bluuebunny/crossref_metadata_2025 huggingface dataset:
Osteosarcoma cell intrinsic PD-L2 signals promote invasion and metastasis via the RhoA-ROCK-LIMK2 and autophagy pathways
Authors: Ren Tingting , Zheng Bingxin , Huang Yi , Wang Shidong , Bao Xing , Liu Kuisheng , Guo Wei
Published: March 2019

Known as co-stimulatory molecule, programmed death ligand-2 (PD-L2) contributes to T-cell exhaustion by interaction with programmed death-1 (PD-1) receptor, but its tumor cell-intrinsic signal effects have been little investigated. PD-L2 expression was detected by immunohistochemistry in 18 pairs of primary osteosarcoma tissues and matching lung metastasis tissues. We also investigated the effects of PD-L2 knockdown on osteosarcoma both in vitro and in vivo. In our study, PD-L2 expression was elevated in lung metastases compared with primary osteosarcoma according to an immunohistochemistry assay. Wound-healing and transwell assays revealed that PD-L2 knockdown  leaded to inhibition of migration and invasion of human osteosarcoma cells in vitro. Mechanistically, we demonstrated that PD-L2 knockdown attenuated migration and invasion by inactivating RhoA-ROCK-LIMK2 signaling, suppressing epithelial–mesenchymal transition (EMT), and inhibiting autophagy by decreasing beclin-1 expression. In support of these observations, beclin-1 knockdown also inhibited activation of the RhoA-ROCK-LIMK2 pathway, leading to autophagy inhibition-induced blockade of migration and invasion. Depletion of PD-L2 in KHOS cells markedly weakens pulmonary metastatic potential in vivo by orthotopic transplantation of nude mice. Our study reveals a pro-metastatic functional mechanism for PD-L2 in osteosarcoma. Furthermore, we demonstrate a regulatory role for PD-L2 on autophagy, as well as a relationship between autophagy and metastasis in osteosarcoma, which may represent a potential therapeutic target for osteosarcoma.
Colorless-to-colorful switching electrochromic polyimides with very high contrast ratio
Authors: Zhang Qiang , Tsai Chou-Yi , Li Lain-Jong , Liaw Der-Jang
Published: March 2019

Colorless-to-colorful switching electrochromic polymers with very high contrast ratio are unattainable and attractive for the applications of smart wearable electronics. Here we report a facile strategy in developing colorless-to-colorful switching electrochromic polyimides by incorporating with alicyclic nonlinear, twisted structures and adjusted conjugated electrochromophores, which minimize the charge transfer complex formation. It is noted that, by controlling the conjugation length of electrochromophore, the colorless-to-black switching electrochromic polymer film (PI-1a) exhibites an ultrahigh integrated contrast ratio up to 91.4% from 380 to 780 nm, especially up to 96.8% at 798 nm. In addition, PI-1a film with asymmetric structure also demonstrates fast electrochemical and electrochromic behaviors (a switching and bleaching time of 1.3 s and 1.1 s, respectively) due to the loose chain stacking, which provides more pathways for the penetration of counterion. Moreover, the colorless-to-black EC device based on PI-1a reveals an overall integrated contrast ratio up to 80%.
Chronic Chlamydia infection in human organoids increases stemness and promotes age-dependent CpG methylation
Authors: Kessler Mirjana , Hoffmann Karen , Fritsche Kristin , Brinkmann Volker , Mollenkopf Hans-Joachim , Thieck Oliver , Teixeira da Costa Ana Rita , Braicu Elena I. , Sehouli Jalid , Mangler Mandy , Berger Hilmar , Meyer Thomas F.
Published: March 2019

Chronic infections of the fallopian tubes with Chlamydia trachomatis (Ctr) cause scarring and can lead to infertility. Here we use human fallopian tube organoids and genital Ctr serovars D, K and E for long-term in vitro analysis. The epithelial monolayer responds with active expulsion of the bacteria into the lumen and with compensatory cellular proliferation—demonstrating a role of epithelial homeostasis in the defense against this pathogen. In addition, Ctr infection activates LIF signaling, which we find to be an essential regulator of stemness in the organoids. Infected organoids exhibit a less differentiated phenotype with higher stemness potential, as confirmed by increased organoid forming efficiency. Moreover, Ctr increases hypermethylation of DNA, which is an indicator of accelerated molecular aging. Thus, the chronic organoid infection model suggests that Ctr has a long-term impact on the epithelium. These heritable changes might be a contributing factor in the development of tubal pathologies, including the initiation of high grade serous ovarian cancer.
UFL1 promotes histone H4 ufmylation and ATM activation
Authors: Qin Bo , Yu Jia , Nowsheen Somaira , Wang Minghui , Tu Xinyi , Liu Tongzheng , Li Honglin , Wang Liewei , Lou Zhenkun
Published: March 2019

