bluuebunny/crossref_metadata_2025_split huggingface dataset:
The SR protein B52/SRp55 regulates splicing of the period thermosensitive intron and mid-day siesta in Drosophila
Authors: Zhang Zhichao , Cao Weihuan , Edery Isaac 
Published: January 2018

AbstractSimilar to many diurnal animals, Drosophila melanogaster exhibits a mid-day siesta that is more robust as temperature increases, an adaptive response that aims to minimize the deleterious effects from exposure to heat. This temperature-dependent plasticity in mid-day sleep levels is partly based on the thermal sensitive splicing of an intron in the 3′ untranslated region (UTR) of the circadian clock gene termed period (per). In this study, we evaluated a possible role for the serine/arginine-rich (SR) splicing factors in the regulation of dmpi8 splicing efficiency and mid-day siesta. Using a Drosophila cell culture assay we show that B52/SRp55 increases dmpi8 splicing efficiency, whereas other SR proteins have little to no effect. The magnitude of the stimulatory effect of B52 on dmpi8 splicing efficiency is modulated by natural variation in single nucleotide polymorphisms (SNPs) in the per 3′ UTR that correlate with B52 binding levels. Down-regulating B52 expression in clock neurons increases mid-day siesta and reduces dmpi8 splicing efficiency. Our results establish a novel role for SR proteins in sleep and suggest that polymorphisms in the per 3′ UTR contribute to natural variation in sleep behavior by modulating the binding efficiencies of SR proteins.
Design of an acoustic superlens using single-phase metamaterials with a star-shaped lattice structure
Authors: Chen Meng , Jiang Heng , Zhang Han , Li Dongsheng , Wang Yuren 
Published: January 2018

AbstractWe propose a single-phase super lens with a low density that can achieve focusing of sound beyond the diffraction limit. The super lens has a star-shaped lattice structure made of steel that offers abundant resonances to produce abnormal dispersive effects as determined by negative parameter indices. Our analysis of the metamaterial band structure suggests that these star-shaped metamaterials have double-negative index properties, that can mediate these effects for sound in water. Simulations verify the effective focusing of sound by a single-phase solid lens with a spatial resolution of approximately 0.39 λ. This superlens has a simple structure, low density and solid nature, which makes it more practical for application in water-based environments.
Identification of OsGGR2, a second geranylgeranyl reductase involved in α-tocopherol synthesis in rice
Authors: Kimura Eiichi , Abe Takumi , Murata Kazumasa , Kimura Toshiyuki , Otoki Yurika , Yoshida Taiji , Miyazawa Teruo , Nakagawa Kiyotaka 
Published: January 2018

AbstractTocopherol (Toc) and tocotrienol (T3) are abundant in rice bran. Geranylgeranyl reductase (GGR) is an essential enzyme for Toc production that catalyzes the reduction of geranylgeranyl pyrophosphate and geranylgeranyl-chlorophyll. However, we found that a rice mutant line with inactivated Os02g0744900 (OsGGR1/LYL1/OsChl P) gene produces Toc, suggesting that rice plants may carry another enzyme with GGR activity. Using an RNA-mediated interference technique, we demonstrated that the Os01g0265000 (“OsGGR2”) gene product has GGR activity. This result supports the existence of two GGR genes (OsGGR1 and OsGGR2) in rice, in contrast to Arabidopsis thaliana (thale cress) and cyanobacterium Synechocystis that each have only one GGR gene. We also produced rice callus with inactivated OsGGR1 and OsGGR2 that produced T3 but not Toc. Such rice callus could be used as a resource for production of pure T3 for nutraceutical applications.
Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation
Authors: Rehman Hafiz Mamoon , Nawaz Muhammad Amjad , Shah Zahid Hussain , Ludwig-Müller Jutta , Chung Gyuhwa , Ahmad Muhammad Qadir , Yang Seung Hwan , Lee Soo In 
Published: January 2018

