bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of CG methylation inMarchantia Polymorphacauses disorganization of cell division and reveals unique DNA methylation regulatory mechanisms of non-CG methylation
Authors: Ikeda Yoko , Nishihama Ryuichi , Yamaoka Shohei , Arteaga-Vazquez Mario A. , Aguilar-Cruz Adolfo , Grimanelli Daniel , Pogorelcnik Romain , Martienssen Robert A. , Yamato Katsuyuki T. , Kohchi Takayuki , Hirayama Takashi , Mathieu Olivier 
Published: July 2018

AbstractDNA methylation is an epigenetic mark that ensures silencing of transposable elements (TEs) and affects gene expression in many organisms. The function of different DNA methylation regulatory pathways has been largely characterized in the model plantArabidopsis thaliana. However, far less is known about DNA methylation regulation and functions in basal land plants. Here we focus on the liverwortMarchantia polymorpha, an emerging model species that represents a basal lineage of land plants. We identified MpMET, theM. polymorphaorthologue of theMETHYLTRANSFERASE 1(MET1) gene required for maintenance of methylation at CG sites in angiosperms. We generated Mpmetmutants using the CRISPR/Cas9 system, which showed a significant loss of CG methylation and severe morphological changes and developmental defects. The mutants developed many adventitious shoot-like structures, suggesting that MpMETis required for maintaining differentiated cellular identities in the gametophyte. Numerous TEs were up-regulated, even though non-CG methylation was highly increased at TEs in the Mpmetmutants. Closer inspection of CHG methylation revealed features unique toM. polymorpha. Methylation of CCG sites inM. polymorphadoes not depend onMET1, unlike inA. thalianaandPhyscomitrella patens. Furthermore, unlikeA. thaliana,M. polymorphashows higher methylation level at CAG sites than at other CHG contexts and CAG/CTG sites are mostly methylated asymmetrically. Interestingly, CAG and CTG methylation reached comparable levels and symmetry upon loss of CG methylation. Our results highlight the diversity of non-CG methylation regulatory mechanisms in plants.
Insulin signalling activates multiple feedback loops to elicit hunger-induced feeding in Drosophila
Authors: Sudhakar Sreesha R. , Varghese Jishy 
Published: July 2018

AbstractInsulin, a highly conserved peptide hormone, links nutrient availability to metabolism and growth in animals. Besides this, in fed states insulin levels are high and insulin acts as a satiety hormone. In animals that are food deprived insulin levels remain low which facilitates hunger induced feeding. Contrary to expectations, we present evidence for persistent Drosophila insulin-like peptide gene expression and insulin signalling during initial phases of starvation. Maintenance of insulin signalling is crucial to sustain feeding responses during initial stages of starvation. Insulin signalling acts in a feedback loop involving the abdominal fatbody to maintain dilp gene expression in the early stages of food deprivation. Furthermore, another feedback regulatory loop between insulin-producing cells (IPCs) and neurons that produce the orectic hormone short-neuropeptide-F (sNPF), maintains sNPF levels and triggers feeding behavior. Thus, insulin acts through multiple feedback regulatory loops to elicit orexigenic responses and aid in efficient utilization of energy stores during early starvation.
Two essential replicative DNA polymerases exchange dynamically during DNA replication and after replication fork arrest
Authors: Li Yilai , Chen Ziyuan , Matthews Lindsay A. , Simmons Lyle A. , Biteen Julie S. 
Published: July 2018

AbstractThe replisome is the multi-protein complex responsible for faithful replication of chromosomal DNA. Using single-molecule super-resolution imaging, we characterized the dynamics of three replisomal proteins in liveBacillus subtiliscells: the two replicative DNA polymerases, PolC and DnaE, and a processivity clamp loader subunit, DnaX. We quantified the protein mobility and dwell times during normal replication and following both damage-independent and damage-dependent replication fork stress. With these results, we report the dynamic and cooperative process of DNA replication based on changes in the measured diffusion coefficients and dwell times. These experiments show that the replisomal proteins are all highly dynamic and that the exchange rate depends on whether DNA synthesis is active or arrested. Our results also suggest coupling between PolC and DnaX in the DNA replication process, and indicate that DnaX provides an important role in synthesis during repair. Furthermore, our results show that DnaE provides a limited contribution to chromosomal replication and repair.
Personalized expression of bitter ‘taste’ receptors in human skin
Authors: Shaw Lauren , Mansfield Corrine , Colquitt Lauren , Lin Cailu , Ferreira Jaime , Emmetsberger Jaime , Reed Danielle R. 
Published: July 2018