The ataxia-telangiectasia mutated (ATM) kinase, an upstream kinase of the DNA damage response (DDR), is rapidly activated following DNA damage, and phosphorylates its downstream targets to launch DDR signaling. However, the mechanism of ATM activation is still not completely understood. Here we report that UFM1 specific ligase 1 (UFL1), an ufmylation E3 ligase, is important for ATM activation. UFL1 is recruited to double strand breaks by the MRE11/RAD50/NBS1 complex, and monoufmylates histone H4 following DNA damage. Monoufmylated histone H4 is important for Suv39h1 and Tip60 recruitment. Furthermore, ATM phosphorylates UFL1 at serine 462, enhancing UFL1 E3 ligase activity and promoting ATM activation in a positive feedback loop. These findings reveal that ufmylation of histone H4 by UFL1 is an important step for amplification of ATM activation and maintenance of genomic integrity.
Inactivation of a CRF-dependent amygdalofugal pathway reverses addiction-like behaviors in alcohol-dependent rats
Authors: de Guglielmo Giordano , Kallupi Marsida , Pomrenze Matthew B. , Crawford Elena , Simpson Sierra , Schweitzer Paul , Koob George F. , Messing Robert O. , George Olivier
Published: March 2019

The activation of a neuronal ensemble in the central nucleus of the amygdala (CeA) during alcohol withdrawal has been hypothesized to induce high levels of alcohol drinking in dependent rats. In the present study we describe that the CeA neuronal ensemble that is activated by withdrawal from chronic alcohol exposure contains ~80% corticotropin-releasing factor (CRF) neurons and that the optogenetic inactivation of these CeA CRF+ neurons prevents recruitment of the neuronal ensemble, decreases the escalation of alcohol drinking, and decreases the intensity of somatic signs of withdrawal. Optogenetic dissection of the downstream neuronal pathways demonstrates that the reversal of addiction-like behaviors is observed after the inhibition of CeA CRF projections to the bed nucleus of the stria terminalis (BNST) and that inhibition of the CRFCeA-BNST pathway is mediated by inhibition of the CRF-CRF1 system and inhibition of BNST cell firing. These results suggest that the CRFCeA-BNST pathway could be targeted for the treatment of excessive drinking in alcohol use disorder.
Magnetization-polarization cross-control near room temperature in hexaferrite single crystals
Authors: Kocsis V. , Nakajima T. , Matsuda M. , Kikkawa A. , Kaneko Y. , Takashima J. , Kakurai K. , Arima T. , Kagawa F. , Tokunaga Y. , Tokura Y. , Taguchi Y.
Published: March 2019

Mutual control of the electricity and magnetism in terms of magnetic (H) and electric (E) fields, the magnetoelectric (ME) effect, offers versatile low power consumption alternatives to current data storage, logic gate, and spintronic devices. Despite its importance, E-field control over magnetization (M) with significant magnitude was observed only at low temperatures. Here we have successfully stabilized a simultaneously ferrimagnetic and ferroelectric phase in a Y-type hexaferrite single crystal up to 450 K, and demonstrated the reversal of large non-volatile M by E field close to room temperature. Manipulation of the magnetic domains by E field is directly visualized at room temperature by using magnetic force microscopy. The present achievement provides an important step towards the application of ME multiferroics.
Low genetic variation is associated with low mutation rate in the giant duckweed
Authors: Xu Shuqing , Stapley Jessica , Gablenz Saskia , Boyer Justin , Appenroth Klaus J. , Sree K. Sowjanya , Gershenzon Jonathan , Widmer Alex , Huber Meret
Published: March 2019

Mutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. Here we investigate genetic diversity, spontaneous mutation rate andNein the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals reveals extremely low intraspecific genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereasNeis large. These results demonstrate that low genetic diversity can be associated with large-Nespecies, where selection can reduce mutation rates to very low levels. This study also highlights that accurate estimates of mutation rate can help to explain seemingly unexpected patterns of genome-wide variation.
Author Correction: Strong indirect coupling between graphene-based mechanical resonators via a phonon cavity
Authors: Luo Gang , Zhang Zhuo-Zhi , Deng Guang-Wei , Li Hai-Ou , Cao Gang , Xiao Ming , Guo Guang-Can , Tian Lin , Guo Guo-Ping
Published: March 2019

The original version of this Article contained a number of errors. As a result of this, changes have been made to both the PDF and the HTML versions of the Article. A full list of these changes is available online
Megaphylogeny resolves global patterns of mushroom evolution
Authors: Varga Torda , Krizsán Krisztina , Földi Csenge , Dima Bálint , Sánchez-García Marisol , Sánchez-Ramírez Santiago , Szöllősi Gergely J. , Szarkándi János G. , Papp Viktor , Albert László , Andreopoulos William , Angelini Claudio , Antonín Vladimír , Barry Kerrie W. , Bougher Neale L. , Buchanan Peter , Buyck Bart , Bense Viktória , Catcheside Pam , Chovatia Mansi , Cooper Jerry , Dämon Wolfgang , Desjardin Dennis , Finy Péter , Geml József , Haridas Sajeet , Hughes Karen , Justo Alfredo , Karasiński Dariusz , Kautmanova Ivona , Kiss Brigitta , Kocsubé Sándor , Kotiranta Heikki , LaButti Kurt M. , Lechner Bernardo E. , Liimatainen Kare , Lipzen Anna , Lukács Zoltán , Mihaltcheva Sirma , Morgado Louis N. , Niskanen Tuula , Noordeloos Machiel E. , Ohm Robin A. , Ortiz-Santana Beatriz , Ovrebo Clark , Rácz Nikolett , Riley Robert , Savchenko Anton , Shiryaev Anton , Soop Karl , Spirin Viacheslav , Szebenyi Csilla , Tomšovský Michal , Tulloss Rodham E. , Uehling Jessie , Grigoriev Igor V. , Vágvölgyi Csaba , Papp Tamás , Martin Francis M. , Miettinen Otto , Hibbett David S. , Nagy László G.
Published: March 2019

Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.
Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil
Authors: Carro Lorena , Castro Jean Franco , Razmilic Valeria , Nouioui Imen , Pan Che , Igual José M. , Jaspars Marcel , Goodfellow Michael , Bull Alan T. , Asenjo Juan A. , Klenk Hans-Peter
Published: March 2019

The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32T, LB39T and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32T and LB39T were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.
Coffee-based colloids for direct solar absorption
Authors: Alberghini Matteo , Morciano Matteo , Bergamasco Luca , Fasano Matteo , Lavagna Luca , Humbert Gabriele , Sani Elisa , Pavese Matteo , Chiavazzo Eliodoro , Asinari Pietro
Published: March 2019

Despite their promising thermo-physical properties for direct solar absorption, carbon-based nanocolloids present some drawbacks, among which the unpleasant property of being potentially cytotoxic and harmful to the environment. In this work, a sustainable, stable and inexpensive colloid based on coffee is synthesized and its photo-thermal properties investigated. The proposed colloid consists of distilled water, Arabica coffee, glycerol and copper sulphate, which provide enhanced properties along with biocompatibility. The photo-thermal performance of the proposed fluid for direct solar absorption is analysed for different dilutions and compared with that of a traditional flat-plate collector. Tailor-made collectors, opportunely designed and realized via 3D-printing technique, were used for the experimental tests. The results obtained in field conditions, in good agreement with two different proposed models, show similar performance of the volumetric absorption using the proposed coffee-based colloids as compared to the classical systems based on a highly-absorbing surface. These results may encourage further investigations on simple, biocompatible and inexpensive colloids for direct solar absorption.
Flow Analysis at the Snow Covered High Altitude Catchment via Distributed Energy Balance Modeling
Authors: Shakoor Abdul , Ejaz Naeem
Published: March 2019

Energy budget-based distributed modeling at high-altitude glacio-nival watersheds is essential to accurately describe hydrological processes and quantify the flow rates. In this study, SNOWPACK model and its distributed version Alpine3D are applied for the first time in Pakistan to simulate the runoff response of a high altitude glaciated catchment. The basic aim was to explore the feasibility of this modeling system and its future applications in the region. Final results demonstrated satisfactory performance of the model between measured and modeled discharges with Nash-Sutcliff Efficiency of 0.54. However, total simulated flow volume differs only 1.3 times as compared to measured discharge of the lake, located at the glacier snout. Flow composition analysis revealed that the runoff regime of the study site is strongly influenced by the snow and glacier melt runoff representing 53% snowmelt and 38% glacier melt contribution. Low model efficiency has been observed during glacier melting season due to inaccurate wind speed distribution and biased input met-data. It is concluded that high performance of this model can be achieved if the model is optimized over the catchment similar to the study site provided with long term data sets. This study leaves a firm foundation for the potential application of a highly accurate distributed energy balance model in the entire Karakoram and Himalaya region to understand the melt dynamics of such a rugged terrain glacier rich mountains.
A neonicotinoid pesticide impairs foraging, but not learning, in free-flying bumblebees
Authors: Muth F. , Leonard A. S.
Published: March 2019

Neonicotinoids are widely-used pesticides implicated in the decline of bees, known to have sub-lethal effects on bees’ foraging and colony performance. One proposed mechanism for these negative effects is impairment to bees’ ability to learn floral associations. However, the effects of neonicotinoids on learning performance have largely been addressed using a single protocol, where immobilized bees learn an association based on a single sensory modality. We thus have an incomplete understanding of how these pesticides affect bee learning in more naturalistic foraging scenarios. We carried out the first free-foraging study into the effects of acute exposure of a neonicotinoid (imidacloprid) on bumblebees’ (Bombus impatiens) ability to learn associations with visual stimuli. We uncovered dose-dependent detrimental effects on motivation to initiate foraging, amount of nectar collected, and initiation of subsequent foraging bouts. However, we did not find any impairment to bees’ ability to learn visual associations. While not precluding the possibility that other forms of learning are impaired, our findings suggest that some of the major effects of acute neonicotinoid exposure on foraging performance may be due to motivational and/or sensory impairments. In light of these findings, we discuss more broadly how pesticide effects on pollinator cognition might be studied.
Anti-Hexokinase 1 Antibody as a Novel Serum Biomarker of a Subgroup of Diabetic Macular Edema
Authors: Yoshitake Tatsuya , Murakami Tomoaki , Yoshitake Shin , Suzuma Kiyoshi , Dodo Yoko , Fujimoto Masahiro , Ito Shinji , Tsujikawa Akitaka
Published: March 2019

