bluuebunny/crossref_metadata_2025 huggingface dataset:
mTORC1 and mTORC2 Differentially Regulate Cell Fate Programs to Coordinate Osteoblastic Differentiation in Mesenchymal Stromal Cells
Authors: Schaub Theres , Gürgen Dennis , Maus Deborah , Lange Claudia , Tarabykin Victor , Dragun Duska , Hegner Björn
Published: December 2019

Vascular regeneration depends on intact function of progenitors of vascular smooth muscle cells such as pericytes and their circulating counterparts, mesenchymal stromal cells (MSC). Deregulated MSC differentiation and maladaptive cell fate programs associated with age and metabolic diseases may exacerbate arteriosclerosis due to excessive transformation to osteoblast-like calcifying cells. Targeting mTOR, a central controller of differentiation and cell fates, could offer novel therapeutic perspectives. In a cell culture model for osteoblastic differentiation of pluripotent human MSC we found distinct roles for mTORC1 and mTORC2 in the regulation of differentiation towards calcifying osteoblasts via cell fate programs in a temporally-controlled sequence. Activation of mTORC1 with induction of cellular senescence and apoptosis were hallmarks of transition to a calcifying phenotype. Inhibition of mTORC1 with Rapamycin elicited reciprocal activation of mTORC2, enhanced autophagy and recruited anti-apoptotic signals, conferring protection from calcification. Pharmacologic and genetic negative interference with mTORC2 function or autophagy both abolished regenerative programs but induced cellular senescence, apoptosis, and calcification. Overexpression of the mTORC2 constituent rictor revealed that enhanced mTORC2 signaling without altered mTORC1 function was sufficient to inhibit calcification. Studies in mice reproduced the in vitro effects of mTOR modulation with Rapamycin on cell fates in vascular cells in vivo. Amplification of mTORC2 signaling promotes protective cell fates including autophagy to counteract osteoblast differentiation and calcification of MSC, representing a novel mTORC2 function. Regenerative approaches aimed at modulating mTOR network activation patterns hold promise for delaying age-related vascular diseases and treatment of accelerated arteriosclerosis in chronic metabolic conditions.
Spin polarization in the phase diagram of a Li–Fe–S system
Authors: Takami Tsuyoshi , Takeuchi Tomonari , Fukunaga Toshiharu
Published: December 2019

Divalent and trivalent states of Fe ions are known to be stable in inorganic compounds. We focus a novel LixFeS5 cathode, in which the Li content (x) changes from 2 to 10 by an electrochemical technique. As x increases from 2, a Pauli paramagnetic conductive Li2FeS5 phase changes into a superparamagnetic insulating Li10FeS5 phase. Density functional theory calculations suggest that Fe+ ions in a high-x phase are responsible for ferromagnetic spin polarization. Reaching the monovalent Fe ion is significant for understanding microscopic chemistry behind operation as Li-ion batteries and the original physical properties resulting from the unique local structure.
High resolution structural and functional analysis of a hemopexin motif protein from Dolichos
Authors: Sharma Sarita Chandan , Kumar Ashish , Vashisht Sharad , Salunke Dinakar M.
Published: December 2019

It is increasingly evident that seed proteins exhibit specific functions in plant physiology. However, many proteins remain yet to be functionally characterized. We have screened the seed proteome of Dolichos which lead to identification and purification of a protein, DC25. The protein was monomeric and highly thermostable in extreme conditions of pH and salt. It was crystallized and structure determined at 1.28 Å resolution using x-ray crystallography. The high-resolution structure of the protein revealed a four-bladed β-propeller hemopexin-type fold containing pseudo four-fold molecular symmetry at the central channel. While the structure exhibited homology with 2S albumins, variations in the loops connecting the outermost strands and the differences in surface-charge distribution may be relevant for distinct functions. Comparative study of the protein with other seed hemopexins revealed the presence of four conserved water molecules in between the blades which cross-link them and maintain the tertiary structure. The protein exhibited intrinsic peroxidase activity, which could be inhibited by binding of a heme analog. The identification of redox-sensitive cysteine and inhibition of peroxidase activity by iodoacetamide facilitated characterization of the possible active site. The determined peroxidase activity of DC25 may be responsible for rescuing germinating seeds from oxidative stress.
Lattice disorder effect on magnetic ordering of iron arsenides
Authors: Sefat Athena S. , Wang Xiaoping P. , Liu Yaohua , Zou Qiang , Fu Mimgming , Gai Zheng , Ganesan Kalaiselvan , Vohra Yogesh , Li Li , Parker David S.
Published: December 2019

