bluuebunny/crossref_metadata_2025_split huggingface dataset:
Behaviour and cold hardiness of the purple stem borer in winter, colonizing more northerly latitudes
Authors: Huang Jianrong , Li Guoping , Lei Haixia , Fan Chunbin , Tian Caihong , Chen Qi , Huang Bo , Li Huilong , Lu Zhaocheng , Feng Hongqiang 
Published: October 2019

AbstractTo escape or alleviate low temperatures in winter, insects have evolved many behavioral and physiological strategies. The rice pest insect, the purple stem borer, Sesamia inferens (Walker) is currently reported to be expanding their northern distributions and causing damage to summer maize in Xinxiang, China. However, their method of coping with the lower temperature in the new northern breeding area in winter is largely unknown. This paper investigates the overwinter site of S. inferens, and identifies the cold hardiness of larvae collected from a new breeding area in winter and explores a potential distribution based on low temperature threshold and on species distribution model, MaxEnt. The results show that the overwintering location of the S. inferens population is more likely to be underground with increasing latitude and,in the north, with the temperature decreasing, the larvae gradually moved down the corn stalk and drilled completely underground by February 18th. Those who were still above ground were all winterkilled. The cold hardiness test shows the species is a moderate freeze-tolerant one, and Supercooling Points (SCP), Freezing Points (FP) and mortality rate during the middle of winter (January, SCP: −7.653, FP: −6.596) were significantly lower than early winter (October) or late winter (March). Distribution in the new expansion area was predicted and the survival probability area was below N 35° for the Air Lower Lethal Temperature (ALLT50) and below N 40° for the Underground Lower Lethal Temperature (ULLT50), The suitable habitat areas for S. inferens with MaxEnt were also below N 40°. This study suggests the overwinter strategies have led to the colonization of up to a five degree more northerly overwintering latitude. This behavior of S. inferens could help maize producers to propose a control method to increase pest mortality by extracting the maize stubble after harvest.
Differences in splicing defects between the grey and white matter in myotonic dystrophy type 1
Authors: Nishi Masamitsu , Kimura Takashi , Furuta Mitsuru , Suenaga Koichi , Matsumura Tsuyoshi , Fujimura Harutoshi , Jinnai Kenji , Yoshikawa Hiroo 
Published: October 2019

AbstractMyotonic dystrophy type 1 (DM1) is a multi-system disorder caused by CTG repeats in the myotonic dystrophy protein kinase (DMPK) gene. This leads to sequestration of the splicing factor, muscleblind-like 2 (MBNL2), and aberrant splicing, mainly in the central nervous system. We investigated the splicing patterns of MBNL1/2 and genes controlled by MBNL2 in several regions of the brain and between the grey matter (GM) and white matter (WM) in DM1 patients using RT-PCR. Compared with the control, the percentage of spliced-in parameter (PSI) for most of the examined exons were significantly altered in most of the brain regions of DM1 patients, except for the cerebellum. The splicing of many genes was differently regulated between the GM and WM in both DM1 and control. The level of change in PSI between DM1 and control was higher in the GM than in the WM. The differences in alternative splicing between the GM and WM may be related to the effect of DM1 on the WM of the brain. We hypothesize that in DM1, aberrantly spliced isoforms in the neuronal cell body of the GM may not be transported to the axon. This might affect the WM as a consequence of Wallerian degeneration secondary to cell body damage. Our findings may have implications for analysis of the pathological mechanisms and exploring potential therapeutic targets.
Alcohol Effects on Globus Pallidus Connectivity: Role of Impulsivity and Binge Drinking
Authors: Fede Samantha J. , Abrahao Karina P. , Cortes Carlos R. , Grodin Erica N. , Schwandt Melanie L. , George David T. , Diazgranados Nancy , Ramchandani Vijay A. , Lovinger David M. , Momenan Reza 
Published: October 2019

