bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-resolution animal tracking with integration of environmental information in aquatic systems
Authors: Francisco Fritz A , Nührenberg Paul , Jordan Alex 
Published: February 2020

AbstractAcquiring high resolution quantitative behavioural data underwater often involves installation of costly infrastructure, or capture and manipulation animals. Aquatic movement ecology can therefore be limited in scope of taxonomic and ecological coverage. Here we present a novel deep-learning based, multi-individual tracking approach, which incorporates Structure-from-Motion in order to determine the 3D location, body position and the visual environment of every recorded individual. The application is based on low-cost cameras and does not require the animals to be confined or handled in any way. Using this approach, single individuals, small heterospecific groups and schools of fish were tracked in freshwater and marine environments of varying complexity. Further, we established accuracy measures, resulting in positional tracking errors as low as 1.09 ± 0.47 cm (RSME) in underwater areas up to 500 m2. This cost-effective and open-source framework allows the analysis of animal behaviour in aquatic systems at an unprecedented resolution. Implementing this versatile approach, quantitative behavioural analysis can employed in a wide range of natural contexts, vastly expanding our potential for examining non-model systems and species.
Whole brain optoacoustic tomography reveals strain-specific regional beta-amyloid densities in Alzheimer’s disease amyloidosis models
Authors: Ni Ruiqing , Dean-Ben Xose Luis , Kirschenbaum Daniel , Rudin Markus , Chen Zhenyue , Crimi Alessandro , Voigt Fabian F. , Nilsson K. Peter R. , Helmchen Fritjof , Nitsch Roger , Aguzzi Adriano , Razansky Daniel , Klohs Jan 
Published: February 2020

AbstractDeposition of beta-amyloid (Aβ) deposits is one major histopathological hallmark of Alzheimer’s disease (AD). Here, we introduce volumetric multi-spectral optoacoustic tomography (vMSOT), which covers 10×10×10 mm3 field-of-view, capable of 3D whole mouse brain imaging. We show for the first time the optoacoustic properties of oxazine-derivative AOI987 probe, which binds to Aβ, and the application of vMSOT for the quantification of brain-wide Aβ deposition. Administration of AOI987 to two common transgenic mouse strains of AD amyloidosis led to a retention of the probe in Aβ-laden brain regions. Co-registered of vMSOT data to a brain atlas revealed strain-specific pattern of AOI987 uptake. A comparison with ex vivo light-sheet microscopy in cleared mouse brains showed a good correspondence in Aβ distribution. Lastly, we demonstrate the specificity of the AOI987 probe by immunohistochemistry. vMSOT with AOI987 facilitates preclinical brain region-specific studies of Aβ spread and accumulation, and the monitoring of putative treatments targeting Aβ.
Biogenic Amine Neurotransmitters Promote Eicosanoid Production And Protein Homeostasis
Authors: Joshi Kishore K. , Matlack Tarmie L. , Pyonteck Stephanie , Menzel Ralph , Rongo Christopher 
Published: February 2020

