bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pseudo-repeats in doublecortin make distinct mechanistic contributions to microtubule regulation
Authors: Manka Szymon W. , Moores Carolyn A. 
Published: October 2019

AbstractDoublecortin (DCX) is a neuronal microtubule-associated protein (MAP) indispensable for brain development. Its flexibly linked DC domains – NDC and CDC – mediate microtubule (MT) nucleation and stabilisation, but it is unclear how. Using high-resolution time-resolved cryo-EM, we mapped NDC and CDC interactions with tubulin at different MT polymerisation stages and studied their functional effects on MT dynamics using TIRF microscopy. Although coupled, each DC repeat appears to have a distinct role in MT nucleation and stabilisation by DCX: CDC is a conformationally plastic tubulin binding module that appears to facilitate MT nucleation by binding tubulin oligomers and stabilising tubulin-tubulin contacts in the nascent MT lattice, while NDC appears to be favoured along the mature lattice, providing enhanced and durable MT stabilisation. Our near-atomic resolution structures of MT-bound DC domains also explain in unprecedented detail the DCX mutation-related brain defects observed in the clinic. This modular composition of DCX reflects a common design principle among MAPs where pseudo-repeats of tubulin/MT binding elements chaperone or stabilise distinct conformational transitions to regulate distinct stages of MT dynamic instability.
Potential Outbreak in Brazil by Equine Herpesvirus Type 2 (EHV-2): Detection, Clinical and Genetic Analysis of Equine Gammaherpesvirus 2
Authors: Cicolo Sofia , de Almeida Campos Angélica Cristine , de Oliveira Cairo Monteiro , Poltronieri Thais , Góes Luiz Gustavo Bentim , da Silveira Vanessa Barbosa , Barbosa Carla Meneguin , Baccarin Raquel Yvonne Arantes , Oliveira Danielle Bruna Leal , Belli Carla Bargi , Durigon Edison Luiz 
Published: October 2019

AbstractEquine herpesvirus (EHV) commonly affects horses causing neurologic and respiratory symptoms beside spontaneous abortions, meaning huge economic losses for equine industry worldwide. In foals the virus can facilitate secondary infections byRhodococcus equi, important in morbidity and mortality in equines. A total of five genotypes of EHV were previously described in Brazil including EHV-1, EHV-2, EHV-3, EHV-4 and EHV-5. EHV-2 genotype had only been previously described in Brazil in asymptomatic animals. We report the dead of 11 foals in Middle-west region of Brazil showing respiratory and neurological symptoms, as well as several abortions in mares from the same farm. Laboratory exams revealed neutrophilia leukocytosis. Necroscopic and histopathologic findings were suppurative bronchopneumonia and ulcerative enteritis. Molecular assays point to the absence of the bacteriaRhodococcus equiand other EHV. The presence of EHV-2 DNA was confirmed by sequencing in serum sample from one foal. This is the first confirmed outbreak of EHV-2 causing disease in Brazilian horses with confirmed presence of the virus. EHV-2 has been neglected and could be highlight the important role of EHV-2 in equine respiratory disease and spontaneous abortions in equid in Brazil.Author SummaryEquid herpesvirus type 2 (EHV-2), a gammaherpesvirus, has been neglected and can cause respiratory infection, abortion and in extreme cases neurologic symptoms and dead.Outbreaks of EHV-2 never was described in Brazil and can be critical to losses in equid industry. Our report provides evidence for a direct link between the EHV-2 strain and the outbreak in foals. We proved the clinical, histopathological and phylogenetic analysis of segment of EHV-2 polymerase.In summary, our study confirm that Gammaherpesvirus 2 is circulating in Brazil and the EHV-2 is a cause of the first outbreak in foals showing the important role of EHV-2 in equid respiratory disease.
Interdependent Allosteric FFA2R Modulators Synergistically Induce Functional Selective Activation and Desensitization in Neutrophils
Authors: Lind Simon , Holdfeldt André , Mårtensson Jonas , Sundqvist Martina , Kenakin Terry P. , Björkman Lena , Forsman Huamei , Dahlgren Claes 
Published: October 2019

