bluuebunny/crossref_metadata_2025 huggingface dataset:
Exosome-mediated uptake of mast cell tryptase into the nucleus of melanoma cells: a novel axis for regulating tumor cell proliferation and gene expression
Authors: Rabelo Melo Fabio , Santosh Martin Sebastin , Sommerhoff Christian P. , Pejler Gunnar
Published: September 2019

It is well established that mast cell accumulation accompanies most malignancies. However, the knowledge of how mast cells functionally impact on tumors is still rudimentary. Here we addressed this issue and show that mast cells have anti-proliferative activity on melanoma cells and that this effect is dependent on tryptase, a tetrameric protease stored in mast cell granules. Mechanistically, tryptase was found to be endocytosed by melanoma cells as cargo of DNA-coated exosomes released from melanoma cells, followed by transport to the nucleus. In the nucleus, tryptase executed clipping of histone 3 and degradation of Lamin B1, accompanied by extensive nuclear remodeling. Moreover, tryptase degraded hnRNP A2/B1, a protein involved in mRNA stabilization and interaction with non-coding RNAs. This was followed by downregulated expression of the oncogene EGR1 and of multiple non-coding RNAs, including oncogenic species. Altogether, these findings establish a new principle for regulation of tumor cell proliferation.
PKAc-directed interaction and phosphorylation of Ptc is required for Hh signaling inhibition in Drosophila
Authors: Fan Jialin , Gao Yajie , Lu Yi , Wu Wenqing , Yuan Shuo , Wu Hailong , Chen Dahua , Zhao Yun
Published: September 2019

Ptc is a gatekeeper to avoid abnormal Hh signaling activation, but the key regulators involved in Ptc-mediated inhibition remain largely unknown. Here, we identify PKAc as a key regulator required for Ptc inhibitory function. In the absence of Hh, PKAc physically interacts with Ptc and phosphorylates Ptc at Ser-1150 and -1183 residues. The presence of Hh unleashes PKAc from Ptc and activates Hh signaling. By combining both in vitro and in vivo functional assays, we demonstrate that such Ptc–PKAc interaction and Ptc phosphorylation are both important for Ptc inhibitory function. Interestingly, we further demonstrate that PKAc is subjected to palmitoylation, contributing to its kinase activity on plasma membrane. Based on those novel findings, we establish a working model on Ptc inhibitory function: In the absence of Hh, PKAc interacts with and phosphorylates Ptc to ensure its inhibitory function; and Hh presence releases PKAc from Ptc, resulting in Hh signaling activation.
ABA-mediated regulation of leaf and root hydraulic conductance in tomato grown at elevated CO2 is associated with altered gene expression of aquaporins
Authors: Fang Liang , Abdelhakim Lamis Osama Anwar , Hegelund Josefine Nymark , Li Shenglan , Liu Jie , Peng Xiaoying , Li Xiangnan , Wei Zhenhua , Liu Fulai
Published: September 2019

Elevated CO2 concentration in the air (e[CO2]) decreases stomatal density (SD) and stomatal conductance (gs) where abscisic acid (ABA) may play a role, yet the underlying mechanism remains largely elusive. We investigated the effects of e[CO2] (800 ppm) on leaf gas exchange and water relations of two tomato (Solanum lycopersicum) genotypes, Ailsa Craig (WT) and its ABA-deficient mutant (flacca). Compared to plants grown at ambient CO2 (400 ppm), e[CO2] stimulated photosynthetic rate in both genotypes, while depressed the gs only in WT. SD showed a similar response to e[CO2] as gs, although the change was not significant. e[CO2] increased leaf and xylem ABA concentrations and xylem sap pH, where the increases were larger in WT than in flacca. Although leaf water potential was unaffected by CO2 growth environment, e[CO2] lowered osmotic potential, hence tended to increase turgor pressure particularly for WT. e[CO2] reduced hydraulic conductance of leaf and root in WT but not in flacca, which was associated with downregulation of gene expression of aquaporins. It is concluded that ABA-mediated regulation of gs, SD, and gene expression of aquaporins coordinates the whole-plant hydraulics of tomato grown at different CO2 environments.
Species-Specific Marker Discovery in Tilapia
Authors: Syaifudin Mochamad , Bekaert Michaël , Taggart John B. , Bartie Kerry L. , Wehner Stefanie , Palaiokostas Christos , Khan M. G. Q. , Selly Sarah-Louise C. , Hulata Gideon , D’Cotta Helena , Baroiller Jean-Francois , McAndrew Brendan J. , Penman David J.
Published: September 2019

Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.
Functional analysis of new human Bardet-Biedl syndrome loci specific variants in the zebrafish model
Authors: Castro-Sánchez Sheila , Suarez-Bregua Paula , Novas Rossina , Álvarez-Satta María , Badano Jose L. , Rotllant Josep , Valverde Diana
Published: September 2019

The multiple genetic approaches available for molecular diagnosis of human diseases have made possible to identify an increasing number of pathogenic genetic changes, particularly with the advent of next generation sequencing (NGS) technologies. However, the main challenge lies in the interpretation of their functional impact, which has resulted in the widespread use of animal models. We describe here the functional modelling of seven BBS loci variants, most of them novel, in zebrafish embryos to validate their in silico prediction of pathogenicity. We show that target knockdown (KD) of known BBS (BBS1, BB5 or BBS6) loci leads to developmental defects commonly associated with ciliopathies, as previously described. These KD pleiotropic phenotypes were rescued by co-injecting human wild type (WT) loci sequence but not with the equivalent mutated mRNAs, providing evidence of the pathogenic effect of these BBS changes. Furthermore, direct assessment of cilia located in Kupffer’s vesicle (KV) showed a reduction of ciliary length associated with all the studied variants, thus confirming a deleterious effect. Taken together, our results seem to prove the pathogenicity of the already classified and unclassified new BBS variants, as well as highlight the usefulness of zebrafish as an animal model for in vivo assays in human ciliopathies.
Electron cryomicroscopy observation of acyl carrier protein translocation in type I fungal fatty acid synthase
Authors: Lou Jennifer W. , Iyer Kali R. , Hasan S. M. Naimul , Cowen Leah E. , Mazhab-Jafari Mohammad T.
Published: September 2019