ABSTRACTMulticellular organisms use multiple pathways to restore protein homeostasis (proteostasis) in response to adverse physiological conditions, changing environment, and developmental aging. The nervous system can regulate proteostasis in different tissues, but it is unclear how it mobilizes proteostasis pathways to offset physiological decline. Here we show thatC. elegansemploys the humoral biogenic amine neurotransmitters dopamine, serotonin, and tyramine to regulate proteostasis and the activity of the Ubiquitin Proteasome System (UPS) in epithelial tissues. Mutants for biogenic amine synthesis show decreased poly-ubiquitination and turnover of a GFP-based UPS substrate. Using RNA-seq, we determined the expression profile of genes regulated by biogenic amine signaling. We find that biogenic amines promote the expression of a subset of cytochrome P450 monooxygenases involved in eicosanoid production from polyunsaturated fatty acids (PUFAs). Mutants for these P450s share the same UPS phenotype observed in biogenic amine mutants. The production of n-3 PUFAs is required for UPS substrate turnover, whereas mutants that accumulate n-3 PUFAs show accelerated turnover of this GFP-based substrate. Our results suggest that neurosecretory sensory neurons release biogenic amines to modulate the lipid signaling profile, which in turn activates stress response pathways to maintain proteostasis.
Search for top-down and bottom-up drivers of latitudinal trends in insect herbivory in oak trees in Europe
Authors: Valdés-Correcher Elena , Moreira Xoaquín , Augusto Laurent , Barbaro Luc , Bouget Christophe , Bouriaud Olivier , Branco Manuela , Centenaro Giada , Csóka György , Damestoy Thomas , Dobrosavljević Jovan , Duduman Mihai-Leonard , Dulaurent Anne-Maïmiti , Eötvös Csaba B. , Faticov Maria , Ferrante Marco , Fürjes-Mikó Ágnes , Galmán Andrea , Gossner Martin M. , Hampe Arndt , Harvey Deborah , Howe Andrew Gordon , Kadiri Yasmine , Kaennel-Dobbertin Michèle , Koricheva Julia , Kozel Alexander , Kozlov Mikhail V. , Löveï Gábor L. , Lupaştean Daniela , Milanović Slobodan , Mrazova Anna , Opgennoorth Lars , Pitkänen Juha-Matti , Popova Anna , Popović Marija , Prinzing Andreas , Queloz Valentin , Roslin Tomas , Sallé Aurélien , Sam Katerina , Scherer-Lorenzen Michael , Schuldt Andreas , Selikhovkin Andrey , Suominen Lassi , Tack Ayco J. M. , Tahadlova Marketa , Thomas Rebecca , Castagneyrol Bastien 
Published: February 2020

AbstractAimThe strength of species interactions is traditionally expected to become stronger toward the Equator. However, recent studies have reported opposite or inconsistent latitudinal trends in the bottom-up (plant quality) and top-down (natural enemies) forces driving insect herbivory, possibly because these forces have rarely been studied concomitantly. This makes previous attempts to understand the effect of large scale climatic gradients on insect herbivory unsuccessful.LocationEuropeTime period2018-2019Major taxa studiedQuercus roburMethodsWe used scholar-based citizen science to simultaneously test for latitudinal variation in plant-herbivore-natural enemy interactions. We further investigated the underlying climatic factors associated with variation in herbivory, leaf chemistry and attack rates inQuercus roburacross its complete latitudinal range in Europe. We quantified insect herbivory and the occurrence of specialist herbivores as well as leaf chemistry and bird attack rates on dummy caterpillars on 261 oak trees.ResultsClimatic factors rather than latitudeper sewere the best predictors of the large-scale (geographical) variation in the incidence of gall-inducers and leaf-miners as well as of leaf nutritional quality. However, insect herbivory, plant chemical defences (leaf phenolics) and bird attack rates were not influenced by latitude or climatic factors. The incidence of leaf-miners increased with increasing concentrations of hydrolysable tannins and decreased with those of condensed tannins, whereas the incidence of gall-inducers increased with increasing leaf soluble sugar concentration and decreased with increasing leaf C:N ratios. However, neither other traits nor bird attack rates varied with insect herbivory.Main conclusionsThese findings help to refine our understanding of the bottom-up and top-down mechanisms driving geographical variation in plant-herbivore interactions, and urge for further examination of the drivers of insect herbivory on trees.
Key histone chaperones have distinct roles in replisome progression and genomic stability
Authors: Tsirkas Ioannis , Dovrat Daniel , Lei Yang , Kalyva Angeliki , Lotysh Diana , Li Qing , Aharoni Amir 
Published: February 2020

