bluuebunny/crossref_metadata_2025_split huggingface dataset:
RESOLFT nanoscopy with photoswitchable organic fluorophores
Authors: Kwon Jiwoong , Hwang Jihee , Park Jaewan , Han Gi Rim , Han Kyu Young , Kim Seong Keun 
Published: December 2015

AbstractFar-field optical nanoscopy has been widely used to image small objects with sub-diffraction-limit spatial resolution. Particularly, reversible saturable optical fluorescence transition (RESOLFT) nanoscopy with photoswitchable fluorescent proteins is a powerful method for super-resolution imaging of living cells with low light intensity. Here we demonstrate for the first time the implementation of RESOLFT nanoscopy for a biological system using organic fluorophores, which are smaller in size and easier to be chemically modified. With a covalently-linked dye pair of Cy3 and Alexa647 to label subcellular structures in fixed cells and by optimizing the imaging buffer and optical parameters, our RESOLFT nanoscopy achieved a spatial resolution of ~74 nm in the focal plane. This method provides a powerful alternative for low light intensity RESOLFT nanoscopy, which enables biological imaging with small organic probes at nanoscale resolution.
Resveratrol Treatment after Status Epilepticus Restrains Neurodegeneration and Abnormal Neurogenesis with Suppression of Oxidative Stress and Inflammation
Authors: Mishra Vikas , Shuai Bing , Kodali Maheedhar , Shetty Geetha A. , Hattiangady Bharathi , Rao Xiaolan , Shetty Ashok K. 
Published: December 2015

AbstractAntiepileptic drug therapy, though beneficial for restraining seizures, cannot thwart status epilepticus (SE) induced neurodegeneration or down-stream detrimental changes. We investigated the efficacy of resveratrol (RESV) for preventing SE-induced neurodegeneration, abnormal neurogenesis, oxidative stress and inflammation in the hippocampus. We induced SE in young rats and treated with either vehicle or RESV, commencing an hour after SE induction and continuing every hour for three-hours on SE day and twice daily thereafter for 3 days. Seizures were terminated in both groups two-hours after SE with a diazepam injection. In contrast to the vehicle-treated group, the hippocampus of animals receiving RESV during and after SE presented no loss of glutamatergic neurons in hippocampal cell layers, diminished loss of inhibitory interneurons expressing parvalbumin, somatostatin and neuropeptide Y in the dentate gyrus, reduced aberrant neurogenesis with preservation of reelin + interneurons, lowered concentration of oxidative stress byproduct malondialdehyde and pro-inflammatory cytokine tumor necrosis factor-alpha, normalized expression of oxidative stress responsive genes and diminished numbers of activated microglia. Thus, 4 days of RESV treatment after SE is efficacious for thwarting glutamatergic neuron degeneration, alleviating interneuron loss and abnormal neurogenesis and suppressing oxidative stress and inflammation. These results have implications for restraining SE-induced chronic temporal lobe epilepsy.
Infectious Progeny of 2009 A (H1N1) Influenza Virus Replicated in and Released from Human Neutrophils
Authors: Zhang Zhang , Huang Tao , Yu Feiyuan , Liu Xingmu , Zhao Conghui , Chen Xueling , Kelvin David J. , Gu Jiang 
Published: December 2015

AbstractVarious reports have indicated that a number of viruses could infect neutrophils, but the multiplication of viruses in neutrophils was abortive. Based on our previous finding that avian influenza viral RNA and proteins were present in the nucleus of infected human neutrophils in vivo, we investigated the possibility of 2009 A (H1N1) influenza viral synthesis in infected neutrophils and possible release of infectious progeny from host cells. In this study we found that human neutrophils in vitro without detectable level of sialic acid expression could be infected by this virus strain. We also show that the infected neutrophils can not only synthesize 2009 A (H1N1) viral mRNA and proteins, but also produce infectious progeny. These findings suggest that infectious progeny of 2009 A (H1N1) influenza virus could be replicated in and released from human neutrophils with possible clinical implications.
High-density lipoprotein contribute to G0-G1/S transition in Swiss NIH/3T3 fibroblasts
Authors: Angius Fabrizio , Spolitu Stefano , Uda Sabrina , Deligia Stefania , Frau Alessandra , Banni Sebastiano , Collu Maria , Accossu Simonetta , Madeddu Clelia , Serpe Roberto , Batetta Barbara 
Published: December 2015