During fatty acid biosynthesis, acyl carrier proteins (ACPs) from type I fungal fatty acid synthase (FAS) shuttle substrates and intermediates within a reaction chamber that hosts multiple spatially-fixed catalytic centers. A major challenge in understanding the mechanism of ACP-mediated substrate shuttling is experimental observation of its transient interaction landscape within the reaction chamber. Here, we have shown that ACP spatial distribution is sensitive to the presence of substrates in a catalytically inhibited state, which enables high-resolution investigation of the ACP-dependent conformational transitions within the enoyl reductase (ER) reaction site. In two fungal FASs with distinct ACP localization, the shuttling domain is targeted to the ketoacyl-synthase (KS) domain and away from other catalytic centers, such as acetyl-transferase (AT) and ER domains by steric blockage of the KS active site followed by addition of substrates. These studies strongly suggest that acylation of phosphopantetheine arm of ACP may be an integral part of the substrate shuttling mechanism in type I fungal FAS.
Effects of early adversity and social discrimination on empathy for complex mental states: An fMRI investigation
Authors: Fourie Melike M. , Stein Dan J. , Solms Mark , Gobodo-Madikizela Pumla , Decety Jean
Published: September 2019

There is extensive evidence of an association between early adversity and enduring neural changes that impact socioemotional processing throughout life. Yet little is known about the effects of on-going social discrimination on socioemotional functioning. Here we examined how cumulative experiences of social discrimination impact brain response during empathic responding—a crucial issue in South Africa, given its historical apartheid context and continuing legacies. White and Black South Africans completed measures of social adversity (early adversity and social discrimination), and underwent fMRI while viewing video clips depicting victims and perpetrators of apartheid crimes. Increased neural response was detected in brain regions associated with cognitive rather than affective empathy, and greater social adversity was associated with reduced reported compassion across participants. Notably, social discrimination (due to income level, weight, gender) in White participants was associated with increased amygdala reactivity, whereas social discrimination (due to race) in Black participants mediated the negative associations of temporoparietal junction and inferior frontal gyrus activation with compassion during emotionally provocative conditions. These findings suggest that (i) social discrimination has comparable associations at the neural level as other psychosocial stressors, and that (ii) the mechanisms underlying empathic responding vary as a function of the type of social discrimination experienced.
Luminescence Studies and Judd–Ofelt Analysis on SiO2@LaPO4:Eu@SiO2 Submicro-spheres with Different Size of Intermediate Shells
Authors: Zhu Xiaowei , Yang Kuisuo , Wu Anping , Bai He , Bao Jinrong , Qiao Yan , Yang Yunjiang , Li Wenxian , Liu Ying
Published: September 2019

The novel submicro-spheres SiO2@LaPO4:Eu@SiO2 with core-shell-shell structures were prepared by connecting the SiO2 submicro-spheres and the rare earth ions through an organosilane HOOCC6H4N(CONH(CH2)3Si(OCH2CH3)3 (MABA-Si). The as-prepared products were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), and infrared spectroscopy (IR). It is found that the intermediate shell of the submicro-spheres was composed by LaPO4:Eu nanoparticles with the size of about 4, 5–7, or 15–34 nm. A possible formation mechanism for the SiO2@LaPO4:Eu@SiO2 submicro-spheres has been proposed. The dependence of the photoluminescence intensity on the size of the LaPO4:Eu nanoparticles has been investigated. The intensity ratios of electrical dipole transition 5D0 → 7F2 to magnetic dipole transition 5D0 → 7F1 of Eu3+ ions were increased with decreasing the size of LaPO4:Eu nanoparticles. According to the Judd-Ofelt (J-O) theory, when the size of LaPO4:Eu nanoparticles was about 4, 5–7 and 15–34 nm, the calculated J-O parameter Ω2 (optical transition intensity parameter) was 2.30 × 10−20, 1.80 × 10−20 and 1.20 × 10−20, respectively. The increase of Ω2 indicates that the symmetry of Eu3+ in the LaPO4 lattice was gradually reduced. The photoluminescence intensity of the SiO2@LaPO4:Eu@SiO2 submicro-spheres was unquenched in aqueous solution even after 15 days.
A new perspective on membrane-embedded Bax oligomers using DEER and bioresistant orthogonal spin labels
Authors: Teucher Markus , Zhang Hui , Bader Verian , Winklhofer Konstanze F. , García-Sáez Ana J. , Rajca Andrzej , Bleicken Stephanie , Bordignon Enrica
Published: September 2019