This study investigates magnetic ordering temperature in nano- and mesoscale structural features in an iron arsenide. Although magnetic ground states in quantum materials can be theoretically predicted from known crystal structures and chemical compositions, the ordering temperature is harder to pinpoint due to potential local lattice variations that calculations may not account for. In this work we find surprisingly that a locally disordered material can exhibit a significantly larger Néel temperature (TN) than an ordered material of precisely the same chemical stoichiometry. Here, a EuFe2As2 crystal, which is a ‘122’ parent of iron arsenide superconductors, is found through synthesis to have ordering below TN = 195 K (for the locally disordered crystal) or TN = 175 K (for the ordered crystal). In the higher TN crystals, there are shorter planar Fe-Fe bonds [2.7692(2) Å vs. 2.7745(3) Å], a randomized in-plane defect structure, and diffuse scattering along the [00 L] crystallographic direction that manifests as a rather broad specific heat peak. For the lower TN crystals, the a-lattice parameter is larger and the in-plane microscopic structure shows defect ordering along the antiphase boundaries, giving a larger TN and a higher superconducting temperature (Tc) upon the application of pressure. First-principles calculations find a strong interaction between c-axis strain and interlayer magnetic coupling, but little impact of planar strain on the magnetic order. Neutron single-crystal diffraction shows that the low-temperature magnetic phase transition due to localized Eu moments is not lattice or disorder sensitive, unlike the higher-temperature Fe sublattice ordering. This study demonstrates a higher magnetic ordering point arising from local disorder in 122.
RETRACTED ARTICLE: High diversity of Morchella and a novel lineage of the Esculenta clade from the north Qinling Mountains revealed by GCPSR-based study
Authors: Phanpadith Phonepaserd , Yu Zhongdong , Li Tao
Published: December 2019

China is a mainland country rich in natural morel recourses, having records of half of the worldwide 61 morel phylospecies. In this study, 31 collections of ascocarps from the north Qinling Mountains, 4 collections of commercial cultivars from the south Qinling Mountains, and 3Morchellamycelium clones from commercial cultivars were investigated using the genealogical concordance phylogenetic species recognition (GCPSR) method. Maximum-likelihood was employed for the construction of phylogenetic trees. A total of five phylogenetic species were found among the 38 collections, namelyMorchellasp. Mes-8, Mes-9, Mes-13, and Mes-25, andMorchella chensiensis(IF556780), in addition to the false morel (Verpa bohemica). The identification of cultivatedMorchellasp. Mel-2, Mel-6, Mel-10, and Mel-12 coincided with that of the commercial farms. A total of 80% (4/5) of yellow morels were new records for the Qinling region, except Mes-19; moreover, a novel monophyletic lineage,Morchella chensiensis, was found to be distinct from the previously reported phylospecies by single gene and combined genes analysis, thus being herein proposed as a new phylospecies. All collections from this study showed continental endemism, and all Qinling Mountains collections were grouped together in rDNA phylogenetic trees. The study provided insights on biodiversities in this key region of China.
A simple analytic model for predicting the wicking velocity in micropillar arrays
Authors: Krishnan Siva Rama , Bal John , Putnam Shawn A.
Published: December 2019

