bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergent evolution of reduced eggshell conductance in avian brood parasites
Authors: McClelland Stephanie C. , Jamie Gabriel A. , Waters Katy , Caldas Lara , Spottiswoode Claire N. , Portugal Steven J. 
Published: February 2019

Brood parasitism has evolved independently in several bird lineages, giving rise to strikingly similar behavioural adaptations that suggest convergent evolution. By comparison, convergence of physiological traits that optimize this breeding strategy has received much less attention, yet these species share many similar physiological traits that optimize this breeding strategy. Eggshell structure is important for embryonic development as it controls the flux of metabolic gases, such as O2, CO2and H2O, into and out of the egg; in particular, water vapour conductance (GH2O) is an essential process for optimal development of the embryo. Previous work has shown that common cuckoos (Cuculus canorus) have a lower than expected eggshellGH2Ocompared with their hosts. Here, we sought to test whether this is a trait found in other independently evolved avian brood parasites, and therefore reflects a general adaptation to a parasitic lifestyle. We analysedGH2Ofor seven species of brood parasites from four unique lineages as well as for their hosts, and combined this with species from the literature. We found lower than expectedGH2Oamong all our observed brood parasites both compared with hosts (except for brown-headed cowbirds (Molothrus ater)) and compared with the expected rates given their phylogenetic positions. These findings suggest that a loweredGH2Omay be a general adaptation for brood parasitism, perhaps helping the parasite nestling to develop greater aerobic fitness.This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Patterns of host use by brood parasiticMaculineabutterflies across Europe
Authors: Tartally András , Thomas Jeremy A. , Anton Christian , Balletto Emilio , Barbero Francesca , Bonelli Simona , Bräu Markus , Casacci Luca Pietro , Csősz Sándor , Czekes Zsolt , Dolek Matthias , Dziekańska Izabela , Elmes Graham , Fürst Matthias A. , Glinka Uta , Hochberg Michael E. , Höttinger Helmut , Hula Vladimir , Maes Dirk , Munguira Miguel L. , Musche Martin , Nielsen Per Stadel , Nowicki Piotr , Oliveira Paula S. , Peregovits László , Ritter Sylvia , Schlick-Steiner Birgit C. , Settele Josef , Sielezniew Marcin , Simcox David J. , Stankiewicz Anna M. , Steiner Florian M. , Švitra Giedrius , Ugelvig Line V. , Van Dyck Hans , Varga Zoltán , Witek Magdalena , Woyciechowski Michal , Wynhoff Irma , Nash David R. 
Published: February 2019

The range of hosts exploited by a parasite is determined by several factors, including host availability, infectivity and exploitability. Each of these can be the target of natural selection on both host and parasite, which will determine the local outcome of interactions, and potentially lead to coevolution. However, geographical variation in host use and specificity has rarely been investigated.Maculinea(=Phengaris) butterflies are brood parasites ofMyrmicaants that are patchily distributed across the Palæarctic and have been studied extensively in Europe. Here, we review the published records of ant host use by the EuropeanMaculineaspecies, as well as providing new host ant records for more than 100 sites across Europe. This comprehensive survey demonstrates that while all but one of theMyrmicaspecies found onMaculineasites have been recorded as hosts, the most common is often disproportionately highly exploited. Host sharing and host switching are both relatively common, but there is evidence of specialization at many sites, which varies amongMaculineaspecies. We show that mostMaculineadisplay the features expected for coevolution to occur in a geographic mosaic, which has probably allowed these rare butterflies to persist in Europe.This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Bacterial Phage Tail-like Structure Kills Eukaryotic Cells by Injecting a Nuclease Effector
Authors: Rocchi Iara , Ericson Charles , Malter Kyle E. , Zargar Sahar , Eisenstein Fabian , Pilhofer Martin , Beyhan Sinem , Shikuma Nicholas J. 
Published: February 2019

ABSTRACTMany bacteria interact with target organisms using syringe-like structures called Contractile Injection Systems (CIS). CIS structurally resemble headless bacteriophages and share evolutionarily related proteins such as the tail tube, sheath, and baseplate complex. Recent evidence shows that CIS are specialized to puncture membranes and often deliver effectors to target cells. In many cases, CIS mediate trans-kingdom interactions between bacteria and eukaryotes, however the effectors delivered to target cells and their mode of action are often unknown. In this work, we establish an in vitro model to study a CIS called Metamorphosis Associated Contractile structures (MACs) that target eukaryotic cells. We show that MACs kill two eukaryotic cell lines, Fall Armyworm Sf9 cells and J774A.1 murine macrophage cells through the action of a newly identified MAC effector, termed Pne1. To our knowledge, Pne1 is the first CIS effector exhibiting nuclease activity against eukaryotic cells. Our results define a new mechanism of CIS-mediated bacteria-eukaryote interaction and are a first step toward understanding structures with the potential to be developed as novel delivery systems for eukaryotic hosts.
Climatic Factors in Relation to Diarrhea for Informed Public Health Decision-Making: A Novel Methodological Approach
Authors: Ikeda Takayoshi , Kapwata Thandi , Behera Swadhin K. , Minakawa Noboru , Hashizume Masahiro , Sweijd Neville , Mathee Angela , Wright Caradee Yael 
Published: February 2019