AbstractHigh density lipoproteins (HDLs) play a crucial role in removing excess cholesterol from peripheral tissues. Although their concentration is lower during conditions of high cell growth rate (cancer and infections), their involvement during cell proliferation is not known. To this aim, we investigated the replicative cycles in synchronised Swiss 3T3 fibroblasts in different experimental conditions: i) contact-inhibited fibroblasts re-entering cell cycle after dilution; ii) scratch-wound assay; iii) serum-deprived cells induced to re-enter G1 by FCS, HDL or PDGF. Analyses were performed during each cell cycle up to quiescence. Cholesterol synthesis increased remarkably during the replicative cycles, decreasing only after cells reached confluence. In contrast, cholesteryl ester (CE) synthesis and content were high at 24 h after dilution and then decreased steeply in the successive cycles. Flow cytometry analysis of DiO-HDL, as well as radiolabeled HDL pulse, demonstrated a significant uptake of CE-HDL in 24 h. DiI-HDL uptake, lipid droplets (LDs) and SR-BI immunostaining and expression followed the same trend. Addition of HDL or PDGF partially restore the proliferation rate and significantly increase SR-BI and pAKT expression in serum-deprived cells. In conclusion, cell transition from G0 to G1/S requires CE-HDL uptake, leading to CE-HDL/SR-BI pathway activation and CEs increase into LDs.
A synthetic modular approach for modeling the role of the 3D microenvironment in tumor progression
Authors: Singh S. P. , Schwartz M. P. , Tokuda E. Y. , Luo Y. , Rogers R. E. , Fujita M. , Ahn N. G. , Anseth K. S. 
Published: December 2015

AbstractHere, we demonstrate the flexibility of peptide-functionalized poly(ethylene glycol) (PEG) hydrogels for modeling tumor progression. The PEG hydrogels were formed using thiol-ene chemistry to incorporate a matrix metalloproteinase-degradable peptide crosslinker (KKCGGPQG↓IWGQGCKK) permissive to proteolytic remodeling and the adhesive CRGDS peptide ligand. Tumor cell function was investigated by culturing WM239A melanoma cells on PEG hydrogel surfaces or encapsulating cells within the hydrogels and either as monocultures or indirect (non-contact) cocultures with primary human dermal fibroblasts (hDFs). WM239A cluster size and proliferation rate depended on the shear elastic modulus for cells cultured on PEG hydrogels, while growth was inhibited by coculture with hDFs regardless of hydrogel stiffness. Cluster size was also suppressed by hDFs for WM239A cells encapsulated in PEG hydrogels, which is consistent with cells seeded on top of hydrogels. Notably, encapsulated WM239A clusters and single cells adopted invasive phenotypes in the hDF coculture model, which included single cell and collective migration modes that resembled invasion from human melanoma patient-derived xenograft tumors encapsulated in equivalent PEG hydrogels. Our combined results demonstrate that peptide-functionalized PEG hydrogels provide a useful platform for investigating aspects of tumor progression in 2D and 3D microenvironments, including single cell migration, cluster growth and invasion.
Characterization of the 26S proteasome network in Plasmodium falciparum
Authors: Wang Lihui , Delahunty Claire , Fritz-Wolf Karin , Rahlfs Stefan , Helena Prieto Judith , Yates John R. , Becker Katja 
Published: December 2015

AbstractIn eukaryotic cells, the ubiquitin-proteasome system as a key regulator of protein quality control is an excellent drug target. We therefore aimed to analyze the 26S proteasome complex in the malaria parasite Plasmodium falciparum, which still threatens almost half of the world’s population. First, we established an affinity purification protocol allowing for the isolation of functional 26S proteasome complexes from the parasite. Subunit composition of the proteasome and component stoichiometry were studied and physiologic interacting partners were identified via in situ protein crosslinking. Furthermore, intrinsic ubiquitin receptors of the plasmodial proteasome were determined and their roles in proteasomal substrate recognition were analyzed. Notably, PfUSP14 was characterized as a proteasome-associated deubiquitinase resulting in the concept that targeting proteasomal deubiquitinating activity in P. falciparum may represent a promising antimalarial strategy. The data provide insights into a profound network orchestrated by the plasmodial proteasome and identified novel drug target candidates in the ubiquitin-proteasome system.
Fragmentation of Fast Josephson Vortices and Breakdown of Ordered States by Moving Topological Defects
Authors: Sheikhzada Ahmad , Gurevich Alex 
Published: December 2015