Hemiwicking is the phenomena where a liquid wets a textured surface beyond its intrinsic wetting length due to capillary action and imbibition. In this work, we derive a simple analytical model for hemiwicking in micropillar arrays. The model is based on the combined effects of capillary action dictated by interfacial and intermolecular pressures gradients within the curved liquid meniscus and fluid drag from the pillars at ultra-low Reynolds numbers $${\boldsymbol{(}}{{\bf{10}}}^{{\boldsymbol{-}}{\bf{7}}}{\boldsymbol{\lesssim }}{\bf{Re}}{\boldsymbol{\lesssim }}{{\bf{10}}}^{{\boldsymbol{-}}{\bf{3}}}{\boldsymbol{)}}$$(10−7≲Re≲10−3). Fluid drag is conceptualized via a critical Reynolds number: $${\bf{Re}}{\boldsymbol{=}}\frac{{{\bf{v}}}_{{\bf{0}}}{{\bf{x}}}_{{\bf{0}}}}{{\boldsymbol{\nu }}}$$Re=v0x0ν, where v0 corresponds to the maximum wetting speed on a flat, dry surface and x0 is the extension length of the liquid meniscus that drives the bulk fluid toward the adsorbed thin-film region. The model is validated with wicking experiments on different hemiwicking surfaces in conjunction with v0 and x0 measurements using Water $${\boldsymbol{(}}{{\bf{v}}}_{{\bf{0}}}{\boldsymbol{\approx }}{\bf{2}}\,{\bf{m}}{\boldsymbol{/}}{\bf{s}}{\boldsymbol{,}}\,{\bf{25}}\,{\boldsymbol{\mu }}{\bf{m}}{\boldsymbol{\lesssim }}{{\bf{x}}}_{{\bf{0}}}{\boldsymbol{\lesssim }}{\bf{28}}\,{\boldsymbol{\mu }}{\bf{m}}{\boldsymbol{)}}$$(v0≈2m/s,25µm≲x0≲28µm), viscous FC-70 $${\boldsymbol{(}}{{\boldsymbol{v}}}_{{\bf{0}}}{\boldsymbol{\approx }}{\bf{0.3}}\,{\bf{m}}{\boldsymbol{/}}{\bf{s}}{\boldsymbol{,}}\,{\bf{18.6}}\,{\boldsymbol{\mu }}{\bf{m}}{\boldsymbol{\lesssim }}{{\boldsymbol{x}}}_{{\bf{0}}}{\boldsymbol{\lesssim }}{\bf{38.6}}\,{\boldsymbol{\mu }}{\bf{m}}{\boldsymbol{)}}$$(v0≈0.3m/s,18.6µm≲x0≲38.6µm) and lower viscosity Ethanol $${\boldsymbol{(}}{{\boldsymbol{v}}}_{{\bf{0}}}{\boldsymbol{\approx }}{\bf{1.2}}\,{\bf{m}}{\boldsymbol{/}}{\bf{s}}{\boldsymbol{,}}\,{\bf{11.8}}\,{\boldsymbol{\mu }}{\bf{m}}{\boldsymbol{\lesssim }}{{\bf{x}}}_{{\bf{0}}}{\boldsymbol{\lesssim }}{\bf{33.3}}\,{\boldsymbol{\mu }}{\bf{m}}{\boldsymbol{)}}$$(v0≈1.2m/s,11.8µm≲x0≲33.3µm).
Characterization of a five-microRNA signature as a prognostic biomarker for esophageal squamous cell carcinoma
Authors: Yu Jun , Zhu Ming , Lv Min , Wu Xiaoliu , Zhang Xiaomei , Zhang Yuanying , Li Jintian , Zhang Qin
Published: December 2019