AbstractBackgroundDiarrheal disease is one of the leading causes of morbidity and mortality globally, particularly in children under 5 years of age. Factors related to diarrheal disease incidence include infection, malnutrition, and exposure to contaminated water and food. Climate factors also contribute to diarrheal disease.ObjectivesWe aimed to explore the relationship between temperature, precipitation and diarrhea case counts of hospital admissions among vulnerable communities living in a rural setting in South Africa.MethodsWe applied a novel approach of ‘contour analysis’ to visually examine simultaneous observations in frequencies of anomalously high and low diarrhea case counts occurring in a season and assigning colors to differences that were statistically significant based on chi-squared test results.ResultsThere was a significantly positive difference between high and low ‘groups’ when there was a lack of rain (0 mm of cumulative rain) for 1 to 2 weeks in winter for children under 5.Diarrhea prevalence was greater among children under 5 years when conditions were hotter than usual during winter and spring.DiscussionDry conditions may lead to increased water storage raising the risks of water contamination. Reduced use of water for personal hygiene and cleaning of outdoor pit latrines affect sanitation quality. Rural communities require adequate and uninterrupted water provision and healthcare providers should raise awareness about potential diarrheal risks especially during the dry season.
Minimal effects of proto-Y chromosomes on house fly gene expression in spite of evidence that selection maintains stable polygenic sex determination
Authors: Son Jae Hak , Kohlbrenner Tea , Heinze Svenia , Beukeboom Leo , Bopp Daniel , Meisel Richard P. 
Published: February 2019

AbstractSex determination is the developmental process by which organismal sex is established. Sex determination evolves fast, often due to changes in the master regulators at the top of the pathway. In addition, some species are polymorphic for multiple different master regulators within natural populations. Understanding the forces that maintain this polygenic sex determination can be informative of the factors that drive the evolution of sex determination. The house fly,Musca domestica, is a well-suited model to those ends because natural populations harbor male-determining loci on each of the six chromosomes and a bi-allelic female-determiner. Multiple lines of evidence suggest that natural selection maintains polygenic sex determination in house fly. However, previous work found that there are very few sequence differences between proto-Y chromosomes and their homologous X chromosomes. This suggests that there is not much genetic variation upon which natural selection could act to maintain polygenic sex determination in house fly. To address this paradox, we performed RNA-seq experiments that examine the effects of the two most common proto-Y chromosomes on gene expression. We find that the proto-Y chromosomes do indeed have a relatively minor effect on gene expression, as expected based on the minimal X-Y sequence differences. Despite these minimal gene expression differences, we identify some patterns that are consistent with sex-specific selection acting on phenotypic effects of proto-Y chromosomes. Our results suggest that, if natural selection maintains polygenic sex determination in house fly, the phenotypic differences under selection are minor and possibly depend on ecological contexts that were not tested in our experimental design.
Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types
Authors: Rieber Lila , Mahony Shaun 
Published: February 2019

AbstractCell-type-specific chromosome conformation is correlated with differential gene regulation. Broad compartmentalization into two compartments (A & B) is proposed to be the main driver of cell-specific chromosome organization. However it is unclear what fraction of chromosome conformation changes between cell types and conditions is independent of changes in compartmentalization and whether any such compartment-independent reorganization is functionally important. We developed MultiMDS to jointly infer and align 3D chromosomal structures, thereby enabling a quantitative comparison of locus-specific changes across Hi-C datasets. We compared Hi-C datasets from yeast, which lack compartmentalization, grown with and without galactose. These comparisons confirmed known relocalizations as well as identifying additional examples. We also compared mammalian datasets across a variety of cell lines. We found a consistent enrichment for changes along the A/B compartment (nuclear interior/nuclear periphery) axis, even when comparing the same cell type from different individuals. Despite the prevalence of compartment changes, we consistently find compartment-independent relocalizations of loci that are within the A compartment in both compared cell types. Some such intra-compartment relocalizations involve loci that display enhancer-associated histone marks in one cell type and polycomb-associated histone marks in the other. MultiMDS thus enables a new way to compare chromosome conformations across two Hi-C datasets.Availabilityhttps://github.com/seqcode/multimds
Volatile organic chemical analyser (eNose) diagnosis of dogs naturally infected with visceral leishmaniasis in Brazil
Authors: Staniek ME , Sedda L , Gibson TD , de Souza CF , Costa EM , Dillon RJ , Hamilton JGC 
Published: February 2019

