bluuebunny/crossref_metadata_2025_split huggingface dataset:
CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data
Authors: Marcelino Vanessa R. , Clausen Philip T.L.C. , Buchmann Jan P. , Wille Michelle , Iredell Jonathan R. , Meyer Wieland , Lund Ole , Sorrell Tania C. , Holmes Edward C. 
Published: May 2019

AbstractHigh-throughput sequencing of DNA and RNA from environmental and host-associated samples (metagenomics and metatranscriptomics) is a powerful tool to assess which organisms are present in a sample. Taxonomic identification software usually align individual short sequence reads to a reference database, sometimes containing taxa with complete genomes only. This is a challenging task given that different species can share identical sequence regions and complete genome sequences are only available for a fraction of organisms. A recently developed approach to map sequence reads to reference databases involves weighing all high scoring read-mappings to the data base as a whole to produce better-informed alignments. We used this novel concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. Using simulated fungal and bacterial metagenomes, we demonstrate that CCMetagen substantially outperforms other commonly used metagenome classifiers, attaining a 3 – 1580 fold increase in precision and a 2 – 922 fold increase in F1 scores for species-level classifications when compared to Kraken2, Centrifuge and KrakenUniq. CCMetagen is sufficiently fast and memory efficient to use the entire NCBI nucleotide collection (nt) as reference, enabling the assessment of species with incomplete genome sequence data from all biological kingdoms. Our pipeline efficiently produced a comprehensive overview of the microbiome of two biological data sets, including both eukaryotes and prokaryotes. CCMetagen is user-friendly and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.
Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay
Authors: Tachiwana Hiroaki , Dacher Mariko , Maehara Kazumitsu , Harada Akihito , Ohkawa Yasuyuki , Kimura Hiroshi , Kurumizaka Hitoshi , Saitoh Noriko 
Published: May 2019

AbstractIn eukaryotes, histone variant distribution within the genome is the key epigenetic feature. To understand how each histone variant is targeted to the genome, we developed a new method, in which epitope-tagged histone complexes are introduced into permeabilized cells and incorporated into their chromatin. We found that the incorporation of histones H2A and H2A.Z mainly occurred at less condensed chromatin (open), suggesting that the condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. This led to the recapitulation of the pre-existing chromatin structure: the genome-wide even distribution of H2A and the exclusion of H2A.Z from the closed chromatin. Intriguingly, an H2A.Z mutant with mutations in the developmentally essential region was incorporated into closed chromatin. Our study revealed that the combination of chromatin structure and DNA replication dictates the differential histone deposition for maintaining the epigenetic chromatin states.
Structural and functional characterisation of SiiA, an auxiliary protein from the SPI4-encoded type 1 secretion system fromSalmonella enterica
Authors: Kirchweger Peter , Weiler Sigrid , Egerer-Sieber Claudia , Blasl Anna-Theresa , Hoffmann Stefanie , Schmidt Christiane , Sander Nathalie , Merker Dorothee , Gerlach Roman G. , Hensel Michael , Muller Yves A. 
Published: May 2019

AbstractSalmonellainvasion is mediated by a concerted action of theSalmonellapathogenicity island 4 (SPI4)-encoded type one secretion system (T1SS) and the SPIl-encoded type three secretion system (T3SS-1). The SPI4-encoded T1SS establishes the first contact to the host membrane. It consists of five proteins (SiiABCDF) that secrete the giant adhesin SiiE. The exact mechanism by which the T1SS enables host cell recognition remains unclear. Here, we investigated structure-function relationships in SiiA, a non-canonical T1SS subunit located at the inner membrane (IM). We observe that SiiA consists of a membrane domain, an intrinsically disordered periplasmic linker region and a folded globular periplasmic domain (SiiA-PD). The crystal structure of SiiA-PD shows homology to that of MotB-PD and other peptidoglycan (PG)-binding domains. Indeed, SiiA-PD binds PGin vitroalbeit at an acidic pH, only, whereas MotB-PD binds PG from pH 5.8 to 8. Mutation of Arg162 in SiiA impedes PG binding and reducesSalmonellainvasion efficacy of polarized epithelial cells. SiiA forms a complex with SiiB at the IM, and the SiiA-MotB homology is likely paralleled by a SiiB-MotA homology. We show that, in addition to PG binding, the SiiAB complex translocates protons across the IM. Substituting Asp13 in SiiA impairs proton translocation. Overall, SiiA displays many properties previously observed in MotB. However, whereas the MotAB complex uses the proton motif force (PMF) to energize the bacterial flagellum, it remains to be shown how the use of the PMF by SiiAB assists T1SS function and ultimatelySalmonellainvasion.
PhenoGMM: Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity
Authors: Rubbens Peter , Props Ruben , Kerckhof Frederiek-Maarten , Boon Nico , Waegeman Willem 
Published: May 2019