AbstractThe integumentary (i.e., skin) and gustatory systems both function to protect the human body and are a first point of contact with poisons and pathogens. These systems may share a similar protective mechanism because both human taste and skin cells express mRNA for bitter ‘taste’ receptors (TAS2Rs). Here, we used gene-specific methods to measure mRNA from all known bitter receptor genes in adult human skin from freshly biopsied samples and from samples collected at autopsy from the Genotype-Tissue Expression project. Human skin expressed some but not all TAS2Rs, and for those that were expressed, the relative amounts differed markedly among individuals. For some TAS2Rs, mRNA abundance was related to sun exposure (TAS2R14, TAS2R30, TAS2R42, and TAS2R60), sex (TAS2R3, TAS2R4, TAS2R8, TAS2R9, TAS2R14, and TAS2R60), and age (TAS2R5), although these effects were not large. These findings contribute to our understanding of extraoral expression of chemosensory receptors.
De novoTranscriptome Analyses Provide Insights into Opsin-based Photoreception in the Lantern sharkEtmopterus spinax
Authors: Delroisse Jérôme , Duchatelet Laurent , Flammang Patrick , Mallefet Jérôme 
Published: July 2018

AbstractThe velvet belly lantern shark (Etmopterus spinax) is a small deep-sea shark commonly found in the Easter Atlantic and the Mediterranean Sea. In this study, paired-end illumina HiSeqTMtechnology has been employed to analyse transcriptome data from eye and ventral skin tissues of the lantershark species. About 64 and 49 million Illumina reads were generated from skin and eyetissues respectively. The assembly allowed us to predict 119,749 total unigenes including 94,569 for the skin transcriptome and 94,365 for the eye transcriptome while 74,753 were commonly found in both transcriptomes. Among unigenes, 60,322 sequences were annotated using classical public databases. The assembled and annotated transcriptomes provide a valuable resource for further understanding of the shark biology. We identified potential “light-interacting toolkit” genes including multiple genes related to ocular and extraocular light perception processes such as opsins. In particular, a single rhodopsin gene mRNA and its potentially associated peropsin were only detected in the eye transcriptome confirming a monochromatic vision of the lantern-shark. Conversely, an encephalopsin mRNA was mainly detected in the skin transcriptome. The encephalopsin was immunolocalized in various shark tissues confirming its wide expression in the shark skin and pinpointing a possible functional relation with the photophore,i.e. epidermal light organs. We hypothesize that extraocular photoreception might be involved in the bioluminescence control possibly acting on the shutter opening and/or the photocyte activity itself.
Structural connectivity facilitates functional connectivity of auditory prediction error generation within a fronto-temporal network
Authors: Oestreich Lena K. L. , Randeniya Roshini , Garrido Marta I. 
Published: July 2018

AbstractAuditory prediction errors, i.e. the mismatch between predicted and actual auditory input, are generated by a hierarchical functional network of cortical sources. This network is also interconnected by auditory white matter pathways. Hence it would be reasonable to assume that these structural and functional networks are quantitatively related, which is what the present study set out to investigate. Specifically, whether structural connectivity of auditory white matter pathways enables effective connectivity of auditory prediction error generation. Eighty-nine participants underwent diffusion weighted magnetic resonance imaging. Anatomically-constrained tractography was used to extract auditory white matter pathways, namely the bilateral arcuate fasciculus, the inferior occipito-frontal fasciculi (IOFF), and the auditory interhemispheric pathway, from which Apparent Fibre Density (AFD) was calculated. The same participants also underwent a stochastic oddball paradigm, which was used to elicit prediction error responses, while undergoing electroencephalographic recordings. Dynamic causal modelling (DCM) was used to investigate the effective connectivity of auditory prediction error generation in brain regions interconnected by the above mentioned auditory white matter pathways. Brain areas interconnected by all auditory white matter pathways best explained the dynamics of auditory prediction error responses. Furthermore, AFD in the right IOFF and right arcuate fasciculus significantly predicted the effective connectivity parameters underlying auditory prediction error generation. In conclusion, the generation of auditory prediction errors within an effectively connected, fronto-temporal network was found to be facilitated by the structural connectivity of auditory white matter pathways. These findings build upon the notion that structural connectivity facilitates dynamic interactions within brain regions that are effectively connected.Significance statementThe brain continuously generates and updates hypotheses that predict forthcoming sensory input. Within the auditory domain, it has repeatedly been reported that these predictions about the auditory environment are facilitated by specific functional cortical connections. These functionally connected brain regions are also structurally connected via auditory white matter pathways. For the first time, this study provides quantitative evidence for a structural basis along which this functional network of auditory prediction error generation operates. This finding provides evidence for the notion that the functional connectivity of dynamically interacting brain areas is facilitated by structural connectivity amongst these brain areas.
Modeling Zika Virus Spread in Colombia Using Google Search Queries and Logistic Power Models
Authors: Brown Mekenna , Cain Christopher , Whitfield James , Ding Edwin , Del Valle Sara Y , Manore Carrie A 
Published: July 2018