AbstractVisceral leishmaniasis (VL) in Brazil is a neglected vector-borne tropical parasitic disease that is responsible for several thousand human deaths every year. The numbers of cases more than doubled between 1990 and 2016. Transmission occurs when sand flies become infected after feeding on infected dogs (the reservoir host) and then subsequently on humans. A major component of the VL control effort is the identification and euthanasia of infected dogs to remove them as a source of infection. Rapid, accurate identification of infected dogs would be key to this strategy.Here we demonstrate the potential of a volatile organic chemical analyser (eNose) to rapidly and accurately identify dogs infected with Leishmania infantum parasites. The eNose could discriminate between the odours present in the hair of infected and uninfected dogs with greater than 95% sensitivity and 95% specificity. The device was sufficiently sensitive to be able to identify infected dogs even when parasite loads in the circulating blood were very low.Future improvements to VOC analyser technology, portability and ease of use suggest that this methodology could significantly improve the diagnosis of VL infected dogs in Brazil and elsewhere and with other parasitic diseases such as Malaria, Chaga’s Disease and Leishmania in humans.
Interacting fruit flies synchronize behavior
Authors: Klibaite Ugne , Shaevitz Joshua W. 
Published: February 2019

AbstractSocial behaviors are ubiquitous and crucial to an animal’s survival and success. The behaviors an animal performs in a social setting are affected by internal factors, inputs from the environment, and interaction with others. To quantify social behaviors, we need to measure both the stochastic nature of behavior of isolated individuals and how these behaviors change as a function of the environment and features of social interaction. We probed the behavior of male and female fruit flies in a circular arena as individuals and within all possible pairings. By combining measurements of the animals’ position in the arena with an unsupervised analysis of their behaviors, we fully define the effects of position in the environment and the presence of a partner on locomotion, grooming, singing, and other behaviors that make up an animal’s repertoire. We find that geometric context tunes behavioral preference, pairs of animals synchronize their behavioral preferences across trials, and paired individuals display signatures of behavioral mimicry.
hilldiv: an R package for the integral analysis of diversity based on Hill numbers
Authors: Alberdi Antton , Gilbert M Thomas P 
Published: February 2019

AbstractHill numbers provide a powerful framework for measuring, comparing and partitioning the diversity of biological systems as characterised using high throughput DNA sequencing approaches. In order to facilitate the implementation of Hill numbers into such analyses, whether focusing on diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses, we present a new R package. ‘Hilldiv’ provides a set of functions to assist analysis of diversity based on Hill numbers, using count tables (e.g. OTU, ASV) and associated phylogenetic trees as inputs. Multiple functionalities of the library are introduced, including diversity measurement, diversity profile plotting, diversity comparison between samples and groups, multi-level diversity partitioning and (dis)similarity measurement. All of these are grounded in abundance-based and incidence-based Hill numbers, and can accommodate phylogenetic or functional correlation among OTUs or ASVs. The package can be installed from CRAN or Github, and tutorials and example scripts can be found in the package’s page (https://github.com/anttonalberdi/hilldiv).
The architect of virus assembly: the portal protein complex nucleates procapsid assembly in bacteriophage P22
Authors: Motwani Tina , Teschke Carolyn M. 
Published: February 2019

AbstractThe genetic material of tailed dsDNA bacteriophages, herpesviruses and adenoviruses is packaged into a precursor capsid through a 12-mer ring-shaped protein complex called the portal protein, located at a unique 5-fold vertex. In several phages and viruses, including T4, Φ29, and HSV-1, the dodecameric portal protein forms a nucleation complex with scaffolding proteins to initiate procapsid assembly, thereby ensuring incorporation of only one portal complex per capsid. However, for bacteriophage P22, the role of its portal protein in initiation of procapsid assembly is unclear. We recently developed anin vitroP22 assembly assay where portal protein is co-assembled into procapsid-like particles. We also showed that scaffolding protein catalyzes oligomerization of monomeric portal protein into 12-mer rings, and possibly forming a scaffolding-protein nucleation complex that results in one portal complex per P22 procapsid. Here, we present evidence substantiating that P22 portal protein, similar to the other dsDNA viruses, can act as an assembly nucleator. We find that the presence of P22 portal protein is able to increase the rate of particle assembly. Additionally, we show that P22 portal protein proper contributes to proper morphology of the assembled particles. Our results highlight a key function of portal protein as an assembly initiator, a feature likely conserved among these classes of dsDNA viruses.
Systematic Analysis of Metabolic Pathway Distributions of Bacterial Energy Reserves
Authors: Wang Liang , Yang Jianye , Huang Yue , Liu Qinghua , Xu Yaping , Piao Xue , Wise Michael J. 
Published: February 2019