AbstractIn plants, UGTs (UDP-glycosyltransferases) glycosylate various phytohormones and metabolites in response to biotic and abiotic stresses. Little is known about stress-responsive glycosyltransferases in plants. Therefore, it is important to understand the genomic and transcriptomic portfolio of plants with regard to biotic and abiotic stresses. Here, we identified 140, 154, and 251 putative UGTs in Brassica rapa, Brassica oleracea, and Brassica napus, respectively, and clustered them into 14 major phylogenetic groups (A–N). Fourteen major KEGG pathways and 24 biological processes were associated with the UGTs, highlighting them as unique modulators against environmental stimuli. Putative UGTs from B. rapa and B. oleracea showed a negative selection pressure and biased gene fractionation pattern during their evolution. Polyploidization increased the intron proportion and number of UGT-containing introns among Brassica. The putative UGTs were preferentially expressed in developing tissues and at the senescence stage. Differential expression of up- and down-regulated UGTs in response to phytohormone treatments, pathogen responsiveness and abiotic stresses, inferred from microarray and RNA-Seq data in Arabidopsis and Brassica broaden the glycosylation impact at the molecular level. This study identifies unique candidate UGTs for the manipulation of biotic and abiotic stress pathways in Brassica and Arabidopsis.
Computer-aided Discovery of Peptides that Specifically Attack Bacterial Biofilms
Authors: Haney Evan F. , Brito-Sánchez Yoan , Trimble Michael J. , Mansour Sarah C. , Cherkasov Artem , Hancock Robert E. W. 
Published: January 2018

AbstractBiofilms represent a multicellular growth state of bacteria that are intrinsically resistant to conventional antibiotics. It was recently shown that a synthetic immunomodulatory cationic peptide, 1018 (VRLIVAVRIWRR-NH2), exhibits broad-spectrum antibiofilm activity but the sequence determinants of antibiofilm peptides have not been systematically studied. In the present work, a peptide library consisting of 96 single amino acid substituted variants of 1018 was SPOT-synthesized on cellulose arrays and evaluated against methicillin resistant Staphylococcus aureus (MRSA) biofilms. This dataset was used to establish quantitative structure-activity relationship (QSAR) models relating the antibiofilm activity of these peptides to hundreds of molecular descriptors derived from their sequences. The developed 3D QSAR models then predicted the probability that a peptide would possess antibiofilm activity from a library of 100,000 virtual peptide sequences in silico. A subset of these variants were SPOT-synthesized and their activity assessed, revealing that the QSAR models resulted in ~85% prediction accuracy. Notably, peptide 3002 (ILVRWIRWRIQW-NH2) was identified that exhibited an 8-fold increased antibiofilm potency in vitro compared to 1018 and proved effective in vivo, significantly reducing abscess size in a chronic MRSA mouse infection model. This study demonstrates that QSAR modeling can successfully be used to identify antibiofilm specific peptides with therapeutic potential.
Evaluation of the osteogenesis and osseointegration of titanium alloys coated with graphene: an in vivo study
Authors: Li Kewen , Wang Chunhui , Yan Jinhong , Zhang Qi , Dang Baoping , Wang Zhuo , Yao Yun , Lin Kaifeng , Guo Zhongshang , Bi Long , Han Yisheng 
Published: January 2018

AbstractThe aim of this study was to investigate whether a surface coating with graphene could enhance the surface bioactivation of titanium alloys (Ti6Al4V) to further accelerate in vivo osteogenesis and osseointegration at the implant surface. In this study, a New Zealand white rabbit femoral condyle defect model was established. After 4, 12 and 24 weeks, biomechanical testing, micro-computed tomography (Micro-CT) analyses and histological observations were performed. At the highest push-out forces during the test, microstructure parameters, such as the bone volume/total volume fraction (BV/TV) and mineral apposition rate (MAR), of the new bone were significantly higher in the graphene-coated Ti6Al4V group (G-Ti6Al4V) than in the Ti6Al4V group (P < 0.05). Van Gieson (VG) staining showed that the G-Ti6Al4V group had more new bone formation than the Ti6Al4V group, and the G-Ti6Al4V group showed a closer fit between the bone and implant. In conclusion, graphene might be a novel type of nano-coating material for enhancing the surface biological activity of Ti-based alloy materials and may further promote in vivo osteogenesis and osseointegration.
A unique inbred rat strain with sustained cephalic hypersensitivity as a model of chronic migraine-like pain
Authors: Munro Gordon , Petersen Steffen , Jansen-Olesen Inger , Olesen Jes 
Published: January 2018