Diabetic retinopathy (DR) induces the breakdown of the blood-retinal barrier and promotes neuroinflammation, although autoimmune responses to sequestered retinal antigens remain poorly understood. In this study, we investigated the autoantibodies for retinal antigens in sera from diabetic macular edema (DME) patients. Screening by immunoblotting demonstrated that IgG from 7 of 10 DME sera samples reacted to an ~102-kDa autoantigen from porcine retinas. Immunoprecipitation with autoantibodies from DME sera and subsequent mass spectrometry enabled us to identify hexokinase 1 as an autoantigen reactive to IgG from DME sera. IgG in 7 of 10 DME sera partially colocalized to hexokinase 1 in the outer plexiform layer of rodent retinas. Quantitative analyses using enzyme-linked immunosorbent assays revealed that the serum titers of this autoantibody were significantly higher in the DME sera than those in the sera from diabetic patients without DME, and 20 (24.1%) of the 83 DME serum samples had higher IgG titers than the cutoff value (mean + 2 standard deviations of the sera from diabetic patients without DR). Multivariate logistic regression analysis confirmed that the higher titer of anti-hexokinase 1 IgG was clinically feasible for the diagnosis of DME. These data identify anti-hexokinase 1 antibody as a serum biomarker of a subset of DME.
Novel catalytically active Pd/Ru bimetallic nanoparticles synthesized by Bacillus benzeovorans
Authors: Omajali Jacob B. , Gomez-Bolivar Jaime , Mikheenko Iryna P. , Sharma Surbhi , Kayode Bayonle , Al-Duri Bushra , Banerjee Dipanjan , Walker Marc , Merroun Mohamed L. , Macaskie Lynne E.
Published: March 2019

Bacillus benzeovoransassisted and supported growth of ruthenium (bio-Ru) and palladium/ruthenium (bio-Pd@Ru) core@shell nanoparticles (NPs) as bio-derived catalysts. Characterization of the bio-NPs using various electron microscopy techniques and high-angle annular dark field (HAADF) analysis confirmed two NP populations (1–2 nm and 5–8 nm), with core@shells in the latter. The Pd/Ru NP lattice fringes, 0.231 nm, corresponded to the (110) plane of RuO2.While surface characterization using X-ray photoelectron spectroscopy (XPS) showed the presence of Pd(0), Pd(II), Ru(III) and Ru(VI), X-ray absorption (XAS) studies of the bulk material confirmed the Pd speciation (Pd(0) and Pd(II)- corresponding to PdO), and identified Ru as Ru(III) and Ru(IV). The absence of Ru–Ru or Ru–Pd peaks indicated Ru only exists in oxide forms (RuO2and RuOH), which are surface-localized. X ray diffraction (XRD) patterns did not identify Pd-Ru alloying. Preliminary catalytic studies explored the conversion of 5-hydroxymethyl furfural (5-HMF) to the fuel precursor 2,5-dimethyl furan (2,5-DMF). Both high-loading (9.7 wt.% Pd, 6 wt.% Ru) and low-loading (2.4 wt.% Pd, 2 wt.% Ru) bio-derived catalysts demonstrated high conversion efficiencies (~95%) and selectivity of ~63% (~20% better than bio-Ru NPs) and 58%, respectively. These materials show promising future scope as efficient low-cost biofuel catalysts.
An fMRI study on the neural correlates of social conformity to a sexual minority
Authors: Liuzza M. T. , Macaluso E. , Chiesa P. A. , Lingiardi V. , Aglioti S. M.
Published: March 2019

Social conformity refers to the tendency to align one’s own behaviors, beliefs and values to those of others. Little is known about social influence coming from a minority group. To test whether social pressure from sexual minorities triggers avoidance-motivated behaviors, we explored how being influenced by the preferences of gay peers modifies the behavioral and neural reactivity of individuals defined as in- vs. out- groups on the basis of sexual orientation. To this aim, we combined fMRI with a social conformity paradigm in which heterosexual and gay/bisexual (hereafter non-exclusively heterosexual, NEH) individuals provided with male body attractiveness ratings by a fictitious group of gay students may or may not alter their previous rating and may or may not conform to the mean. Behaviorally, conformity to the minority preference was found in in-group NEH more than in out-group heterosexuals. Analysis of BOLD signal showed that social pressure brought about increased brain activity in frontal and parietal regions associated with the detection of social conflict. These results show that members of a sexual majority group display a smaller level of conformity when a sexual minority group exerts social influence. However, the neural correlates of this modulation are yet to be clarified.
A Mycobacterium tuberculosis Beijing strain persists at high rates and extends its geographic boundaries 20 years after importation
Authors: Pérez-Lago Laura , Campos-Herrero María Isolina , Cañas Fernando , Copado Rodolfo , Sante Laura , Pino Berta , Lecuona María , Gil Óscar Díez , Martín Carlos , Muñoz Patricia , García-de-Viedma Darío , Samper Sofía
Published: March 2019

Transmission of Beijing Mycobacterium tuberculosis can be investigated based on genotypic analysis of clinical isolates. A Beijing strain began to spread on Gran Canaria Island, Spain, at the end of the last century. In 1996, only 3 years after its importation to the island, its frequency had increased to 27.1% of all the isolates. The strain was tracked during the following years, and the most recent data obtained corresponded to 2007-8, when its presence continued to be alarming (21%). In the current study, we updated data on the distribution of this strain 20 years (2013–2014) after it was first detected on the island and extended the analysis for the first time to all the mycobacteriology laboratories covering the population of the Canary Island archipelago. Rapid updating was enabled by means of 2 different strain-specific PCRs: one targeting a peculiar feature of the strain, which was identified based on an IS6110 copy mapping in the Rv2180c gene, and a newly defined strain-specific single nucleotide polymorphism, which was identified by whole-genome sequencing. The results showed that the strain has remained highly prevalent (20.90% of all isolates), has spread throughout the neighbouring islands, and has also reached high representativeness in them (11–32%).
Guided STED nanoscopy enables super-resolution imaging of blood stage malaria parasites
Authors: Schloetel Jan-Gero , Heine Jörn , Cowman Alan F. , Pasternak Michał
Published: March 2019

