bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA-seq of HaHV-1-infected abalones reveals a common transcriptional signature of Malacoherpesviruses
Authors: Bai Chang-Ming , Rosani Umberto , Li Ya-Nan , Zhang Shu-Min , Xin Lu-Sheng , Wang Chong-Ming 
Published: January 2019

AbstractHaliotid herpesvirus-1 (HaHV-1) is the viral agent causative of abalone viral ganglioneuritis, a disease that has severely affected gastropod aquaculture. Although limited, the sequence similarity between HaHV-1 and Ostreid herpesvirus-1 supported the assignment of both viruses to Malacoherpesviridae, a Herpesvirales family distantly related with other viruses. In this study, we reported the first transcriptional data of HaHV-1, obtained from an experimental infection of Haliotis diversicolor supertexta. We also sequenced the genome draft of the Chinese HaHV-1 variant isolated in 2003 (HaHV-1-CN2003) by PacBio technology. Analysis of 13 million reads obtained from 3 RNA samples at 60 hours post injection (hpi) allowed the prediction of 51 new ORFs for a total of 117 viral genes and the identification of 207 variations from the reference genome, consisting in 135 Single Nucleotide Polymorphisms (SNPs) and 72 Insertions or Deletions (InDels). The pairing of genomic and transcriptomic data supported the identification of 60 additional SNPs, representing viral transcriptional variability and preferentially grouped in hotspots. The expression analysis of HaHV-1 ORFs revealed one putative secreted protein, two putative capsid proteins and a possible viral capsid protease as the most expressed genes and demonstrated highly synchronized viral expression patterns of the 3 infected animals at 60 hpi. Quantitative reverse transcription data of 37 viral genes supported the burst of viral transcription at 30 and 60 hpi during the 72 hours of the infection experiment, and allowed the distinction between early and late viral genes.
Regulation of osteogenesis and osteoclastogenesis by zoledronic acid loaded on biodegradable magnesium-strontium alloy
Authors: Li Mei , Wan Peng , Wang Weidan , Yang Ke , Zhang Yu , Han Yong 
Published: January 2019

AbstractInhibiting osteoclasts and osteoclast precursors to reduce bone resorption is an important strategy to treat osteoclast-related diseases, such as peri-prosthetic osteolysis. In this study, our objective was to study the role of zoledronic acid (ZA), as a highly potent and nitrogen-containing bisphosphonate, in promoting osteogenesis and inhibiting osteoclastogenesis properties of magnesium (Mg)-based implants. ZA was chemically associated with calcium phosphate (CaP) deposited on magnesium-strontium (Mg-Sr) alloy, which was confirmed by the morphological observation, phase composition and drug releasing via SEM, XRD spectrum and High Performance Liquid Chromatography (HPLC), respectively. The in vitro performances indicated that ZA-CaP bilayer coating Mg-Sr alloy could enhance the proliferation and the osteogenic differentiation as well as the mineralization of pre-osteoblasts, however, induce the apoptosis and inhibit the osteoclast differentiation. We further investigated the possible molecular mechanisms by using Quantitative real-time PCR (qRT-PCR) and Western Blotting, and the results showed that ZA-CaP bilayer coating Mg-Sr alloy could regulate the osteogenesis and osteoclastogenesis through the Estrogen Receptor α (ERα) and NF-κB signaling pathway. Moreover, ZA-CaP bilayer coating Mg-Sr alloy could regulate the cross talk of osteoblast-osteoclast and increase the ratio of OPG: RANKL in the co-culture system through OPG/RANKL/RANK signaling pathway, which promoting the balance of bone remodeling process. Therefore, these promising results suggest the potential clinical applications of ZA pretreated Mg-Sr alloys for bone defect repairs and periprosthetical osteolysis due to the excessive differentitation and maturation of osteoclasts.
The nuclear variant of bone morphogenetic protein 2 (nBMP2) is expressed in macrophages and alters calcium response
Authors: Tellez Freitas Claudia M. , Burrell Haley R. , Valdoz Jonard C. , Hamblin Garrett J. , Raymond Carlee M. , Cox Tyler D. , Johnson Deborah K. , Andersen Joshua L. , Weber K. Scott , Bridgewater Laura C. 
Published: January 2019