AbstractReplication-coupled (RC) nucleosome assembly is an essential process in eukaryotic cells in order to maintain chromatin structure during DNA replication. The deposition of newly synthesized H3/H4 histones during DNA replication is facilitated by specialized histone chaperones. Although the contribution of these histone chaperones to genomic stability has been thoroughly investigated, their effect on replisome progression is much less understood. By exploiting a time-lapse microscopy system for monitoring DNA replication in individual live cells, we examined how mutations in key histone chaperones includingCAC1,RTT106,RTT109andASF1, affect replication fork progression. Our experiments revealed that mutations inCAC1orRTT106that directly deposit histones on the DNA, slowdown replication fork progression. In contrast, analysis of cells mutated in the intermediaryASF1orRTT109histone chaperones revealed that replisome progression is not affected. We found that mutations in histone chaperones includingASF1andRTT109lead to extended G2/M duration, elevated number of RPA foci and in some cases, increased spontaneous mutation rate. Our research suggests that histone chaperones have distinct roles in enabling high replisome progression and maintaining genome stability during cell cycle progression.Author SummaryHistone chaperones (HC) play key roles in maintaining the chromatin structure during DNA replication in eukaryotic cells. Despite extensive studies on HCs, little is known regarding their importance for replication fork progression during S-phase. Here, we utilized a live-cell imaging approach to measure the progression rates of single replication forks in individual yeast cells mutated in key histone chaperones. Using this approach, we show that mutations inCAC1orRTT106HCs that directly deposit histones on the DNA lead to slowdown of replication fork progression. In contrast, mutations inASF1orRTT109HCs that transfers H3/H4 toCAC1orRTT106, do not affect replisome progression but lead to post replication defects. Our results reveal distinct functions of HCs in replication fork progression and maintaining genome stability.
Coupling of conformational switches in calcium sensor unraveled with local Markov models and transfer entropy
Authors: Hempel Tim , Plattner Nuria , Noé Frank 
Published: February 2020

AbstractProteins often have multiple switching domains that are coupled to each other and to binding of ligands in order to realize signaling functions. Here we investigate the C2A domain of Synaptotagmin-1 (Syt-1), a calcium sensor in the neurotransmitter release machinery and a model system for the large family of C2 membrane binding domains. We combine extensive molecular dynamics (MD) simulations and Markov modeling in order to model conformational switching domains, their states and their dependence on bound calcium ions. Using transfer entropy, we characterize how the switching domains are coupled via directed or allosteric mechanisms and give rise to the calcium sensing function of the protein. Our switching mechanism contributes to the understanding of the neurotransmitter release machinery and the proposed methodological approach serves as a template to analyze conformational switching domains and study their coupling in macromolecular machines in general.
Evaluation of a new probiotic concept for broilers
Authors: Jørgensen S. L. , Poulsen L. L. , Bisgaard M. , Christensen H. 
Published: February 2020

SUMMARYProbiotics were introduced as a spray directly in the hatcher when chickens started to leave the eggs which potentially could reduce the horizontal transmission and colonization with pathogenic bacteria. The single introduction of probiotics could limit the cost compared to multiple introductions with feed and/or water. A mixture of five probiotic strains belonging toEscherichia coli, Enterococcus faecalis, Lactobacillus agilisandLactobacillus rhamnosuswas tested with two independent flocks of broilers (Ross 308). For each experiment, a comparison was made to an untreated control flock on the same farm. At day 14 of production the probiotic strains were re-isolated from ileum of euthanized chickens. The first week mortality was slightly increased in the probiotic flock (0.42%) compared to the control (0.35%) in experiment 1, however, it was higher in the control flock (1.45%) compared to the probiotic flock (1.12%) in experiment 2. The average weight of chickens that could be slaughtered for consumption was increased by 3.5% in the probiotic flocks compared to the control flocks, resulting in a 1.9% higher total weight of slaughtered chickens in the probiotics treated flocks compared to the control as a mean of the two experiments. The number of condemned animals was within the normal range for the production system and could not directly be related to effects of probiotics. Although one probiotic strain ofE. coliwas isolated from dead animals, the probiotics did not affect the proportion of chickens which died due toE. coliduring the first week compared to the control.Primary audienceplant managers, veterinarians, nutritionists
Gut microbiome, diet and symptom interactions in irritable bowel syndrome
Authors: Tap Julien , Störsrud Stine , Nevé Boris Le , Cotillard Aurélie , Pons Nicolas , Doré Joël , Öhman Lena , Törnblom Hans , Derrien Muriel , Simren Magnus 
Published: February 2020