Malaria remains a major burden world-wide, but the disease-causing parasites from the genus Plasmodium are difficult to study in vitro. Owing to the small size of the parasites, subcellular imaging poses a major challenge and the use of super-resolution techniques has been hindered by the parasites’ sensitivity to light. This is particularly apparent during the blood-stage of the Plasmodium life cycle, which presents an important target for drug research. The iron-rich food vacuole of the parasite undergoes disintegration when illuminated with high-power lasers such as those required for high resolution in Stimulated Emission Depletion (STED) microscopy. This causes major damage to the sample precluding the use of this super-resolution technique. Here we present guided STED, a novel adaptive illumination (AI) STED approach, which takes advantage of the highly-reflective nature of the iron deposit in the cell to identify the most light-sensitive parts of the sample. Specifically in these parts, the high-power STED laser is deactivated automatically to prevent local damage. Guided STED nanoscopy finally allows super-resolution imaging of the whole Plasmodium life cycle, enabling multicolour imaging of blood-stage malaria parasites with resolutions down to 35 nm without sample destruction.
Optical clumped isotope thermometry of carbon dioxide
Authors: Prokhorov Ivan , Kluge Tobias , Janssen Christof
Published: March 2019

Simultaneous analysis of carbon dioxide isotopologues involved in the isotope exchange between the doubly substituted 13C16O18O molecule and 12C16O2 has become an exciting new tool for geochemical, atmospheric and paleoclimatic research with applications ranging from stratospheric chemistry to carbonate-based geothermometry studies. Full exploitation of this isotope proxy and thermometer is limited due to time consuming and costly analysis using mass spectrometric instrumentation. Here, we present an all optical clumped CO2 isotopologue thermometer with capability for rapid analysis and simplified sample preparation. The current development also provides the option for analysis of additional multiply-substituted isotopologues, such as 12C18O2. Since the instrument unambiguously measures all isotopologues of the 12C16O2 + 13C16O18O $$\rightleftharpoons $$⇌ 13C16O2 + 12C16O18O exchange, its equilibrium constant and the corresponding temperature are measured directly. Being essentially independent of the isotope composition of the calibration gas, an uncalibrated working reference is sufficient and usage of international calibration standards is obsolete. Other isotopologues and molecules can be accessed using the methodology, opening up new avenues in isotope research. Here we demonstrate the high-precision performance of the instrument with first gas temperature measurements of carbon dioxide samples from geothermal sources.
Profiling of gallbladder carcinoma reveals distinct miRNA profiles and activation of STAT1 by the tumor suppressive miRNA-145-5p
Authors: Goeppert Benjamin , Truckenmueller Felicia , Ori Alessandro , Fritz Valerie , Albrecht Thomas , Fraas Angelika , Scherer Dominique , Silos Rosa González , Sticht Carsten , Gretz Norbert , Mehrabi Arianeb , Bewerunge-Hudler Melanie , Pusch Stefan , Bermejo Justo Lorenzo , Dietrich Peter , Schirmacher Peter , Renner Marcus , Roessler Stephanie
Published: March 2019

Gallbladder carcinoma (GBC) is a biliary tract cancer with few treatment options and poor prognosis. Radical surgery is the only potentially curative treatment option but most patients diagnosed with GBC are unresectable. Thus, there is a great need for the development of new treatment options including targeted therapy. Here, we aimed at identifying deregulated miRNAs and affected pathways involved in GBC development and progression. We performed global miRNA profiling of 40 GBC and 8 normal gallbladder tissues and identified large differences with 30% of miRNAs being differentially expressed (false discovery rate: FDR < 0.001). We found 24 miRNAs to be differentially regulated in GBC with poor outcome (p < 0.05) of which miR-145-5p was the most downregulated miRNA. Overexpression of miR-145-5p significantly reduced cell proliferation and colony formation. Gene expression analysis of cells expressing miR-145-5p mimics revealed activation of the Signal transducer and activator of transcription 1 (STAT1) signaling pathway which is mainly tumor suppressive. Furthermore, the activation of STAT1 by miR-145-5p was specifically observed in gallbladder carcinoma and cholangiocarcinoma but not in hepatocellular carcinoma cells. The Protein Tyrosine Phosphatase Receptor Type F (PTPRF) is downregulated upon miR-145 expression and may be involved in STAT1 regulation. In addition, we found that the STAT1-regulated protein IRF7 is downregulated in GBC compared to normal gallbladder tissue and low IRF7 expression is associated with significantly lower overall survival of GBC patients. Thus, this study identified GBC patient subgroups and provides new mechanistic insights in the tumor suppressive function of miR-145-5p leading to activation of STAT1 signaling.
The tricyclic antidepressant clomipramine inhibits neuronal autophagic flux
Authors: Cavaliere Federica , Fornarelli Alessandra , Bertan Fabio , Russo Rossella , Marsal-Cots Anaïs , Morrone Luigi Antonio , Adornetto Annagrazia , Corasaniti Maria Tiziana , Bano Daniele , Bagetta Giacinto , Nicotera Pierluigi
Published: March 2019