Bax is a Bcl-2 protein crucial for apoptosis initiation and execution, whose active conformation is only partially understood. Dipolar EPR spectroscopy has proven to be a valuable tool to determine coarse-grained models of membrane-embedded Bcl-2 proteins. Here we show how the combination of spectroscopically distinguishable nitroxide and gadolinium spin labels and Double Electron-Electron Resonance can help to gain new insights into the quaternary structure of active, membrane-embedded Bax oligomers. We show that attaching labels bulkier than the conventional MTSL may affect Bax fold and activity, depending on the protein/label combination. However, we identified a suitable pair of spectroscopically distinguishable labels, which allows to study complex distance networks in the oligomers that could not be disentangled before. Additionally, we compared the stability of the different spin-labeled protein variants in E. coli and HeLa cell extracts. We found that the gem-diethyl nitroxide-labeled Bax variants were reasonably stable in HeLa cell extracts. However, when transferred into human cells, Bax was found to be mislocalized, thus preventing its characterization in a physiological environment. The successful use of spectroscopically distinguishable labels on membrane-embedded Bax-oligomers opens an exciting new path towards structure determination of membrane-embedded homo- or hetero-oligomeric Bcl-2 proteins via EPR.
Rhythmic pattern facilitates speech production: An ERP study
Authors: Zhang Ning , Zhang Qingfang
Published: September 2019

Rhythm affects the speech perception of events unfolding over time. However, it is not clear to what extent the rhythm could affect the processes of sentence speech production. In this event-related potential (ERP) study, we examined whether a particular rhythmic pattern could affect the planning of speech production before articulation. We recorded electrophysiological (EEG) and behavioural (reaction time) data while participants read aloud a target speech in Chinese. Target speeches were sentences or phrases consisting four characters, with regular (e.g., the 2 + 2 pattern; numbers in the brackets represent the number of syllables) or irregular (e.g., 1 + 3) rhythmic patterns, which were preceded by congruent or incongruent musical rhythmic patterns formed by simple pure tones with different temporal intervals. Behavioural and ERP findings indicated a rhythmic priming effect in comparing congruent and incongruent conditions in the regular target speeches, but not in the irregular ones. An early component (N100) that was elicited in response to target speeches that were rhythmically mismatched to primes was linked to the detection of hierarchical linguistic units, which did not conform to expectations. A later negative component (N400) was thought to reflect the violation of expectation on rhythmic pattern in speech production. These findings suggest that rhythmic pattern constrains grammatical and prosodic encoding during speech production, and support the hypothesis that speakers form a grammatical or a prosodic abstract frame before articulation.
Quantitative mathematical modeling of clinical brain metastasis dynamics in non-small cell lung cancer
Authors: Bilous M. , Serdjebi C. , Boyer A. , Tomasini P. , Pouypoudat C. , Barbolosi D. , Barlesi F. , Chomy F. , Benzekry S.
Published: September 2019

Brain metastases (BMs) are associated with poor prognosis in non-small cell lung cancer (NSCLC), but are only visible when large enough. Therapeutic decisions such as whole brain radiation therapy would benefit from patient-specific predictions of radiologically undetectable BMs. Here, we propose a mathematical modeling approach and use it to analyze clinical data of BM from NSCLC. Primary tumor growth was best described by a gompertzian model for the pre-diagnosis history, followed by a tumor growth inhibition model during treatment. Growth parameters were estimated only from the size at diagnosis and histology, but predicted plausible individual estimates of the tumor age (2.1–5.3 years). Multiple metastatic models were further assessed from fitting either literature data of BM probability (n = 183 patients) or longitudinal measurements of visible BMs in two patients. Among the tested models, the one featuring dormancy was best able to describe the data. It predicted latency phases of 4.4–5.7 months and onset of BMs 14–19 months before diagnosis. This quantitative model paves the way for a computational tool of potential help during therapeutic management.
Dynamics of centriole amplification in centrosome-depleted brain multiciliated progenitors
Authors: Mercey Olivier , Al Jord Adel , Rostaing Philippe , Mahuzier Alexia , Fortoul Aurélien , Boudjema Amélie-Rose , Faucourt Marion , Spassky Nathalie , Meunier Alice
Published: September 2019

Reproductive and respiratory organs, along with brain ventricles, are lined by multiciliated epithelial cells (MCC) that generate cilia-powered fluid flows. MCC hijack the centrosome duplication pathway to form hundreds of centrioles and nucleate motile cilia. In these cells, the large majority of procentrioles are formed associated with partially characterized organelles called deuterosomes. We recently challenged the paradigm that deuterosomes and procentrioles are formed de novo by providing data, in brain MCC, suggesting that they are nucleated from the pre-existing centrosomal younger centriole. However, the origin of deuterosomes and procentrioles is still under debate. Here, we further question centrosome importance for deuterosome and centriole amplification. First, we provide additional data confirming that centriole amplification occurs sequentially from the centrosomal region, and that the first procentriole-loaded deuterosomes are associated with the daughter centriole or in the centrosomal centriole vicinity. Then, to further test the requirement of the centrosome in deuterosome and centriole formation, we depleted centrosomal centrioles using a Plk4 inhibitor. We reveal unexpected limited consequences in deuterosome/centriole number in absence of centrosomal centrioles. Notably, in absence of the daughter centriole only, deuterosomes are not seen associated with the mother centriole. In absence of both centrosomal centrioles, procentrioles are still amplified sequentially and with no apparent structural defects. They seem to arise from a focal region, characterized by microtubule convergence and pericentriolar material (PCM) assembly. The relevance of deuterosome association with the daughter centriole as well as the role of the PCM in the focal and sequential genesis of centrioles in absence of centrosomal centrioles are discussed.
The double inhibition of PDK1 and STAT3-Y705 prevents liver metastasis in colorectal cancer
Authors: Qin Wenjuan , Tian Yun , Zhang Jing , Liu Wenjian , Zhou Qiming , Hu Sheng , Yang Fei , Lu Li , Lu Haijie , Cui Shuzhong , Wen Lu , Wei Shaozhong
Published: September 2019