AbstractPublic health agencies generally have a small window to respond to burgeoning disease outbreaks in order to mitigate the potential impact. There has been significant interest in developing forecasting models that can predict how and where a disease will spread. However, since clinical surveillance systems typically publish data with a lag of two or more weeks, there is a need for complimentary data streams that can close this gap. We examined the usefulness of Google Trends search data for analyzing the 2016 Zika epidemic in Colombia and evaluating their ability to predict its spread. We calculated the correlation and the time delay between the reported case data and the Google Trends data using variations of the logistic growth model, and showed that the data sets were systematically offset from each other, implying a lead time in the Google Trends data. Our study showed how Internet data can potentially complement clinical surveillance data and may be used as an effective early detection tool for disease outbreaks.
RNAi screening identifies a new Toll from shrimp that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides
Authors: Li Haoyang , Yin Bin , Wang Sheng , Fu Qihui , Xiao Bang , Lǚ Kai , He Jianguo , Li Chaozheng 
Published: July 2018

ABSTRACTThe function of Toll pathway defense against bacterial infection has been well established in shrimp, however how this pathway responds to viral infection is still largely unknown. In this study, we report the Toll4-Dorsal-AMPs cascade restricts the white spot syndrome virus (WSSV) infection of shrimp. A total of nine Tolls fromLitopenaeus vannameinamely Toll1-9 are identified, and RNAi screeningin vivoreveals the Toll4 is important for shrimp to oppose WSSV infection. Knockdown of Toll4 results in elevated viral loads and renders shrimp more susceptible to WSSV. Furthermore, Toll4 could be a one of upstream pattern recognition receptor (PRR) to detect WSSV, and thereby leading to nuclear translocation and phosphorylation of Dorsal, the known NF-κB transcription factor of the canonical Toll pathway. More importantly, silencing of Toll4 and Dorsal contributes to impaired expression of a specific set of antimicrobial peptides (AMPs) such as anti-LPS-factor (ALF) and lysozyme (LYZ) family, which exert potent anti-WSSV activity. Two AMPs of ALF1 and LYZ1 as representatives are demonstrated to have the ability to interact with several WSSV structural proteins. Taken together, we therefore identify the Toll4-Dorsal pathway mediates strong resistance to WSSV infection by inducing some specific AMPs.Author summaryThe TLR pathway mediated antiviral immune response is well identified in mammals, yet, Toll pathway governing this protection in invertebrates remains unknown. In the present study, we uncover that a shrimp Toll4 from a total of nine Tolls inL. vannameiconfers resistance to WSSV thought inducing the NF-κB transcription factor Dorsal to inspiring the production of some antimicrobial peptides (AMPs) with antiviral activity. The anti-LPS-factor (ALF) and lysozyme (LYZ) family are identified as the Toll4-Dorsal pathway targeted genes with the ability to interact with viral structural proteins in response to WSSV infection. These results suggest that the Toll receptor induces the expression of AMPs with antiviral activity could be a general antiviral mechanism in invertebrates and Toll pathway established antiviral defense could be conserved during evolution.
Effect of NaCl-Stressed Bt Cotton on the Feeding Behaviors and Nutritional Parameters of Helicoverpa armigera
Authors: Luo Jun-Yu , Zhang Shuai , Zhu Xiang-Zhen , Ji Ji-Chao , Zhang Kai-Xin , Wang Chun-Yi , Zhang Li-Juan , Wang Li , Cui Jin-Jie 
Published: July 2018

AbstractSaline-alkali soil is an arable land resource on which transgenic Bt cotton has been planted on a large scale in accordance with food security strategies, but there are concerns about the insecticidal effects of Bt cotton on target insect pests. In this study, a Bacillus thuringiensis (Bt) cotton variety, GK19, and its nontransgenic parent variety, Simian-3, were used as experimental materials to study the effect of the expression of exogenous insecticidal proteins in Bt cotton under NaCl stress on the feeding behavior and nutritional parameters of Helicoverpa armigera. The results showed that the expression of exogenous insecticidal proteins in GK19 was significantly inhibited under NaCl stress. However, on GK19 Bt cotton, the feeding, crawling, resting and spinning down of the 5th instar H. armigera larvae, as well as the food consumption and feces amount of these larvae, did not markedly differ under different NaCl concentrations. In contrast, the mean relative growth rate (MRGR), relative growth rate (RGR), approximate digestibility (AD), efficiency of conversion of ingested food (ECI) and efficiency of conversion of digested food (ECD) of the larvae decreased markedly in response to NaCl stress. Under the same concentration of NaCl, the nutritional parameters of the bollworm larvae on GK19 Bt cotton or Simian-3 nontransgenic cotton were different. However, the interaction between salt stress and cotton variety had no significant effect on the feeding behavior or nutritional parameters of H. armigera larvae. These results may provide a scientific basis for determining the effect of exogenous insecticidal protein expression in Bt cotton under NaCl stress on H. armigera and can therefore be useful for the effective application of Bt cotton in saline-alkali soils to prevent and control H. armigera.
Amyloid-ß promotes neurotoxicity by Cdk5-induced p53 stabilization
Authors: Lapresa Rebeca , Agulla Jesús , Sánchez-Morán Irene , Bolaños Juan P. , Almeida Angeles 
Published: July 2018

