bluuebunny/crossref_metadata_2025_split huggingface dataset:
A step towards valid detection and quantification of lung cancer volume in experimental mice with contrast agent-based X-ray microtomography
Authors: Bidola Pidassa , Martins de Souza e Silva Juliana , Achterhold Klaus , Munkhbaatar Enkhtsetseg , Jost Philipp J. , Meinhardt Anna-Lena , Taphorn Kirsten , Zdora Marie-Christine , Pfeiffer Franz , Herzen Julia 
Published: February 2019

AbstractTumor volume is a parameter used to evaluate the performance of new therapies in lung cancer research. Conventional methods that are used to estimate tumor size in mouse models fail to provide fast and reliable volumetric data for tumors grown non-subcutaneously. Here, we evaluated the use of iodine-staining combined with micro-computed tomography (micro-CT) to estimate the tumor volume ofex vivotumor-burdened lungs. We obtained fast high spatial resolution three-dimensional information of the lungs, and we demonstrated that iodine-staining highlights tumors and unhealthy tissue. We processed iodine-stained lungs for histopathological analysis with routine hematoxylin and eosin (H&E) staining. We compared the traditional tumor burden estimation performed manually with H&E histological slices with a semi-automated method using micro-CT datasets. In mouse models that develop lung tumors with well precise boundaries, the method that we describe here enables to perform a quick estimation of tumorous tissue volume in micro-CT images. Our method overestimates the tumor burden in tumors surrounded by abnormal tissue, while traditional histopathological analysis underestimates tumor volume. We propose to embed micro-CT imaging to the traditional workflow of tumorous lung analyses in preclinical cancer research as a strategy to obtain a more accurate estimation of the total lung tumor burden.
Extracellular polysaccharide synthesis in a bloom-forming strain of Microcystis aeruginosa: implications for colonization and buoyancy
Authors: Chen Meng , Tian Li-Li , Ren Chong-Yang , Xu Chun-Yang , Wang Yi-Ying , Li Li 
Published: February 2019

AbstractMicrocystis, the dominant species among cyanobacterial blooms, normally forms colonies under natural conditions but exists as single cells or paired cells in axenic laboratory cultures after long-term cultivation. Here, a bloom-forming Microcystis aeruginosa strain CHAOHU 1326 was studied because it presents a colonial morphology and grows on the water surface during axenic laboratory culturing. We first examined the morphological features of strain CHAOHU 1326 and three other unicellular M. aeruginosa strains FACHB-925, FACHB-940, and FACHB-975 cultured under the same conditions by scanning and transmission electron microscopy. Then, we compared the extracellular polysaccharide (EPS)-producing ability of colonial strain CHAOHU 1326 to that of the three unicellular M. aeruginosa strains, and found that strain CHAOHU 1326 produced a higher amount of EPS than the other strains during growth. Moreover, based on genome sequencing, multiple gene clusters implicated in EPS biosynthesis and a cluster of 12 genes predicted to be involved in gas vesicle synthesis in strain CHAOHU 1326 were detected. These predicted genes were all functional and expressed in M. aeruginosa CHAOHU 1326 as determined by reverse transcription PCR. These findings provide a physiological and genetic basis to better understand colony formation and buoyancy control during M. aeruginosa blooming.
Astrocytic endfeet re-cover blood vessels after removal by laser ablation
Authors: Kubotera Hideaki , Ikeshima-Kataoka Hiroko , Hatashita Yoshiki , Allegra Mascaro Anna Letizia , Pavone Francesco Saverio , Inoue Takafumi 
Published: February 2019

AbstractThe astrocyte, one of the glial cells, plays many functional roles. These include provision of nutrients from blood vessels to neurons, supply of neurotransmitters and support of blood–brain barrier (BBB) integrity. Astrocytes are known to support the integrity of BBB through maintenance of the tight junction between endothelial cells of blood vessels. However, evidence of its direct contribution to BBB is lacking owing to technical limitations. In this study, astrocytic endfeet covering blood vessels were removed by the laser ablation method with two photon laser scanning microscopy in in vivo mouse brain, and the re-covering of blood vessels with the astrocytic endfeet was observed in about half of the cases. Blood vessels kept their integrity without astrocytic endfoot covers: leakage of plasma marker dyes, Evans Blue or dextran-conjugated fluorescein, was not observed from stripped blood vessels, while ablation of vascular walls induced extravasation of Evans Blue. These results suggest that the astrocytic endfeet covering blood vessels do not contribute to the immediate BBB barrier.
A cancer-associated point mutation disables the steric gate of human PrimPol
Authors: Díaz-Talavera Alberto , Calvo Patricia A. , González-Acosta Daniel , Díaz Marcos , Sastre-Moreno Guillermo , Blanco-Franco Luis , Guerra Susana , Martínez-Jiménez Maria I. , Méndez Juan , Blanco Luis 
Published: February 2019