AbstractDespite the harm caused by binge drinking, the neural mechanisms leading to risky and disinhibited intoxication-related behaviors are not well understood. Evidence suggests that the globus pallidus externus (GPe), a substructure within the basal ganglia, participates in inhibitory control processes, as examined in stop-signaling tasks. In fact, studies in rodents have revealed that alcohol can change GPe activity by decreasing neuronal firing rates, suggesting that the GPe may have a central role in explaining impulsive behaviors and failures of inhibition that occur during binge drinking. In this study, twenty-five healthy volunteers underwent intravenous alcohol infusion to achieve a blood alcohol level of 0.08 g/dl, which is equivalent to a binge drinking episode. A resting state functional magnetic resonance imaging scan was collected prior to the infusion and at binge-level exposure. Functional connectivity analysis was used to investigate the association between alcohol-induced changes in GPe connectivity, drinking behaviors, and impulsivity traits. We found that individuals with greater number of drinks or heavy drinking days in the recent past had greater alcohol-induced deficits in GPe connectivity, particularly to the striatum. Our data also indicated an association between impulsivity and alcohol-induced deficits in GPe – frontal/precentral connectivity. Moreover, alcohol induced changes in GPe-amygdala circuitry suggested greater vulnerabilities to stress-related drinking in some individuals. Taken together, these findings suggest that alcohol may interact with impulsive personality traits and drinking patterns to drive alterations in GPe circuitry associated with behavioral inhibition, possibly indicating a neural mechanism by which binge drinking could lead to impulsive behaviors.
GSMN-ML- a genome scale metabolic network reconstruction of the obligate human pathogenMycobacterium leprae
Authors: Borah Khushboo , Kearney Jacque-Lucca , Banerjee Ruma , Vats Pankaj , Wu Huihai , Dahale Sonal , Sunitha Manjari K , Joshi Rajendra , Bonde Bhushan , Ojo Olabisi , Lahiri Ramanuj , Williams Diana L. , McFadden Johnjoe 
Published: October 2019

AbstractLeprosy, caused byMycobacterium leprae, has plagued humanity for thousands of years and continues to cause morbidity, disability and stigmatization in two to three million people today. Although effective treatment is available, the disease incidence has remained approximately constant for decades so new approaches, such as vaccine or new drugs, are urgently needed for control. Research is however hampered by the pathogen’s obligate intracellular lifestyle and the fact that it has never been grownin vitro. Consequently, despite the availability of its complete genome sequence, fundamental questions regarding the biology of the pathogen, such as its metabolism, remain largely unexplored. In order to explore the metabolism of the leprosy bacillus with a long-term aim of developing a medium to grow the pathogenin vitro, we reconstructed anin silicogenome scale metabolic model of the bacillus, GSMN-ML. The model was used to explore the growth and biomass production capabilities of the pathogen with a range of nutrient sources, such as amino acids, glucose, glycerol and metabolic intermediates. We also used the model to analyze RNA-seq data fromM. lepraegrown in mouse foot pads, and performed Differential Producibility Analysis (DPA) to identify metabolic pathways that appear to be active during intracellular growth of the pathogen, which included pathways for central carbon metabolism, co-factor, lipids, amino acids, nucleotides and cell wall synthesis. The GSMN-ML model is thereby a usefulin silicotool that can be used to explore the metabolism of the leprosy bacillus, analyze functional genomic experimental data, generate predictions of nutrients required for growth of the bacillusin vitroand identify novel drug targets.Author SummaryMycobacterium leprae, the obligate human pathogen is uncultivable in axenic growth medium, and this hinders research on this pathogen, and the pathogenesis of leprosy. The development of novel therapeutics relies on the understanding of growth, survival and metabolism of this bacterium in the host, the knowledge of which is currently very limited. Here we reconstructed a metabolic network ofM. leprae-GSMN-ML, a powerfulin silicotool to study growth and metabolism of the leprosy bacillus. We demonstrate the application of GSMN-ML to identify the metabolic pathways, and metabolite classes thatM. lepraeutilizes during intracellular growth.
Common alleles ofCMT2andNRPE1are major determinants ofde novoDNA methylation variation inArabidopsis thaliana
Authors: Sasaki Eriko , Kawakatsu Taiji , Ecker Joseph , Nordborg Magnus 
Published: October 2019