This study aims to identify a miRNAs signature for predicting overall survival (OS) in esophageal squamous cell carcinoma (ESCC) patients. MiRNA expression profiles and corresponding clinical information of 119 ESCC patients were obtained from NCBI GEO and used as the training set. Differentially expressed miRNAs (DEmiRNAs) were screened between early-stage and late-stage samples. Cox regression analysis, recursive feature elimination (RFE)-support vector machine (SVM) algorithm, and LASSO Cox regression model were used to identify prognostic miRNAs and consequently build a prognostic scoring model. Moreover, promising target genes of these prognostic miRNAs were predicted followed by construction of miRNA-target gene networks. Functional relevance of predicted target genes of these prognostic miRNAs in ESCC was analyzed by performing function enrichment analyses. There were 46 DEmiRNAs between early-stage and late-stage samples in the training set. A risk score model based on five miRNAs was built. The five-miRNA risk score could classify the training set into a high-risk group and a low-risk group with significantly different OS time. Risk stratification ability of the five-miRNA risk score was successfully validated on an independent set from the Cancer Genome Atlas (TCGA). Various biological processes and pathways were identified to be related to these miRNAs, such as Wnt signaling pathway, inflammatory mediator regulation of TRP channels pathway, and estrogen signaling pathway. The present study suggests a pathological stage-related five-miRNA signature that may have clinical implications in predicting prognosis of ESCC patients.
Recurrent Mobility: Urban Conduits for Diffusion of Energy Efficiency
Authors: Mohammadi Neda , Taylor John E.
Published: December 2019

Recent advances in energy technologies, policies, and practices have accelerated the global rate of improvements in energy efficiency, bringing the energy targets identified in the 2030 United Nations (UN) Sustainable Development Agenda within reach. However, Target 7.3 requires this rate to double by 2030, demanding a more substantial response to energy interventions. At present, energy interventions are failing to reach optimal levels of adoption in buildings, which are the largest urban energy consumers. This is due to a combination of direct and indirect effects generally referred to as the energy efficiency gap. Here, we compare over 18.8 million positional records of individuals against Greater London’s buildings energy consumption records over the course of one year. We demonstrate that indirect (i.e., spillover) effects, arising fromrecurrent mobility, govern the diffusion of urban buildings’ energy efficiency, far outpacing direct effects. This has been understood as a consequence of underlying spatiotemporal dependencies at the intersection of energy use and social interactions. We add to this the critical role of recurrent mobility (i.e., the mobility of those urban populations who repeatedly visit certain locations, such as home and work) as a diffusion conduit. These findings suggest that in order to improve the current levels of adoption, interventions must target times and locations that function as dense hubs of energy consumption and social interactions. Recurrent mobility thus provides a viable complement to existing targeted intervention approaches aimed at improving energy efficiency, supporting efforts to meet the UN’s 2030 energy targets.
Association of imaging factors derived from convolutional neural network with visual outcomes in age-related macular degeneration and polypoidal choroidal vasculopathy
Authors: Lee Hyungwoo , Jang Minsu , Kim Hyung Chan , Chung Hyewon
Published: December 2019

We investigated the association of visual outcome in typical neovascular age-related macular degeneration (nAMD) and polypoidal choroidal vasculopathy (PCV) with or without pachychoroid with lesion areas on optical coherence tomography (OCT) quantified by convolutional neural network (CNN) analysis. Treatment-naïve 132 nAMD and 45 PCV eyes treated with ranibizumab or aflibercept for at least 12 months were retrospectively reviewed. Significant factors, including intraretinal fluid (IRF), subretinal fluid (SRF), pigment epithelial detachment (PED) and subretinal hyperreflective material (SHRM) area quantified by CNN at baseline and 12 months, were analyzed by logistic regression analyses for 3-line visual gain or maintenance of 20/30 Snellen vision. Visual gain at the final visit in nAMD was associated with a smaller SHRM at baseline (OR 0.167, P = 0.03), greater decrease in SRF and SHRM from baseline to month 12 (OR 1.564, P = 0.02; OR 12.877, P = 0.01, respectively). Visual gain in nAMD without pachychoroid was associated with a greater decrease in SRF and SHRM (OR 1.574, P = 0.03, OR 1.775, P = 0.04). No association was found in nAMD with pachychoroid and any type of PCV. Greater decrease in SRF and SHRM from baseline to month 12 was associated with favorable visual outcomes in nAMD without pachychoroid but not in nAMD with pachychoroid and PCV.
Simulation studies for characterizing ultrashort bunches using novel polarizable X-band transverse deflection structures
Authors: Marx Daniel , Assmann Ralph W. , Craievich Paolo , Floettmann Klaus , Grudiev Alexej , Marchetti Barbara
Published: December 2019