AbstractPrimPol is a human primase/polymerase specialized in re-starting stalled forks by repriming beyond lesions such as pyrimidine dimers, and replication-perturbing structures including G-quadruplexes and R-loops. Unlike most conventional primases, PrimPol proficiently discriminates against ribonucleotides (NTPs), being able to start synthesis using deoxynucleotides (dNTPs), yet the structural basis and physiological implications for this discrimination are not understood. In silico analyses based on the three-dimensional structure of human PrimPol and related enzymes enabled us to predict a single residue, Tyr100, as the main effector of sugar discrimination in human PrimPol and a change of Tyr100 to histidine to boost the efficiency of NTP incorporation. We show here that the Y100H mutation profoundly stimulates NTP incorporation by human PrimPol, with an efficiency similar to that for dNTP incorporation during both primase and polymerase reactions in vitro. As expected from the higher cellular concentration of NTPs relative to dNTPs, Y100H expression in mouse embryonic fibroblasts and U2OS osteosarcoma cells caused enhanced resistance to hydroxyurea, which decreases the dNTP pool levels in S-phase. Remarkably, the Y100H PrimPol mutation has been identified in cancer, suggesting that this mutation could be selected to promote survival at early stages of tumorigenesis, which is characterized by depleted dNTP pools.
Structural biology workflow for the expression and characterization of functional human sodium glucose transporter type 1 in Pichia pastoris
Authors: Suades Albert , Alcaraz Antonio , Cruz Esteban , Álvarez-Marimon Elena , Whitelegge Julian P. , Manyosa Joan , Cladera Josep , Perálvarez-Marín Alex 
Published: February 2019

AbstractHeterologous expression of human membrane proteins is a challenge in structural biology towards drug discovery. Here we report a complete expression and purification process of a functional human sodium/D-glucose co-transporter 1 (hSGLT1) in Pichia pastoris as representative example of a useful strategy for any human membrane protein. hSGLT1 gene was cloned in two different plasmids to develop parallel strategies: one which includes green fluorescent protein fusion for screening optimal conditions, and another for large scale protein production for structural biology and biophysics studies. Our strategy yields at least 1 mg of monodisperse purified recombinant hSGLT1 per liter of culture, which can be characterized by circular dichroism and infrared spectroscopy as an alpha-helical fold protein. This purified hSGLT1 transports co-substrates (Na+ and glucose) and it is inhibited by phlorizin in electrophysiological experiments performed in planar lipid membranes.
Contribution of syndecans to cellular internalization and fibrillation of amyloid-β(1–42)
Authors: Letoha Tamás , Hudák Anett , Kusz Erzsébet , Pettkó-Szandtner Aladár , Domonkos Ildikó , Jósvay Katalin , Hofmann-Apitius Martin , Szilák László 
Published: February 2019