AbstractThe non-activating allosteric modulator AZ1729, specific for free fatty acid receptor 2 (FFA2R), transfers the orthosteric FFA2R agonists propionate and the P2Y2R specific agonist ATP into activating ligands that trigger an assembly of the neutrophil superoxide generating NADPH-oxidase. The homologous priming effect on the propionate response and the heterologous receptor cross-talk sensitized ATP response mediated by AZ1729 are functional characteristics shared with Cmp58, another non-activating allosteric FFA2R modulator. In addition, AZ1729 also turned Cmp58 into a potent activator of the superoxide generating neutrophil NADPH-oxidase, and in agreement with the allosteric modulation concept, the effect was reciprocal in that Cmp58 turned AZ1729 into a potent activating allosteric agonist. The activation signals down-stream of FFA2R when stimulated by the two interdependent allosteric modulators were biased in that, unlike for orthosteric agonists, the two complementary modulators together triggered an activation of the NADPH-oxidase, but not any transient rise in the cytosolic concentration of free Ca2+. In addition, following AZ1729/Cmp58 activation, signaling by the desensitized FFA2Rs was functionally selective in that the orthosteric agonist propionate could still induce a transient rise in intracellular Ca2+. The novel neutrophil activation and receptor down-stream signaling pattern mediated by the two cross-sensitizing allosteric FFA2R modulators represents a new regulatory mechanism that controls receptor signaling.Significance StatementA novel activation mechanism of a G-protein coupled free fatty acid receptor (FFA2R), is synergistically triggered by two otherwise non-activating allosteric modulators in the absence of orthosteric agonists. The receptor down-stream signaling proved to be functionally selective (biased); a superoxide generating enzyme is assembled and activated without involvement of the Ca2+signaling pathway. The novel activation mechanism and the receptor down-stream signaling pattern mediated by the two cross-sensitizing allosteric FFA2R modulators, represents a new regulatory mechanism for control of GPCR-signaling.
The Swedish example of food animal production without extensive use of antibiotics – or “healthy animals do not need antibiotics”
Authors: Björkman Ingeborg , Röing Marta , Eriksen Jaran , Lundborg Cecilia Stålsby 
Published: October 2019

AbstractObjectiveTo describe how stakeholders at different levels in food animal production in Sweden work to contain antibiotic resistance, with a special focus on poultry production. The stakeholders’ perceptions of antibiotic resistance and awareness of the One Health concept were also studied.MethodsThis is an interview study with thirteen informants. They represent policymakers, trade organisations, and veterinarians and farmers in the poultry industry. Interview transcripts were analysed using content analysis. The analysis continued until a latent theme emerged, and then the content was rearranged in four domains.FindingsA latent theme “Working in unison” emerged, based on the consistency expressed by the informants when they discussed antibiotic resistance, use of antibiotics and food animal production methods. The theme was built on four domains, representing the content of the interviews: Knowledge and engagement; Cooperation; Animal health concept; and Development in balance with economic prerequisites. The work for healthy animals started in Sweden already in the 1920-ies and continued step by step in cooperation and with support from the government. In 1986 Sweden became the first country to ban antibiotics for growth promotion. Veterinarians were considered important drivers of processes by spreading knowledge and working close to the farmers. Farmers felt involved in the development of production methods. The One Health concept was well known among stakeholders working at national level but not among veterinarians in production or farmers.ConclusionsSweden has come far in work to contain antibiotic resistance in the animal sector by practicing restrictive use of antibiotics in food animal production. This practise is based on a long tradition of cooperation among stakeholders, from policymakers to farmers, and with a primary focus on animal health and welfare.
Quantifying the individual impact of artificial barriers in freshwaters: A standardized and absolute genetic index of fragmentation
Authors: Prunier Jérôme G. , Poesy Camille , Dubut Vincent , Veyssière Charlotte , Loot Géraldine , Poulet Nicolas , Blanchet Simon 
Published: October 2019