AbstractMicrobial flow cytometry allows to rapidly characterize microbial communities. Recent research has demonstrated a moderate to strong connection between the cytometric diversity and taxonomic diversity based on 16S rRNA gene amplicon sequencing data. This creates the opportunity to integrate both types of data to study and predict the microbial community diversity in an automated and efficient way. However, microbial flow cytometry data results in a number of unique challenges that need to be addressed. The results of our work are threefold: i) We expand current microbial cytometry fingerprinting approaches by proposing and validating a model-based fingerprinting approach based upon Gaussian Mixture Models, which we calledPhenoGMM. ii) We show that microbial diversity can be rapidly estimated byPhenoGMM. In combination with a supervised machine learning model, diversity estimations based on 16S rRNA gene amplicon sequencing data can be predicted. iii) We evaluate our method extensively by using multiple datasets from different ecosystems and compare its predictive power with a generic binning fingerprinting approach that is commonly used in microbial flow cytometry. These results demonstrate the strong connection between the genetic make-up of a microbial community and its phenotypic properties as measured by flow cytometry. Our workflow facilitates the study of microbial diversity and community dynamics using flow cytometry in a fast and quantitative way.ImportanceMicroorganisms are vital components in various ecoystems on Earth. In order to investigate the microbial diversity, researchers have largely relied on the analysis of 16S rRNA gene sequences from DNA. Flow cytometry has been proposed as an alternative technique to characterize microbial community diversity and dynamics. It is an optical technique, able to rapidly characterize a number of phenotypic properties of individual cells. So-called fingerprinting techniques are needed in order to describe microbial community diversity and dynamics based on flow cytometry data. In this work, we propose a more advanced fingerprinting strategy based on Gaussian Mixture Models. When samples have been analyzed by both flow cytometry and 16S rRNA gene amplicon sequencing, we show that supervised machine learning models can be used to find the relationship between the two types of data. We evaluate our workflow on datasets from different ecosystems, illustrating its general applicability for the analysisof microbial flow cytometry data.PhenoGMMfacilitates the rapid characterization and predictive modelling of microbial diversity using flow cytometry.
Effects of mid-frontal brain stimulation on sustained attention
Authors: van Schouwenburg Martine R. , Sligte Ilja G. , Giffin Michael R. , Günther Franziska , Koster Dirk , Spronkers Floortje S. , Vos Anna , Slagter Heleen A. 
Published: May 2019

AbstractSustained attention is defined as the ability to maintain attention over longer periods of time, which typically declines with time on task (i.e., the vigilance decrement). Previous studies have suggested an important role for the dorsomedial prefrontal cortex (mPFC) in sustained attention. In two experiments, we aimed to enhance sustained attention by applying transcranial electrical current stimulation over the mPFC during a sustained attention task. In the first experiment, we applied transcranial direct current stimulation (tDCS) in a between-subject design (n=97): participants received either anodal, cathodal, or sham stimulation. Contrary to our prediction, we found no effect of stimulation on the vigilance decrement. In the second experiment, participants received theta and alpha transcranial alternating current stimulation (tACS) in two separate sessions (n=47, within-subject design). Here, we found a frequency-dependent effect on the vigilance decrement, such that contrary to our expectation, participants’ performance over time became worse after theta compared to alpha stimulation. However, this result needs to be interpreted with caution given that this effect could be driven by differential side effects between the two stimulation frequencies. To conclude, across two studies, we were not able to reduce the vigilant decrement using tDCS or theta tACS.
Higher surfaces of a crop in the landscape increase outbreak risks the following growing season
Authors: Delaune T. , Ballot R. , Sausse C. , Felix I. , Chen M. , Maupas F. , Valantin-Morison M. , Makowski D. , Barbu C. 
Published: May 2019