Antidepressants are commonly prescribed psychotropic substances for the symptomatic treatment of mood disorders. Their primary mechanism of action is the modulation of neurotransmission and the consequent accumulation of monoamines, such as serotonin and noradrenaline. However, antidepressants have additional molecular targets that, through multiple signaling cascades, may ultimately alter essential cellular processes. In this regard, it was previously demonstrated that clomipramine, a widely used FDA-approved tricyclic antidepressant, interferes with the autophagic flux and severely compromises the viability of tumorigenic cells upon cytotoxic stress. Consistent with this line of evidence, we report here that clomipramine undermines autophagosome formation and cargo degradation in primary dissociated neurons. A similar pattern was observed in the frontal cortex and liver of treated mice, as well as in the nematode Caenorhabditis elegans exposed to clomipramine. Together, our findings indicate that clomipramine may negatively regulate the autophagic flux in various tissues, with potential metabolic and functional implications for the homeostatic maintenance of differentiated cells.
Distinct triterpene synthases in the laticifers of Euphorbia lathyris
Authors: Forestier Edith , Romero-Segura Carmen , Pateraki Irini , Centeno Emilio , Compagnon Vincent , Preiss Myriam , Berna Anne , Boronat Albert , Bach Thomas J. , Darnet Sylvain , Schaller Hubert
Published: March 2019

Euphorbia lathyriswas proposed about fifty years ago as a potential agroenergetic crop. The tremendous amounts of triterpenes present in its latex has driven investigations for transforming this particular biological fluid into an industrial hydrocarbon source. The huge accumulation of terpenes in the latex of many plant species represent a challenging question regarding cellular homeostasis. In fact, the enzymes, the mechanisms and the controllers that tune the amount of products accumulated in specialized compartments (to fulfill ecological roles) or deposited at important sites (as essential factors) are not known. Here, we have isolated oxidosqualene cyclases highly expressed in the latex ofEuphorbia lathyris. This triterpene biosynthetic machinery is made of distinct paralogous enzymes responsible for the massive accumulation of steroidal and non-steroidal tetracyclic triterpenes. More than eighty years after the isolation of butyrospermol from shea butter (Heilbronn IM, Moffet GL, and Spring FSJ.Chem.Soc. 1934, 1583), a butyrospermol synthase is characterized in this work using yeast andin foliaheterologous expression assays.
Simulations of Protein Adsorption on Nanostructured Surfaces
Authors: Manzi Berardo M. , Werner Marco , Ivanova Elena P. , Crawford Russell J. , Baulin Vladimir A.
Published: March 2019

Recent technological advances have allowed the development of a new generation of nanostructured materials, such as those displaying both mechano-bactericidal activity and substrata that favor the growth of mammalian cells. Nanomaterials that come into contact with biological media such as blood first interact with proteins, hence understanding the process of adsorption of proteins onto these surfaces is highly important. The Random Sequential Adsorption (RSA) model for protein adsorption on flat surfaces was modified to account for nanostructured surfaces. Phenomena related to the nanofeature geometry have been revealed during the modelling process; e.g., convex geometries can lead to lower steric hindrance between particles, and hence higher degrees of surface coverage per unit area. These properties become more pronounced when a decrease in the size mismatch between the proteins and the surface nanostructures occurs. This model has been used to analyse the adsorption of human serum albumin (HSA) on a nano-structured black silicon (bSi) surface. This allowed the Blocking Function (the rate of adsorption) to be evaluated. The probability of the protein to adsorb as a function of the occupancy was also calculated.
Dual-FRET imaging of IP3 and Ca2+ revealed Ca2+-induced IP3 production maintains long lasting Ca2+ oscillations in fertilized mouse eggs
Authors: Matsu-ura Toru , Shirakawa Hideki , Suzuki Kenichi G. N. , Miyamoto Akitoshi , Sugiura Kotomi , Michikawa Takayuki , Kusumi Akihiro , Mikoshiba Katsuhiko
Published: March 2019

In most species, fertilization induces Ca2+ transients in the egg. In mammals, the Ca2+ rises are triggered by phospholipase Cζ (PLCζ) released from the sperm; IP3 generated by PLCζ induces Ca2+ release from the intracellular Ca2+ store through IP3 receptor, termed IP3-induced Ca2+ release. Here, we developed new fluorescent IP3 sensors (IRIS-2s) with the wider dynamic range and higher sensitivity (Kd = 0.047–1.7 μM) than that we developed previously. IRIS-2s employed green fluorescent protein and Halo-protein conjugated with the tetramethylrhodamine ligand as fluorescence resonance energy transfer (FRET) donor and acceptor, respectively. For simultaneous imaging of Ca2+ and IP3, using IRIS-2s as the IP3 sensor, we developed a new single fluorophore Ca2+ sensor protein, DYC3.60. With IRIS-2s and DYC3.60, we found that, right after fertilization, IP3 concentration ([IP3]) starts to increase before the onset of the first Ca2+ wave. [IP3] stayed at the elevated level with small peaks followed after Ca2+ spikes through Ca2+ oscillations. We detected delays in the peak of [IP3] compared to the peak of each Ca2+ spike, suggesting that Ca2+-induced regenerative IP3 production through PLC produces small [IP3] rises to maintain [IP3] over the basal level, which results in long lasting Ca2+ oscillations in fertilized eggs.
Historical BCG vaccination combined with drug treatment enhances inhibition of mycobacterial growth ex vivo in human peripheral blood cells
Authors: Prabowo Satria A. , Zelmer Andrea , Stockdale Lisa , Ojha Utkarsh , Smith Steven G. , Seifert Karin , Fletcher Helen A.
Published: March 2019

