bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colonizations drive host shifts, diversification of preferences and expansion of herbivore diet breadth
Authors: Singer Michael C , Parmesan Camille 
Published: April 2020

ABSTRACTDynamics of herbivorous insect diet breadth are important in generation of novel pests, biological control of weeds and as indicators of global change impacts. But what forces and events drive these dynamics? Here we present evidence for a novel scenario: that specialization increases in persistent populations, but that, at the species level, this trend is countered by effects of colonizations. Colonizations cause host shifts, which are followed by non-adaptive evolutionary expansions of diet breadth, adding transitory hosts during adaptation to the principal novel host.We base this thesis on long-term study of 15 independently-evolving populations of Edith’s Checkerspot butterfly, eight of which used fewer host genera in recent censuses than in the 1980’s, while none used more - a significant increase in specializaton. At the same time, two extintion/recolonization events were followed by temporary expansions of diet breadth. Behavioural experiments showed that these expansions were driven by within-population diversification of individual oviposition preferences. These results may explain an old puzzle: a significant negative association between population-level diet breadth and mtDNA diversity. Populations with fewer mtDNA haplotypes had broader diets, suggesting that diet breadth increases in younger, recently-colonized populations.A recent global meta-analysis of butterfly diets, using biogeographic data, explains latitudinal patterns of diet breadth by showing that poleward range expansions have caused reduced specialization. This implies broad applicability of our results, which provide a plausible mechanism for the latitudinal trends: colonizations at expanding range margins would increase population-level diet breadths, while population persistence in range interiors would facilitate increasing specialization.
Biological characterization of Euscelidius variegatus iflavirus 1
Authors: Ottati Sara , Persico Alberto , Rossi Marika , Bosco Domenico , Vallino Marta , Abbà Simona , Molinatto Giulia , Palmano Sabrina , Balestrini Raffaella , Galetto Luciana , Marzachì Cristina 
Published: April 2020

AbstractVirus-based biocontrol technologies represent sustainable alternatives to pesticides and insecticides. Phytoplasmas are prokaryotic plant pathogens causing severe losses to crops worldwide. Novel approaches are needed since insecticides against their insect vectors and rogueing of infected plants are the only available strategies to counteract phytoplasma diseases. A new iflavirus, named EVV-1, has been described in the leafhopper phytoplasma vectorEuscelidius variegatus, raising the potential to use virus-based application strategies against phytoplasma disease. Here transmission routes of EVV-1 are characterized, and localization within the host reveals the mechanism of insect tolerance to virus infection. Both vertical and horizontal transmission of EVV-1 occur and vertical transmission was more efficient. The virus is systemic and occurs in all life-stages, with the highest loads measured in ovaries and first to third instar nymphs. The basic knowledge gained here on the biology of the virus is crucial for possible future application of iflaviruses as biocontrol agents.
The MPS1 kinase NTE region has helical propensity and preferred conformations towards the TPR domain
Authors: Hiruma Yoshitaka , Matsoukas Minos-Timotheos , Touw Wouter G. , Spyroulias Georgios , Kops Geert J.P.L. , Ubbink Marcellus , Perrakis Anastassis 
Published: April 2020

