bluuebunny/crossref_metadata_2025_split huggingface dataset:
FBL17 targets CDT1a for degradation in early S-phase to prevent Arabidopsis genome instability
Authors: Desvoyes Bénédicte , Noir Sandra , Masoud Kinda , López María Isabel , Genschik Pascal , Gutierrez Crisanto 
Published: September 2019

AbstractMaintenance of genome integrity depends on controlling the availability of DNA replication initiation proteins, e.g., CDT1, a component of the pre-replication complexes that regulates chromatin licensing for replication. To understand the evolutionary history of CDT1 regulation, we have identified the mechanisms involved in CDT1 dynamics. During cell cycle, CDT1a starts to be loaded early after mitotic exit and maintains high levels until the G1/S transition. Soon after the S-phase onset, CDT1a is rapidly degraded in a proteasome-dependent manner. Plant cells use a specific SCF-mediated pathway that relies on the FBL17 F-box protein for CDT1a degradation, which is independent of CUL4a-containing complexes. A similar oscillatory pattern occurs in endoreplicating cells, where CDT1a is loaded just after finishing the S-phase. CDT1a is necessary to maintain genome stability, an ancient strategy although unique proteins and mechanisms have evolved in different eukaryotic lineages to ensure its degradation during S-phase.Impact statementThe DNA replication protein CDT1a is crucial for genome integrity and is targeted for proteasome degradation just after S-phase initiation by FBL17 in proliferating and endoreplicating cells of Arabidopsis
Blind spots in global soil biodiversity and ecosystem function research
Authors: Guerra Carlos A. , Heintz-Buschart Anna , Sikorski Johannes , Chatzinotas Antonis , Guerrero-Ramírez Nathaly , Cesarz Simone , Beaumelle Léa , Rillig Matthias C. , Maestre Fernando T. , Delgado-Baquerizo Manuel , Buscot François , Overmann Jörg , Patoine Guillaume , Phillips Helen R. P. , Winter Marten , Wubet Tesfaye , Küsel Kirsten , Bardgett Richard D. , Cameron Erin K. , Cowan Don , Grebenc Tine , Marín César , Orgiazzi Alberto , Singh Brajesh K. , Wall Diana H. , Eisenhauer Nico 
Published: September 2019

AbstractSoils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and governance. Here we identify and characterize the existing gaps in soil biodiversity and ecosystem function data across soil macroecological studies and >11,000 sampling sites. These include significant spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.6% of all sampling sites having a non-systematic coverage of both biodiversity and function datasets. Based on this information, we provide clear priorities to support and expand soil macroecological research.
Differential effects of farming practice on cuckoo bumblebee communities in relation to their hosts
Authors: Howard Charlotte E. , Austin Alexander J. , Gilbert James D. J. 
Published: September 2019

ABSTRACTBees are important for vital pollination of wild and crop plants, but are in decline worldwide. Intensification of agriculture is a major driver of bee decline. Organic farming practices are designed to limit environmental impacts of agriculture and can increase bee abundance and species diversity. However, studies have been heavily focused towards some guilds of bees, overlooking others. This includes social brood parasites, cuckoo bumblebees, an understudied bee lineage. Little is known about bumblebee host and cuckoo population dynamics, and the effects of farming practice on cuckoo bumblebees have never previously been evaluated.To compare the effects of farming practice (organic vs conventional) on the abundance, species diversity, and community dissimilarity of cuckoo bumblebees and their hosts, we compared host and cuckoo community metrics across ten matched pairs of organic and conventional farms in Yorkshire, UK.As found by many previous studies, host bumblebees were more abundant on organic farms than on conventional farms. Despite this, cuckoo bumblebees were equally abundant on both farm types. Contrary to prediction, community dissimilarity and species diversity were unaffected by farm type for both host and cuckoo communities.Synthesis and applications:Results suggest that cuckoo bumblebee community metrics are not solely driven by host community metrics, and that cuckoos may respond differently from their hosts to differences among farming practices. This could, in turn, indicate that a unified management practice is not sufficient to conserve all bumblebee species.
Single-cell atlas of major haematopoietic tissues sheds light on blood cell formation from embryonic endothelium
Authors: Shvartsman Maya , Pavlovich Polina V. , Oatley Morgan , Ganter Kerstin , McKernan Rachel , Prialgauskaite Radvile , Adamov Artem , Chukreev Konstantin , Descostes Nicolas , Buness Andreas , Cabezas-Wallscheid Nina , Lancrin Christophe 
Published: September 2019