AbstractThe use of fungicides and insecticides by farmers represents a major threat to biodiversity1, endangering agriculture itself2,3. Landscapes could be designed4to take advantage of the dependencies of pests5,6, pathogens7and their natural enemies8on landscape elements. However, the complexity of the interactions makes it difficult to establish general rules. Despite initial enthusiasm9, the many studies opposing cultivated and semi-natural habitats have not revealed a homogeneous response of pests10and pathogens11to semi-natural habitats. In addition, the question of the impact of crop diversity on pests and pathogens remains largely open12. Based on about half a million observations over nine years on 30 major field crop pests and pathogens spread over all latitudes of metropolitan France, we show that the outbreak risk increases with the area of the host crop in the landscape the previous growing season. The impact on the risk of the host crop area the ongoing growing season diverges between animal pests and pathogens. We also confirm that woodlands, scrublands, hedgerows and grasslands do not have a consistent effect over the spectrum of pests. The spatial and temporal distribution of the resource, the host crop, generally prevails over the effects of potential alternative habitats. Territorial and temporal coordination generally promoting crop diversity but excluding a crop at risk a given year may prove to be key levers for reducing pesticide use14.
Follicular regulatory T cells can access the germinal centre independently of CXCR5
Authors: Vanderleyden Ine , Fra-Bido Sigrid C. , Innocentin Silvia , Okkenhaug Hanneke , Evans-Bailey Nicola , Pierson Wim , Linterman Michelle A. 
Published: May 2019

SummaryThe germinal centre (GC) response is critical for generating high-affinity humoral immunity and immunological memory, which forms the basis of successful immunisation. Control of the GC response is thought to require follicular regulatory T (Tfr) cells, a subset of suppressive Foxp3+ Treg cells located within GCs. Relatively little is known about the exact role of Tfr cells within the GC, and the mechanism/s through which they exert their suppressive function. A unique feature of Tfr cells is their reported CXCR5-dependent localisation to the GC. Here we show that the lack of CXCR5 on Foxp3+ regulatory T cells resulted in a reduced frequency, but not an absence of, GC-localised Tfr cells. This demonstrates that additional, CXCR5-independent mechanisms facilitate Treg cell homing to the GC.
SYCP2translocation-mediated dysregulation and frameshift variants cause human male infertility
Authors: Schilit Samantha L.P. , Menon Shreya , Friedrich Corinna , Kammin Tammy , Wilch Ellen , Hanscom Carrie , Jiang Sizun , Kliesch Sabine , Talkowski Michael E. , Tüttelmann Frank , MacQueen Amy J. , Morton Cynthia C. 
Published: May 2019

ABSTRACTInfertility is one of the most common disorders for men of reproductive age. To identify novel genetic etiologies, we studied a male with severe oligozoospermia and 46, XY,t(20;22)(q13.3;q11.2). We identified exclusive overexpression ofSYCP2from the der(20) allele that is hypothesized to result from enhancer adoption. Modeling the dysregulation in budding yeast resulted in disruption of the synaptonemal complex, a common cause of defective spermatogenesis in mammals. Exome sequencing of infertile males revealed three novel heterozygousSYCP2frameshift variants in additional subjects with cryptozoospermia and azoospermia. This study provides the first evidence ofSYCP2-mediated male infertility in humans.
Using citizen science data to define and track restoration targets in urban areas
Authors: Callaghan Corey T. , Major Richard E. , Lyons Mitchell B. , Martin John M. , Wilshire John H. , Kingsford Richard T. , Cornwell William K. 
Published: May 2019

Abstract

Habitat fragmentation and land degradation, directly and indirectly caused by urbanization, are drastically altering the world's ecosystems and are therefore driving an imperative for ecological restoration within the world's cities. Current methods for the implementation and monitoring of restoration are limited. Restoration ecology needs cost‐effective and repeatable tools for tracking changes at global scales, but with local relevance.