AbstractThe mitotic spindle assembly checkpoint (SAC) ensures accurate segregation of chromosomes by preventing onset of anaphase until all chromosomes are properly attached to spindle microtubules. The Monopolar spindle 1 (MPS1) kinase is one of the SAC components, localizing at unattached kinetochores by an N-terminal localization module. This module comprises a flexible NTE module and the TPR domain, which we previously characterized for their contribution to kinetochore binding. Here we discuss the conformations of the highly flexible NTE with respect to the TPR domain, using paramagnetic NMR. The distance restraints derived from paramagnetic relaxation enhancements (PREs) show that the mobile NTE can be found in proximity of a large but specific part of the surface area of the TPR domain. To sample the conformational space of the NTE in the context of the NTE-TPR module, we used theab initioRosetta approach supplemented by paramagnetic NMR restraints. We find that many NTE residues have a propensity to form helical structures and that the module localizes at the convex surface of the TPR domain. This work demonstrates the highly dynamic nature of the interactions between the NTE and TPR domains and it shows that the convex rather than the canonical concave TPR surface mediates interactions, leading to the auto-inhibition that the TPR exerts upon the NTE region in the context of SAC signaling.
Deubiquitylase UCHL3 drives error correction at kinetochores and chromosome segregation independent of spindle assembly checkpoint
Authors: Jerabkova Katerina , Liao Yongrong , Kleiss Charlotte , Fournane Sadek , Durik Matej , Agote-Arán Arantxa , Brino Laurent , Sedlacek Radislav , Sumara Izabela 
Published: April 2020

AbstractEqual segregation of chromosomes during mitosis ensures euploidy of daughter cells. Defects in this process may result in imbalance in chromosomal composition and cellular transformation. Two surveillance pathways, the spindle assembly checkpoint (SAC) and the error-correction (EC), exist at kinetochores that monitor microtubule attachment and faithful segregation of chromosomes at the metaphase to anaphase transition. However, the molecular understanding of the interplay between EC and SAC signaling remains limited. Here we describe a role of deubiquitylase UCHL3 in the regulation of EC pathway during mitosis. Downregulation or inhibition of UCHL3 leads to improper attachments of chromosomes to spindle microtubules and to chromosome alignment defects during metaphase. Frequent segregation errors during anaphase and consequently aneuploidy is also observed upon inactivation of UCHL3. Surprisingly, UCHL3 is not involved in SAC signaling as both recruitment of SAC proteins to kinetochores and timely anaphase onset are not perturbed in UCHL3-deficient cells. Mechanistically, UCHL3 interacts with and deubiquitylates the mitotic kinase Aurora B known to drive both SAC and EC signaling. UCHL3 promotes interaction of Aurora B with MCAK, important EC factor but does not regulate Aurora B binding to other interacting partners or subcellular localization of Aurora B. Our results thus suggest that UCHL3-mediated deubiquitylation functionally separates EC from SAC signaling during mitosis and is critical for maintenance of euploidy in human cells.
CO2enhances the ability ofCandida albicansto form biofilms, overcome nutritional immunity and resist antifungal treatment
Authors: Pentland Daniel R. , Mühlschlegel Fritz A. , Gourlay Campbell W. 
Published: April 2020

AbstractC. albicansis the predominant fungal pathogen of humans and frequently colonises medical devices, such as voice prosthesis, as a biofilm. It is a dimorphic yeast that can switch between yeast and hyphal forms in response to environmental cues, a property that is essential during biofilm establishment and maturation. One such cue is the elevation of CO2levels, as observed in exhaled breath.. However, despite the clear medical relevance, the effects of CO2onC. albicansbiofilm growth has not been investigated to date. Here, we show that physiologically relevant CO2elevation enhances each stage of theC. albicansbiofilm forming process;from attachment through to maturation and dispersion.. The effects of CO2are mediated via the Ras/cAMP/PKA signalling pathway and the central biofilm regulators Efg1, Brg1, Bcr1 and Ndt80. Biofilms grown under elevated CO2conditions also exhibit increased azole resistance, tolerance to nutritional immunity and enhanced glucose uptake to support their rapid growth. These findings suggest thatC. albicanshas evolved to utilise the CO2signal to promote biofilm formation within the host. We investigate the possibility of targeting CO2activated processes and propose 2-Deoxyglucose as a drug that may be repurposed to preventC. albicansbiofilm formation on medical airway management implants. We thus characterise the mechanisms by which CO2promotesC. albicansbiofilm formation and suggest new approaches for future preventative strategies.
Integration of behavioral and biological variables using penalized regression: an application to the maternal immune activation model of autism
Authors: Paraschivescu Cristina , Barbosa Susana , Lorivel Thomas , Glaichenhaus Nicolas , Davidovic Laetitia 
Published: April 2020