As a key glycolysis enzyme, the significance of pyruvate dehydrogenase kinase 1 (PDK1) in the development of colorectal cancer (CRC) remains unknown. This study revealed that the prognosis of CRC patients with high levels of PDK1 was poor, and PDK1 knockdown significantly reduced liver metastasis of CRC in both nude mice and immune competent BALB/C mice. When combined with cryptotanshinone (CPT), an inhibitor of STAT3-p-Y705, the liver metastasis was further inhibited. PDK1 knockdown obviously increased reactive oxygen species level in anoikis conditions and subsequently resulted in an elevated anoikis, but the combination of PDK1 knockdown and CPT showed a reduced effect on anoikis. Based on this discrepancy, the adherence ability of CRC cells to matrix protein fibronectin was further detected. It showed that PDK1 knockdown significantly decreased the adherence of CRC cells to fibronectin when combined with CPT. These results suggest that inhibition of PDK1 can decrease the surviving CRC cells in blood circulation via up-regulation of anoikis, and inhibition of STAT3-p-Y705 can prevent it to settle down on the liver premetastatic niche, which ultimately reduces liver metastasis.
Exchange bias in ferromagnetic bilayers with orthogonal anisotropies: the case of GaMnAsP/GaMnAs combination
Authors: Choi Suho , Bac Seul-Ki , Liu Xinyu , Lee Sanghoon , Dong Sining , Dobrowolska M. , Furdyna J. K.
Published: September 2019

We report the observation of exchange bias in a ferromagnetic Ga0.94Mn0.06As0.77P0.23/ Ga0.94Mn0.06As bilayer, in which the easy axis in one layer is oriented out-of-plane, and in the other in-plane. Magnetization reversal in this system is explored using planar Hall effect (PHE) measurements under various initial conditions and with various field-cooling orientations. Our results show that the two magnetic layers are ferromagnetically exchange-coupled, and that such coupling results in pronounced exchange-bias-like shifts of magnetic hysteresis loops during reversal of in-plane magnetization. The presence of exchange bias in this system can be understood on the basis of magnetic closure domains formed in the layer with the out-of-plane easy axis.
High Fluence Chromium and Tungsten Bowtie Nano-antennas
Authors: Morshed Monir , Li Ziyuan , Olbricht Benjamin C. , Fu Lan , Haque Ahasanul , Li Li , Rifat Ahmmed A. , Rahmani Mohsen , Miroshnichenko Andrey E. , Hattori Haroldo T.
Published: September 2019

Nano-antennas are replicas of antennas that operate at radio-frequencies, but with considerably smaller dimensions when compared with their radio frequency counterparts. Noble metals based nano-antennas have the ability to enhance photoinduced phenomena such as localized electric fields, therefore-they have been used in various applications ranging from optical sensing and imaging to performance improvement of solar cells. However, such nano-structures can be damaged in high power applications such as heat resisted magnetic recording, solar thermo-photovoltaics and nano-scale heat transfer systems. Having a small footprint, nano-antennas cannot handle high fluences (energy density per unit area) and are subject to being damaged at adequately high power (some antennas can handle just a few milliwatts). In addition, given that nano-antennas are passive devices driven by external light sources, the potential damage of the antennas limits their use with high power lasers: this liability can be overcome by employing materials with high melting points such as chromium (Cr) and tungsten (W). In this article, we fabricate chromium and tungsten nano-antennas and demonstrate that they can handle 110 and 300 times higher fluence than that of gold (Au) counterpart, while the electric field enhancement is not significantly reduced.
Recent decline in vegetative regeneration of bamboo (Yushania alpina), a key food plant for primates in Volcanoes National Park, Rwanda
Authors: van der Hoek Yntze , Emmanuel Faida , Eckardt Winnie , Kwizera Innocent , Derhé Mia , Caillaud Damien , Stoinski Tara S. , Tuyisingize Deogratias
Published: September 2019

The African montane bamboo Yushania alpina provides both habitat and food for many species in the Albertine Rift region. In Volcanoes National Park (VNP), Rwanda, it is especially important as a key food resource for the Endangered mountain gorilla Gorilla beringei beringei and Endangered golden guenon Cercopithecus mitis kandti. We examined temporal and spatial variation in bamboo shoots regeneration and consumption by primates, monitored between 2013 and 2018 in 82 16-m2 plots located along transects in VNP. Our analyses revealed a decline in vegetative regeneration of bamboo in recent years, which is mirrored by a decline in bamboo shoot consumption by primates; but an increase in proportional intake. Local declines in regeneration are potentially due to high intensities of herbivory, decreased amounts of rainfall during growing seasons, and natural processes that form part of the life cycle of bamboo. Moreover, spatial variation in bamboo regeneration can be explained by elevation, as well as by stand-level variation in soil acidity, vegetation density, and the density of dead bamboo culms. We discuss the potential mechanisms underlying observed temporal and spatial variations and outline possible effects of a decline in bamboo regeneration for primates and other aspects of biodiversity in VNP.
Transcriptome profiles of hypothalamus and adrenal gland linked to haplotype related to coping behavior in pigs
Authors: Gley Kevin , Murani Eduard , Trakooljul Nares , Zebunke Manuela , Puppe Birger , Wimmers Klaus , Ponsuksili Siriluck
Published: September 2019