AbstractIntraneuronal accumulation of amyloid-β(1–42) (Aβ1–42) is one of the earliest signs of Alzheimer’s disease (AD). Cell surface heparan sulfate proteoglycans (HSPGs) have profound influence on the cellular uptake of Aβ1–42 by mediating its attachment and subsequent internalization into the cells. Colocalization of amyloid plaques with members of the syndecan family of HSPGs, along with the increased expression of syndecan-3 and -4 have already been reported in postmortem AD brains. Considering the growing evidence on the involvement of syndecans in the pathogenesis of AD, we analyzed the contribution of syndecans to cellular uptake and fibrillation of Aβ1–42. Among syndecans, the neuron specific syndecan-3 isoform increased cellular uptake of Aβ1–42 the most. Kinetics of Aβ1–42 uptake also proved to be fairly different among SDC family members: syndecan-3 increased Aβ1–42 uptake from the earliest time points, while other syndecans facilitated Aβ1–42 internalization at a slower pace. Internalized Aβ1–42 colocalized with syndecans and flotillins, highlighting the role of lipid-rafts in syndecan-mediated uptake. Syndecan-3 and 4 also triggered fibrillation of Aβ1–42, further emphasizing the pathophysiological relevance of syndecans in plaque formation. Overall our data highlight syndecans, especially the neuron-specific syndecan-3 isoform, as important players in amyloid pathology and show that syndecans, regardless of cell type, facilitate key molecular events in neurodegeneration.
Mechanism of action of the moonlighting protein EfTu as a Substance P sensor in Bacillus cereus
Authors: N’Diaye Awa R. , Borrel Valerie , Racine Pierre-Jean , Clamens Thomas , Depayras Segolene , Maillot Olivier , Schaack Beatrice , Chevalier Sylvie , Lesouhaitier Olivier , Feuilloley Marc G. J. 
Published: February 2019

AbstractThe striking feature of the ubiquitous protein EfTu (Thermo unstable ribosomal Elongation factor) is its moonlighting (multifunctional) activity. Beyond its function at the ribosomal level it should be exported to the bacterial surface and act as an environmental sensor. In Bacillus cereus, and other cutaneous bacteria, it serves as a Substance P (SP) receptor and is essential for bacterial adaptation to the host. However, the modus operandi of EfTu as a bacterial sensor remains to be investigated. Studies realized by confocal and transmission electron microscopy revealed that, in the absence of an exogenous signal, EfTu is not exposed on the bacterial surface but is recruited under the effect of SP. In addition, SP acts as a transcriptional regulator of the tuf gene encoding for EfTu. As observed using gadolinium chloride, an inhibitor of membrane mechanosensitive channels (Msc), Msc control EfTu export and subsequently the bacterial response to SP both in terms of cytotoxicity and biofilm formation activity. Microscale thermophoresis revealed that in response to SP, EfTu can form homopolymers. This event should occur after EfTu export and, as shown by proteo-liposome reconstruction studies, SP appears to promote EfTu polymers association to the membrane, leading subsequently to the bacterial response. Molecular modeling suggests that this mechanism should involve EfTu unfolding and insertion into the bacterial cytoplasmic membrane, presumably through formation of homopolymers. This study is unraveling the original mechanism action of EfTu as a bacterial sensor but also reveals that this protein should have a broader role, including in eukaryotes.
Laser- synthesized TiN nanoparticles as promising plasmonic alternative for biomedical applications
Authors: Popov Anton A. , Tselikov Gleb , Dumas Noé , Berard Charlotte , Metwally Khaled , Jones Nicola , Al-Kattan Ahmed , Larrat Benoit , Braguer Diane , Mensah Serge , Da Silva Anabela , Estève Marie-Anne , Kabashin Andrei V. 
Published: February 2019

AbstractExhibiting a red-shifted absorption/scattering feature compared to conventional plasmonic metals, titanium nitride nanoparticles (TiN NPs) look as very promising candidates for biomedical applications, but these applications are still underexplored despite the presence of extensive data for conventional plasmonic counterparts. Here, we report the fabrication of ultrapure, size-tunable TiN NPs by methods of femtosecond laser ablation in liquids and their biological testing. We show that TiN NPs demonstrate strong and broad plasmonic peak around 640–700 nm with a significant tail over 800 nm even for small NPs sizes (<7 nm). In vitro tests of laser-synthesized TiN NPs on cellular models evidence their low cytotoxicity and excellent cell uptake. We finally demonstrate a strong photothermal therapy effect on U87–MG cancer cell cultures using TiN NPs as sensitizers of local hyperthermia under near-infrared laser excitation. Based on absorption band in the region of relative tissue transparency and acceptable biocompatibility, laser-synthesized TiN NPs promise the advancement of biomedical modalities employing plasmonic effects, including absorption/scattering contrast imaging, photothermal therapy, photoacoustic imaging and SERS.
High-velocity impact of solid objects on Non-Newtonian Fluids
Authors: de Goede Thijs C. , de Bruin Karla G. , Bonn Daniel 
Published: February 2019