AbstractFragmentation by artificial barriers is an important threat to freshwater biodiversity. Mitigating the negative aftermaths of fragmentation is of crucial importance, and it is now essential for environmental managers to benefit from a precise estimate of the individual impact of weirs and dams on river connectivity. Although the indirect monitoring of fragmentation using molecular data constitutes a promising approach, it is plagued with several constraints preventing a standardized and individual quantification of barrier effects. Indeed, observed levels of genetic differentiation depend on both the age of the obstacle and the effective size of the populations it separates, making difficult comparisons of the actual barrier effect of different obstacles. Here, we developed a standardized genetic index of fragmentation (FINDEX), allowing an absolute and independent assessment of the individual effects of obstacles on connectivity. TheFINDEXis the standardized ratio (expressed as a percentage) between the observed genetic differentiation between pairs of populations located on either side of an obstacle and the genetic differentiation expected if this obstacle completely prevented gene flow. The expected genetic differentiation is calculated from simulations taking into account two nuisance parameters: the number of generations since barrier creation (the age of the obstacle) and the expected heterozygosity of the targeted populations, a proxy for effective population sizes. Using both simulated and published empirical datasets, we explored and discussed the validity and the limits of theFINDEX. We demonstrated that it allows quantifying genetic effects of fragmentation only from a few generations after barrier creation and provides valid comparisons among populations (or species) of different effective populations sizes and obstacles of different ages. The computation of theFINDEXrequires a minimum amount of fieldwork and genotypic data, and solves some of the difficulties inherent to the study of artificial fragmentation in rivers and potentially in other ecosystems. This makes theFINDEXa promising and objective tool for managers aiming at at planning restoration programs and at evaluating the efficiency of these programs.
Alzheimer’s Disease risk modifier genes do not impact tau aggregate uptake, seeding or maintenance in cell models
Authors: Kolay Sourav , Diamond Marc I. 
Published: October 2019

ABSTRACTAlzheimer’s disease (AD) afflicts millions of people worldwide, and is caused by accumulated amyloid beta and tau pathology. Progression of tau pathology in AD may utilize prion mechanisms of propagation in which pathological tau aggregates released from one cell are taken up by neighboring or connected cells and act as templates for their own replication, a process termed “seeding.” In cultured cells we have modeled various aspects of pathological tau propagation, including uptake of aggregates, induced (naked) seeding by exogenous aggregates, seeding caused by Lipofectamine-mediated delivery to the cell interior, and chronic maintenance of aggregates in cells through mother-to-daughter transmission. The factors that regulate these processes are not well understood, and we hypothesized that AD risk modifier genes might play a role. We identified 22 genes strongly linked to AD via meta-analysis of genome-wide association studies (GWAS). We used CRISPR/Cas-9 to individually knock out each in gene in HEK293T cells, and verified disruption using genomic sequencing. We then tested the effect of gene knockout in tau aggregate uptake, naked and Lipofectamine-mediated seeding, and aggregate maintenance in cultured cell lines. GWAS gene knockouts had no effect on these models of tau pathology. With obvious caveats due to the model systems used, these results imply that these 22 AD risk modifier genes do not directly modulate tau uptake, seeding, or aggregate maintenance.
In vivodeuterated water labeling allows tumor visualization via deuterium magnetic resonance spectroscopic imaging of cholesterol
Authors: Assmann Julian C. , Brender Jeffrey R. , Farthing Don E. , Saito Keita , Kishimoto Shun , Warrick Kathrynne A. , Maglakelidze Natella , Crooks Daniel R. , Merkle Hellmut , Gress Ronald E. , Krishna Murali C. , Buxbaum Nataliya P. 
Published: October 2019

AbstractWater is an essential component of many biochemical reactions. Deuterated water (D2O) has been used to study cell kinetics, protein synthesis, and metabolism. We hypothesized that rapidly proliferating cancer cells would become preferentially labeled with deuterium due to high metabolic activity, thus allowing imaging of biosynthetically labeled metabolites within tumorsin vivo. We initiated systemic D2O labeling in two established tumor xenograft models, HT-29 and MiaPaCa-2 and imaged mice by deuterium magnetic resonance spectroscopic imaging (dMRSI). After 14 days of tumor growth and 7 days ofin vivolabeling, a clear contrast was demonstrated between the xenograft and the contralateral control limb in both models. The origin of the contrast was traced to an aliphatic peak at 1.8 ppm, which was identified byex vivoNMR analysis to originate from cholesterol and cholesterol esters. Cholesterol is important for tumor cell proliferation, signaling, and malignant transformation, while current methods to monitor cholesterol synthesis and accumulation are limited. This deuterated water labeling-imaging approach could complement current cancer imaging techniques, allowing not only imaging of uptake but also synthesis of cholesterol to elucidate effects on tumor cholesterol metabolismin vivo.
Nectins rather than E-cadherin anchor the actin belts at cell-cell junctions of epithelia
Authors: Mangeol Pierre , Massey-Harroche Dominique , Bivic André Le , Lenne Pierre-François 
Published: October 2019