AbstractTopological defects such as vortices, dislocations or domain walls define many important effects in superconductivity, superfluidity, magnetism, liquid crystals and plasticity of solids. Here we address the breakdown of the topologically-protected stability of such defects driven by strong external forces. We focus on Josephson vortices that appear at planar weak links of suppressed superconductivity which have attracted much attention for electronic applications, new sources of THz radiation and low-dissipative computing. Our numerical simulations show that a rapidly moving vortex driven by a constant current becomes unstable with respect to generation of vortex-antivortex pairs caused by Cherenkov radiation. As a result, vortices and antivortices become spatially separated and accumulate continuously on the opposite sides of an expanding dissipative domain. This effect is most pronounced in thin film edge Josephson junctions at low temperatures where a single vortex can switch the whole junction into a resistive state at currents well below the Josephson critical current. Our work gives a new insight into instability of a moving topological defect which destroys global long-range order in a way that is remarkably similar to the crack propagation in solids.
Evolutionary conserved brainstem circuits encode category, concentration and mixtures of taste
Authors: Vendrell-Llopis Nuria , Yaksi Emre 
Published: December 2015

AbstractEvolutionary conserved brainstem circuits are the first relay for gustatory information in the vertebrate brain. While the brainstem circuits act as our life support system and they mediate vital taste related behaviors, the principles of gustatory computations in these circuits are poorly understood. By a combination of two-photon calcium imaging and quantitative animal behavior in juvenile zebrafish, we showed that taste categories are represented by dissimilar brainstem responses and generate different behaviors. We also showed that the concentration of sour and bitter tastes are encoded by different principles and with different levels of sensitivity. Moreover, we observed that the taste mixtures lead to synergistic and suppressive interactions. Our results suggest that these interactions in early brainstem circuits can result in non-linear computations, such as dynamic gain modulation and discrete representation of taste mixtures, which can be utilized for detecting food items at broad range of concentrations of tastes and rejecting inedible substances.
The orphan response regulator EpsW is a substrate of the DifE kinase and it regulates exopolysaccharide in Myxococcus xanthus
Authors: Black Wesley P. , Wang Lingling , Davis Manli Y. , Yang Zhaomin 
Published: December 2015

AbstractHere we attempted to identify the downstream target of the DifE histidine kinase in the regulation of exopolysaccharide (EPS) production in the Gram-negative bacterium Myxococcus xanthus. This bacterium is an important model system for the studies of Type IV pilus (T4P) because it is motile by social (S) motility which is powered by T4P retraction. EPS is critical for S motility because it is the preferred anchor for T4P retraction in this bacterium. Previous studies identified the Dif chemosensory pathway as crucial for the regulation of EPS production. However, the downstream target of the DifE kinase in this pathway was unknown. In this study, EpsW, an orphan and single-domain response regulator (RR), was identified as a potential DifE target first by bioinformatics. Subsequent experiments demonstrated that epsW is essential for EPS biosynthesis in vivo and that EpsW is directly phosphorylated by DifE in vitro. Targted mutagenesis of epsW suggests that EpsW is unlikely the terminal RR of the Dif pathway. We propose instead that EpsW is an intermediary in a multistep phosphorelay that regulates EPS in M. xanthus.
The Origin of The Acheulean: The 1.7 Million-Year-Old Site of FLK West, Olduvai Gorge (Tanzania)
Authors: Diez-Martín F. , Sánchez Yustos P. , Uribelarrea D. , Baquedano E. , Mark D. F. , Mabulla A. , Fraile C. , Duque J. , Díaz I. , Pérez-González A. , Yravedra J. , Egeland C. P. , Organista E. , Domínguez-Rodrigo M. 
Published: December 2015

AbstractThe appearance of the Acheulean is one of the hallmarks of human evolution. It represents the emergence of a complex behavior, expressed in the recurrent manufacture of large-sized tools, with standardized forms, implying more advance forethought and planning by hominins than those required by the precedent Oldowan technology. The earliest known evidence of this technology dates back toc. 1.7 Ma. and is limited to two sites (Kokiselei [Kenya] and Konso [Ethiopia]), both of which lack functionally-associated fauna. The functionality of these earliest Acheulean assemblages remains unknown. Here we present the discovery of another early Acheulean site also dating toc. 1.7 Ma from Olduvai Gorge. This site provides evidence of the earliest steps in developing the Acheulean technology and is the oldest Acheulean site in which stone tools occur spatially and functionally associated with the exploitation of fauna. Simple and elaborate large-cutting tools (LCT) and bifacial handaxes co-exist at FLK West, showing that complex cognition was present from the earliest stages of the Acheulean. Here we provide a detailed technological study and evidence of the use of these tools on the butchery and consumption of fauna, probably by earlyHomo erectus sensu lato.
Dielectric behaviors of Aurivillius Bi5Ti3Fe0.5Cr0.5O15 multiferroic polycrystals: Determining the intrinsic magnetoelectric responses by impedance spectroscopy
Authors: Bai Wei , Chen Chao , Yang Jing , Zhang Yuanyuan , Qi Ruijuan , Huang Rong , Tang Xiaodong , Duan Chun-Gang , Chu Junhao 
Published: December 2015