Transverse deflection structures are useful devices for characterizing the longitudinal properties of bunches in electron accelerators. With efforts to produce ever-shorter bunches for applications such as external injection into novel accelerator structures, e.g. plasma cells or dielectric structures, the applicability of deflection structures to measuring ultrashort bunches has been considered. In this paper, charge-density and bunch-length measurements of femtosecond and subfemtosecond bunches at the ARES linac at the SINBAD facility at DESY are studied with simulations and the limitations discussed in detail. The novel polarizable X-band transverse deflection structure (PolariX-TDS) will allow the streaking of bunches at all transverse angles, making a 3D charge-density reconstruction of bunches possible, in addition to the standard 1D charge-density reconstruction and bunch-length measurements. These various measurements of the charge-density distributions of bunches have been simulated, and it is shown that useful information about ultrashort bunches down to subfemtosecond lengths may be obtained using the setup planned for the ARES linac.
Blockade of ROCK inhibits migration of human primary keratinocytes and malignant epithelial skin cells by regulating actomyosin contractility
Authors: Srinivasan Srisathya , Das Sreya , Surve Vishakha , Srivastava Ankita , Kumar Sushant , Jain Nikita , Sawant Abhijeet , Nayak Chitra , Purwar Rahul
Published: December 2019

Actomyosin contractility, crucial for several physiological processes including migration, is controlled by the phosphorylation of myosin light chain (MLC). Rho-associated protein kinase (ROCK) and Myosin light chain kinase (MLCK) are predominant kinases that phosphorylate MLC. However, the distinct roles of these kinases in regulating actomyosin contractility and their subsequent impact on the migration of healthy and malignant skin cells is poorly understood. We observed that blockade of ROCK in healthy primary keratinocytes (HPKs) and epidermal carcinoma cell line (A-431 cells) resulted in loss of migration, contractility, focal adhesions, stress fibres, and changes in morphology due to reduction in phosphorylated MLC levels. In contrast, blockade of MLCK reduced migration, contractile dynamics, focal adhesions and phosphorylated MLC levels of HPKs alone and had no effect on A-431 cells due to the negligible MLCK expression. Using genetically modified A-431 cells expressing phosphomimetic mutant of p-MLC, we show that ROCK dependent phosphorylated MLC controls the migration, focal adhesion, stress fibre organization and the morphology of the cells. In conclusion, our data indicate that ROCK is the major kinase of MLC phosphorylation in both HPKs and A-431 cells, and regulates the contractility and migration of healthy as well as malignant skin epithelial cells.
Hto, Tritiated Amino Acid Exposure and External Exposure Induce Differential Effects on Hematopoiesis and Iron Metabolism
Authors: Bertho Jean-Marc , Kereselidze Dimitri , Manens Line , Culeux Cécile , Magneron Victor , Surette Joel , Blimkie Melinda , Bertrand Linsdey , Wyatt Heather , Souidi Maâmar , Dublineau Isabelle , Priest Nicholas , Jourdain Jean-René
Published: December 2019