We propose the Urban Greenspace Integrity Index—a locally relevant measure of an urban greenspace's response to urbanization, derived from widely accessible citizen science data. Unlike classical measurements of biodiversity (e.g. species richness, species diversity), this index measures species‐specific responses to continuous measures of urbanization.

Increases in this index are evidence of a successful urban restoration project; that is, restoration results in a community shift that favours urban‐sensitive species. Importantly, data for this index are easily and efficiently collected by citizen scientists, providing long‐term repeatable data. This urban index, calculated from greenspace surveys, correlates with and complements traditional biodiversity metrics.

Synthesis and applications. Policymakers and practitioners can use the index—a measure of the urbanness of the local bird community—to define and track restoration of urban ecosystems, effectively measuring changes in biodiversity in response to urbanization: measuring whether the urbanness of the bird community changes through time. Importantly, this index can be calculated using citizen science data, providing a potentially long‐term monitoring effort of restoration projects.
Bird services and disservices to strawberry farming in Californian agricultural landscapes
Authors: Gonthier David J. , Sciligo Amber R. , Karp Daniel S. , Lu Adrian , Garcia Karina , Juarez Gila , Chiba Taiki , Gennet Sasha , Kremen Claire 
Published: May 2019

Abstract

Bird conservation in agricultural settings can be controversial. While some bird species damage some crops, others suppress insect pests. Few studies have simultaneously compared bird services and disservices to assess their net impact.

Using an exclusion experiment in six California strawberry farms, we show that bird suppression of berry damage by insect pests (about 3.8% of berries) is similar in magnitude to the damage birds inflict on strawberries (about 3.2% of berries).

Across 27 farms, we found that bird species richness and the relative abundance of insectivorous birds increased, while the relative abundance of strawberry‐eating birds and bird damage decreased on farms with more semi‐natural land cover in the surrounding landscapes (1000 m radius).

Relative to homogeneous farms, those that implemented diversification practices, such as hedgerows, flower strips or increased crop diversity, had greater bird species richness, total relative abundance, insectivore abundance and strawberry‐eating bird abundance.

Synthesis and applications. Conserving semi‐natural land cover in the surrounding landscape benefits bird species richness locally and aids farmers through reduced abundance of strawberry‐eating birds and bird damage. These results highlight the need to consider both the services and disservices of birds when making management decisions.
Predicting the spatial dynamics of Wolbachia infections in Aedes aegypti arbovirus vector populations in heterogeneous landscapes
Authors: Hancock Penelope A. , Ritchie Scott A. , Koenraadt Constantianus J. M. , Scott Thomas W. , Hoffmann Ary A. , Godfray H. Charles J. 
Published: May 2019

Abstract

A promising strategy for reducing the transmission of dengue and other arboviral human diseases by Aedes aegypti mosquito vector populations involves field introductions of the endosymbiotic bacteria Wolbachia. Wolbachia infections inhibit viral transmission by the mosquito, and can spread between mosquito hosts to reach high frequencies in the vector population. Wolbachia spreads by maternal transmission, and spread dynamics can be variable and highly dependent on natural mosquito population dynamics, population structure and fitness components.

We develop a mathematical model of an A. aegypti metapopulation that incorporates empirically validated relationships describing density‐dependent mosquito fitness components. We assume that density dependent relationships differ across subpopulations, and construct heterogeneous landscapes for which model‐predicted patterns of variation in mosquito abundance and demography approximate those observed in field populations. We then simulate Wolbachia release strategies similar to that used in field trials.

We show that our model can produce rates of spatial spread of Wolbachia similar to those observed following field releases.

We then investigate how different types of spatio‐temporal variation in mosquito habitat, as well as different fitness costs incurred by Wolbachia on the mosquito host, influence predicted spread rates. We find that fitness costs reduce spread rates more strongly when the habitat landscape varies temporally due to stochastic and seasonal processes.