ABSTRACTThe p53 tumor suppressor protein, a key regulator of cell apoptosis, has been described to accumulate in affected brain areas from Alzheimer’s disease (AD) patients. However, whether p53 plays any role in AD pathogenesis remains unknown. Here, we found that exposure of neurons to oligomers of the amyloidogenic fragment 25-35 of the Aß peptide (Aβ25-35) activated Cdk5, which promoted p53 protein phosphorylation and stabilization. Moreover, Aβ25-35-mediated mitochondrial dysfunction and neuronal apoptosis were prevented by both genetic and pharmacological inhibition of either p53 or Cdk5 activities. To confirm this mechanism in vivo, Aβ25-35 was stereotaxically injected in the cerebral right ventricle of mice, a treatment that caused p53 protein accumulation, dendrite disruption and neuronal death. Furthermore, these effects were prevented in p53 knockout mice or by pharmacologically inhibiting p53. Thus, Aβ25-35 triggers Cdk5 activation to induce p53 phosphorylation and stabilization, which leads to neuronal damage. Inhibition of the Cdk5-p53 pathway may therefore represent a novel therapeutic strategy against Aβ-induced neurodegeneration.
Connections between freshwater carbon and nutrient cycles revealed through reconstructed population genomes
Authors: Linz Alexandra M. , He Shaomei , Stevens Sarah L. R. , Anantharaman Karthik , Rohwer Robin R. , Malmstrom Rex R. , Bertilsson Stefan , McMahon Katherine D. 
Published: July 2018

AbstractMetabolic processes at the microbial scale influence ecosystem functions because microbes are responsible for much of the carbon and nutrient cycling in freshwater. One approach to predict the metabolic capabilities of microbial communities is to search for functional marker genes in metagenomes. However, this approach does not provide context about co-occurrence with other metabolic traits within an organism or detailed taxonomy about those organisms. Here, we combine a functional marker gene analysis with metabolic pathway prediction of microbial population genomes (MAGs) assembled from metagenomic time series in eutrophic Lake Mendota and humic Trout Bog to identify how carbon and nutrient cycles are connected in freshwater. We found that phototrophy, carbon fixation, and nitrogen fixation pathways co-occurred in Cyanobacteria MAGs in Lake Mendota and in Chlorobiales MAGs in Trout Bog. Cyanobacteria MAGs also had strong temporal correlations to functional marker genes for nitrogen fixation in several years. Genes encoding steps in the nitrogen and sulfur cycles varied in abundance and taxonomy by lake, potentially reflecting the availability and composition of inorganic nutrients in these systems. We were also able to identify which populations contained the greatest density and diversity of genes encoding glycoside hydrolases. Populations with many glycoside hydrolases also encoded pathways for sugar degradation. By using both MAGs and marker genes, we were better able to link functions to specific taxonomic groups in our metagenomic time series, enabling a more detailed understanding of freshwater microbial carbon and nutrient cycling.
Excellence models as complex management systems
Authors: Edgeman Rick 
Published: July 2018

Purpose
When appropriately implemented, excellence models such as the Shingo operational excellence model (SOEM), Baldrige performance excellence model and EFQM business excellence model aid enterprise quests for sustained superior results across varied dimensions. Evidence supporting this statement abounds in the literature and in practice. The models, however, tend to be driven by experience, rather than grounded in theory. The purpose of this paper is to explore theoretical underpinnings for such models, with the SOEM used for illustrative purposes.

Design/methodology/approach
Management theory, systems theory and excellence modeling are integrated to yield a complex management systems based operational excellence model. Correspondence of this model with the SOEM is explored. Key elements considered include contextual factors external to the enterprise, diverse stakeholders, mediating forces, enterprise culture and representative enterprise processes.

Findings
Understanding the theoretical underpinnings of excellence models—their elements and the interactions and synergies of these elements—enables more sure adaptation of such models to specific enterprise contexts, and more sure course corrections whenever corrections are needed.

Originality/value
Many excellence models exist, their usefulness largely validated by anecdotal or empirical evidence. Such validation is important, but falls short of theoretically grounding these models. The approach taken herein serves to unify theory, empirical evidence and anecdotes, thus placing excellence models on more solid ground.