AbstractMetabolism of energy reserves are essential for bacterial functions such as pathogenicity, metabolic adaptation, and environmental persistence, etc. Previous bioinformatics studies have linked gain or loss of energy reserves such as glycogen and polyphosphate (polyP) with host-pathogen interactions and bacterial virulence based on a comparatively small number of bacterial genomes or proteomes. Thus, understanding the distribution patterns of energy reserves metabolism across bacterial species provides a shortcut route to look into bacterial lifestyle and physiology theoretically. So far, five major energy reserves have been identified in bacteria due to their effective capacity to support bacterial persistence under nutrient deprivation conditions, which include wax ester (WE), triacylglycerol (TAG), polyhydroxyalkanoates (PHA), polyphosphate, and glycogen. Although unknown pathways directly involved in energy reserves keep being discovered with the continuous endeavour of molecular microbiologists and it is currently rather clear about the enzymes related with the metabolism of energy reserves, there is a lack of systematic study of the pathway or key enzyme distributions of the five energy reserves in bacteria from an evolutionary point of view. With the fast development of sequencing technology, abundant bacterial proteomes are available in public database now. In this study, we sourced 8214 manually reviewed bacterial reference proteomes from UniProt database and used statistical models to search homologous sequences of key enzymes related with energy reserves. The distribution patterns of the pathways for energy reserves metabolism are visualized in taxonomy-based phylogenetic trees. According to the study, it was revealed that specific pathways and enzymes are associated with certain types of bacterial groups, which provides evolutionary insights into the understanding of their origins and functions. In addition, the study also confirmed that loss of energy reserves is correlated with bacterial genome reduction. Through this analysis, a much clearer picture about energy reserves metabolism in bacteria is present, which could serve a guide for further theoretical and experimental analyses of energy reserves metabolism in bacteria.
Enhanced TF binding site maps improve regulatory networks learned from accessible chromatin data
Authors: Kulkarni Shubhada R. , Jones D. Marc , Vandepoele Klaas 
Published: February 2019

ABSTRACTDetermining where transcription factors (TF) bind in genomes provides insights into which transcriptional programs are active across organs, tissue types, and environmental conditions. Recent advances in high-throughput profiling of regulatory DNA have yielded large amounts of information about chromatin accessibility. Interpreting the functional significance of these datasets requires knowledge of which regulators are likely to bind these regions. This can be achieved by using information about TF binding preferences, or motifs, to identify TF binding events that are likely to be functional. Although different approaches exist to map motifs to DNA sequences, a systematic evaluation of these tools in plants is missing. Here we compare four motif mapping tools widely used in the Arabidopsis research community and evaluate their performance using chromatin immunoprecipitation datasets for 40 TFs. Downstream gene regulatory network (GRN) reconstruction was found to be sensitive to the motif mapper used. We further show that the low recall of FIMO, one of the most frequently used motif mapping tools, can be overcome by using an Ensemble approach, which combines results from different mapping tools. Several examples are provided demonstrating how the Ensemble approach extends our view on transcriptional control for TFs active in different biological processes. Finally, a new protocol is presented to efficiently derive more complete cell type-specific GRNs through the integrative analysis of open chromatin regions, known binding site information, and expression datasets.
Classifying drugs by their arrhythmogenic risk using machine learning
Authors: Costabal Francisco Sahli , Seo Kinya , Ashley Euan , Kuhl Ellen 
Published: February 2019

Abstract.An undesirable side effect of drugs are cardiac arrhythmias, in particular a condition called torsades de pointes. Current paradigms for drug safety evaluation are costly, lengthy, and conservative, and impede efficient drug development. Here we combine multiscale experiment and simulation, high-performance computing, and machine learning to create an easy-to-use risk assessment diagram to quickly and reliable stratify the pro-arrhythmic potential of new and existing drugs. We capitalize on recent developments in machine learning and integrate information across ten orders of magnitude in space and time to provide a holistic picture of the effects of drugs, either individually or in combination with other drugs. We show, both experimentally and computationally, that drug-induced arrhythmias are dominated by the interplay of two currents with opposing effects: the rapid delayed rectifier potassium current and the L-type calcium current. Using Gaussian process classification, we create a classifier that stratifies safe and arrhythmic domains for any combinations of these two currents. We demonstrate that our classifier correctly identifies the risk categories of 23 common drugs, exclusively on the basis of their concentrations at 50% current block. Our new risk assessment diagram explains under which conditions blocking the L-type calcium current can delay or even entirely suppress arrhythmogenic events. Using machine learning in drug safety evaluation can provide a more accurate and comprehensive mechanistic assessment of the pro-arrhythmic potential of new drugs. Our study shapes the way towards establishing science-based criteria to accelerate drug development, design safer drugs, and reduce heart rhythm disorders.