bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synergism between the Black Queen effect and the proteomic constraint on genome size reduction in the photosynthetic picoeukaryotes
Authors: Derilus D. , Rahman M. Z. , Pinero F. , Massey S. E. 
Published: June 2020

AbstractThe photosynthetic picoeukaryotes (PPEs) comprise a rare example of free-living eukaryotes that have undergone genome reduction. Here, we examine a duality in the process; the proposed driver of genome reduction (the Black Queen hypothesis, BQH), and the resultant impact of genome information loss (the Proteomic Constraint hypothesis, PCH). The BQH predicts that some metabolites may be shared in the open ocean, thus driving loss of redundant metabolic pathways in individual genomes. In contrast, the PCH predicts that as the information content of a genome is reduced, the total mutation load is also reduced, leading to loss of DNA repair genes due to the resulting reduction in selective constraint. Consistent with the BQH, we observe that biosynthetic pathways involved with soluble metabolites such as amino acids and carotenoids are preferentially lost from the PPEs, in contrast to biosynthetic pathways involved with insoluble metabolites, such as lipids, which are retained. Consistent with the PCH, a correlation between proteome size and the number of DNA repair genes, and numerous other informational categories, is observed. While elevated mutation rates resulting from the loss of DNA repair genes have been linked to reduced effective population sizes in intracellular bacteria, this remains to be established. This study shows that in microbial species with large population sizes, an underlying factor in modulating their DNA repair capacity appears to be information content.
Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia
Authors: Weldenegodguad Melak , Pokharel Kisun , Ming Yao , Honkatukia Mervi , Peippo Jaana , Reilas Tiina , Røed Knut H. , Kantanen Juha 
Published: June 2020

AbstractReindeer are semi-domesticated ruminants that have adapted to the challenging northern Eurasian environment characterized by long winters and marked annual fluctuations in daylight. We explored the genetic makeup behind their unique characteristics by de novo sequencing the genome of a male reindeer and conducted gene family analyses with nine other mammalian species. We performed a population genomics study of 23 additional reindeer representing both domestic and wild populations and several ecotypes from various geographic locations. We assembled 2.66 Gb (N50 scaffold of 5 Mb) of the estimated 2.92 Gb reindeer genome, comprising 27,332 genes. The results from the demographic history analysis suggested marked changes in the effective population size of reindeer during the Pleistocene period. We detected 160 reindeer-specific and expanded genes, of which zinc finger proteins (n = 42) and olfactory receptors (n = 13) were the most abundant. Comparative genome analyses revealed several genes that may have promoted the adaptation of reindeer, such as those involved in recombination and speciation (PRDM9), vitamin D metabolism (TRPV5, TRPV6), retinal development (PRDM1, OPN4B), circadian rhythm (GRIA1), immunity (CXCR1, CXCR2, CXCR4, IFNW1), tolerance to cold-triggered pain (SCN11A) and antler development (SILT2). The majority of these characteristic reindeer genes have been reported for the first time here. Moreover, our population genomics analysis suggested at least two independent reindeer domestication events with genetic lineages originating from different refugial regions after the Last Glacial Maximum. Taken together, our study has provided new insights into the domestication, evolution and adaptation of reindeer and has promoted novel genomic research of reindeer.
Zika Virus NS3 Protease Pharmacophore Anchor Model and Drug Discovery
Authors: Pathak Nikhil , Kuo Yi-Ping , Chang Teng-Yuan , Huang Chin-Ting , Hung Hui-Chen , Hsu John Tsu-An , Yu Guann-Yi , Yang Jinn-Moon 
Published: June 2020

