreversibly lost.HighlightsFor a given glucose concentration, a dormant yeast spore has a well-defined probability of germinating (“germination ability”).A spore’s germination ability positively correlates with its RNAP I-III levels and the gene-expression (GFP) level it can realize when the expression is forced without nutrients.Ageing during dormancy means gradual decreases in germination ability, RNAP levels, and GFP-level realizable when expression is forced.Spores die after sufficiently losing gene-expressing ability and drugs that inhibit gene expression during dormancy shorten spores’ lifespans (e.g., from months to a day).
Heterospecific song quality as social information for settlement decisions: an experimental approach in a wild bird
Authors: Morinay Jennifer , Forsman Jukka T. , Doligez Blandine 
Published: August 2019

AbstractAssessing local habitat quality via social cues provided by con- or heterospecific individuals sharing the same needs is a widespread strategy of social information use for breeding habitat selection. However, gathering information about putative competitors may involve agonistic costs. The use of social cues reflecting local habitat quality acquired from a distance, such as acoustic cues, could therefore be favoured. Bird songs are conspicuous signals commonly assumed to reliably reflect producer quality, and thereby local site quality. Birds of different species have been shown to be attracted to breeding sites by heterospecific songs, but whether they can use fine heterospecific song features as information on producer (and by extension habitat) quality remains unknown. We used a playback experiment in a wild population of collared flycatchers (Ficedula albicollis), a species known to eavesdrop on dominant great tits’ (Parus major) presence and performance, to test whether flycatchers preferred to settle near broadcasts of a high quality great tit song (i.e. song with large repertoire size, long strophes, high song rate), a low quality great tit song or a chaffinch song (control). Among old females, aggressive ones preferred to settle near broadcasts of high quality tit song and avoided broadcasts of low quality tit song, while less aggressive females preferred to settle near broadcasts of low quality tit song. Male personality or age did not influence settlement decisions. Our results show that collared flycatcher females use great tit song quality features as information for settlement decisions, though differently depending on their own competitive ability and/or previous experience with great tit songs. Our study therefore further illustrates the complex condition-dependent use of heterospecific social information for breeding habitat selection.
Genetic variation in parental effects contribute to the evolutionary potential of prey responses to predation risk
Authors: Tigreros Natasha , Agrawal Anurag A. , Thaler Jennifer S. 
Published: August 2019

ABSTRACTDespite the ubiquity of parental effects and their potential impact on evolutionary dynamics, their contribution to the evolution of ecologically relevant adaptations remains poorly understood. Using quantitative genetics, here we demonstrate that parental effects contribute substantially to the evolutionary potential of larval antipredator responses in a leaf beetle (Leptinotarsa decemlineata). Previous research showed that largerL. decemlineatalarvae elicit stronger antipredator responses, and mothers perceiving predators improved offspring responses by increasing intraclutch cannibalism –an extreme form of offspring provisioning. We now report substantial additive genetic variation underlying maternal ability to induce intraclutch cannibalism, indicating the potential of this adaptive maternal effect to evolve by natural selection. We also show that paternal size, a heritable trait, impacted larval responses to predation risk, but that larval responses themselves had little additive genetic variation. Together, these results demonstrate how larval responses to predation risk can evolve via two types of parental effects, both of which provide indirect sources of genetic variation for offspring traits.
Nanopore sequencing of the glucocerebrosidase (GBA) gene in a New Zealand Parkinson’s disease cohort
Authors: Graham O.E.E. , Pitcher T.L. , Liau Y. , Miller A.L. , Dalrymple-Alford J.C. , Anderson T.J. , Kennedy M.A. 
Published: August 2019

AbstractIntroductionBi-allelic mutations in the gene for glucocerebrosidase (GBA) cause Gaucher disease, an autosomal recessive lysosomal storage disorder. Gaucher disease causing GBA mutations in the heterozygous state are also high risk factors for Parkinson’s disease (PD). GBA analysis is challenging due to a related pseudogene and structural variations (SVs) that can occur at this locus. We have applied and refined a recently developed nanopore DNA sequencing method to analyze GBA variants in a clinically assessed New Zealand longitudinal cohort of PD.MethodWe examined amplicons encompassing the coding region of GBA (8.9kb) from 229 PD cases and 50 healthy controls using the GridION nanopore sequencing platform, and Sanger validation.ResultsWe detected 23 variants in 21 PD cases (9.2% of patients). We detected modest PD risk variant p.N409S (rs76763715) in one case, p.E365K (rs2230288) in 12 cases, and p.T408M (rs75548401) in seven cases, one of whom also had p.E365K. We additionally detected the possible risk variants p.R78C (rs146774384) in one case, p.D179H (rs147138516) in one case which occurred on the same haplotype as p.E365K, and one novel variant c.335C>T or p.(L335=), that potentially impacts splicing of GBA transcripts. Additionally, we found a higher prevalence of dementia among patients with GBA variants.ConclusionThis work confirmed the utility of nanopore sequencing as a high-throughput method to identify known and novel GBA variants, and to assign precise haplotypes. Our observations may contribute to improved understanding of the effects of variants on disease pathogenesis, and to the development of more targeted treatments.
LaeA controls citric acid production through regulation of a citrate exporter encodingcexAinAspergillus luchuensismut.kawachii
Authors: Kadooka Chihiro , Nakamura Eri , Mori Kazuki , Okutsu Kayu , Yoshizaki Yumiko , Takamine Kazunori , Goto Masatoshi , Tamaki Hisanori , Futagami Taiki 
Published: August 2019