AbstractCell-cell junctions support the mechanical integrity of epithelia by enabling adhesion and tension transmission between neighboring cells. The prevailing mechanistic dogma is that E-cadherin supports and transmits mechanical tension between cells through actin belts in a region named thezonula adherens. Using super-resolution microscopy on human intestinal biopsies and Caco-2 cells, we show that thezonula adherensconsists of E-cadherin and nectin belts that are separated by about 150 nm along the apico-basal direction, the nectin belt being in the immediate vicinity of the actin belt. The segregation of nectins and E-cadherin increases as the tissue matures. Our data redefine the structure of thezonula adherensand show that nectins, rather than E-cadherin, are the major connectors of actin belts in epithelia.
Conserved nuclear receptors controlling a novel trait target fast-evolving genes expressed in a single cell
Authors: Sieriebriennikov Bogdan , Sun Shuai , Lightfoot James W. , Witte Hanh , Moreno Eduardo , Rödelsperger Christian , Sommer Ralf J. 
Published: October 2019

AbstractEnvironment shapes development through a phenomenon called developmental plasticity. Deciphering its genetic basis has implications for understanding evolution and adaptation to novel environments, yet molecular studies are scarce. Here, we expanded the gene regulatory network controlling predatoryvs.non-predatory morphology in the nematodePristionchus pacificus. First, we isolated a mutant in the nuclear hormone receptornhr-1with a previously unseen phenotypic effect. It disrupts mouth-form determination and results in animals combining features of both wild-type morphs. Further, we identified common targets of NHR-1 and the previously identified nuclear hormone receptor NHR-40 through transcriptomics. Unlike their highly conserved regulators, the target genes have no orthologs inCaenorhabditis elegansand likely result from lineage-specific expansions. An array of transcriptional reporters revealed co-expression of all tested targets in the same pharyngeal gland cell. The morphological remodeling of this cell accompanied the evolution of teeth and predation, linking rapid gene turnover with morphological innovations.
A two-way molecular dialogue between embryo and endosperm required for seed development
Authors: Doll N. M. , Royek S. , Fujita S. , Okuda S. , Stintzi A. , Widiez T. , Hothorn M. , Schaller A. , Geldner N. , Ingram G. 
Published: October 2019

AbstractThe plant embryonic cuticle is a hydrophobic barrier depositedde novoby the embryo during seed development. At germination it protects the seedling from water loss and is thus critical for survival. Embryonic cuticle formation is controlled by a signaling pathway involving the protease ALE1 and the receptor-like kinases GSO1 and GSO2. We show that a sulfated peptide, TWISTED SEED1 (TWS1) acts as a GSO1/GSO2 ligand. Cuticle surveillance depends on the action of ALE1 which, unlike TWS1 and GSO1/2, is not produced in the embryo but in the neighboring endosperm. Cleavage of an embryo-derived TWS1 precursor by ALE1 releases the active peptide, triggering GSO1/2-dependent cuticle reinforcement in the embryo. A bidirectional molecular dialogue between embryo and endosperm thus safeguards cuticle integrity prior to germination.One Sentence SummarySubtilase-mediated activation of the TWISTED SEED1 peptide provides spatial cues during embryo cuticle integrity monitoring.
Plants with self-sustained luminescence
Authors: Mitiouchkina Tatiana , Mishin Alexander S. , Gonzalez Somermeyer Louisa , Markina Nadezhda M. , Chepurnyh Tatiana V. , Guglya Elena B. , Karataeva Tatiana A. , Palkina Kseniia A. , Shakhova Ekaterina S. , Fakhranurova Liliia I. , Chekova Sofia V. , Tsarkova Aleksandra S. , Golubev Yaroslav V. , Negrebetsky Vadim V. , Dolgushin Sergey A. , Shalaev Pavel V. , Melnik Olesya A. , Shipunova Victoria O. , Deyev Sergey M. , Bubyrev Andrey I. , Pushin Alexander S. , Choob Vladimir V. , Dolgov Sergey V. , Kondrashov Fyodor A. , Yampolsky Ilia V. , Sarkisyan Karen S. 
Published: October 2019