The increased potential for tritium releases from either nuclear reactors or from new facilities raises questions about the appropriateness of the current ICRP and WHO recommendations for tritium exposures to human populations. To study the potential toxicity of tritium as a function of dose, including at a regulatory level, mice were chronically exposed to tritium in drinking water at one of three concentrations, 10 kBq.l−1, 1 MBq.l−1 or 20 MBq.l−1. Tritium was administered as either HTO or as tritiated non-essential amino acids (TAA). After one month’s exposure, a dose-dependent decrease in red blood cells (RBC) and iron deprivation was seen in all TAA exposed groups, but not in the HTO exposed groups. After eight months of exposure this RBC decrease was compensated by an increase in mean globular volume - suggesting the occurrence of an iron deficit-associated anemia. The analysis of hematopoiesis, of red blood cell retention in the spleen and of iron metabolism in the liver, the kidneys and the intestine suggested that the iron deficit was due to a decrease in iron absorption from the intestine. In contrast, mice exposed to external gamma irradiation at equivalent dose rates did not show any change in red blood cell numbers, white blood cell numbers or in the plasma iron concentration. These results showed that health effects only appeared following chronic exposure to concentrations of tritium above regulatory levels and the effects seen were dependent upon the speciation of tritium.
Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers
Authors: Schneider Tobias , Berg Andrej , Ulusoy Zeynel , Gamerdinger Martin , Peter Christine , Kovermann Michael
Published: December 2019

Ubiquitylation is an eminent posttranslational modification referring to the covalent attachment of single ubiquitin molecules or polyubiquitin chains to a target protein dictating the fate of such labeled polypeptide chains. Here, we have biochemically produced artificially Lys11-, and Lys27-, and Lys63-linked ubiquitin dimers based on click-chemistry generating milligram quantities in high purity. We show that the artificial linkage used for the conjugation of two ubiquitin moieties represents a fully reliable surrogate of the natural isopeptide bond by acquiring highly resolved nuclear magnetic resonance (NMR) spectroscopic data including ligand binding studies. Extensive coarse grained and atomistic molecular dynamics (MD) simulations allow to extract structures representing the ensemble of domain-domain conformations used to verify the experimental data. Advantageously, this methodology does not require individual isotopic labeling of both ubiquitin moieties as NMR data have been acquired on the isotopically labeled proximal moiety and complementary MD simulations have been used to fully interpret the experimental data in terms of domain-domain conformation. This combined approach intertwining NMR spectroscopy with MD simulations makes it possible to describe the conformational space non-canonically Lys11-, and Lys27-linked ubiquitin dimers occupy in a solution averaged ensemble by taking atomically resolved information representing all residues in ubiquitin dimers into account.
9-ING-41, a small molecule inhibitor of GSK-3beta, potentiates the effects of anticancer therapeutics in bladder cancer
Authors: Kuroki Hiroo , Anraku Tsutomu , Kazama Akira , Bilim Vladimir , Tasaki Masayuki , Schmitt Daniel , Mazar Andrew P. , Giles Francis J , Ugolkov Andrey , Tomita Yoshihiko
Published: December 2019

Glycogen synthase kinase-3 beta (GSK-3β), a serine/threonine kinase, has been identified as a potential therapeutic target in human bladder cancer. In the present study, we investigated the antitumor effect of a small molecule GSK-3β inhibitor, 9-ING-41, currently in clinical studies in patients with advanced cancer, in bladder cancer cell lines. We found that treatment with 9-ING-41 leads to cell cycle arrest, autophagy and apoptosis in bladder cancer cells. The autophagy inhibitor chloroquine potentiated the antitumor effects of 9-ING-41 when tested in combination studies. Our findings also demonstrate that 9-ING-41 enhanced the growth inhibitory effects of gemcitabine or cisplatin when used in combination in bladder cancer cells. Finally, we found that 9-ING-41 sensitized bladder cancer cells to the cytotoxic effects of human immune effector cells. Our results provide a rationale for the inclusion of patients with advanced bladder cancer in clinical studies of 9-ING-41.
Computational assessment of the retinal vascular tortuosity integrating domain-related information
Authors: Ramos L. , Novo J. , Rouco J. , Romeo S. , Álvarez M. D. , Ortega M.
Published: December 2019