ABSTRACTThe putative methyltransferase LaeA is a global regulator of metabolic and development processes in filamentous fungi. We characterized the homologouslaeAgenes of the white koji fungusAspergillus luchuensismut.kawachii(A. kawachii) to determine their role in the hyperproduction of citric acid. The ΔlaeAstrain exhibited a significant reduction in citric acid productivity. Cap-analysis gene expression (CAGE) revealed thatlaeAis required for the gene expression of a putative citrate exporter encodingcexA, which is critical for citric acid production. The deficit in the productivity of citric acid by the ΔlaeAstrain was rescued by the overexpression ofcexAto a level comparable with that of thecexA-overexpressing ΔcexAstrain. In addition, chromatin immunoprecipitation coupled with quantitative PCR (ChIP-qPCR) analysis indicated that LaeA regulates the expression ofcexAvia methylation levels of the histones H3K4 and H3K9. These results indicate that LaeA is involved in citric acid production through epigenetic regulation ofcexAinA. kawachii.IMPORTANCEA. kawachiihas been traditionally used for production of the distilled spirit shochu in Japan. Citric acid produced byA. kawachiiplays an important role in preventing microbial contamination during the shochu fermentation process. This study characterized homologouslaeAgenes; using CAGE, complementation test, and ChIP-qPCR, it was found thatlaeAis required for citric acid production though regulation ofcexAinA. kawachii. The epigenetic regulation of citrate production elucidated in this study will be useful for controlling the fermentation processes of shochu.
Colonization and extinction dynamics and their link to the distribution of European trees at continental scale
Authors: Guyennon Arnaud , Reineking Björn , Dahlgren Jonas , Lehtonen Aleksi , Ratcliffe Sophia , Ruiz-Benito Paloma , Zavala Miguel A. , Kunstler Georges 
Published: August 2019

AbstractAimProcesses driving current tree species distribution are still largely debated. Attempts to relate species distribution and population demography metrics have shown mixed results. In this context, we would like to test the hypotheses that the metapopulation processes of colonization and extinction are linked to species distribution models.LocationEurope: Spain, France, Germany, Finland, and Sweden.TaxonAngiosperms and Gymnosperms.MethodsFor the 17 tree species analyzed we fitted species distribution model (SDM) relating environmental variables to presence absence data across Europe. Then using independent data from national forest inventories across Europe we tested whether colonization and extinction probabilities are related to occurrence probability estimated by the SDMs. Finally, we tested how colonization and extinction respectively drive probability of presence at the metapopulation equilibrium.ResultsWe found that for most species at least one process (colonization/extinction) is related to the occurrence probability, but rarely both.Main conclusionsOur study supports the view that metapopulation dynamics are partly related to SDM occurrence probability through one of the metapopulation probabilities. However these links are relatively weak and the metapopulation models tend to overestimate the occurrence probability. Our results call for caution in model extrapolating SDM models to metapopulation dynamics.
SeqBreed: a python tool to evaluate genomic prediction in complex scenarios
Authors: Pérez-Enciso M. , Ramírez-Ayala L. C. , Zingaretti L.M. 
Published: August 2019

AbstractBackgroundGenomic Prediction (GP) is the procedure whereby molecular information is used to predict complex phenotypes. Although GP can significantly enhance predictive accuracy, it can be expensive and difficult to implement. To help in designing optimum experiments, including genome wide association studies and genomic selection experiments, we have developed SeqBreed, a generic and flexible python3 forward simulator.ResultsSeqBreed accommodates sex and mitochondrion chromosomes as well as autopolyploidy. It can simulate any number of complex phenotypes determined by any number of causal loci. SeqBreed implements several GP methods, including single step GBLUP. We demonstrate its functionality with Drosophila Genome Reference Panel (DGRP) sequence data and with tetraploid potato genotypes.ConclusionsSeqBreed is a flexible and easy to use tool appropriate for optimizing GP or genome wide association studies. It incorporates some of the most popular GP methods and includes several visualization tools. Code is open and can be freely modified. Software, documentation and examples are available at https://github.com/miguelperezenciso/SeqBreed.
A novel methodology for defining stromal expression of atypical chemokine receptors in vivo
Authors: Hansell Christopher A.H. , Love Samantha , Pingen Marieke , Wilson Gillian J , MacLeod Megan , Graham Gerard J. 
Published: August 2019

AbstractAnalysis of chemokine receptor, and atypical chemokine receptor, expression is frequently hampered by the lack of availability of high-quality antibodies and the species-specificity of those that are available. We have previously described methodology utilising Alexa-Fluor labelled chemokine ligands as versatile reagents to detect receptor expression. Previously this has been limited to haematopoietic cells and methodology for assessing expression of receptors on stromal cells has been lacking. Amongst chemokine receptors the ones most frequently expressed on stromal cells belong to the atypical chemokine receptor subfamily. These receptors do not signal in the classic sense in response to ligand but scavenge their ligands and degrade them and thus sculpt in vivo chemokine gradients. Here we demonstrate the ability to use either intratracheal, or intravenous, Alexa-Fluor labelled chemokine administration to detect stromal cell populations expressing the atypical chemokine receptor ACKR2. Using this methodology we demonstrate, for the first time, expression of ACKR2 on blood endothelial cells. This observation sets the lung aside from other tissues in which ACKR2 is exclusively expressed on lymphatic endothelial cells. In summary therefore we described a novel method for the in situ labelling of atypical chemokine receptor expressing cells appropriate for subsequent flow cytometric analysis. We propose that this methodology will work in a range of species and for a range of receptors and therefore will have significant versatility