AbstractWe investigate which property of non-Newtonian fluids determines the deceleration of a high-speed impacting object. Using high-speed camera footage, we measure the velocity decrease of a high-speed spherical object impacting a typical Newtonian fluid (water) as a reference and compare it with a shear thickening fluid (cornstarch) and a shear thinning viscoelastic fluid (a weakly cross-linked polymer gel). Three models describing the kinetic energy loss of the object are considered: fluid inertia, shear thickening and viscoelasticity. By fitting the three models to the experimental data, we conclude that the viscoelastic model works best for both the cornstarch and the polymer gel. Since the cornstarch is also viscoelastic, we conclude that the ability to stop objects of these complex fluids is given by their viscoelasticity rather than shear thickening or shear thinning.
An ADAMTS Sol narae is required for cell survival in Drosophila
Authors: Tsogtbaatar Orkhon , Won Jong-Hoon , Kim Go-Woon , Han Jeong-Hoon , Bae Young-Kyung , Cho Kyung-Ok 
Published: February 2019

AbstractCell survival is essential for all living organisms to cope against multiple environmental insults. Intercellular signaling between dying and surviving cells plays an important role to ensure compensatory proliferation, preventing tissue loss after environmental stresses. Here, we show that Sol narae (Sona), a Disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) in Drosophila is required for cell survival. sona exhibited a positive genetic interaction with Death-associated inhibitor of apoptosis 1 (Diap1), and a negative genetic interaction with reaper (rpr). Transcription patterns of sona, Diap1, and rpr genes in the pouch region of wing discs were coordinately changed after irradiation. Interestingly, there was a negative correlation in the expression levels of Sona and DIAP1, and both cell types, one with high Sona level and the other with high Diap1 level, were resistant to irradiation-induced cell death. The sona-expressing cells rarely entered into cell cycle themselves but promoted the nearby cells to proliferate in irradiation conditions. We found that these sona-expressing cells are able to upregulate Cyclin D (Cyc D) and increase tissue size. Furthermore, transient Sona overexpression increased survival rate and promoted development of flies in irradiation conditions. We propose that the two types of radiation-resistant cells, one with high Sona level and the other with high Diap1 level, communicate with dying cells and between each other for cell survival and proliferation in response to irradiation.
Ultra-High Efficiency and Broad Band Operation of Infrared Metasurface Anomalous Reflector based on Graphene Plasmonics
Authors: Soleymani Sina , Güngördü M. Zeki , Kung Patrick , Kim Seongsin M. 
Published: February 2019

AbstractInfrared metasurface anomalous reflector with ultra-high efficiency and broad band operation is designed via multi-sheet graphene layer with triangular holes. The anomalous reflection angle covers the range of 10° to 90° with the efficiency higher than 80%, over a broad spectral range from 7 μm–40 μm of infrared spectrum. It reaches above 92% at the center wavelength in the spectral response. By increasing the periodicity of phase gradient, we can expand this frequency band even further without losing efficiency. The compact design of metasurface affords the adjustability of the electrochemical potential level of graphene by means of gating. Additionally, the impact of the number of graphene sheets for the optimum efficiency of the proposed structure is investigated. By adding the secondary graphene metasurface with opposite direction of phase gradient, we demonstrated the tunability of the reflection angle from θr to −θr with bias voltage.
Distinct impacts of the 1997–98 and 2015–16 extreme El Niños on Japanese eel larval catch
Authors: Lin Yong-Fu , Wu Chau-Ron 
Published: February 2019

AbstractExtraordinarily poor recruitment of Japanese eels in East Asia has been generally reported during extreme El Niño years. However, the scenario failed to take place during the 2015–16 extreme event. In this study, we examined possible factors responsible for differing eel abundance in East Asia during the two strongest recent extreme El Niños, which occurred in 1997–98 and 2015–16. Numerical tracer experiments were carried out to determine why the impacts on eel catches seen in 1997–98 were not repeated in 2015–16. Among physical factors, two scenarios are likely responsible for extremely poor recruitment in East Asia: southward migration of the North Equatorial Current (NEC) or southward movement of eel spawning grounds. Comparing the latitudinal shift of NEC locations between the 1997–98 and 2015–16 El Niños, we conclude that NEC migration may be a factor, but is not chiefly responsible, for lower eel catches. Our findings pointed to southward movement of spawning grounds as the dominant factor. The northward movement of spawning grounds during 2015–16 meant that eel larvae were preferentially transported into the NEC-Kuroshio system, which resulted in a higher rate of recruitment success. The distinct evolution and dynamics of these two El Niño events led to different spawning ground locations, impacting eel abundance in East Asian countries.
The NOP-1 peptide derived from the central regulator of ethylene signaling EIN2 delays floral senescence in cut flowers
Authors: Hoppen Claudia , Müller Lena , Albrecht Anna Christina , Groth Georg 
Published: February 2019