AbstractZika virus (ZIKV) of the flaviviridae family, is the cause of emerging infections characterized by fever, Guillain-Barré syndrome (GBS) in adults and microcephaly in newborns. There exists an urgent unmet clinical need for anti-ZIKV drugs for the treatment of infected individuals. In the current work, we aimed at the promising virus drug target, ZIKV NS3 protease and constructed a Pharmacophore Anchor (PA) model for the active site. The PA model reveals a total of 12 anchors (E, H, V) mapped across the active site subpockets. We further identified five of these anchors to be critical core anchors (CEH1, CH3, CH7, CV1, CV3) conserved across flaviviral proteases. The ZIKV protease PA model was then applied in anchor-enhanced virtual screening yielding 14 potential antiviral candidates, which were tested by in vitro assays. We discovered FDA drugs Asunaprevir and Simeprevir to have potent anti-ZIKV activities with EC50 values 4.7 µM and 0.4 µM, inhibiting the viral protease with IC50 values 6.0 µM and 2.6 µM respectively. Additionally, the PA model anchors aided in the exploration of inhibitor binding mechanisms. In conclusion, our PA model serves as a promising guide map for ZIKV protease targeted drug discovery and the identified ‘previr’ FDA drugs are promising for anti-ZIKV treatments.
Saturation of radiative heat transfer due to many-body thermalization
Authors: Latella Ivan , Messina Riccardo , Biehs Svend-Age , Rubi J. Miguel , Ben-Abdallah Philippe 
Published: June 2020

AbstractRadiative heat transfer between two bodies saturates at very short separation distances due to the nonlocal optical response of the materials. In this work, we show that the presence of radiative interactions with a third body or external bath can also induce a saturation of the heat transfer, even at separation distances for which the optical response of the materials is purely local. We demonstrate that this saturation mechanism is a direct consequence of a thermalization process resulting from many-body interactions in the system. This effect could have an important impact in the field of nanoscale thermal management of complex systems and in the interpretation of measured signals in thermal metrology at the nanoscale.
Drug response analysis for scaffold-free cardiac constructs fabricated using bio-3D printer
Authors: Arai Kenichi , Murata Daiki , Takao Shoko , Nakamura Anna , Itoh Manabu , Kitsuka Takahiro , Nakayama Koichi 
Published: June 2020

AbstractCardiac constructs fabricated using human induced pluripotent stem cells-derived cardiomyocytes (iPSCs-CMs) are useful for evaluating the cardiotoxicity of and cardiac response to new drugs. Previously, we fabricated scaffold-free three-dimensional (3D) tubular cardiac constructs using a bio-3D printer, which can load cardiac spheroids onto a needle array. In this study, we developed a method to measure the contractile force and to evaluate the drug response in cardiac constructs. Specifically, we measured the movement of the needle tip upon contraction of the cardiac constructs on the needle array. The contractile force and beating rate of the cardiac constructs were evaluated by analysing changes in the movement of the needle tip. To evaluate the drug response, contractile properties were measured following treatment with isoproterenol, propranolol, or blebbistatin, in which the movement of the needle tip was increased following isoproterenol treatment, but was decreased following propranolol or blebbistain, treatments. To evaluate cardiotoxicity, contraction and cell viability of the cardiac constructs were measured following doxorubicin treatment. Cell viability was found to decrease with decreasing movement of the needle tip following doxorubicin treatment. Collectively, our results show that this method can aid in evaluating the contractile force of cardiac constructs.
PLGA nanoparticles loaded with Gallic acid- a constituent of Leea indica against Acanthamoeba triangularis
Authors: Mahboob Tooba , Nawaz Muhammad , de Lourdes Pereira Maria , Tian-Chye Tan , Samudi Chandramathi , Sekaran Shamala Devi , Wiart Christophe , Nissapatorn Veeranoot 
Published: June 2020

AbstractAcanthamoeba, a genus that contains at least 24 species of free-living protozoa, is ubiquitous in nature. Successful treatment of Acanthamoeba infections is always very difficult and not always effective. More effective drugs must be developed, and medicinal plants may have a pivotal part in the future of drug discovery. Our research focused on investigating the in vitro anti- acanthamoebic potential of Leea indica and its constituent gallic acid in different concentrations. Water and butanol fractions exhibited significant amoebicidal activity against trophozoites and cysts. Gallic acid (100 µg/mL) revealed 83% inhibition of trophozoites and 69% inhibition of cysts. The butanol fraction induced apoptosis in trophozoites, which was observed using tunnel assay. The cytotoxicity of the fractions and gallic acid was investigated against MRC-5 and no adverse effects were observed. Gallic acid was successfully loaded within poly (D,L-lactide-co-glycolide) (PLGA) nanoparticles with 82.86% encapsulation efficiency, while gallic acid showed 98.24% in vitro release at 48 hours. Moreover, the gallic acid encapsulated in the PLGA nanoparticles exhibited 90% inhibition against trophozoites. In addition, gallic acid encapsulated nanoparticles showed reduced cytotoxicity towards MRC-5 compared to gallic acid, which evidenced that natural product nanoencapsulation in polymeric nanoparticles could play an important role in the delivery of natural products.
Synthesis and characterization of Magnesium-Iron-Cobalt complex hydrides
Authors: Barale Jussara , Deledda Stefano , Dematteis Erika M. , Sørby Magnus H. , Baricco Marcello , Hauback Bjørn C. 
Published: June 2020