AbstractWe previously identified a nuclear variant of bone morphogenetic protein 2 (BMP2), named nBMP2, that is translated from an alternative start codon. Decreased nuclear localization of nBMP2 in the nBmp2NLStmmouse model leads to muscular, neurological, and immune phenotypes—all of which are consistent with aberrant intracellular calcium (Ca2+) response. Ca2+response in these mice, however, has yet to be measured directly. Because a prior study suggested impairment of macrophage function in nBmp2NLStmmutant mice, bone marrow derived (BMD) macrophages and splenic macrophages were isolated from wild type and nBmp2NLStmmutant mice. Immunocytochemistry revealed that nuclei of both BMD and splenic macrophages from wild type mice contain nBMP2, while the protein is decreased in nuclei of nBmp2NLStmmutant macrophages. Live-cell Ca2+imaging and engulfment assays revealed that Ca2+response and phagocytosis in response to bacterial supernatant are similar in BMD macrophages isolated from naïve (uninfected) nBmp2NLStmmutant mice and wild type mice, but are deficient in splenic macrophages isolated from mutant mice after secondary systemic infection withStaphylococcus aureus, suggesting progressive impairment as macrophages respond to infection. This direct evidence of impaired Ca2+handling in nBMP2 mutant macrophages supports the hypothesis that nBMP2 plays a role in Ca2+response.
Clonal dynamics monitoring during clinical evolution in chronic lymphocytic leukaemia
Authors: González-Rincón Julia , Gómez Sagrario , Martinez Nerea , Troulé Kevin , Perales-Patón Javier , Derdak Sophia , Beltrán Sergi , Fernández-Cuevas Belén , Pérez-Sanz Nuria , Nova-Gurumeta Sara , Gut Ivo , Al-Shahrour Fátima , Piris Miguel A. , García-Marco José A. , Sánchez-Beato Margarita 
Published: January 2019

AbstractChronic lymphocytic leukaemia is the most prevalent leukaemia in Western countries. It is an incurable disease characterized by a highly variable clinical course. Chronic lymphocytic leukaemia is an ideal model for studying clonal heterogeneity and dynamics during cancer progression, response to therapy and/or relapse because the disease usually develops over several years. Here we report an analysis by deep sequencing of sequential samples taken at different times from the affected organs of two patients with 12- and 7-year disease courses, respectively. One of the patients followed a linear pattern of clonal evolution, acquiring and selecting new mutations in response to salvage therapy and/or allogeneic transplantation, while the other suffered loss of cellular tumoral clones during progression and histological transformation.
Imaginal disc growth factor 4 regulates development and temperature adaptation in Bactrocera dorsalis
Authors: Gu Xinyue , Li Zhihong , Su Yun , Zhao Yan , Liu Lijun 
Published: January 2019

AbstractThe oriental fruit flyBactrocera dorsalis(Hendel) (Diptera: Tephritidae) is an important invasive pest with high reproductive capacity and invasiveness; it has shown remarkable range expansion and brings higher risk to the environment and agriculture. The insect cuticle serves as skin and skeleton, protecting insects against numerous harmful stresses. One gene named imaginal disc growth factor 4 (idgf4) which is involved in cuticle formation, plays an important role in organizing proteins in the chitin-matrix, as well as in adult molting. This gene in the poorly-described glycoside hydrolase 18 (GH 18) family was chosen to study the function of chitinases in insect defense barrier against heat and molting using quantitative real-time PCR (qRT-PCR) and RNA interference (RNAi). qRT- PCR showed thatidgf4was expressed in all nine developmental stages and was mainly expressed in the early and late pupal, as well as adult stages. Knocking down theidgf4gene via RNAi in 3rdinstar larvae led to the decreased survival of larvae under high temperatures and malformed individuals as adults. The results indicated the function of theidgf4gene in the fruit fly’s defense barrier and development. It can provide new insights into understanding the function of one member in the GH 18 family, and may reveal a new potential gene for pest control.
The evolutionary consequences for seawater performance and its hormonal control when anadromous Atlantic salmon become landlocked
Authors: McCormick Stephen D. , Regish Amy M. , Ardren William R. , Björnsson Björn Thrandur , Bernier Nicholas J. 
Published: January 2019