AbstractThe Yolk Sac (YS) and Aorta-Gonad-Mesonephros (AGM) are two major haematopoietic regions during embryonic development. Interestingly, AGM is the only one generating haematopoietic stem cells (HSCs). To identify the difference between AGM and YS, we compared them using single-cell RNA sequencing between 9.5 and 11.5 days of mouse embryonic development and identified cell populations using CONCLUS, a new computational tool. The AGM was the only one containing neurons and a specific mesenchymal population, while the YS major component was an epithelial population expressing liver marker genes. In addition, the YS contained a major endothelial population expressing Stab2, a hyaluronan receptor, also highly expressed by liver endothelium. We demonstrated that the YS haematopoietic potential was restricted to Stab2-negative cells and that ectopic expression of Stab2 could reduce blood cell formation from endothelium. Our results indicate that the AGM is a tissue more favourable to HSCs development than the YS because of its microenvironment and the nature of its endothelial cells.
A multi-seasonal model of plant-nematode interactions and its use to identify optimal plant resistance deployment strategies
Authors: Nilusmas Samuel , Mercat Mathilde , Perrot Thomas , Djian-Caporalino Caroline , Castagnone-Sereno Philippe , Touzeau Suzanne , Calcagno Vincent , Mailleret Ludovic 
Published: September 2019

SummaryRoot-knot nematodes (RKNs) are soil-borne polyphagous pests with major impact on crop yield worlwide. Resistant crops efficiently control avirulent RKNs, but favour the emergence of virulent forms. Virulence being associated with fitness costs, susceptible crops counter-select virulent RKNs. In this study we identify optimal rotation strategies between susceptible and resistant crops to control RKNs and maximize crop yield.We developed an epidemiological model describing the within-season dynamics of avirulent and virulent RKNs on susceptible or resistant plant root-systems, and their between-season survival. The model was fitted to experimental data and used to predict yield-maximizing rotation strategies, with special attention to the impact of epidemic and genetic parameters.Crop rotations were found to be efficient under realistic parameter ranges. They were characterised by low ratios of resistant plants, and were robust to parameter uncertainty. Rotations provide significant gain over resistant-only strategies, especially under intermediate fitness costs and severe epidemic contexts.Switching from the current general deployment of resistant crops to custom rotation strategies could not only maintain or increase crop yield, but also preserve the few and valuable R-genes available to us.
GWAS and Fine-Mapping of Livability and Six Disease Traits in Holstein Cattle
Authors: Freebern Ellen , Santos Daniel JA , Fang Lingzhao , Jiang Jicai , Parker Gaddis Kristen L. , Liu George E. , Vanraden Paul M. , Maltecca Christian , Cole John B. , Ma Li 
Published: September 2019