AbstractDNA cytosine methylation is an epigenetic mark associated with silencing of transposable elements (TEs) and heterochromatin formation. In plants, it occurs in three sequence contexts: CG, CHG, and CHH (where H is A, T, or C). The latter does not allow direct inheritance of methylation during DNA replication due to lack of symmetry, and methylation must therefore be re-established every cell generation. Genome-wide association studies (GWAS) have previously shown thatCMT2andNRPE1are major determinants of genome-wide patterns of TE CHH-methylation. Here we instead focus on CHH-methylation of individual TEs and TE-families, allowing us to identify the pathways involved in CHH-methylation simply from natural variation and confirm the associations by comparing them with mutant phenotypes. Methylation at TEs targeted by the RNA-directed DNA methylation (RdDM) pathway is unaffected byCMT2variation, but is strongly affected by variation atNRPE1, which is largely responsible for the longitudinal cline in this phenotype. In contrast, CMT2-targeted TEs are affected by both loci, which jointly explain 7.3% of the phenotypic variation (13.2% of total genetic effects). There is no longitudinal pattern for this phenotype, however, because the geographic patterns appear to compensate for each other in a pattern suggestive of stabilizing selection.Author SummaryDNA methylation is a major component of transposon silencing, and essential for genomic integrity. Recent studies revealed large-scale geographic variation as well as the existence of majortrans-acting polymorphisms that partly explained this variation. In this study, we re-analyze previously published data (The 1001 Epigenomes), focusing onde novoDNA methylation patterns of individual TEs and TE families rather than on genome-wide averages (as was done in previous studies). GWAS of the patterns reveals the underlying regulatory networks, and allowed us to comprehensively characterizetrans-regulation ofde novoDNA methylation and its role in the striking geographic pattern for this phenotype.
Plasmodiophora brassicae in its environment-effects of temperature and light on resting spore survival in soil
Authors: Zahr Kher , Sarkes Alian , Yang Yalong , Zhou Qixing , Feindel David , Harding Michael W. , Feng Jie 
Published: October 2019

AbstractClubroot caused by Plasmodiophora brassicae is an important disease on cruciferous crops worldwide. Management of clubroot has been challenging, due largely to the millions of resting spores produced within an infected root that can survive dormant in the soil for many years. This study was conducted to investigate some of the environmental conditions that may affect the survival of resting spores in the soil. Soil samples containing clubroot resting spores (1 × 107 spores g-1 soil) were stored at various temperatures for two years. Additionally, other samples were buried in soil, or kept on the soil surface in the field. The content of P. brassicae DNA and the numbers of viable spores in the samples were assessed by quantitative polymerase chain reaction (qPCR) and pathogenicity bioassays, respectively. The results indicated that 4°C, 20°C and being buried in the soil were better conditions for spore survival than were −20°C, 30°C and at the soil surface. Most of the spores kept on the soil surface were killed, suggesting the negative effect of light on spore viability. Additional experiments confirmed that ultraviolet (UV) light contributed a large negative effect on spore viability as lower pathogenicity and less DNA content were observed from the 2-and 3-hour UV light treated spores compared to the untreated control. Finally, this work demonstrated that DNA-based quantification methods such as qPCR can be poor predictors of P. brassicae disease potential due to the presence and persistence of DNA from dead spores.
Phylogeography of two Andean frogs: Test of vicariance versus elevational gradient models of diversification
Authors: Koscinski Daria , Handford Paul , Tubaro Pablo L. , Li Peiwen , Lougheed Stephen C. 
Published: October 2019