AbstractPopulations of anadromous fish have become landlocked in relatively recent geological history (<14,000 years), but the evolutionary impacts of this altered lifecycle on traits underlying seawater performance have not been established. In order to examine the effects of relaxed selection on seawater traits, anadromous and landlocked Atlantic salmon were reared under identical conditions and examined for differences in seawater performance and its underlying physiological and endocrine control during the time of spring downstream migration. Salinity tolerance, survival and initial growth in seawater were greater in anadromous than in landlocked salmon. Abundance of the seawater isoform of gill Na+/K+-ATPase increased in spring in both strains but was greater in anadromous salmon. Hormones associated with seawater acclimation (adrenocorticotropic hormone, cortisol and growth hormone) increased in spring in both strains but were higher in anadromous salmon, whereas plasma thyroid hormones did not differ. Hypothalamic urotensin I mRNA levels also increased in spring and were higher in the anadromous strain. The results provide evidence that salinity tolerance and associated physiological traits are regulated by seasonal stimulation of the hypothalamic-pituitary-interrenal axis, and that relaxed selection on seawater entry traits has decreased this stimulation in landlocked salmon.
TROPOMI enables high resolution SO2 flux observations from Mt. Etna, Italy, and beyond
Authors: Queißer Manuel , Burton Mike , Theys Nicolas , Pardini Federica , Salerno Giuseppe , Caltabiano Tommaso , Varnam Matthew , Esse Benjamin , Kazahaya Ryunosuke 
Published: January 2019

AbstractThe newly launched imaging spectrometer TROPOMI onboard the Sentinel-5 Precursor satellite provides atmospheric column measurements of sulfur dioxide (SO2) and other gases with a pixel resolution of 3.5 × 7 km2. This permits mapping emission plumes from a vast number of natural and anthropogenic emitters with unprecedented sensitivity, revealing sources which were previously undetectable from space. Novel analysis using back-trajectory modelling of satellite-based SO2 columns allows calculation of SO2 flux time series, which would be of great utility and scientific interest if applied globally. Volcanic SO2 emission time series reflect magma dynamics and are used for risk assessment and calculation of the global volcanic CO2 gas flux. TROPOMI data make this flux time series reconstruction approach possible with unprecedented spatiotemporal resolution, but these new data must be tested and validated against ground-based observations. Mt. Etna (Italy) emits SO2 with fluxes ranging typically between 500 and 5000 t/day, measured automatically by the largest network of scanning UV spectrometers in the world, providing the ideal test-bed for this validation. A comparison of three SO2 flux datasets, TROPOMI (one month), ground-network (one month), and ground-traverse (two days) shows acceptable to excellent agreement for most days. The result demonstrates that reliable, nearly real-time, high temporal resolution SO2 flux time series from TROPOMI measurements are possible for Etna and, by extension, other volcanic and anthropogenic sources globally. This suggests that global automated real-time measurements of large numbers of degassing volcanoes world-wide are now possible, revolutionizing the quantity and quality of magmatic degassing data available and insights into volcanic processes to the volcanological community.
High temperatures affect the hypersensitive reaction, disease resistance and gene expression induced by a novel harpin HpaG-Xcm
Authors: Zhou Xiaoyun , Liu Yue , Huang Jiamin , Liu Qinghuan , Sun Jianzhang , Cai Xinfeng , Tang Peng , Liu Wenbo , Miao Weiguo 
Published: January 2019

AbstractHarpin proteins are produced by plant-pathogenic Gram-negative bacteria and regulate bacterial pathogenicity by inducing plant growth and defence responses in non-hosts. HpaG-Xcm, a novel harpin protein, was identified from Xanthomonas citri pv. mangiferaeindicae, which causes bacterial black spot of mango. Here, we describe the predicted structure and functions of HpaG-Xcm and investigate the mechanism of heat resistance. The HpaG-Xcm amino acid sequence contains seven motifs and two α-helices, in the N- and C-terminals, respectively. The N-terminal α-helical region contains two heptads, which form the coiled-coil (CC) structure. The CC region, which is on the surface of HpaG-Xcm, forms oligomeric aggregates by forming hydrophobic interactions between hydrophobic amino acids. Like other harpins, HpaG-Xcm was heat stable, promoted root growth and induced a hypersensitive response (HR) and systemic acquired resistance in non-host plants. Subjecting HpaG-Xcm to high temperatures altered the gene expression induced by HpaG-Xcm in tobacco leaves, probably due to changes in the spatial structure of HpaG-Xcm. Phenotypic tests revealed that the high-temperature treatments reduced the HR and disease resistance induced by HpaG-Xcm but had little effect on growth promotion. These findings indicate that the stability of interactions between CC and plants may be associated with thermal stability of HpaG-Xcm.
High metabolic variation for seaweeds in response to environmental changes: a case study of the brown algae Lobophora in coral reefs
Authors: Gaubert Julie , Payri Claude E. , Vieira Christophe , Solanki Hiren , Thomas Olivier P. 
Published: January 2019