AbstractBackgroundHealth traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to identify associated genomic variants and thus reveal insights into the genetic architecture of complex traits and diseases. The objective of this study is to investigate the genetic basis of seven health traits in dairy cattle and to identify potential candidate genes associated with cattle health using GWAS, fine mapping, and analyses of multitissue transcriptome data.ResultsWe studied cow livability and six direct disease traits, mastitis, ketosis, hypocalcemia, displaced abomasum, metritis, and retained placenta, using de-regressed breeding values and more than three million imputed DNA sequence variants. After data edits and filtering on reliability, phenotypes for 11,880 to 24,699 Holstein bulls were included in the analyses of the seven traits. GWAS was performed using a mixed-model association test, and a Bayesian fine-mapping procedure was conducted to calculate a posterior probability of causality to each variant and gene in the candidate regions. The GWAS results detected a total of eight genome-wide significant associations for three traits, cow livability, ketosis, and hypocalcemia, including the bovine MHC region associated with livability. Our fine-mapping of associated regions reported 20 candidate genes with the highest posterior probabilities of causality for cattle health. Combined with transcriptome data across multiple tissues in cattle, we further exploited these candidate genes to identify specific expression patterns in disease-related tissues and relevant biological explanations such as the expression ofGCin the liver and association with mastitis as well as theCCDC88Cexpression in CD8 cells and association with cow livability.ConclusionsCollectively, our analyses report six significant associations and 20 candidate genes of cattle health. With the integration of multi-tissue transcriptome data, our results provide useful information for future functional studies and better understanding of the biological relationship between genetics and disease susceptibility in cattle.
Testosterone secretion varies in a sex- and stage-specific manner: insights on the regulation of competitive traits from a sex-role reversed species
Authors: Lipshutz Sara E. , Rosvall Kimberly A. 
Published: September 2019

AbstractTestosterone (T) mediates a variety of traits that function in competition for mates, including territorial aggression, ornaments, armaments, and gametogenesis. The link between T and mating competition has been studied mainly in males, but females also face selection pressures to compete for mates. Sex-role reversed species, in which females are the more competitive sex, provide a unique perspective on the role of T in promoting competitive traits. Here, we examine patterns of T secretion in sex-role reversed Northern Jacanas (Jacana spinosa) during breeding, when females are fertile and males are either seeking copulations or conducting parental care. We measured baseline levels of T in circulation along with a suite of behavioral and morphological traits putatively involved in mating competition. We evaluated hypotheses that levels of T track gonadal sex and parental role, and we begin to investigate whether T and competitive traits co-vary in a sex- and stage-specific manner. Although females had higher expression of competitive traits than males at either breeding stage, we found that females and incubating males had similar levels of T secretion, which were lower than those observed in copulating males. T was correlated with wing spur length in females and testes mass in copulating males, but was otherwise uncorrelated with other competitive traits. These findings suggest that levels of T in circulation alone do not predict variation in competitive traits across levels of analysis, including gonadal sex and parental role. Instead, our findings coupled with prior research indicate that selection for female mating competition and male care may generate different physiological regulation of competitive traits in jacanas.HighlightsIn role reversed species, females face stronger competition and males care for offspringWe examine testosterone (T) and competitive traits in female and male jacanasCirculating T is similar in females and incubating males, but higher in copulating malesBoth gonadal sex and parental role shape patterns of T secretionPhysiological regulation of competitive traits may differ in female and male jacanas
Transcriptional changes suggest a major involvement of Gibberellins in Trifolium pratense regrowth after mowing
Authors: Herbert Denise Brigitte , Gross Thomas , Rupp Oliver , Becker Annette 
Published: September 2019

AbstractRed clover (Trifolium pratense) is used worldwide as a fodder plant due its high nutritional value. In response to mowing, red clover exhibits specific morphological traits to compensate the loss of biomass. The morphological reaction is well described, but knowledge of the underlying molecular mechanisms are still lacking. Here we characterize the molecular genetic response to mowing of red clover by using comparative transcriptomics in greenhouse conditions and agriculturally used field. The analysis of mown and control plants revealed candidate genes possibly regulating crucial steps of the genetic network governing the regrowth reaction. In addition, multiple identified gibberellic acid (GA) related genes suggest a major role for GA in establishing the regrowth morphology of red clover. Mown red clover plants showing this regrowth morphology were partially “rescued” by exogenous GA application, demonstrating the influence of GA during regrowth. Our findings provide insights into the physiological and genetic processes of mowing red clover, to serve as a base for red clover yield improvement.
Effect of integrated health system leading-managing-and-governing for results model on institutional delivery: Team-based quasi-experiment
Authors: Ambelie Yeshambel Agumas , Alene Getu Degu , Gebrekiros Damen Hailemariam 
Published: September 2019