AbstractMaternal immune activation (MIA) during pregnancy increases the odds of developing neuropsychiatric disorders such as autism spectrum disorder (ASD) later in life. In pregnant mice, MIA can be induced by injecting the viral mimic polyinosinic:polycytidylic acid (poly(I:C) to pregnant dams resulting in altered fetal neurodevelopmental and behavioral changes in their progeny. Although the murine MIA model has been extensively studied worldwide, the underlying mechanisms have only been partially elucidated. Furthermore, the murine MIA model suffers from lack of reproducibility, at least in part because it is highly influenced by subtle changes in environmental conditions. In human studies, multivariable (MV) statistical analysis is widely used to control for covariates including sex, age, exposure to environmental factors and many others. We reasoned that animal studies in general, and studies on the MIA model in particular, could therefore benefit from MV analyzes to account for complex phenotype interactions and high inter-individual variability. Here, we used a dataset consisting of 26 variables collected on 67 male pups during the course of several independent experiments on the MIA model. We then analyzed this dataset using penalized regression to identify variables associated within uteroexposure to MIA. In addition to confirming the association between some previously described biological variables and MIA, we identified new variables that could play a role in neurodevelopment alterations. Aside from providing new insights into variable interactions in the MIA model, this study highlights the importance of extending the use of MV statistics to animal studies.
Polygenic adaptation of rosette growth inArabidopsis thaliana
Authors: Wieters Benedict , Steige Kim A. , He Fei , Koch Evan M. , Ramos-Onsins Sebastián E. , Gu Hongya , Guo Ya-Long , Sunyaev Shamil , de Meaux Juliette 
Published: April 2020

AbstractThe rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate ofArabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four broad regions, including an outgroup set of genotypes from China. A field experiment conducted under natural conditions confirmed the ecological relevance of the observed variation. All genotypes markedly expanded their rosette diameter when the light supply was decreased, demonstrating that environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions. Yet, we detected significant levels of genetic variation both in growth rate and growth plasticity. Genome-wide association studies revealed that only 2 single nucleotide polymorphisms associate with genetic variation for growth above Bonferroni confidence levels. However, marginally associated variants were significantly enriched among genes with an annotated role in growth and stress reactions. Polygenic scores computed from marginally associated variants confirmed the polygenic basis of growth variation. For both light regimes, phenotypic divergence between the most distantly related population (China) and the various regions in Europe is smaller than the variation observed within Europe, indicating that some level of stabilizing selection constrains the evolution of growth rate. We observed that Spanish genotypes, however, reach a significantly larger size than Northern European genotypes. Tests of adaptive divergence and analysis of the individual burden of deleterious mutations reveal that adaptive processes have played a more important role in shaping regional differences in rosette growth than maladaptive evolution.
EXPRESSION OFMycobacterium tuberculosisRpsA INMycobacterium smegmatisINCREASES SUSCEPTIBILITY TO PYRAZINAMIDE
Authors: Antiparra Ricardo , Santos Marco , Toledo Angie , Gilman Robert H. , Kirwan Daniela E. , Sheen Patricia , Zimic Mirko 
Published: April 2020