AbstractThe formation, structure and deuterium desorption properties of Mg2FexCo(1−x)Dy (0 ≤ x ≤ 1 and 5 ≤ y ≤ 6) complex hydrides were investigated. The synthesis was carried out by reactive ball milling, using a mixture of powders of the parent elements in D2 atmosphere. The formation of quaternary deuterides was identified from Rietveld refinements of powder X-Ray diffraction and powder neutron diffraction patterns, and from infrared attenuated total reflectance analysis. It was observed that the crystal structure of deuterides depends on the transition metal fraction. For Co-rich compositions, i.e. up to x = 0.1, hydrides have the tetragonal distorted CaF2-type structure (space group P4/nmm) of Mg2CoD5 at room temperature. For Fe-rich compositions, i.e. x ≥ 0.5, a cubic hydride is observed, with the same K2PtCl6-type structure (space group Fm$$\bar{{\bf{3}}}$$3¯m) as Mg2FeD6 and as Mg2CoD5 at high temperatures. For x = 0.3, both the cubic and the tetragonal deuterides are detected. Differential scanning calorimetry coupled with thermogravimetric and temperature programmed desorption analyses show rather similar deuterium desorption properties for all samples, without significant changes as a function of composition. Finally, hydrogen sorption experiments performed for Mg2Fe0.5Co0.5H5.5 at 30 bar of H2 and 673 K showed reversible reactions, with good kinetic for both absorption and desorption of hydrogen.
New Synthesis Route for Complex Borides; Rapid Synthesis of Thermoelectric Yttrium Aluminoboride via Liquid-Phase Assisted Reactive Spark Plasma Sintering
Authors: Son Hyoung-Won , Berthebaud David , Yubuta Kunio , Yoshikawa Akira , Shishido Toetsu , Suzuta Keiko , Mori Takao 
Published: June 2020

AbstractYxAlyB14 ceramics are of high interest as high temperature thermoelectric materials with excellent p, n control. In this study, direct synthesis of dense polycrystalline YxAlyB14 (x ~0.64, 0.52 ≤ y ≤ 0.67) ceramics was successfully carried out by spark plasma sintering using commercially available precursors. YB4, AlB2 and B powders were reactively sintered with an additive AlF3 at 1773 K for 5–60 min in reduced Ar atmosphere. The sinterability was remarkably enhanced by liquid phase sintering comparing to conventional synthesis techniques. Phase composition analysis by X-ray diffraction showed that main peaks belong to YxAlyB14 with the MgAlB14 structure type and no peaks of AlF3 were detected. The thermoelectric behavior was changed from p-type to n-type with increasing Al occupancy. Power factor and ZT values measured in this study were found to be in the same range as the best values previously reported. This original synthesis process is found to be less precursor-consuming as compared to previous synthesis processes, and strikingly, less time-consuming, as the synthesis time, is shortened from 8 h to 5 min for p-type and to 1 h for n-type. The total process time is shortened from ≥3 days to ~4–5 h. This discovery opens the door for more accessible synthesis of complex borides.
Extracellular vesicles produced by NFAT3-expressing cells hinder tumor growth and metastatic dissemination
Authors: de Camargo Lívia Cardoso Bueno , Guaddachi Frédéric , Bergerat David , Ourari Nadia , Coillard Lucie , Parietti Veronique , Le Bras Morgane , Lehmann-Che Jacqueline , Jauliac Sébastien 
Published: June 2020