AbstractIn contrast to fluorescent proteins, light emission from luciferase reporters requires exogenous addition of a luciferin substrate. Bacterial bioluminescence has been the single exception, where an operon of five genes is sufficient to produce light autonomously. Although commonly used in prokaryotic hosts, toxicity of the aldehyde substrate has limited its use in eukaryotes1. Here we demonstrate autonomous luminescence in a multicellular eukaryotic organism by incorporating a recently discovered fungal bioluminescent system2into tobacco plants. We monitored these light-emitting plants from germination to flowering, observing temporal and spatial patterns of luminescence across time scales from seconds to months. The dynamic patterns of luminescence reflected progression through developmental stages, circadian oscillations, transport, and response to injuries. As with other fluorescent and luminescent reporters, we anticipate that this system will be further engineered for varied purposes, especially where exogenous addition of substrate is undesirable.
Cascabel: a flexible, scalable and easy-to-use amplicon sequence data analysis pipeline
Authors: Asbun Alejandro Abdala , Besseling Marc A , Balzano Sergio , van Bleijswijk Judith , Witte Harry , Villanueva Laura , Engelmann Julia C 
Published: October 2019

ABSTRACTMarker gene sequencing of the rRNA operon (16S, 18S, ITS) or cytochrome c oxidase I (CO1) is a popular means to assess microbial communities of the environment, microbiomes associated with plants and animals, as well as communities of multicellular organisms via environmental DNA sequencing. Since this technique is based on sequencing a single gene rather than the entire genome, the number of reads needed per sample is lower than that required for metagenome sequencing, making marker gene sequencing affordable to nearly any laboratory. Despite the relative ease and cost-efficiency of data generation, analyzing the resulting sequence data requires computational skills that may go beyond the standard repertoire of a current molecular biologist/ecologist. We have developed Cascabel, a flexible and easy-to-use amplicon sequence data analysis pipeline, which uses Snakemake and a combination of existing and newly developed solutions for its computational steps. Cascabel takes the raw data as input and delivers a table of operational taxonomic units (OTUs) and a representative sequence tree. Our pipeline allows customizing the analyses by offering several choices for most of the steps, for example different OTU generating methods. The pipeline can make use of multiple computing nodes and scales from personal computers to computing servers. The analyses and results are fully reproducible and documented in an HTML and optional pdf report. Cascabel is freely available at Github: https://github.com/AlejandroAb/CASCABEL and licensed under GNU GPLv3.
A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells
Authors: Dias José M. , Alekseenko Zhanna , Jeggari Ashwini , Boareto Marcelo , Vollmer Jannik , Kozhevnikova Mariya , Wang Hui , Matise Michael P. , Alexeyenko Andrey , Iber Dagmar , Ericson Johan 
Published: October 2019

AbstractHow time is measured by neural stem cells during temporal neurogenesis has remained unresolved. By combining experiments and computational modelling, we here define a Shh/Gli-driven three-node timer underlying the sequential generation of motor neurons (MNs) and serotonergic neurons in the brainstem. The timer is founded on temporal decline of Gli-activator and Gli-repressor activities established through downregulation of Gli transcription. The circuitry conforms an incoherent feedforward loop, whereby Gli proteins promote expression of Phox2b and thereby MN-fate, but also account for a delayed activation of a self-promoting Tgfβ-node triggering a fate switch by repressing Phox2b. Hysteresis and spatial averaging by diffusion of Tgfβ counteracts noise and increases temporal accuracy at the population level. Our study defines how time is reliably encoded during the sequential specification of neurons.