The retinal vascular tortuosity presents a valuable potential as a clinical biomarker of many relevant vascular and systemic diseases. Commonly, the existent approaches face the tortuosity quantification by means of fully mathematical representations of the vessel segments. However, the specialists, based on their diagnostic experience, commonly analyze additional domain-related information that is not represented in these mathematical metrics of reference. In this work, we propose a novel computational tortuosity metric that outperforms the mathematical metrics of reference also incorporating anatomical properties of the fundus image such as the distinction between arteries and veins, the distance to the optic disc, the distance to the fovea, and the vessel caliber. The evaluation of its prognostic performance shows that the integration of the anatomical factors provides an accurate tortuosity assessment that is more adjusted to the specialists’ perception.
Lyse-Reseal Erythrocytes for Transfection of Plasmodium falciparum
Authors: Govindarajalu Gokulapriya , Rizvi Zeba , Kumar Deepak , Sijwali Puran Singh
Published: December 2019

Simple and efficient transfection methods for genetic manipulation of Plasmodium falciparum are desirable to identify, characterize and validate the genes with therapeutic potential and better understand parasite biology. Among the available transfection techniques for P. falciparum, electroporation-based methods, particularly electroporation of ring-infected RBCs is routinely used. Nonetheless, transfection of P. falciparum remains a resource-intensive procedure. Here, we report a simple and economic transfection method for P. falciparum, which is termed as the lyse-reseal erythrocytes for transfection (LyRET). It involved lysis of erythrocytes with a hypotonic RBC lysis buffer containing the desired plasmid DNA, followed by resealing by adding a high salt buffer. These DNA-encapsulated lyse-reseal erythrocytes were mixed with P. falciparum trophozoite/schizont stages and subjected to selection for the plasmid-encoded drug resistance. In parallel, transfections were also done by the methods utilizing electroporation of DNA into uninfected RBCs and parasite-infected RBCs. The LyRET method successfully transfected 3D7 and D10 strains with different plasmids in 63 of the 65 attempts, with success rate similar to transfection by electroporation of DNA into infected RBCs. The cost effectiveness and comparable efficiency of LyRET method makes it an alternative to the existing transfection methods for P. falciparum, particularly in resource-limited settings.
De novo Comparative Transcriptome Analysis of Genes Differentially Expressed in the Scion of Homografted and Heterografted Tomato Seedlings
Authors: Wang Hui , Zhou Peng , Zhu Wenying , Wang Fu
Published: December 2019

Tomato is an important vegetable crop grown worldwide. Grafting is an agricultural technique that is used to improve growth, yield, and resistance to diverse stresses in tomato production. Here, we examined the differences between the scion of heterografted (‘Provence’/‘Haomei’) and homografted (‘Provence’/‘Provence’) tomato seedlings. We observed anatomical changes during the graft-union healing process in heterografted and homografted tomato seedlings and conducted transcriptome analyses of the ‘Provence’ scion from both graft combinations. With the development of calli from both graft partners, the isolation layer became thinner at 16 d after grafting (DAG). Compared with that of homografts, the healing in heterografts was slightly delayed, but the graft union had completely healed at 21 DAG. In total, 858 significantly differentially expressed genes were detected between the transcriptomes of heterografts and homografts at 16 DAG. Functional pathways identified by GO and KEGG enrichment analyses were associated with primary and secondary metabolism, hormone signalling, transcription factor regulation, transport, and responses to stimuli. Many differentially expressed genes were involved in pathways associated with mitogen-activated protein kinase signalling, plant hormone signalling, and oxidative stress. A number of transcription factors were up-regulated in the scion of heterografted seedlings. The results provide a valuable resource for the elucidation of the molecular mechanisms, and candidate genes for functional analyses, of heterograft and homograft systems.
Probing Charge Transport Difference in Parallel and Vertical Layered Electronics with Thin Graphite Source/Drain Contacts
Authors: Li Jiayi , Lee Ko-Chun , Hsieh Meng-Hsun , Yang Shih-Hsien , Chang Yuan-Ming , Chang Jen-Kuei , Lin Che-Yi , Lin Yen-Fu
Published: December 2019