AbstractAnimal models of migraine-like pain enabling ongoing study of behaviour typically involve the systemic administration of chemical vasodilators or dural administration of inflammatory algogens. However, neither method mediates prolonged effects on behavior indicative of enduring pathophysiological changes occurring within dural or trigeminal pain circuits. We generated successive generations of a unique inbred rat strain, spontaneous trigeminal allodynia (STA) rats, previously reported to exhibit an episodic migraine-like behavioural phenotype. We show that both male and female STA rats display robust and sustained reductions in periorbital thresholds to cutaneous mechanical stimulation. Otherwise, the general behavior (e.g. locomotor, grooming) of these rats appeared normal. In female STA rats, the mechanical hypersensitivity was confined to the cephalic region, manifested after puberty through adolescence, and was sustained into adulthood recapitulating the clinical manifestation of migraine. We exploited this hitherto unidentified chronic phenotype to show that the migraine-specific drugs sumatriptan (5-HT1B/1D receptor agonist) and olcegepant (CGRP receptor antagonist) could completely reverse cephalic hypersensitivity using a within subject cross-over paradigm. Our findings indicate that STA rats actually possess a phenotype indicative of migraine chronicity which is exquisitely sensitive to migraine therapeutics. This unique strain could prove to be an invaluable resource in preclinical migraine drug discovery.
White matter hyperintensity shape and location feature analysis on brain MRI; proof of principle study in patients with diabetes
Authors: de Bresser Jeroen , Kuijf Hugo J. , Zaanen Karlijn , Viergever Max A. , Hendrikse Jeroen , Biessels Geert Jan ,   Utrecht Vascular Cognitive Impairment Study Group, Algra A. , van den Berg E. , Bouvy W. , Brundel M. , Heringa S. , Kappelle L. J. , Leemans A. , Luijten P. R. , Mali W. P. Th. M. , Rutten G. E. H. M. , Vincken K. L. , Zwanenburg J. 
Published: January 2018

AbstractCerebral small vessel disease is a heterogeneous disease in which various underlying etiologies can lead to different types of white matter hyperintensities (WMH). WMH shape features might aid in distinguishing these different types. In this proof of principle study in patients with type 2 diabetes mellitus (T2DM), we present a novel approach to assess WMH using shape features. Our algorithm determines WMH volume and different WMH shape and location features on 3T MRI scans. These features were compared between patients with T2DM (n = 60) and a matched control group (n = 54). Although a more traditional marker (WMH volume) was not significantly different between groups (natural log transformed Beta (95% CI): 0.07 (−0.11↔0.24)), patients with T2DM showed a larger number of non-punctuate WMH (median (10th–90th percentile), patients: 40 lesions per person (16–86); controls: 26 (5–58)) and a different shape (eccentricity) of punctuate deep WMH (Beta (95% CI): 0.40 (0.23↔0.58)) compared to controls. In conclusion, our algorithm identified WMH features that are not part of traditional WMH assessment, but showed to be distinguishing features between patients with T2DM and controls. Future studies could address these features to further unravel the etiology and functional impact of WMH.
Activated Biomass-derived Graphene-based Carbons for Supercapacitors with High Energy and Power Density
Authors: Jung SungHoon , Myung Yusik , Kim Bit Na , Kim In Gyoo , You In-Kyu , Kim TaeYoung 
Published: January 2018

AbstractHere, we present a facile and low-cost method to produce hierarchically porous graphene-based carbons from a biomass source. Three-dimensional (3D) graphene-based carbons were produced through continuous sequential steps such as the formation and transformation of glucose-based polymers into 3D foam-like structures and their subsequent carbonization to form the corresponding macroporous carbons with thin graphene-based carbon walls of macropores and intersectional carbon skeletons. Physical and chemical activation was then performed on this carbon to create micro- and meso-pores, thereby producing hierarchically porous biomass-derived graphene-based carbons with a high Brunauer-Emmett-Teller specific surface area of 3,657 m2 g−1. Owing to its exceptionally high surface area, interconnected hierarchical pore networks, and a high degree of graphitization, this carbon exhibited a high specific capacitance of 175 F g−1 in ionic liquid electrolyte. A supercapacitor constructed with this carbon yielded a maximum energy density of 74 Wh kg−1 and a maximum power density of 408 kW kg−1, based on the total mass of electrodes, which is comparable to those of the state-of-the-art graphene-based carbons. This approach holds promise for the low-cost and readily scalable production of high performance electrode materials for supercapacitors.
Establishing rapid analysis of Pu isotopes in seawater to study the impact of Fukushima nuclear accident in the Northwest Pacific
Authors: Men Wu , Zheng Jian , Wang Hai , Ni Youyi , Aono Tatsuo , Maxwell Sherrod L. , Tagami Keiko , Uchida Shigeo , Yamada Masatoshi 
Published: January 2018