The hypothalamic-pituitary-adrenal (HPA) axis is an important component of neuroendocrine stress regulation and coping behavior. Transcriptome profiles of the hypothalamus and adrenal gland were assessed to identify molecular pathways and candidate genes for coping behavior in pigs. Ten each of high- (HR) and low- (LR) reactive pigs (n = 20) were selected for expression profiling based haplotype information of a prominent QTL-region on SSC12 discovered in our previous genome-wide association study (GWAS) on coping behavior. Comparing the HR and LR pigs showed 692 differentially expressed genes (DEGs) in the adrenal gland and 853 DEGs in the hypothalamus, respectively. Interestingly, 47% (17 out of 36) of DEGs found in both tissues were located in GWAS regions identified on SSC12, indicating that there are significant functional positional candidate genes for coping behaviour. Pathway analysis assigned DEGs to glucocorticoid receptor signaling in the adrenal gland. Furthermore, oxidative phosphorylation, mitochondrial dysfunction, and NGF signaling as well as cholecystokinin/Gastrin-mediated were identified in the hypothalamus. We narrowed the list of candidate genes in GWAS regions by analyzing their DEGs in the HPA axis. The top identified transcripts, including ATP1B2, AURKB, MPDU1 and NDEL1 provide evidence for molecular correlates of coping behavior in GWAS regions.
Root water uptake and its pathways across the root: quantification at the cellular scale
Authors: Zarebanadkouki Mohsen , Trtik Pavel , Hayat Faisal , Carminati Andrea , Kaestner Anders
Published: September 2019

The pathways of water across root tissues and their relative contribution to plant water uptake remain debated. This is mainly due to technical challenges in measuring water flux non-invasively at the cellular scale under realistic conditions. We developed a new method to quantify water fluxes inside roots growing in soils. The method combines spatiotemporal quantification of deuterated water distribution imaged by rapid neutron tomography with an inverse simulation of water transport across root tissues. Using this non-invasive technique, we estimated for the first time the in-situ radial water fluxes [m s−1] in apoplastic and cell-to-cell pathways. The water flux in the apoplast of twelve days-old lupins (Lupinus albus L. cv. Feodora) was seventeen times faster than in the cell-to-cell pathway. Hence, the overall contribution of the apoplast in water flow [m3 s−1] across the cortex is, despite its small volume of 5%, as large as 57 ± 8% (Mean ± SD for n = 3) of the total water flow. This method is suitable to non-invasively measure the response of cellular scale root hydraulics and water fluxes to varying soil and climate conditions.
Influence of temperature on the displacement threshold energy in graphene
Authors: Chirita Mihaila Alexandru Ionut , Susi Toma , Kotakoski Jani
Published: September 2019

The atomic structure of nanomaterials is often studied using transmission electron microscopy. In addition to image formation, the energetic electrons impinging on the sample may also cause damage. In a good conductor such as graphene, the damage is limited to the knock-on process caused by elastic electron-nucleus scattering. This process is determined by the kinetic energy an atom needs to be sputtered, i.e. its displacement threshold energy Ed. This is typically assumed to have a fixed value for all electron impacts on equivalent atoms within a crystal. Here we show using density functional tight-binding simulations that the displacement threshold energy is affected by thermal perturbations of atoms from their equilibrium positions. This effect can be accounted for in the estimation of the displacement cross section by replacing the constant threshold energy value with a distribution. Our refined model better describes previous precision measurements of graphene knock-on damage, and should be considered also for other low-dimensional materials.
Soil temperature and hydric potential influences the monthly variations of soil Tuber aestivum DNA in a highly productive orchard
Authors: Todesco Flora , Belmondo Simone , Guignet Yoann , Laurent Liam , Fizzala Sandrine , Le Tacon François , Murat Claude
Published: September 2019

Tuber aestivum, also known as the summer or Burgundy truffle, is an ectomycorrhizal Ascomycete associated with numerous trees and shrubs. Its life cycle occurs in the soil, and thus soil parameters such as temperature and water availability could influence it.T.aestivumcultivation has started in several countries, but ecological and agronomic requirements for the establishment and management of orchards are largely unknown. The aims of this work were: 1) to design a specific qPCR protocol using genomic data to trace and quantifyT.aestivumDNA in the soil; and 2) to assess the monthly soil DNA dynamic according to soil parameters (i.e. soil hydric potential and temperature) in this orchard. The study was conducted in a highly productiveT.aestivumorchard (hazels, oaks, pines, lime and hornbeam). The production started five years after the plantation and then increased exponentially to reach a maximum of 320 kg/ha in 2017. The soil hydric potential and temperature partially explained the monthlyT.aestivumsoil DNA variability. The data presented here offer new insights intoT.aestivumecology and cultivation.
Demonstration of polarization control GaN-based micro-cavity lasers using a rigid high-contrast grating reflector
Authors: Chang Tsu-Chi , Hong Kuo-Bin , Kuo Shuo-Yi , Lu Tien-Chang
Published: September 2019

We reported on GaN microcavity (MC) lasers combined with one rigid TiO2 high-contrast grating (HCG) structure as the output mirror. The HCG structure was directly fabricated on the GaN structure without an airgap. The entire MC structure comprised a bottom dielectric distributed Bragg reflector; a GaN cavity; and a top HCG reflector, which was designed to yield high reflectance for transverse magnetic (TM)- or transverse electric (TE)-polarized light. The MC device revealed an operation threshold of approximately 0.79 MW/cm2 when pulsed optical pumping was conducted using the HCG structure at room temperature. The laser emission was TM polarized with a degree of polarization of 99.2% and had a small divergence angle of 14° (full width at half maximum). This laser operation demonstration for the GaN-based MC structure employing an HCG exhibited the advantages of HCGs in semiconductor lasers at wavelengths from green to ultraviolet.
Down-regulation of cyclin-dependent kinase 5 attenuates p53-dependent apoptosis of hippocampal CA1 pyramidal neurons following transient cerebral ischemia
Authors: Shin Bich Na , Kim Dae Won , Kim In Hye , Park Joon Ha , Ahn Ji Hyeon , Kang Il Jun , Lee Yun Lyul , Lee Choong-Hyun , Hwang In Koo , Kim Young-Myeong , Ryoo Sungwoo , Lee Tae-Kyeong , Won Moo-Ho , Lee Jae-Chul
Published: September 2019