AbstractObjectiveThe objective of this study is to examine, based on theory of change, whether integrated leading-managing-and-governing for results model is plausible cause of improved institutional delivery.MethodsA team-based quasi-experimental study was conducted. One-hundred-thirty-four health facility teams were enrolled in the study. Teams were allocated to intervention and control groups in a 1:1 ratio, non-randomly. End line institutional delivery was the dependent variable while the group (main predictor) and the baseline institutional delivery (covariate) were independent variables. The intervention that was given over six months was integrated leading-managing-and-governing for results model. The institutional deliveries were measured with percentages whilst the group was measured with exposure status (yes or no) to the intervention. Data, from both groups, were collected at baseline and end line. Data were analyzed using analysis of covariance. Statistical significance was determined at (p<.05). The main effect of the intervention was determined by 95% CI, presented in the contrast results.ResultsThe adjusted mean institutional deliveries with 95% CI were 47.4 (46.2, 48.6) and 33.4 (32.2, 34.6) in the intervention and control groups, respectively. Contrast results showed that having an intervention group, p = .000, 95% CI (12.2, 15.8), of integrated leading-managing-and governing for results model significantly increased mean institutional delivery compared to having a control group.ConclusionsThis study provides some guidance regarding the plausible causation of integrated leading-managing-and-governing for results model on institutional delivery. It would serve as a baseline in identifying true causation using a randomized design.
A Neural Network Based Algorithm for Dynamically Adjusting Activity Targets to Sustain Exercise Engagement Among People Using Activity Trackers
Authors: Mohammadi Ramin , Centi Amanda Jayne , Atif Mursal , Agboola Stephen , Jethwani Kamal , Kvedar Joseph C , Kamarthi Sagar 
Published: September 2019

AbstractIt is well established that lack of physical activity is detrimental to overall health of an individual. Modern day activity trackers enable individuals to monitor their daily activity to meet and maintain targets and to promote activity encouraging behavior. However, the benefits of activity trackers are attenuated over time due to waning adherence. One of the key methods to improve adherence to goals is to motivate individuals to improve on their historic performance metrics. In this work we developed a machine learning model to dynamically adjust the activity target for the forthcoming week that can be realistically achieved by the activity-tracker users. This model prescribes activity target for the forthcoming week. We considered individual user-specific personal, social, and environmental factors, daily step count through the current week (7 days). In addition, we computed an entropy measure that characterizes the pattern of daily step count for the current week. Data for training the machine learning model was collected from 30 participants over a duration of 9 weeks. The model predicted target daily count with mean absolute error of 1545 steps. The proposed work can be used to set personalized goals in accordance with the individual’s level of activity and thereby improving adherence to fitness tracker.
System-Level Quantification and Phenotyping of Early Embryonic Morphogenesis ofCaenorhabditis elegans
Authors: Guan Guoye , Wong Ming-Kin , Ho Vincy Wing Sze , An Xiaomeng , Chan Lu-Yan , Tian Binghui , Li Zhiyuan , Tang Leihan , Zhao Zhongying , Tang Chao 
Published: September 2019