Tuberculosis (TB) is a leading infectious cause of death globally. Drug treatment and vaccination, in particular with Bacillus Calmette-Guérin (BCG), remain the main strategies to control TB. With the emergence of drug resistance, it has been proposed that a combination of TB vaccination with pharmacological treatment may provide a greater therapeutic value. We implemented an ex vivo mycobacterial growth inhibition assay (MGIA) to discriminate vaccine responses in historically BCG-vaccinated human volunteers and to assess the contribution of vaccine-mediated immune response towards the killing effect of mycobacteria in the presence of the antibiotics isoniazid (INH) and rifampicin (RIF), in an attempt to develop the assay as a screening tool for therapeutic TB vaccines. BCG vaccination significantly enhanced the ability of INH to control mycobacterial growth ex vivo. The BCG-vaccinated group displayed a higher production of IFN-γ and IP-10 when peripheral blood mononuclear cells (PBMC) were co-cultured with INH, with a similar trend during co-culture with RIF. A higher frequency of IFN-γ+ and TNF-α+ CD3− CD4− CD8− cells was observed, suggesting the contribution of Natural Killer (NK) cells in the combined effect between BCG vaccination and INH. Taken together, our data indicate the efficacy of INH can be augmented following historical BCG vaccination, which support findings from previous observational and animal studies.
Spin Torque Efficiency and Analytic Error Rate Estimates of Skyrmion Racetrack Memory
Authors: Suess Dieter , Vogler Christoph , Bruckner Florian , Heistracher Paul , Slanovc Florian , Abert Class
Published: March 2019

In this paper, the thermal stability of skyrmion bubbles and the critical currents to move them over pinning sites were investigated. For the used pinning geometries and the used parameters, the unexpected behavior is reported that the energy barrier to overcome the pinning site is larger than the energy barrier of the annihilation of a skyrmion. The annihilation takes place at boundaries by current driven motion, as well as due to the excitation over energy barriers, in the absence of currents, without forming Bloch points. It is reported that the pinning sites, which are required to allow thermally stable bits, significantly increase the critical current densities to move the bits in skyrmion-like structures to aboutjcrit = 0.62 TA/m². The simulation shows that the applied spin transfer model predicts experimentally obtained critical currents to move stable skyrmions at room temperature well, which is in contrast to simulations based on spin orbit torque that predict significantly too low critical currents. By calculating the thermal stability, as well as the critical current, we can derive the spin torque efficiency η = ΔE/Ic = 0.19 kBT300/μA, which is in a similar range to the simulated spin torque efficiency of MRAM structures. Finally, it is shown that the stochastic depinning process of any racetrack-like device requires an extremely narrow depinning time distribution smaller than ~6% of the current pulse length to reach bit error rates smaller than 10−9.
Laue three dimensional neutron diffraction
Authors: Raventós Marc , Tovar Michael , Medarde Marisa , Shang Tian , Strobl Markus , Samothrakitis Stavros , Pomjakushina Ekaterina , Grünzweig Christian , Schmidt Søren
Published: March 2019

This article presents a measurement technique and data analysis tool to perform 3D grain distribution mapping and indexing of oligocrystalline samples using neutrons: Laue three-dimensional neutron diffraction (Laue3DND). The approach builds on forward modelling used for correlation and multiple fitting of the measured diffraction spots relative to individual grains. This enables not only to identify individual grains, but also their position and orientation in the sample. The feasibility and performance of the Laue3DND approach are tested using multi-grain synthetic datasets from cubic (α-Fe) and tetragonal (YBaCuFeO5) symmetries. Next, experimental results from two data sets measured at the FALCON instrument of Helmholtz-Zentrum Berlin are presented: A cylindrical alpha iron (α-Fe) reference sample with 5 mm diameter and 5 mm height, as well as a 2 mm3layered perovskite (YBaCuFeO5). Using Laue3DND, we were able to retrieve the position and orientation of 97 out of 100 grains from a syntheticα-Fe data set, as well as 24 and 9 grains respectively from theα-Fe and YBaCuFeO5sample measured at FALCON. Results from the synthetic tests also indicate that Laue3DND is capable of indexing 10 out of 10 grains for both symmetries in two extreme scenarios: using only 6 Laue projections and using 360 projections with extremely noisy data. The precision achieved in terms of spatial and orientation resolution for the current version of the method is 430 μm and 1° respectively. Based on these results obtained, we are confident to present a tool that expands the capabilities of standard Laue diffraction, providing the number, position, orientation and relative size of grains in oligocrystalline samples.
Definition of network types – Prediction of dough mechanical behaviour under shear by gluten microstructure
Authors: Lucas Isabelle , Petermeier Hannes , Becker Thomas , Jekle Mario
Published: March 2019