AbstractIn order to assess the impact of the Fukushima derived Pu isotopes on seawater, a new analytical method to rapidly determine Pu isotopes in seawater by SF-ICP-MS including Fe(OH)2 primary co-precipitation, CaF2/LaF3 secondary co-precipitation and TEVA+UTEVA+DGA extraction chromatographic separation was established. High concentration efficiency (~100%) and high U decontamination factor (~107) were achieved. The plutonium chemical recoveries were 74–88% with the mean of 83 ± 5%. The precisions for both 240Pu/239Pu atom ratios and 239+240Pu activity concentrations were less than 5% when 15 L of seawater samples with the typical 239+240Pu activity of the Northwest Pacific were measured. It just needs 12 hours to determine plutonium using this new method. The limit of detection (LOD) for 239Pu and 240Pu were both 0.08 fg/mL, corresponding to 0.01 mBq/m3 for 239Pu and 0.05 mBq/m3 for 240Pu when a 15 L volume of seawater was measured. This method was applied to determine the seawater samples collected 446–1316 km off the FDNPP accident site in the Northwest Pacific in July of 2013. The obtained 239+240Pu activity concentrations of 1.21–2.19 mBq/m3 and the 240Pu/239Pu atom ratios of 0.198–0.322 suggested that there was no significant Pu contamination from the accident to the Northwest Pacific.
Ergodicity breaking transition in a glassy soft sphere system at small but non-zero temperatures
Authors: Maiti Moumita , Schmiedeberg Michael 
Published: January 2018

AbstractWhile the glass transition at non-zero temperature seems to be hard to access for experimental, theoretical, or simulation studies, jamming at zero temperature has been studied in great detail. Motivated by the exploration of the energy landscape that has been successfully used to investigate athermal jamming, we introduce a new method that includes the possibility of the thermally excited crossing of energy barriers. We then determine whether the ground state configurations of a soft sphere system are accessible or not and as a consequence whether the system is ergodic or effectively non-ergodic. Interestingly, we find an transition where the system becomes effectively non-ergodic if the density is increased. The transition density in the limit of small but non-zero temperatures is independent of temperature and below the transition density of athermal jamming. This confirms recent computer simulation studies where athermal jamming occurs deep inside the glass phase. In addition, we show that the ergodicity breaking transition is in the universality class of directed percolation. Therefore, our approach not only makes the transition from an ergodic to an effectively non-ergodic systems easily accessible and helps to reveal its universality class but also shows that it is fundamentally different from athermal jamming.
Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Authors: Pagerols Mireia , Richarte Vanesa , Sánchez-Mora Cristina , Rovira Paula , Soler Artigas María , Garcia-Martínez Iris , Calvo-Sánchez Eva , Corrales Montse , da Silva Bruna Santos , Mota Nina Roth , Victor Marcelo Moraes , Rohde Luis Augusto , Grevet Eugenio Horacio , Bau Claiton Henrique Dotto , Cormand Bru , Casas Miguel , Ramos-Quiroga Josep Antoni , Ribasés Marta 
Published: January 2018

AbstractMethylphenidate (MPH) is the most frequently used pharmacological treatment in children with attention-deficit/hyperactivity disorder (ADHD). However, a considerable interindividual variability exists in clinical outcome. Thus, we performed a genome-wide association study of MPH efficacy in 173 ADHD paediatric patients. Although no variant reached genome-wide significance, the set of genes containing single-nucleotide polymorphisms (SNPs) nominally associated with MPH response (P < 0.05) was significantly enriched for candidates previously studied in ADHD or treatment outcome. We prioritised the nominally significant SNPs by functional annotation and expression quantitative trait loci (eQTL) analysis in human brain, and we identified 33 SNPs tagging cis-eQTL in 32 different loci (referred to as eSNPs and eGenes, respectively). Pathway enrichment analyses revealed an over-representation of genes involved in nervous system development and function among the eGenes. Categories related to neurological diseases, psychological disorders and behaviour were also significantly enriched. We subsequently meta-analysed the association with clinical outcome for the 33 eSNPs across the discovery sample and an independent cohort of 189 ADHD adult patients (target sample) and we detected 15 suggestive signals. Following this comprehensive strategy, our results provide a better understanding of the molecular mechanisms implicated in MPH treatment effects and suggest promising candidates that may encourage future studies.
Eye region surface temperature reflects both energy reserves and circulating glucocorticoids in a wild bird
Authors: Jerem Paul , Jenni-Eiermann Susanne , Herborn Katherine , McKeegan Dorothy , McCafferty Dominic J. , Nager Ruedi G. 
Published: January 2018