ABSTRACTPyrazinamide (PZA) is one of the most important drugs used in combined antituberculous therapy. After the drug entersMycobacterium tuberculosisit is hydrolyzed by pyrazinamidase (PZAse) to the bactericidal molecule pyrazinoic acid (POA). Ribosomal protein S1 (RpsA) was recently identified as a possible target of PZA based on its binding activity to POA and capacity to inhibit trans-translation. However, its role is not completely understood.It has been proposed thatMycobacterium smegmatisRpsA is not capable of binding POA, unlikeM. tuberculosisRpsA. This may be due to the different amino acid sequence in the carboxy-terminal region of the two molecules: inM. smegmatisRpsA it is much closer to the sites that may interact with POA than inM. tuberculosisRpsA. These differences could be contributing, along with the presence of highly active POA efflux, to the natural resistance to PZA inM. smegmatis.To further understand the mechanisms of action of PZA and the role of RpsA in PZA susceptibility, we evaluated the effect of complementingM. tuberculosisRpsA expression inM. smegmatisusing pNIT mycobacterial non-integrative expression vector and then performed a PZA susceptibility test determining the minimum inhibitory concentration (MIC) of PZA. It was expected that chimeric ribosomes comprisingM. tuberculosisRpsA may be present and may affect PZA susceptibility.Our results showed a reduction in PZA MIC inM. smegmatiscomplemented with overexpressedM. tuberculosisRpsA compared to non-overexpressedM. smegmatis(468 µg/mL and >7500 µg/mL respectively).
The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA
Authors: Hao Jingjie , Chai Yen Ning , Ordóñez Raziel A. , Wright Emily E. , Archontoulis Sotirios , Schachtman Daniel P. 
Published: April 2020

AbstractThe determination of how microbial community structure changes within the soil profile, will be beneficial to understanding the long-term health of agricultural soil ecosystems and will provide a first step towards elucidating how deep soil microbial communities contribute to carbon sequestration. This study aimed to investigate the differences in the microbial community abundance, composition and diversity throughout from the surface layers down to deep soils in corn and soybean fields in Iowa, USA. We used 16S rRNA amplicon sequencing of soil samples to characterize the change in microbial community structure. Our results revealed decreased richness and diversity in bacterial community structure with increasing soil depth. We also observed distinct distribution patterns of bacterial community composition along soil profiles. Soil and root data at different depths enabled us to demonstrate that the soil organic matter, soil bulk density and plant water availability were all significant factors in explaining the variation in soil microbial community composition. Our findings provide valuable insights in the changes in microbial community structure to depths of 180 cm in one of the most productive agricultural regions in the world. This knowledge will be important for future management and productivity of agroecosystems in the face of increasing demand for food and climate change.
Cortical stiffness of keratinocytes measured by lateral indentation with optical tweezers
Authors: Jokhadar Špela Zemljič , Stojković Biljana , Vidak Marko , Liovic Mirjana , Gouveia Marcos , Travasso Rui D.M. , Derganc Jure 
Published: April 2020

AbstractKeratin intermediate filaments are the principal structural element of epithelial cells. Their importance in providing bulk cellular stiffness is well recognized, but their role in the mechanics of cell cortex is less understood. In this study, we therefore compared the cortical stiffness of three keratinocyte lines: primary wild type cells (NHEK2), immortalized wild type cells (NEB1) and immortalized mutant cells (KEB7). The cortical stiffness was measured by lateral indentation of cells with AOD-steered optical tweezers without employing any moving mechanical elements. The method was validated on fixed cells and Cytochalasin-D treated cells to ensure that the observed variations in stiffness within a single cell line were not a consequence of low measurement precision. The measurements of the cortical stiffness showed that primary wild type cells were significantly stiffer than immortalized wild type cells, which was also detected in previous studies of bulk elasticity. In addition, a small difference between the mutant and the wild type cells was detected, showing that mutation of keratin impacts also the cell cortex. Thus, our results indicate that the role of keratins in cortical stiffness is not negligible and call for further investigation of the mechanical interactions between keratins and elements of the cell cortex.
Conservation genomics reveals low genetic diversity and multiple parentage in the threatened freshwater mussel,Margaritifera hembeli
Authors: Garrison Nicole L. , Johnson Paul D. , Whelan Nathan V. 
Published: April 2020