AbstractBismuth layer ferroelectrics (BLFs) pioneered by Aurivillius about sixty years ago have been revived recently because of the fatigue- and lead-free behaviors and high Curie temperature and especially the robust magnetoelectric (ME) effect. However, discerning the intrinsic ME nature and the inherence between charged defect dipole induced relaxation and spin-related behaviors are still an arduous task. Here, we report a quantitative analysis to reveal the intrinsic spin-lattice coupling in Aurivillius Cr-doped Bi5Ti3FeO15 (BTFCO) multiferroic polycrystals. Dielectric responses are systemically investigated by the temperature-dependent dielectric, module, impedance spectroscopy and equivalent circuit model and two different dielectric relaxation processes occurred in grain interior of Aurivillius BTFCO polycrystals are clarified. One relaxation is proposed to associate with localized transfer of electrons between Fe3+ and Fe2+ while another one arises from the competition interaction of localized hopping of electrons between Fe3+ and Fe2+ and short-range migration of holes between Cr3+ and Cr6+. The variation of the intrinsic permittivity unambiguously confirms the coupling between spin and dipolar orderings in BTFCO polycrystals. These results offer a vital avenue for identifying the intrinsic and extrinsic signals of the electric and ME responses and will give significant impetus to exploring the ME electronic devices of Aurivillius materials.
The effect of temperature on organic carbon degradation in marine sediments
Authors: Malinverno Alberto , Martinez Ernesto A. 
Published: December 2015

AbstractThe degradation of sedimentary particulate organic carbon (POC) is a key carbon cycle process that fuels the deep subseafloor biosphere. The reactivity of POC is expected to decrease with increasing sediment age, severely restricting the energy available to microorganisms. Conversely, increasing temperatures during burial have been proposed to stimulate POC degradation, possibly supplying significant energy to the deep biosphere. To test the importance of temperature, we assembled POC measurements in two global sets of drill sites where sediments underwent either relatively low or high temperatures during burial, which should have resulted in different rates of POC degradation. For ages 5–10 Ma, the decrease of the average POC content with burial is clearly more pronounced in the sites with high temperature histories. Our results support the hypothesis that temperature is one of the fundamental controls on the rate of POC degradation within deeply buried marine sediments.
Genetic diversity and antimicrobial susceptibility of Nocardia species among patients with nocardiosis
Authors: Hashemi-Shahraki Abodolrazagh , Heidarieh Parvin , Bostanabad Saeed Zaker , Hashemzadeh Mohamad , Feizabadi Mohamad Mehdi , Schraufnagel Dean , Mirsaeidi Mehdi 
Published: December 2015

AbstractThe aim of this multicenter study was to determine the genetic diversity and antibiotic susceptibility of clinically isolated Nocardia species. One hundred twenty-seven patients with nocardiosis were randomly selected from 5 provinces of Iran. Molecular diagnosis of Nocardia species was performed using multilocus sequence analysis of gyrase B of the β subunit of DNA topoisomerase (gyrB) and 16S rRNA and subunit A of SecA preproteintranslocase (secA1). Antimicrobial susceptibility testing was performed following the Clinical and Laboratory Standards Institute recommendations. Thirty-five N. cyriacigeorgica, 30 N. asteroides, 26 N. farcinica, 12 N. otitidiscaviarum, and 10 N. abscessus cultures were studied. All isolates were susceptible to linezolid. All isolates of N. cyriacigeorgica, N. asteroides, N. abscessus and N. otitidiscaviarum were susceptible to trimethoprim-sulfamethoxazole, while 8% of N. farcinica isolates were resistant to this drug. All N. otitidiscaviarum isolates were highly resistant to imipenem, but N. cyriacigeorgica, N. asteroides, N. farcinica and N. abscessus were only moderate resistant. The susceptibility patterns vary with different species of Nocardia. Resistance to trimethoprim-sulfamethoxazole in Iran is low and this drug should be first line therapy, unless drug susceptibility testing shows resistance. Linezolid also covers Nocardia well and could be a second line agent.
Climate and soil properties limit the positive effects of land use reversion on carbon storage in Eastern Australia
Authors: Rabbi S.M.F. , Tighe Matthew , Delgado-Baquerizo Manuel , Cowie Annette , Robertson Fiona , Dalal Ram , Page Kathryn , Crawford Doug , Wilson Brian R. , Schwenke Graeme , Mcleod Malem , Badgery Warwick , Dang Yash P. , Bell Mike , O’Leary Garry , Liu De Li , Baldock Jeff 
Published: December 2015