AbstractBody temperature of endotherms shows substantial within- and between-individual variation, but the sources of this variation are not fully understood in wild animals. Variation in body temperature can indicate how individuals cope with their environment via metabolic or stress-induced effects, both of which may relate to depletion of energy reserves. Body condition can reflect heat production through changes to metabolic rate made to protect energy reserves. Additionally, changes in metabolic processes may be mediated by stress-related glucocorticoid secretion, which is associated with altered blood-flow patterns that affect regional body temperatures. Accordingly, both body condition and glucocorticoid secretion should relate to body temperature. We used thermal imaging, a novel non-invasive method of temperature measurement, to investigate relationships between body condition, glucocorticoid secretion and body surface temperature in wild blue tits (Cyanistes caeruleus). Individuals with lower body condition had lower eye-region surface temperature in both non-breeding and breeding seasons. Eye-region surface temperature was also negatively correlated with baseline circulating glucocorticoid levels in non-breeding birds. Our results demonstrate that body surface temperature can integrate multiple aspects of physiological state. Consequently, remotely-measured body surface temperature could be used to assess such aspects of physiological state non-invasively in free-living animals at multiple life history stages.
Rational CCL5 mutagenesis integration in a lactobacilli platform generates extremely potent HIV-1 blockers
Authors: Secchi Massimiliano , Grampa Valentina , Vangelista Luca 
Published: January 2018

AbstractEfforts to improve existing anti-HIV-1 therapies or develop preventatives have identified CCR5 as an important target and CCL5 as an ideal scaffold to sculpt potent HIV-1 entry inhibitors. We created novel human CCL5 variants that exhibit exceptional anti-HIV-1 features using recombinant lactobacilli (exploited for live microbicide development) as a screening platform. Protein design, expression and anti-HIV-1 activity flowed in iterative cycles, with a stepwise integration of successful mutations and refinement of an initial CCL5 mutant battery towards the generation of two ultimate CCL5 derivatives, a CCR5 agonist and a CCR5 antagonist with similar anti-HIV-1 potency. The CCR5 antagonist was tested in human macrophages and against primary R5 HIV-1 strains, exhibiting cross-clade low picomolar IC50 activity. Moreover, its successful combination with several HIV-1 inhibitors provided the ground for conceiving therapeutic and preventative anti-HIV-1 cocktails. Beyond HIV-1 infection, these CCL5 derivatives may now be tested against several inflammation-related pathologies where the CCL5:CCR5 axis plays a relevant role.
A viroid-derived system to produce large amounts of recombinant RNA in Escherichia coli
Authors: Daròs José-Antonio , Aragonés Verónica , Cordero Teresa 
Published: January 2018

AbstractViruses have been engineered into useful biotechnological tools for gene therapy or to induce the synthesis of products of interest, such as therapeutic proteins and vaccines, in animal and fungal cells, bacteria or plants. Viroids are a particular class of infectious agents of higher plants that exclusively consist of a small non-protein-coding circular RNA molecule. In the same way as viruses have been transformed into useful biotechnological devices, can viroids be converted into beneficial tools? We show herein that, by expressing Eggplant latent viroid (ELVd) derived RNAs in Escherichia coli together with the eggplant tRNA ligase, this being the enzyme involved in viroid circularization in the infected plant, RNAs of interest like aptamers, extended hairpins, or other structured RNAs are produced in amounts of tens of milligrams per liter of culture. Although ELVd fails to replicate in E. coli, ELVd precursors self-cleave through the embedded hammerhead ribozymes and the resulting monomers are, in part, circularized by the co-expressed enzyme. The mature viroid forms and the protein likely form a ribonucleoprotein complex that transitorily accumulates in E. coli cells at extraordinarily amounts.