AbstractMargaritifera hembeliis a federally threatened freshwater mussel species restricted to three central Louisiana drainages. Currently, management efforts are being formulated without an understanding of population-level genetic patterns, which could result in sub-optimal conservation outcomes. In particular, information about riverscape genetic patterns is needed to design effective propagation and reintroduction plans. We apply a genomic approach (RADseq) to assess genetic diversity and structure among four wild populations sampled from across the species range. We also assess the genetic diversity of a captively reared cohort produced from a single female. We recovered population differentiation between individuals sampled to the north and south of the Red River. All sites had similarly low levels of heterogeneity and other measures of genetic diversity. The captive cohort displayed higher levels of genetic diversity than expected and likely represents a case of multiple paternity. Future propagation efforts will likely be able to produce genetically diverse cohorts from a small number of wild-caught females, and we recommend future reintroduction efforts utilize brooders within the sub-drainage closest to the reintroduction effort.
Staufen1 localizes to the mitotic spindle and controls the transport of RNA populations to the spindle
Authors: Hassine Sami , Bonnet-Magnaval Florence , Benoit-Bouvrette Louis-Philip , Doran Bellastrid , Ghram Mehdi , Bouthillette Mathieu , Lecuyer Eric , DesGroseillers Luc 
Published: April 2020

ABSTRACTStaufen1 (STAU1) is an RNA-binding protein involved in the posttranscriptional regulation of mRNAs. We report that a large fraction of STAU1 localizes to the mitotic spindle in the colorectal cancer HCT116 and in the non-transformed hTERT-RPE1 cells. Spindle-associated STAU1 partly co-localizes with ribosomes and active sites of translation. We mapped the molecular determinant required for STAU1/spindle association within the first 88 N-terminal amino acids, a domain that is not required for RNA binding. Interestingly, transcriptomic analysis of purified mitotic spindles reveals that 1054 mRNAs as well as the precursor ribosomal RNA and lncRNAs and snoRNAs involved in ribonucleoprotein assembly and processing are enriched on spindles compared to cell extracts. STAU1 knockout causes the displacement of the pre-rRNA and of 154 mRNAs coding for proteins involved in actin cytoskeleton organization and cell growth, highlighting a role for STAU1 in mRNA trafficking to spindle. These data demonstrate that STAU1 controls the localization of sub-populations of RNAs during mitosis and suggests a novel role of STAU1 in pre-rRNA maintenance during mitosis, ribogenesis and/or nucleoli reassembly.SUMMARY STATEMENTProper localization and functions of macromolecules during cell division are crucial to ensure survival and proliferation of daughter cells.
iCellR: Combined Coverage Correction and Principal Component Alignment for Batch Alignment in Single-Cell Sequencing Analysis
Authors: Khodadadi-Jamayran Alireza , Pucella Joseph , Zhou Hua , Doudican Nicole , Carucci John , Heguy Adriana , Reizis Boris , Tsirigos Aristotelis 
Published: April 2020

SUMMARYUnder-sampling RNA molecules and low-coverage sequencing in some single cell sequencing technologies introduce zero counts (also known as drop-outs) into the expression matrices. This issue may complicate the processes of dimensionality reduction and clustering, often forcing distinct cell types to falsely resemble one another, while eliminating subtle, but important differences. Considering the wide range in drop-out rates from different sequencing technologies, it can also affect the analysis at the time of batch/sample alignment and other downstream analyses. Therefore, generating an additional harmonized gene expression matrix is important. To address this, we introduce two separate batch alignment methods: Combined Coverage Correction Alignment (CCCA) and Combined Principal Component Alignment (CPCA). The first method uses a coverage correction approach (analogous to imputation) in a combined or joint fashion between multiple samples for batch alignment, while also correcting for drop-outs in a harmonious way. The second method (CPCA) skips the coverage correction step and uses k nearest neighbors (KNN) for aligning the PCs from the nearest neighboring cells in multiple samples. Our results of nine scRNA-seq PBMC samples from different batches and technologies shows the effectiveness of both these methods. All of our algorithms are implemented in R, deposited into CRAN, and available in the iCellR package.