AbstractIn the marine environment, macroalgae face changing environmental conditions and some species are known for their high capacity to adapt to the new factors of their ecological niche. Some macroalgal metabolites play diverse ecological functions and belong to the adaptive traits of such species. Because algal metabolites are involved in many processes that shape marine biodiversity, understanding their sources of variation and regulation is therefore of utmost relevance. This work aims at exploring the possible sources of metabolic variations with time and space of four common algal species from the genus Lobophora (Dictyotales, Phaeophyceae) in the New Caledonian lagoon using a UHPLC-HRMS metabolomic fingerprinting approach. While inter-specific differences dominated, a high variability of the metabolome was noticed for each species when changing their natural habitats and types of substrates. Fatty acids derivatives and polyolefins were identified as chemomarkers of these changing conditions. The four seaweeds metabolome also displayed monthly variations over the 13-months survey and a significant correlation was made with sea surface temperature and salinity. This study highlights a relative plasticity for the metabolome of Lobophora species.
Fluorescence Polarization of Methylene Blue as a Quantitative Marker of Breast Cancer at the Cellular Level
Authors: Yaroslavsky Anna N. , Feng Xin , Muzikansky Alona , Hamblin Michael R. 
Published: January 2019

AbstractA quantitative technique to detect cancer in single cells could transform cancer diagnosis. Current cancer diagnosis utilizes histopathology, which requires tissue acquisition, extensive processing and, in most cases, relies on the qualitative morphological analysis of tissues and cells. Molecular biomarkers are only available for a few specific tumor subtypes. We discovered that the fluorescence polarization (Fpol) of Methylene Blue (MB) is significantly higher in cancer than in normal human breast tissues and cells. We confirmed that fluorescence polarization imaging did not affect the viability of the cells and yielded highly significant differences between cancer and normal cells using MB concentrations as low as 0.05 and 0.01 mg/ml. To explain this phenomenon we examined intracellular localization of MB and its fluorescence lifetime. We determined that higher fluorescence polarization of MB occurs due to its increased accumulation in mitochondria of cancer cells, as well as shorter fluorescence lifetime in cancer relative to normal cells. As quantitative MB Fpol imaging can be performed in vivo and in real time, it holds the potential to provide an accurate quantitative marker of cancer at the cellular level.
Zinc binding regulates amyloid-like aggregation of GAPR-1
Authors: Sheng Jie , Olrichs Nick K. , Geerts Willie J. , Li Xueyi , Rehman Ashfaq Ur , Gadella Barend M. , Kaloyanova Dora V. , Helms J. Bernd 
Published: January 2019

Abstract
Members of the CAP superfamily (Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1 proteins) are characterized by the presence of a CAP domain that is defined by four sequence motifs and a highly conserved tertiary structure. A common structure–function relationship for this domain is hitherto unknown. A characteristic of several CAP proteins is their formation of amyloid-like structures in the presence of lipids. Here we investigate the structural modulation of Golgi-Associated plant Pathogenesis Related protein 1 (GAPR-1) by known interactors of the CAP domain, preceding amyloid-like aggregation. Using isothermal titration calorimetry (ITC), we demonstrate that GAPR-1 binds zinc ions. Zn2+ binding causes a slight but significant conformational change as revealed by CD, tryptophan fluorescence, and trypsin digestion. The Zn2+-induced conformational change was required for the formation of GAPR-1 oligomers and amyloid-like assemblies in the presence of heparin, as shown by ThT fluorescence and TEM. Molecular dynamics simulations show binding of Zn2+ to His54 and His103. Mutation of these two highly conserved residues resulted in strongly diminished amyloid-like aggregation. Finally, we show that proteins from the cysteine-rich secretory protein (CRISP) subfamily are also able to form ThT-positive structures in vitro in a heparin- and Zn2+-dependent manner, suggesting that oligomerization regulated by metal ions could be a common structural property of the CAP domain.
Signs of outflow feedback from a nearby young stellar object on the protostellar envelope around HL Tauri
Authors: Yen Hsi-Wei , Takakuwa Shigehisa , Gu Pin-Gao , Hirano Naomi , Lee Chin-Fei , Liu Hauyu Baobab , Liu Sheng-Yuan , Wu Chun-Ju 
Published: January 2019