AbstractMetastases are the main cause of cancer-induced deaths worldwide. To block tissue invasion, development of extracellular vesicles (EVs) as therapeutic carriers, appears as an exciting challenge. To this aim, we took advantage of the anti-invasive function of NFAT3 transcription factor we identified previously in breast cancer and addressed the opportunity to transfer this inhibitory function by EVs. We show here that EVs produced by poorly invasive NFAT3-expressing breast cancer cell lines are competent to block in vitro invasion of aggressive cancer cells from different origins and, in cooperation with macrophages, inhibit cell proliferation and induce apoptosis. Moreover, this inhibitory effect can be improved by overexpression of NFAT3 in the EVs-producing cells. These results were extended in a mouse breast cancer model, with clear impact of inhibitory EVs on tumor growth and metastases spreading. This work identifies EVs produced by NFAT3-expressing breast cancer cells as an anti-tumoral tool to tackle cancer development and metastases dissemination.
Binding of Filamentous Actin to CaMKII as Potential Regulation Mechanism of Bidirectional Synaptic Plasticity by β CaMKII in Cerebellar Purkinje Cells
Authors: Pinto Thiago M. , Schilstra Maria J. , Roque Antonio C. , Steuber Volker 
Published: June 2020

AbstractCalcium-calmodulin dependent protein kinase II (CaMKII) regulates many forms of synaptic plasticity, but little is known about its functional role during plasticity induction in the cerebellum. Experiments have indicated that the β isoform of CaMKII controls the bidirectional inversion of plasticity at parallel fibre (PF)-Purkinje cell (PC) synapses in cerebellar cortex. Because the cellular events that underlie these experimental findings are still poorly understood, we developed a simple computational model to investigate how β CaMKII regulates the direction of plasticity in cerebellar PCs. We present the first model of AMPA receptor phosphorylation that simulates the induction of long-term depression (LTD) and potentiation (LTP) at the PF-PC synapse. Our simulation results suggest that the balance of CaMKII-mediated phosphorylation and protein phosphatase 2B (PP2B)-mediated dephosphorylation of AMPA receptors can determine whether LTD or LTP occurs in cerebellar PCs. The model replicates experimental observations that indicate that β CaMKII controls the direction of plasticity at PF-PC synapses, and demonstrates that the binding of filamentous actin to CaMKII can enable the β isoform of the kinase to regulate bidirectional plasticity at these synapses.
AFM Imaging of Protein Aggregation in Studying the Impact of Knotted Electromagnetic Field on A Peroxidase
Authors: Ivanov Yuri D. , Pleshakova Tatyana O. , Shumov Ivan D. , Kozlov Andrey F. , Ivanova Irina A. , Valueva Anastasia A. , Tatur Vadim Yu. , Smelov Mikhail V. , Ivanova Nina D. , Ziborov Vadim S. 
Published: June 2020

AbstractThe phenomenon of knotted electromagnetic field (KEMF) is now actively studied, as such fields are characterized by a nontrivial topology. The research in this field is mainly aimed at technical applications – for instance, the development of efficient communication systems. Until present, however, the influence of KEMF on biological objects (including enzyme systems) was not considered. Herein, we have studied the influence of KEMF on the aggregation and enzymatic activity of a protein with the example of horseradish peroxidase (HRP). The test HRP solution was irradiated in KEMF (the radiation power density was 10−12 W/cm2 at 2.3 GHz frequency) for 40 min. After the irradiation, the aggregation of HRP was examined by atomic force microscopy (AFM) at the single-molecule level. The enzymatic activity was monitored by conventional spectrophotometry. It has been demonstrated that an increased aggregation of HRP, adsorbed on the AFM substrate surface, was observed after irradiation of the protein sample in KEMF with low (10−12 W/cm2) radiation power density; at the same time, the enzymatic activity remained unchanged. The results obtained herein can be used in the development of models describing the interaction of enzymes with electromagnetic field. The obtained data can also be of importance considering possible pathological factors that can take place upon the influence of KEMF on biological objects— for instance, changes in hemodynamics due to increased protein aggregation are possible; the functionality of protein complexes can also be affected by aggregation of their protein subunits. These effects should also be taken into account in the development of novel highly sensitive systems for human serological diagnostics of breast cancer, prostate cancer, brain cancer and other oncological pathologies, and for diagnostics of diseases in animals, and crops.
General and feature-based semantic representations in the semantic network
Authors: Liuzzi Antonietta Gabriella , Aglinskas Aidas , Fairhall Scott Laurence 
Published: June 2020