AbstractThe plant hormone ethylene was identified as important triggering factor and primary regulator of flower senescence in many species. Consequently, application of chemical inhibitors of ethylene biosynthesis and action is used to extend the longevity of ethylene-sensitive flowers. Here, we show that the peptide NOP-1, a biological derived from the nuclear localization signal of ethylene regulator EIN2 tightly binds to the ethylene receptor of carnation plants - a model to study flower senescence. When applied on cut flowers the peptide biological delays petal senescence similar to previously identified and currently used chemical inhibitors, but offers significant advances to these chemicals in biodegradability, sustainability and ecotoxicity. Our bioinformatic analysis of a wide range of ethylene receptors indicates complete sequence conservation of the anticipated NOP-1 binding site in flower species supporting a widespread use of the peptide on flowering ornamentals to delay senescence and decay in cut flowers. We anticipate our innovative approach to extend flower longevity by a new class of biomolecules such as peptides, peptide analogues and peptide mimetics will significantly advance our technological capability to delay flower senescence and expand vase-life of cut flowers in a sustainable and environmentally friendly manner.
Self-assembly of dental surface nanofilaments and remineralisation by SnF2 and CPP-ACP nanocomplexes
Authors: Fernando James R. , Shen Peiyan , Sim Christina P. C. , Chen Yu-Yen , Walker Glenn D. , Yuan Yi , Reynolds Coralie , Stanton David P. , MacRae Colin M. , Reynolds Eric C. 
Published: February 2019

AbstractDental caries, erosion and hypersensitivity are major public health problems. SnF2 is used widely in oral care products to help prevent/treat these conditions. Casein phosphopeptide-stabilised amorphous calcium phosphate nanocomplexes (CPP-ACP) are a biomimetic nanotechnology of salivary phosphopeptide-ACP complexes that deliver bioavailable calcium and phosphate ions to promote dental remineralisation (repair). We show here using in vitro studies and a double-blind, randomised controlled, cross-over design in situ clinical trial that SnF2 and CPP-ACP interact to form a nanofilament coating on the tooth surface and that together they are superior in their ability to promote dental remineralisation. Sn(II) by cross-linking the CPP-ACP helps to stabilise the complexes which improves delivery to the tooth surface and enhances binding and ion incorporation into tooth mineral. The combination of SnF2 and CPP-ACP in oral care products may significantly improve their efficacy in prevention/treatment of dental caries/erosion and hypersensitivity.
Sol-gel derived boehmite nanostructures is a versatile nanoplatform for biomedical applications
Authors: Solovev Yaroslav V. , Prilepskii Artur Y. , Krivoshapkina Elena F. , Fakhardo Anna F. , Bryushkova Ekaterina A. , Kalikina Polina A. , Koshel Elena I. , Vinogradov Vladimir V. 
Published: February 2019

AbstractAlumina is one of the most promising carriers for drug delivery due to the long history of its usage as a vaccine adjuvant. Sol-gel synthesis provides excellent conditions for entrapment of biomolecules within an inorganic cage providing stabilization of proteins under the extremal conditions. In this paper, we show in vitro investigation of monodisperse alumina xerogel nanocontainers (AXNCs) using bovine serum albumin as a model protein entrapped in sol-gel alumina building blocks. Particularly, dose and cell-type dependent cytotoxicity in HeLa and A549 cancer cell lines were employed as well as investigation of antibacterial effect and stability of AXNCs in different biological media. It was shown, that the release of entrapped protein could be provided only in low pH buffer (as in cancer cell cytoplasm). This property could be applied for anticancer drug development. We also discovered boehmite nanoparticles effect on horizontal gene transfer and observed the appearance of antibiotic resistance by means of exchanging of the corresponding plasmid between two different E. coli strains. The present work may help to understand better the influence of AXNCs on various biological systems, such as prokaryotic and eukaryotic cells, and the activity of AXNCs in different biological media.