AbstractWhile several studies have documented associations between dietary habits and microbiota composition and function in healthy subjects, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially in relation to symptoms. Here, we used a novel approach that combined data from 4-day food diary, integrated into a food tree, together with gut microbiota (shotgun metagenomic) for IBS patients (N=149) and healthy subjects (N=52). Paired microbiota and food-based trees allowed to detect new association between subspecies and diet. Combining co-inertia analysis and linear regression models, exhaled gas levels and symptom severity could be predicted from metagenomic and dietary data. IBS patients with severe symptoms had a diet enriched in food items of poorer quality, a high abundance of gut microbial enzymes involved in hydrogen metabolism in correlation with animal carbohydrate (mucin/meat-derived) metabolism. Our study provides unprecedented resolution of diet-microbiota-symptom interactions and ultimately paves the way for personalized nutritional recommendations.
The evolution of mechanisms to produce phenotypic heterogeneity in microorganisms
Authors: Cooper Guy Alexander , Liu Ming , Peña Jorge , West Stuart Andrew 
Published: February 2020

ABSTRACTIn bacteria and other microorganisms, the cells within a population often show extreme phenotypic variation. Different species use different mechanisms to determine how distinct phenotypes are allocated between individuals, including coordinated, random, and genetic determination. However, it is not clear if this diversity in mechanisms is adaptive—arising because different mechanisms are favoured in different environments—or is merely the result of non-adaptive artifacts of evolution. We use theoretical models to analyse the relative advantages of the two dominant mechanisms to divide labour between reproductives and helpers in microorganisms. We show that coordinated specialisation is more likely to evolve over random specialisation in well-mixed groups when: (i) social groups are small; (ii) helping is more “essential”; and (iii) there is a low metabolic cost to coordination. We find analogous results when we allow for spatial structure with a more detailed model of cellular filaments. More generally, this work shows how diversity in the mechanisms to produce phenotypic heterogeneity could have arisen as adaptations to different environments.
Inference of sexual selection from pairwise contests
Authors: Yu Thomas , Clark Andrew G. 
Published: February 2020

AbstractSexual selection, whether mediated by male-male competition, female choice, or male choice, is often realized through a series of pairwise contests. Experimental evolutionists have long applied male-choice and female-choice experiments to quantify the relative mating abilities of genotypes, an important component of fitness. Here, we consider Drosophila mate-choice experiments and apply two mathematical models, the Bradley-Terry and the Élő models, which have been explicitly designed to quantify the merits of contestants and establish a ranking based on results from pairwise contests. Methods such as the Bradley-Terry model and Élő ratings also provide a way to predict the outcome of contests that have not yet taken place. Leave-one-out validation approaches allow us to assess the utility of these models to quantify relative fitnesses, how well the models fit the data, and how well they perform at prediction. After applying these methods to Drosophila mate-choice experiments, we interpret the results in terms of sexual selection, and discuss the implications of departures of the data from good fits to the models.
Functional remodeling of lysosomes by type I interferon modifies host defense
Authors: Zhang Hailong , Zoued Abdelrahim , Liu Xu , Sit Brandon , Waldor Matthew K. 
Published: February 2020

SUMMARYOrganelle remodeling is critical for cellular homeostasis, but host factors that control organelle function during microbial infection remain largely uncharacterized. Here, a genome-scale CRISPR/Cas9 screen in intestinal epithelial cells with the prototypical intracellular bacterial pathogenSalmonellaled us to discover that type I interferon (IFN-I) remodels lysosomes. Even in the absence of infection, IFN-I signaling modified the localization, acidification, protease activity and proteomic profile of lysosomes. Proteomic and genetic analyses revealed that multiple IFN-I-stimulated genes includingIfitm3, Slc15a3, andCnpcontribute to lysosome acidification. IFN-I-dependent lysosome acidification stimulated intracellularSalmonellavirulence gene expression, leading to rupture of theSalmonella-containing vacuole and host cell death. Moreover, IFN-I signaling promotedin vivo Salmonellapathogenesis in the intestinal epithelium, whereSalmonellainitiates infection. Our findings explain how an intracellular bacterial pathogen co-opts epithelial IFN-I signaling. We propose that IFN-I control of lysosome function broadly impacts host defense against diverse viral and microbial pathogens.
Modelling FtsZ nucleation, hydrolysis and treadmilling activity with Monte Carlo methods
Authors: Corbin L. , Erickson H.P. 
Published: February 2020