ABSTRACTThe tropical and subtropical Andes have among the highest levels of biodiversity in the world. Understanding the forces that underlie speciation and diversification in the Andes is a major focus of research. Here we tested two hypotheses of species origins in the Andes: 1. Vicariance mediated by orogenesis or shifting habitat distribution. 2. Parapatric diversification along elevational environmental gradients. We also sought insights on the factors that impacted the phylogeography of co-distributed taxa, and the influences of divergent species ecology on population genetic structure. We used phylogeographic and coalescent analyses of nuclear and mitochondrial DNA sequence data to compare genetic diversity and evolutionary history of two frog species:Pleurodema borellii(Family: Leiuperidae, 130 individuals; 20 sites), andHypsiboas riojanus(Family: Hyllidae, 258 individuals; 23 sites) across their shared range in northwestern Argentina. The two showed concordant phylogeographic structuring, and our analyses support the vicariance model over the elevational gradient model. However,Pleurodema borelliiexhibited markedly deeper temporal divergence (≥4 Ma) thanH. riojanus(1-2 Ma). The three main mtDNA lineages ofP. borelliiwere nearly allopatric and diverged between 4-10 Ma. At similar spatial scales, differentiation was less in the putatively more habitat-specializedH. riojanusthan in the more generalistP. borellii. Similar allopatric distributions of major lineages for both species implies common causes of historical range fragmentation and vicariance. However, different divergence times among clades presumably reflect different demographic histories, permeability of different historical barriers at different times, and/or difference in life history attributes and sensitivities to historical environmental change. Our research enriches our understanding of the phylogeography of the Andes in northwestern Argentina.
Cooperation between MYC and β-catenin in liver tumorigenesis requires Yap/Taz
Authors: Bisso Andrea , Filipuzzi Marco , Gamarra Figueroa Gianni Paolo , Brumana Giulia , Biagioni Francesca , Doni Mirko , Ceccotti Giorgia , Tanaskovic Nina , Morelli Marco Jacopo , Pendino Vera , Chiacchiera Fulvio , Pasini Diego , Olivero Daniela , Campaner Stefano , Sabò Arianna , Amati Bruno 
Published: October 2019

AbstractBackground & AimsActivation of MYC and CTNNB1 (encoding β-catenin) can co-occur in liver cancer, but how these oncogenes cooperate in tumorigenesis remains unclear.Approach & ResultsWe generated a mouse model allowing conditional activation of MYC and WNT/β-catenin signaling (through either β-catenin activation or Apc loss) upon expression of CRE recombinase in the liver, and monitored their effects on hepatocyte proliferation, apoptosis, gene expression profiles and tumorigenesis. Conditional activation of WNT/β-catenin signaling strongly accelerated MYC-driven carcinogenesis in the mouse liver. Both pathways also cooperated in promoting cellular transformation in vitro, demonstrating their cell-autonomous action. Short-term induction of MYC and β-catenin in hepatocytes followed by RNA-seq profiling allowed the identification of a “Myc/β-catenin signature”, composed of a discrete set of Myc-activated genes whose expression increased in presence of active β-catenin. Notably this signature enriched for targets of Yap and Taz, two transcriptional co-activators known to be activated by WNT/β-catenin signaling, and to cooperate with MYC in mitogenic activation and liver transformation. Consistent with these regulatory connections, Yap/Taz accumulated upon Myc/β-catenin activation and were required not only for the ensuing proliferative response, but also for tumor cell growth and survival. Finally, the Myc/β-catenin signature was enriched in a subset of human hepatocellular carcinomas characterized by comparatively poor prognosis.ConclusionsYap and Taz mediate the cooperative action of Myc and β-catenin in liver tumorigenesis. This warrants efforts toward therapeutic targeting of Yap/Taz in aggressive liver tumors marked by elevated Myc/β-catenin activity.
Transient deSUMOylation of IRF2BP proteins controls early transcription in EGFR signaling
Authors: Barysch Sina V. , Stankovic-Valentin Nicolas , Karaca Samir , Doppel Judith , Nait Achour Thiziri , Sticht Carsten , Urlaub Henning , Melchior Frauke 
Published: October 2019

SummaryMolecular switches are essential modules in signaling networks and transcriptional reprogramming. Here, we describe a role for small ubiquitin-related-modifier SUMO as a molecular switch in epidermal growth factor receptor (EGFR) signaling. Using quantitative mass spectrometry, we compared the endogenous SUMO-proteomes of Hela cells before and after EGF-stimulation. Thereby, we identified a small group of transcriptional co-regulators including IRF2BP1, IRF2BP2 and IRF2BPL as novel players in EGFR signaling. Comparison of cells expressing wildtype or SUMOylation deficient IRF2BP1 indicated that transient deSUMOylation of IRF2BP1 is important for appropriate expression of immediate early genes including Dual specificity phosphatase 1 (DUSP1, MKP-1), an important feedback regulator of EGFR signaling. We find that IRF2BP1 is a SUMO-dependent repressor, whose transient deSUMOylation on the DUSP1 promotor allows - and whose timely reSUMOylation restricts - DUSP1 expression. Our work thus provides a paradigm how comparative SUMO proteome analyses serve to reveal novel regulators in signal transduction and transcription.
SECAT: Quantifying differential protein-protein interaction states by network-centric analysis
Authors: Rosenberger George , Heusel Moritz , Bludau Isabell , Collins Ben , Martelli Claudia , Williams Evan , Xue Peng , Liu Yansheng , Aebersold Ruedi , Califano Andrea 
Published: October 2019