Abnormal activation of cyclin-dependent kinase 5 (Cdk5) is associated with pathophysiological conditions. Ischemic preconditioning (IPC) can provide neuroprotective effects against subsequent lethal ischemic insult. The objective of this study was to determine how Cdk5 and related molecules could affect neuroprotection in the hippocampus of gerbils after with IPC [a 2-min transient cerebral ischemia (TCI)] followed by 5-min subsequent TCI. Hippocampal CA1 pyramidal neurons were dead at 5 days post-TCI. However, treatment with roscovitine (a potent inhibitor of Cdk5) and IPC protected CA1 pyramidal neurons from TCI. Expression levels of Cdk5, p25, phospho (p)-Rb and p-p53 were increased in nuclei of CA1 pyramidal neurons at 1 and 2 days after TCI. However, these expressions were attenuated by roscovitine treatment and IPC. In particular, Cdk5, p-Rb and p-p53 immunoreactivities in their nuclei were decreased. Furthermore, TUNEL-positive CA1 pyramidal neurons were found at 5 days after TCI with increased expression levels of Bax, PUMA, and activated caspase-3. These TUNEL-positive cells and increased molecules were decreased by roscovitine treatment and IPC. Thus, roscovitine treatment and IPC could protect CA1 pyramidal neurons from TCI through down-regulating Cdk5, p25, and p-p53 in their nuclei. These findings indicate that down-regulating Cdk5 might be a key strategy to attenuate p53-dependent apoptosis of CA1 pyramidal neurons following TCI.
Annurca apple polyphenol extract selectively kills MDA-MB-231 cells through ROS generation, sustained JNK activation and cell growth and survival inhibition
Authors: Martino Elisa , Vuoso Daniela Cristina , D’Angelo Stefania , Mele Luigi , D’Onofrio Nunzia , Porcelli Marina , Cacciapuoti Giovanna
Published: September 2019

Polyphenols represent the most studied class of nutraceuticals that can be therapeutics for a large spectrum of diseases, including cancer. In this study, we investigated for the first time the antitumor activities of polyphenol extract from Annurca apple (APE) in MDA-MB-231 triple negative breast cancer cells, and we explored the underlying mechanisms. APE selectively inhibited MDA-MB-231 cell viability and caused G2/M phase arrest associated with p27 and phospho-cdc25C upregulation and with p21 downregulation. APE promoted reactive oxygen species (ROS) generation in MDA-MB-231 cells while it acted as antioxidant in non-tumorigenic MCF10A cells. We demonstrated that ROS generation represented the primary step of APE antitumor activity as pretreatment with antioxidant N-acetylcysteine (NAC) prevented APE-induced G2/M phase arrest, apoptosis, and autophagy. APE downregulated Dusp-1 and induced a significant increase in JNK/c-Jun phosphorylation that were both prevented by NAC. Moreover, downregulation of JNK by its specific inhibitor SP600125 significantly diminished the anticancer activity of APE indicating that ROS generation and sustained JNK activation represented the main underlying mechanism of APE-induced cell death. APE also inhibited AKT activation and downregulated several oncoproteins, such as NF-kB, c-myc, and β-catenin. In light of these results, APE may be an attractive candidate for drug development against triple negative breast cancer.
Preparation of a novel Fe3O4/HCO composite adsorbent and the mechanism for the removal of antimony (III) from aqueous solution
Authors: Zhang Jun , Deng Ren-jian , Ren Bo-zhi , Hou Baolin , Hursthouse Andrew
Published: September 2019

A novel adsorbent (Fe3O4/HCO) was prepared via co-precipitation from a mix of ferriferrous oxide and a Ce-rich waste industrial sludge recovered from an optical polishing activity. The effect of system parameters including reaction time, pH, dose, temperature as well as initial concentration on the adsorption of Sb(III) were investigated by sequential batch tests. The Sb(III)/Fe3O4/HCO system quickly reached adsorption equilibrium within 2 h, was effective over a wide pH (3–7) and demonstrated excellent removal at a 60 mg/L Sb(III) concentration. Three isothermal adsorption models were assessed to describe the equilibrium data for Sb(III) with Fe3O4/HCO. Compared to the Freundlich and dubinin-radushkevich, the Langmuir isotherm model showed the best fit, with a maximum adsorption capacity of 22.853 mg/g, which exceeds many comparable absorbents. Four kinetic models, Pseudo-first-order, Pseudo-second-order, Elovich and Intra-particle, were used to fit the adsorption process. The analysis showed that the mechanism was pseudo-second-order and chemical adsorption played a dominant role in the adsorption of Sb(III) by Fe3O4/HCO (correlation coefficient R2 = 0.993). Thermodynamic calculations suggest that adsorption of Sb(III) ions was endothermic, spontaneous and a thermodynamically feasible process. The mechanism of the adsorption of Sb(III) on Fe3O4/HCO could be described by the synergistic adsorption of Sb (III) on Fe3O4, FeCe2O4 and hydrous ceric oxide. The Fe3O4/HCO sorbent appears to be an efficient and environment-friendly material for the removal of Sb(III) from wastewater.
Impacts of atmospheric vertical structures on transboundary aerosol transport from China to South Korea
Authors: Lee Hyo-Jung , Jo Hyun-Young , Kim Sang-Woo , Park Moon-Soo , Kim Cheol-Hee
Published: September 2019