AbstractCell lineage consists of cell division timing, cell migration and cell fate, and is highly conserved during development of nematode species. An outstanding question is how differentiated cells are genetically and physically regulated in order to migrate to their precise destination among individuals. Here, we first generated a reference embryo using time-lapse 3 dimensional images of 222 wild-typeC. elegansembryos at about 1.5-minute interval. This was achieved by automatic tracing and quantitative analysis of cellular phenotypes from 4- to 24-cell stage, including cell cycle duration, division orientation and migration trajectory. We next characterized cell division timing and cell kinematic state, which suggests that eight groups of cells can be clustered based on invariant and distinct division sequence. Cells may still be moving while others start to divide, indicating strong robustness against motional noise in developing embryo. We then devised a system-level phenotyping method for detecting mutant defect in global growth rate, cell cycle duration, division orientation and cell arrangement. A total of 758 genes were selected for perturbation by RNA interference followed by automatic phenotyping, which suggests a cryptic genetic architecture coordinating early morphogenesis spatially and temporally. The high-quality wild-type reference supports a conceptual close-packing model for cell arrangement during 4- to 8-cell stage, implying fundamental mechanical laws regulating the topological structure of earlyC. elegansembryo. Also, we observed a series of remarkable morphogenesis phenomena such as induced defect or recovery from defect in mutant embryo. To facilitate use of this quantification system, we built a software namedSTAR 1.0for visualizing the wild-type reference and mutant phenotype. It also allows automatic phenotyping of new mutant embryo. Taken together, we not only provide a statistical wild-type reference with defined variability, but also shed light on both genetic and physical mechanisms coordinating early embryonic morphogenesis ofC. elegans. The statistical reference permits a sensitive approach for mutant phenotype analysis, with which we phenotype a total of 1818 mutant embryos by depletion of 758 genes.Highlights & Graphical Abstract● Spatial-Temporal Wild-Type Reference for Early Embryonic Morphogenesis ofC. elegans● Variability (Noise) of Division Timing, Division Orientation and Cell Arrangement● A Conceptual Close-Packing Model for Cell Arrangement Up to 8-Cell Stage● Quantitative Phenotyping Methods at Embryo and Cellular Level● Cellular Phenotypes of 1818 Mutant Embryos (758 Genes) Before Gastrulation● Categorized Phenotypes upon Gene Perturbation
Efficient use of harvest data: An integrated population model for exploited animal populations
Authors: Gamelon Marlène , Baubet Éric , Besnard Aurélien , Gaillard Jean-Michel , Lebreton Jean-Dominique , Touzot Laura , Veylit Lara , Gimenez Olivier 
Published: September 2019

AbstractMany populations are affected by hunting or fishing. Models designed to assess the sustainability of harvest management require accurate estimates of demographic parameters (e.g. survival, reproduction) hardly estimable with limited data collected on exploited populations. The joint analysis of different data sources with integrated population models (IPM) is an optimal framework to obtain reliable estimates for parameters usually difficult to estimate, while accounting for imperfect detection and observation error. The IPM built so far for exploited populations have integrated count-based surveys and catch-at-age data into ageclass structured population models. But the age of harvested individuals is difficult to assess and often not recorded, and population counts are often not performed on a regular basis, limiting their use for the monitoring of exploited populations.Here, we propose an IPM that makes efficient use of data commonly collected in exploited marine and terrestrial populations of vertebrates. As individual measures of body mass at both capture and death are often collected in fish and terrestrial game species, our model integrates capture-mark-recapture-recovery data and data collected at death into a body mass-structured population model. It allows the observed number of individuals harvested to be compared with the expected number and provides accurate estimates of demographic parameters.We illustrate the usefulness of this IPM using an emblematic game species distributed worldwide, the wild boarSus scrofa, as a case study. For this species that has increased in distribution and abundance over the last decades, the model provides accurate and precise annual estimates of key demographic parameters (survival, reproduction, growth) and of population size while accounting for imperfect detection and observation error.To avoid an overexploitation of declining populations or an under-exploitation of increasing populations, it is crucial to gain a good understanding of the dynamics of exploited populations. When managers or conservationists have limited demographic data, the IPM offers a powerful framework to assess population dynamics. Being highly flexible, the approach is broadly applicable to both terrestrial and marine exploited populations for which measures of body mass are commonly recorded and more generally, to all populations suffering from anthropogenic mortality causes.