ABSTRACTBacterial cell division is tightly coupled to the dynamic behavior of FtsZ, a tubulin homolog. Recent experimental workin vitroandin vivohas attributed FtsZ’s assembly dynamics to treadmilling, where subunits add to the bottom and dissociate from the top of protofilaments. However, the molecular mechanisms producing treadmilling have yet to be characterized and quantified. We have developed a Monte Carlo model for FtsZ assembly that explains treadmilling and assembly nucleation by the same mechanisms. A key element of the model is a conformational change from R (relaxed), which is highly favored for monomers, to T (tense), which is favored for subunits in a protofilament. This model was created in MATLAB. Kinetic parameters were converted to probabilities of execution during single, small time steps, and these were used to stochastically determine FtsZ dynamics. Our model is able to accurately describe the results of severalin vitroandin vivostudies for a variety of FtsZ flavors. With standard conditions, the model FtsZ polymerized and produced protofilaments that treadmilled at 28 nm/s, hydrolyzed GTP at 2.8 to 4.2 GTP min-1FtsZ-1, and had an average length of 25 to 54 subunits, all similar to experimental results. Adding a bottom capper resulted in shorter protofilaments and higher GTPase, similar to the effect of the known the bottom capper protein MciZ. The model could match nucleation kinetics of several flavors of FtsZ using the same parameters as treadmilling and varying only the R to T transition of monomers.SIGNIFICANCEFtsZ assembly dynamics are now known to be governed by treadmilling, where subunits add to the bottom and dissociate from the top of protofilaments. We have generated a Monte Carlo model of treadmilling based on (a) a conformational transition of FtsZ subunits between two states, and (b) stochastic GTP hydrolysis. Importantly, the nucleation of new protofilaments is explained by the same mechanisms as treadmilling. We have determined kinetic parameters that match a wide range of experimental data. The model is available to users for their ownin silicoexperiments.
Epigenetic silencing of clustered tDNAs in Arabidopsis
Authors: Hummel Guillaume , Berr Alexandre , Graindorge Stéfanie , Cognat Valérie , Ubrig Elodie , Pflieger David , Molinier Jean , Drouard Laurence 
Published: February 2020

AbstractBeyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) andcis-elements,trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. Our data highlight that the combination of both genomic environment and epigenomic landscape contribute to fine tune the differential expression of dispersed versus clustered tDNAs in Arabidopsis.
The differentiated effect of information on the sensorial appreciation of wine
Authors: Saïdi Monia , Giraud Georges 
Published: February 2020

PurposeThis paper investigates how giving additional information to consumers changes their appreciation of wine, and how this effect changes with their knowledge of wine and their characteristics.Design/methodology/approachA survey of 415 French consumers was carried-out in 2014, focusing on the sensory evaluation of 37 red Bourgogne wines. Two sensorial evaluations (visual, and smell & taste) are investigated, first without any information about the wine and then with the presentation of the wine bottle with its labels.FindingsThe majority of participants are significantly influenced by the information displayed. The influence of information depends on their initial knowledge and individual characteristics (gender, age, and home area). This influence is robust, whatever be the means of evaluation.Research limitations/implicationsThe study was carried out with red Bourgogne wines and focused on the village and regional appellations, with a low and medium price range. The results need a broader investigation to be generalizable.Practical implicationsInformation does not have the same influence depending on individual characteristics and on knowledge of wine. Promoting different wines to different consumers who do not have the same knowledge and do not use the same distribution channels is challenging as consumers do not all have the same expectations of red Bourgogne wines. The results provide directions for better targeting consumers through the information on the bottle labels.Originality/valueBy cross-tabulating sensory tastings and knowledge tests, this research contributes to measuring the holistic effect of information on the hedonic appreciation of wine across a significant range of consumers issued from two big cities.