Aims. HL Tau is a Class I–II protostar embedded in an infalling and rotating envelope and possibly associated with a planet forming disk, and it is co-located in a 0.1 pc molecular cloud with two nearby young stellar objects with projected distance of ~20′′–30′′ (2800–4200 au) to HL Tau. Our observations with the Atacama Large Millimeter/Submillimeter Array (ALMA) revealed two arc-like structures on a 1000 au scale connected to the disk, and their kinematics could not be explained with any conventional model of infalling and rotational motions. In this work, we investigate the nature of these arc-like structures connected to the HL Tau disk.
Methods. We carried out new observations in the 13CO and C18O (3–2; 2–1) lines with the James Clerk Maxwell Telescope and the IRAM 30m telescope, and obtained the data with the 7-m array of the Atacama Compact Array (ACA). With the single-dish, ACA, and ALMA data, we analyzed the gas motions on both 0.1 pc and 1000 au scales in the HL Tau region. We constructed new kinematical models of an infalling and rotating envelope with the consideration of relative motion between HL Tau and the envelope.
Results. By including the relative motion between HL Tau and its protostellar envelope, our kinematical model can explain the observed velocity features in the arc-like structures. The morphologies of the arc-like structures can also be explained with an asymmetric initial density distribution in our model envelope. In addition, our single-dish results support the scenario that HL Tau is located at the edge of a largescale (0.1 pc) expanding shell driven by the wind or outflow from XZ Tau, as suggested in the literature. The estimated expanding velocity of the shell is comparable to the relative velocity between HL Tau and its envelope in our kinematical model. These results hint that the largescale expanding motion likely impacts the protostellar envelope around HL Tau and affects its gas kinematics. We found that the mass infalling rate from the envelope onto the HL Tau disk can be decreased by a factor of two due to this impact by the largescale expanding shell.
Measuring the local matter density usingGaiaDR2
Authors: Widmark A. 
Published: January 2019

Aims.We determine the total dynamical matter density in the solar neighbourhood using the secondGaiadata release (DR2).Methods.The dynamical matter density distribution is inferred in a framework of a Bayesian hierarchical model, which accounts for position and velocity of all individual stars, as well as the full error covariance matrix of astrometric observables, in a joint fit of the vertical velocity distribution and stellar number density distribution. This was done for eight separate data samples, with different cuts in observed absolute magnitude, each containing about 25 000 stars. The model for the total matter density does not rely on any underlying baryonic model, although we assumed that it is symmetrical, smooth, and monotonically decreasing with distance from the mid-plane.Results.We infer a density distribution which is strongly peaked in the region close to the Galactic plane (≲60 pc), for all eight stellar samples. Assuming a baryonic model and a dark matter halo of constant density, this corresponds to a surplus surface density of approximately 5–9M⊙pc−2. For the Sun’s position and vertical velocity with respect to the Galactic plane, we inferZ⊙ = 4.76 ± 2.27 pc andW⊙ = 7.24 ± 0.19 km s−1.Conclusions.These results suggest a surplus of matter close to the Galactic plane, possibly explained by an underestimated density of cold gas. We discuss possible systematic effects that could bias our result, for example unmodelled non-equilibrium effects, and how to account for such effects in future extensions of this work.
TESS exoplanet candidates validated with HARPS archival data
Authors: Trifonov Trifon , Rybizki Jan , Kürster Martin 
Published: January 2019

Aims. We aim at the discovery of new planetary systems by exploiting the transit light-curve results from observations made in TESS orbital observatory Sectors 1 and 2 and validating them with precise Doppler measurements obtained from archival HARPS data.
Methods. Taking advantage of the reported TESS transit events around GJ 143 (TOI 186) and HD 23472 (TOI 174), we modeled their HARPS precise Doppler measurements and derived orbital parameters for these two systems.
Results. For the GJ 143 system, TESS has reported only a single transit, and thus its period is unconstrained from photometry. Our radial velocity analysis of GJ 143 reveals the full Keplerian solution of the system, which is consistent with an eccentric planet with a mass almost twice that of Neptune and a period of Pb = 35.59−0.1+0.1 days. Our estimates of the GJ 143 b planet are fully consistent with the transit timing from TESS. We confirm the two-planet system around HD 23472, which according to our analysis is composed of two Neptune-mass planets in a possible 5:3 mean motion resonance.