AbstractHow semantic representations are manifest over the brain remains a topic of active debate. A semantic representation may be determined by specific semantic features (e.g. sensorimotor information), or may abstract away from specific features and represent generalized semantic characteristics (general semantic representation). Here we tested whether nodes of the semantic system code for a general semantic representation and/or possess representational spaces linked to particular semantic features. In an fMRI study, eighteen participants performed a typicality judgment task with written words ﻿drawn from sixteen different categories. Multivariate pattern analysis (MVPA) and representational similarity analysis (RSA) were adopted to investigate the sensitivity of the brain regions to semantic content and the type of semantic representation coded (general or feature-based). We replicated previous findings of sensitivity to general semantic similarity in posterior middle/inferior temporal gyrus (pMTG/ITG) and precuneus (PC) and additionally observed general semantic representations in ventromedial prefrontal cortex (PFC). Finally, two brain regions of the semantic network were sensitive to semantic features: the left pMTG/ITG was sensitive to haptic perception and the left ventral temporal cortex (VTC) to size. This finding supports the involvement of both general semantic representation and feature-based representations in the brain’s semantic system.
Challenging human somatic testicular cell reassembly by protein kinase inhibition –setting up a functional in vitro test system
Authors: Mincheva M. , Wistuba J. , Brenker C. , Schlatt S. 
Published: June 2020

AbstractSignalling pathways and cellular interactions defining initial processes of testis morphogenesis, i.e. cord formation, are poorly understood. In vitro cell-based systems modelling cord formation can be utilised as platforms to interrogate processes of tubulogenesis. We aimed at testing our established cord formation in vitro model using adult human testicular cells as a quantitative assay that can facilitate future studies on cord morphogenesis. We challenged the responsiveness of our system with a broad-spectrum protein kinase inhibitor, K252a. Cultured testicular cells were treated with various K252a concentrations under constant exposure and compound withdrawal. To quantify cell reaggregation changes, we performed computer-assisted phase-contrast image analysis of aggregate size and number. Cell reaggregation was analysed in detail by categorisation of aggregates into size groups and accounting for changes in aggregate number per size category. We found a dose-related disturbance of testicular cell reaggregation. K252a decreased aggregate size (IC50 of 203.3 nM) and reduced the large aggregate numbers. Video recordings revealed that treatment with K252a at a concentration above IC50 interfered with aggregate coalescence into cords. Short-term exposure and compound wash-out induced irreversible decrease in large aggregates. We propose our in vitro model as a functional platform to quantitatively investigate seminiferous tubulogenesis under pharmacological impact.
Good performance of turquoise killifish (Nothobranchius furzeri) on pelleted diet as a step towards husbandry standardization
Authors: Žák Jakub , Dyková Iva , Reichard Martin 
Published: June 2020

AbstractDietary alteration is one of the most universally effective aging interventions, making its standardization a fundamental need for model organisms in aging. In this dietetic study we address the current lack of standardized formulated diet for turquoise killifishNothobranchius furzeri– a promising model organism. We first demonstrated thatN. furzerican be fully weaned at the onset of puberty onto a commercially available pelleted diet as the sole nutrition when kept in social tanks. We then compared nine somatic and six reproductive parameters between fish fed a typical laboratory diet - frozen chironomid larvae (bloodworms) and fish weaned from bloodworms to BioMar pellets. Both dietary groups had comparable somatic and reproductive performance. There was no difference between diet groups in adult body size, specific growth rate, condition or extent of hepatocellular vacuolation. Fish fed a pelleted diet had higher juvenile body mass and more visceral fat. Pellet-fed males had lower liver mass and possessed a lipid type of hepatocellular vacuolation instead of the prevailing glycogen-like vacuolation in the bloodworm-fed group. No considerable effect was found on reproductive parameters. The negligible differences between dietary groups and good acceptance of pellets indicate their suitability as a useful starting point for the development of standardized diet forNothobranchius furzeri.