To forecast haze pollution episodes caused by high concentrations of long-range transported pollutants emitted in the areas upstream of South Korea, it is crucial to study and identify their behaviour. We analysed the three-dimensional air quality structure in Seoul using ground observation data and aerosol lidar measurements to identify vertical aerosol intrusion into the Korean Peninsula during the spring of 2016. The intrusions were particularly affected by the development of the atmospheric boundary layer (ABL) in the leeward regions. The nocturnal pollutant intrusion into the Korean peninsula via the Yellow Sea was examined using measured data. The pollutants first reached the area above the nocturnal boundary layer (548 ± 180 m) and approached ground level on the following day due to convective mixing depending on the convective ABL growth (1182 ± 540 m) in daytime. These intrusion mechanisms were mostly attributed to extremely high concentrations (i.e. >100 μg m−3) of fine particulate matter in the leeward regions, accounting for four of the total of six cases for which the warnings and alerts were issued in Seoul Metropolitan Area over a year-long period (2016). The horizontal and vertical pathways of the long-range transported pollutants and the atmospheric vertical structure were identified as key factors affecting the surface air quality concentration in the leeward regions.
Enabling Web-scale data integration in biomedicine through Linked Open Data
Authors: Kamdar Maulik R. , Fernández Javier D. , Polleres Axel , Tudorache Tania , Musen Mark A.
Published: September 2019

The biomedical data landscape is fragmented with several isolated, heterogeneous data and knowledge sources, which use varying formats, syntaxes, schemas, and entity notations, existing on the Web. Biomedical researchers face severe logistical and technical challenges to query, integrate, analyze, and visualize data from multiple diverse sources in the context of available biomedical knowledge. Semantic Web technologies and Linked Data principles may aid toward Web-scale semantic processing and data integration in biomedicine. The biomedical research community has been one of the earliest adopters of these technologies and principles to publish data and knowledge on the Web as linked graphs and ontologies, hence creating the Life Sciences Linked Open Data (LSLOD) cloud. In this paper, we provide our perspective on some opportunities proffered by the use of LSLOD to integrate biomedical data and knowledge in three domains: (1) pharmacology, (2) cancer research, and (3) infectious diseases. We will discuss some of the major challenges that hinder the wide-spread use and consumption of LSLOD by the biomedical research community. Finally, we provide a few technical solutions and insights that can address these challenges. Eventually, LSLOD can enable the development of scalable, intelligent infrastructures that support artificial intelligence methods for augmenting human intelligence to achieve better clinical outcomes for patients, to enhance the quality of biomedical research, and to improve our understanding of living systems.
Zwitterionic chitooligosaccharide-modified ink-blue titanium dioxide nanoparticles with inherent immune activation for enhanced photothermal therapy
Authors: Zhang Yahui , Sha Weizhou , Zhang Xiaolei , Cheng Mingbo , Wu Qiang , Wang Wei , Yuan Zhi
Published: September 2019

Zwitterionic chitooligosaccharide-modified BTC NPs can re-educate TAMs to a tumoricidal M1 subtype, thus improving the antitumor effect of PTT.
Biomagnification of perfluoroalkyl acids (PFAAs) in the food web of an urban river: assessment of the trophic transfer of targeted and unknown precursors and implications
Authors: Simonnet-Laprade Caroline , Budzinski Hélène , Maciejewski Kevin , Le Menach Karyn , Santos Raphaël , Alliot Fabrice , Goutte Aurélie , Labadie Pierre
Published: September 2019

In the Orge River, the contribution of PFAA precursors decreases between the base and the top of the trophic web.
Evidencing under-barrier phenomena in a Yb(iii) SMM: a joint luminescence/neutron diffraction/SQUID study
Authors: Guégan Frédéric , Jung Julie , Le Guennic Boris , Riobé François , Maury Olivier , Gillon Béatrice , Jacquot Jean-François , Guyot Yannick , Morell Christophe , Luneau Dominique
Published: September 2019

The synthesis, spectroscopic and magnetic characterisation and ab initio investigation of a new Yb based complex, [YbTp2NO3], are reported and exploited to rationalise its field-induced SMM behaviour.
Broadband photocatalysis using a Z-scheme heterojunction of Au/NaYF4:Yb,Er/WO3·0.33H2O-W18O49via a synergetic strategy of upconversion function and plasmonic effect
Authors: Li Xiaoxiao , Yang Kai , Yu Changlin , Zhang Kailian , Yang Shi , Zhu Lihua , Ji Hongbing , Dai Wenxin , Fan Qizhe , Huang Weiya
Published: September 2019

Employing upconversion hosts and plasmonic Au, this work deals with the synthesis of a novel heterojunction via a hydrothermal followed by a photo-reduction method.
A case of multifunctional intermetallic compounds: negative thermal expansion coupling with magnetocaloric effect in (Gd,Ho)(Co,Fe)2
Authors: Hu Jinyu , Lin Kun , Cao Yili , Huang Rongjin , Matsukawa Takeshi , Ishigaki Toru , Fischer Henry E. , Kato Kenichi , Honda Takashi , Ikeda Kazutaka , Otomo Toshiya , Ohoyama Kenji , Deng Jinxia , Chen Jun , Xing Xianran
Published: September 2019

The negative thermal expansion (NTE) and magnetocaloric effect (MCE) are highly correlated in (Gd,Ho)(Co,Fe)2, both of which are governed by the rare earth moment, whereas the MCE is further reinforced through an intermediate contribution from NTE.
Water-compatible fluorescent [2]rotaxanes for Au3+ detection and bioimaging
Authors: Chan Sing-Ming , Tang Fung-Kit , Kwan Chak-Shing , Lam Ching-Yau , Hau Sam C. K. , Leung Ken Cham-Fai
Published: September 2019