AbstractProtein-protein interactions (PPIs) play critical functional and regulatory roles in virtually all cellular processes. They are essential for the formation of macromolecular complexes, which in turn constitute the basis for extended protein interaction networks that determine the functional state of a cell. We and others have previously shown that chromatographic fractionation of native protein complexes in combination with bottom-up mass spectrometric analysis of consecutive fractions supports the multiplexed characterization and detection of state-specific changes of protein complexes.In this study, we describe a computational approach that extends the analysis of data from the co-fractionation / mass spectrometric analysis of native complexes to the level of PPI networks, thus enabling a qualitative and quantitative comparison of the proteome organization between samples and states. The Size-Exclusion Chromatography Algorithmic Toolkit (SECAT) implements a novel, network-centric strategy for the scalable and robust differential analysis of PPI networks. SECAT and its underlying statistical framework elucidate differential quantitative abundance and stoichiometry attributes of proteins in the context of their PPIs. We validate algorithm predictions using publicly available datasets and demonstrate that SECAT represents a more scalable and effective methodology to assess protein-network state and that our approach thus obviates the need to explicitly infer individual protein complexes. Further, by differential analysis of PPI networks of HeLa cells in interphase and mitotic state, respectively, we demonstrate the ability of the algorithm to detect PPI network differences and to thus suggest molecular mechanisms that differentiate cellular states.
Haptic assistance that restricts use of redundant solutions is detrimental to motor learning
Authors: Lokesh Rakshith , Ranganathan Rajiv 
Published: October 2019

AbstractUnderstanding the use of haptic assistance to facilitate motor learning is a critical issue, especially in the context of tasks requiring control of motor variability. However, the question of how haptic assistance should be designed in tasks with redundancy, where multiple solutions are available, is currently unknown. Here we examined the effect of haptic assistance that either allowed or restricted the use of redundant solutions on the learning of a bimanual steering task. 60 college-aged participants practiced steered a single cursor placed in between their hands along a smooth W-shaped track of a certain width as quickly as possible. Haptic assistance was either applied at the ‘task’ level using a force channel that only constrained the cursor to the track, allowing for the use of different hand trajectories, or (ii) the ‘individual effector’ level using a force channel that constrained each hand to a specific trajectory. In addition, we also examined the effect of ‘fading’ – i.e., decreasing assistance with practice to reduce dependence on haptic assistance. Results showed all groups improved with practice - however, groups with haptic assistance at the individual effector level performed worse than those at the task level. Moreover, fading of assistance did not offer learning benefits over constant assistance. Overall, the results suggest that haptic assistance is not effective for motor learning when it restricts the use of redundant solutions.
The Electrophysiological Signature of Mind Wandering
Authors: Arnau Stefan , Löffler Christoph , Rummel Jan , Hagemann Dirk , Wascher Edmund , Schubert Anna-Lena 
Published: October 2019

AbstractMind wandering during ongoing tasks can impede task performance and increase the risk of failure in laboratory as well as in daily-life tasks and work environments. Neurocognitive measures like the electroencephalography (EEG) offer the opportunity to assess mind wandering non-invasively without interfering with the primary task. However, the literature on electrophysiological correlates of mind wandering is rather inconsistent. The present study aims towards clarifying this picture by breaking down the temporal dynamics of mind-wandering encounters using a cluster-based permutation approach. Participants performed a switching task during which mind wandering was occasionally assessed via thought probes applied after trial completion at random time points. In line with previous studies, response accuracy was reduced during mind wandering. Moreover, alpha power during the inter-trial interval was significantly increased on those trials on which participants reported that they had been mind-wandering. This spatially widely distributed effect is theoretically well in line with recent findings linking an increased alpha power to an internally oriented state of attention. Measurements of alpha power may therefore be used to detect mind wandering online during critical tasks in traffic and industry in order to prevent failures.