AbstractAustralia’s “Direct Action” climate change policy relies on purchasing greenhouse gas abatement from projects undertaking approved abatement activities. Management of soil organic carbon (SOC) in agricultural soils is an approved activity, based on the expectation that land use change can deliver significant changes in SOC. However, there are concerns that climate, topography and soil texture will limit changes in SOC stocks. This work analyses data from 1482 sites surveyed across the major agricultural regions of Eastern Australia to determine the relative importance of land use vs. other drivers of SOC. Variation in land use explained only 1.4% of the total variation in SOC, with aridity and soil texture the main regulators of SOC stock under different land uses. Results suggest the greatest potential for increasing SOC stocks in Eastern Australian agricultural regions lies in converting from cropping to pasture on heavy textured soils in the humid regions.
Coordinated loss of microRNA group causes defenseless signaling in malignant lymphoma
Authors: Yamagishi Makoto , Katano Harutaka , Hishima Tsunekazu , Shimoyama Tatsu , Ota Yasunori , Nakano Kazumi , Ishida Takaomi , Okada Seiji , Watanabe Toshiki 
Published: December 2015

AbstractBiological robustness is exposed to stochastic perturbations, which should be controlled by intrinsic mechanisms; the promiscuous signaling network without appropriate alleviation is the true nature of cancer cells. B cell receptor (BCR) signaling is a major source of gene expression signature important for B cell. It is still unclear the mechanism by which the expression of functionally important genes is continuously deregulated in malignant lymphomas. Using RISC-capture assay, we reveal that multiple BCR signaling factors are persistently regulated by microRNA (miRNA) in human B cells. Clinical samples from patients with diffuse large B-cell lymphoma (DLBCL, n = 83) show loss of an essential miRNA set (miR-200c, miR-203, miR-31). Conventional screening and RISC profiling identify multiple targets (CD79B, SYK, PKCβII, PLCγ1, IKKβ, NIK, MYD88, PI3K class I (α/β/δ/γ), RasGRP3); signaling network habitually faces interference composed by miRNA group in normal B cells. We demonstrate that simultaneous depletion of the key miRNAs enhances translation of the multiple targets and causes chronic activation of NF-κB, PI3K-Akt and Ras-Erk cascades, leading to B cell transformation. This study suggests that compensatory actions by multiple miRNAs rather than by a single miRNA ensure robustness of biological processes.
Production and application of polyclonal and monoclonal antibodies against Spiroplasma eriocheiris
Authors: Zhang Ying , Bao Haixun , Miao Fengqin , Peng Yaqin , Shen Yuqing , Gu Wei , Meng Qingguo , Wang Wen , Zhang Jianqiong 
Published: December 2015

AbstractA new species of spiroplasma, Spiroplasma eriocheiris (S. eriocheiris), was identified as a lethal pathogen of tremor disease (TD) in Chinese mitten crab recently. In order to acquire appropriate biological and diagnostic tools for characterizing this newly discovered pathogen, 5 monoclonal antibodies (mAbs) and a polyclonal antibody (pAb) against S. eriocheiris were produced. Among the mAbs, 6F5, 7C8 and 12H5 lead to the deformation of S. eriocheiris. A peptide sequence, YMRDMQSGLPRY was identified as a mimic motif of MreB that is the cell shape determining protein of S. eriocheiris interacting with 3 mAbs. Furthermore, a double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) for detection of S. eriocheiris was established using the mAb and pAb we prepared. It detected as low as 0.1 μg/mL of S. eriocheiris. No cross-reaction was observed with three other common bacteria (Pseudomonas aeruginosa, Escherichia coli and Bacillus subtilis) and the hemolymph samples of healthy Eriocheir sinensis. Collectively, our results indicated that the mAbs and pAb we prepared could be used in the analysis of S. eriocheiris membrane proteins mimotope and development of a diagnostic kit for S. eriocheiris infections.