Rotaxanes were studied for their selective sensing to trivalent metal ions and Au3+ with turn-on fluorescence and for bioimaging.
Synthesis and immunological studies of group AStreptococcuscell-wall oligosaccharide–streptococcal C5a peptidase conjugates as bivalent vaccines
Authors: Zhao Yisheng , Wang Subo , Wang Guirong , Li Hui , Guo Zhongwu , Gu Guofeng
Published: September 2019

A convergent synthesis of GAS cell-wall oligosaccharides and their efficient conjugation with the ScpA193 carrier protein to generate glycoconjugates as potential bivalent vaccines were reported.
Synthesis of CeO2 assemblies through interaction with short-chain dicarboxylic acids under facile hydrothermal conditions
Authors: Huang Xinsong , Li Liping , Li Guangshe
Published: September 2019

CeO2 assemblies with various morphologies are hydrothermally synthesized using short-chain dicarboxylic acids as the only added agent.
Surface hardness and flammability of Na2SiO3and nano-TiO2reinforced wood composites
Authors: Garskaite Edita , Karlsson Olov , Stankeviciute Zivile , Kareiva Aivaras , Jones Dennis , Sandberg Dick
Published: September 2019

Scots pine sapwood reinforced with Na2SiO3and nano-TiO2shows a potential for the exploration of a broader range of wood hardness and flame-retardancy properties in a concept of sustainable material management.
The photooxidative sensitization of bis(p-substituted diphenyl)iodonium salts in the radical polymerization of acrylates
Authors: Balcerak Alicja , Kabatc Janina
Published: September 2019

The ability of two-component dyeing photoinitiating systems for the radical polymerization of 1,6-hexanediol diacrylate (HDDA) and 2-ethyl-2-(hydroxymethyl)-1,3-propanediol triacrylate (TMPTA) is presented.
In situ mass change and gas analysis of 3D manganese oxide/graphene aerogel for supercapacitors
Authors: Suktha Phansiri , Chiochan Poramane , Krittayavathananon Atiweena , Sarawutanukul Sangchai , Sethuraman Sathyamoorthi , Sawangphruk Montree
Published: September 2019

Manganese oxide nanoparticles decorated on 3D reduced graphene oxide aerogels (3D MnOx/rGOae) for neutral electrochemical capacitors were successfully produced by a rapid microwave reduction process within 20 s.
Microwave-assisted iodine-catalyzed oxidative coupling of dibenzyl(difurfuryl)disulfides with amines: a rapid and efficient protocol for thioamides
Authors: Chen Jinyang , Mei Lan , Liu Jialing , Zhong Chuntao , Yuan Binfang , Li Qiang
Published: September 2019

Rapid and efficient protocol for thioamides via microwave-assisted iodine-catalyzed oxidative coupling of dibenzyl(difurfuryl)disulfides with amines.
Grid-scale energy storage with net-zero emissions: comparing the options
Authors: Yao Joseph G. , Bui Mai , Dowell Niall Mac
Published: September 2019

Carbon-neutral energy storage will be an essential technology in delivering a decarbonised, resilient energy system.
Improving the electrocatalytic N2 reduction activity of Pd nanoparticles through surface modification
Authors: Deng Guorong , Wang Ting , Alshehri Abdulmohsen Ali , Alzahrani Khalid Ahmad , Wang Yan , Ye Hejiang , Luo Yonglan , Sun Xuping
Published: September 2019

Tannic acid (TA)-modified Pd nanoparticles (Pd-TA) are efficient for ambient electrocatalytic N2-to-NH3 fixation with an NH3 yield of 24.12 μg h−1 mgcat.−1 and a faradaic efficiency of 9.49%.
Covalent triazine frameworks for carbon dioxide capture
Authors: Wang Han , Jiang Danni , Huang Danlian , Zeng Guangming , Xu Piao , Lai Cui , Chen Ming , Cheng Min , Zhang Chen , Wang Ziwei
Published: September 2019

Covalent triazine frameworks, as a newly emerging class of porous materials, have great potential in the area of CO2 capture.
Photoluminescent metal–organic frameworks and their application for sensing biomolecules
Authors: Dong Jing , Zhao Dan , Lu Yi , Sun Wei-Yin
Published: September 2019

This review focuses on the recent development of luminescent MOFs with synthetic approaches and their application in sensing biomolecules.
The influence of gradient and statistical arrangements of guanidinium or primary amine groups in poly(methacrylate) copolymers on their DNA binding affinity
Authors: Tabujew Ilja , Cokca Ceren , Zartner Leon , Schubert Ulrich S. , Nischang Ivo , Fischer Dagmar , Peneva Kalina
Published: September 2019

Herein, we report the first gradient guanidinium containing cationic copolymers and investigate their binding ability to plasmid DNA (pDNA).
Optimizing domain size and phase purity in all-polymer solar cells by solution ordered aggregation and confinement effect of the acceptor
Authors: Zhang Qiang , Chen Zhenyu , Ma Wei , Xie Zhiyuan , Han Yanchun
Published: September 2019

We optimized the domain size and phase purity of J51:N2200 blends by changing solvent to promote solution ordered aggregation and the confinement of acceptor N2200 to J51 during phase separation.
Multi-colored hollow carbon-containing titania nanoshells for anti-counterfeiting applications
Authors: Yao Xiaxi , Bai Yaocai , Lee Yoon Jae , Qi Zhimin , Liu Xiaoheng , Yin Yadong
Published: September 2019

Hollow nanoshells composed of titania and carbon have been fabricated, displaying striking colors with considerably high contrast by Mie resonance. They respond rapidly and reversibly to the changes in the refractive index of the surrounding medium.