This study defines network types of wheat gluten to describe spatial arrangements of gluten networks in relation to dough mechanical behaviour. To achieve a high variety in gluten arrangements, ten specific and unspecific gluten-modifying agents in increasing concentrations were added to wheat dough. Gluten microstructure was visualized by confocal laser scanning microscopy and quantified by protein network analysis. Dough rheological behaviour was determined by both oscillatory and creep-recovery tests. Based on correlation matrices and principal component analysis, six different network types were identified and associated to their rheological characteristics: a cleaved (low viscous), rigid (highly viscous), spread (viscoelastic), strengthened (viscoelastic), particulate and dense (highly viscous) or particulate and loose (low viscous) network. Furthermore, rheological dough properties of specifically gluten-modified samples were predicted with five microstructural gluten attributes (lacunarity, branching rate, end-point rate, protein width, average protein length) and assigned properly by the obtained partial least square model with an accuracy up to 90% (e.g., R2Y = 0.84 for G*, 0.85 for tanδ, 0.90 for Jmax). As a result, rheological properties of wheat doughs were predicted from microstructural investigations. This novel, quantitative definition of the relation between structure and mechanical behaviour can be used for developments of new wheat products with targeted properties.
Activity and structural analysis of GRL-117C: a novel small molecule CCR5 inhibitor active against R5-tropic HIV-1s
Authors: Nakata Hirotomo , Maeda Kenji , Das Debananda , Chang Simon B. , Matsuda Kouki , Rao Kalapala Venkateswara , Harada Shigeyoshi , Yoshimura Kazuhisa , Ghosh Arun K. , Mitsuya Hiroaki
Published: March 2019

CCR5 is a member of the G-protein coupled receptor family that serves as an essential co-receptor for cellular entry of R5-tropic HIV-1, and is a validated target for therapeutics against HIV-1 infections. In the present study, we designed and synthesized a series of novel small CCR5 inhibitors and evaluated their antiviral activity. GRL-117C inhibited the replication of wild-type R5-HIV-1 with a sub-nanomolar IC50 value. These derivatives retained activity against vicriviroc-resistant HIV-1s, but did not show activity against maraviroc (MVC)-resistant HIV-1. Structural modeling indicated that the binding of compounds to CCR5 occurs in the hydrophobic cavity of CCR5 under the second extracellular loop, and amino acids critical for their binding were almost similar with those of MVC, which explains viral cross-resistance with MVC. On the other hand, one derivative, GRL-10018C, less potent against HIV-1, but more potent in inhibiting CC-chemokine binding, occupied the upper region of the binding cavity with its bis-THF moiety, presumably causing greater steric hindrance with CC-chemokines. Recent studies have shown additional unique features of certain CCR5 inhibitors such as immunomodulating properties and HIV-1 latency reversal properties, and thus, continuous efforts in developing new CCR5 inhibitors with unique binding profiles is necessary.
Risk Factors for Delayed Isolation of Patients with Active Pulmonary Tuberculosis in an Acute-care Hospital
Authors: Han Jaijun , Nam Bo Da , Park Se Yoon , Park Jebyung , Lee Eunyoung , Lee Eun Jung , Hwang Jung Hwa , Kim Tae Hyong
Published: March 2019

The objective of the current study was to determine the factors associated with delayed isolation of pulmonary tuberculosis (TB). In this retrospective study, data of patients newly diagnosed with pulmonary TB from January 2015 through December 2017 at a referral hospital were reviewed. Delayed recognition of pulmonary TB was defined as failure to initiate airborne isolation within the first 3 days of admission. We analyzed the clinical, microbiological, and radiological factors associated with delayed isolation of pulmonary TB. A total of 134 patients with positive sputum acid-fast bacilli (AFB) cultures were analyzed, of which 44 (33%) were isolated within 3 days after admission. In multivariate logistic regression analysis, older age (p = 0.01), admission to departments other than Infectious Disease or Pulmonology (p = 0.005), and presence of malignancy (p = 0.02) were associated with delayed isolation. Patients with a radiologic diagnosis of active pulmonary TB were likely to be isolated early (p = 0.01). Better awareness of pulmonary TB among attending practitioners in hospital settings is required. Delay in isolation is associated with older age, malignancy, hospitalization to departments other than Infectious Disease or Pulmonology, and non-confident radiologic diagnosis of active pulmonary TB.
Unbalanced calcium channel activity underlies selective vulnerability of nigrostriatal dopaminergic terminals in Parkinsonian mice
Authors: Sgobio Carmelo , Sun Lixin , Ding Jinhui , Herms Jochen , Lovinger David M. , Cai Huaibin
Published: March 2019

Dopamine (DA) release in striatum is functionally segregated across a dorsolateral/ventromedial axis. Interestingly, nigrostriatal DA signaling disruption in Parkinson’s disease (PD) preferentially affects the dorsolateral striatum. The relationship between afferent presynaptic calcium transients (PreCaTs) in DA terminals and DA release in dorsolateral (Caudato-Putamen, DLS) and ventromedial (Nucleus Accumbens Shell, VS) striatal subregions was examined by ex vivo real-time dual-recording in conditional transgenic mice expressing the calcium indicator protein GCaMP3. In DLS, minimal increases in cytosolic calcium trigger steep DA release while PreCaTs and DA release in VS both were proportional to the number of pulses in burst stimulation. Co-expressing α-synuclein with the Parkinson’s disease (PD)-associated A53T mutation and GCaMP3 in midbrain DA neurons revealed augmented cytosolic steady state and activity-dependent intra-terminal calcium levels preferentially in DLS, as well as hyperactivation and enhanced expression of N-type calcium channels. Thus, unbalanced calcium channel activity is a presynaptic mechanism to consider in the multifaceted pathogenic pathways of progressive neurodegeneration.