Synthesis and applications: Our empirically based modelling approach represents effects of environmental heterogeneity on the spatial spread of Wolbachia. The models can assist in interpreting observed spread patterns following field releases and in designing suitable release strategies for targeting spatially heterogeneous vector populations.
Ecosystem services and disservices by birds, bats and monkeys change with macadamia landscape heterogeneity
Authors: Linden Valerie M. G. , Grass Ingo , Joubert Elsje , Tscharntke Teja , Weier Sina M. , Taylor Peter J. 
Published: May 2019

AbstractThe relative importance of ecosystem services and disservices can change with landscape structure in a poorly understood way.We compare the impact of biocontrol, provided by bats and birds, with that of crop raiding by vervet monkeys on yield in South African macadamia orchards. Insectivorous bats and birds are known to feed on macadamia pest insect species, like the macadamia nut borer or the green vegetable bug. Vervet monkeys move into the orchards during the day to feed on premature macadamia nuts. Bats, birds and monkeys benefit from patches of natural vegetation adjacent to orchards.With exclusion experiments (four treatments: day, night, day and night, control) we quantified the relative importance of biocontrol and crop raiding on yield, comparing two different landscape settings of the orchards, a natural and a human‐modified.Crop raiding occurred only close to natural vegetation and caused yield losses of about 26%. Biocontrol by bats and birds was higher near natural vegetation, but still significant in human‐modified landscapes, at up to 530 m distance to forest patches. Prevented biocontrol through the exclusion of bats and birds resulted in yield losses of up to 60%.Effects of biocontrol by bats and birds (USD ~5,000 ha/year) were economically more important than the losses of crop raiding (USD ~1,600 ha/year). As both are linked to the vicinity of forest patches, the removal of natural vegetation to limit monkey abundances would also limit biocontrol service provision.Synthesis and applications. This study highlights the high economic benefits of biocontrol by bats and birds, which outweighed negative impacts through yield losses caused by crop raiding monkeys. Management practices to prevent crop damage, such as guarding, excluding vertebrates or removal of adjacent natural vegetation, would also limit access for bats and birds and the great economic benefits provided by their biocontrol. Ecosystem services by bats and birds can be promoted by the exposure of artificial roost and nest sites, but research into species‐specific preferences is needed. The education of farmers is crucial, as many are unaware of the benefits from birds and bats and the fact that these benefits can outweigh the disadvantages of the monkeys’ crop raiding.
Cyclo(tetrahydroxybutyrate) production is sufficient to distinguish between Xenorhabdus and Photorhabdus isolates in Thailand
Authors: Tobias Nicholas J. , Parra‐Rojas César , Shi Yan‐Ni , Shi Yi‐Ming , Simonyi Svenja , Thanwisai Aunchalee , Vitta Apichat , Chantratita Narisara , Hernandez‐Vargas Esteban A. , Bode Helge B. 
Published: May 2019

SummaryBacteria of the genera Photorhabdus and Xenorhabdus produce a plethora of natural products to support their similar symbiotic life cycles. For many of these compounds, the specific bioactivities are unknown. One common challenge in natural product research when trying to prioritize research efforts is the rediscovery of identical (or highly similar) compounds from different strains. Linking genome sequence to metabolite production can help in overcoming this problem. However, sequences are typically not available for entire collections of organisms. Here, we perform a comprehensive metabolic screening using HPLC‐MS data associated with a 114‐strain collection (58 Photorhabdus and 56 Xenorhabdus) across Thailand and explore the metabolic variation among the strains, matched with several abiotic factors. We utilize machine learning in order to rank the importance of individual metabolites in determining all given metadata. With this approach, we were able to prioritize metabolites in the context of natural product investigations, leading to the identification of previously unknown compounds. The top three highest ranking features were associated with Xenorhabdus and attributed to the same chemical entity, cyclo(tetrahydroxybutyrate). This work also addresses the need for prioritization in high‐throughput metabolomic studies and demonstrates the viability of such an approach in future research.