In the present study, we aim to help improve the design of van der Waals stacking, i.e., vertical 2D electronics, by probing charge transport differences in both parallel and vertical conducting channels of layered molybdenum disulfide (MoS2), with thin graphite acting as source and drain electrodes. To avoid systematic errors and variable contact contributions to the MoS2 channel, parallel and vertical electronics are all fabricated and measured on the same conducting material. Large differences in the on/off current ratio, mobility, and charge fluctuations, between parallel and vertical electronics are evident in electrical performance as well as in charge transport mechanisms. Further insights are drawn from a well-constrained analysis of both temperature-dependent current-voltage characteristics and low-frequency (LF) current fluctuations. This work offers significant insight into the fundamental understanding of charge transport and the development of future layered-materials-based integration technology.
Analogue Orientation Control of a Carbon Fibre in a Nematic Liquid Crystal
Authors: Lee Jun-Yong , Lev Bohdan , Kim Jong-Hyun
Published: December 2019

A carbon fibre is a rod-like microstructure, the longitudinal axis of which is aligned with the orientation of the director in a nematic liquid crystal. A nematic liquid crystal with negative dielectric anisotropy is mixed with carbon fibres. By applying an electric field perpendicular to the director, the carbon fibres tend to rotate in response to the electric field, and the directors around the carbon fibres tends to suppress the rotation. We control individual carbon fibres to obtain an expected orientation by handling the competition of two actions. The carbon fibre barely reacts in a small electric field. Meanwhile, when the threshold electric field is exceeded, the carbon fibre rotates with a steep gradient in the direction of the electric field. The change in the rotation shows little hysteresis. As the length of the carbon fibre is increased, the threshold electric field decreases. We analysed the above process with a theoretical model considering the response of the carbon fibre and liquid crystal. This study shows the possibility of accurate analogue orientation control of individual rod-like microstructures.
Citrulline prevents age-related LTP decline in old rats
Authors: Ginguay Antonin , Regazzetti Anne , Laprevote Olivier , Moinard Christophe , De Bandt Jean-Pascal , Cynober Luc , Billard Jean-Marie , Allinquant Bernadette , Dutar Patrick
Published: December 2019

The prevalence of cognitive decline is increasing as the ageing population is considerably growing. Restricting this age-associated process has become a challenging public health issue. The age-related increase in oxidative stress plays a major role in cognitive decline, because of its harmful effect on functional plasticity of the brain, such as long-term potentiation (LTP). Here, we show that citrulline (Cit) has powerful antioxidant properties that can limit ex vivo oxidative stress-induced LTP impairment in the hippocampus. We also illustrate that a three-month Cit supplementation has a protective effect on LTP in aged rats in vivo. The identification of a Cit oxidation byproduct in vitro suggests that the antioxidant properties of Cit could result from its own oxidation. Cit supplementation may be a promising preventive nutritional approach to limit age-related cognitive decline.
Association between Upper-airway Surgery and Ameliorative Risk Markers of Endothelial Function in Obstructive Sleep Apnea
Authors: Wang Fan , Liu Yuenan , Xu Huajun , Qian Yingjun , Zou Jianyin , Yi Hongliang , Guan Jian , Yin Shankai
Published: December 2019

The objective of our study was to evaluate the effects of upper-airway surgery on improvement of endothelial function-related markers in patients with obstructive sleep apnea (OSA). Subjects with moderate to severe OSA who underwent upper-airway surgery, with a follow-up duration of at least 6 months, were included. Pre- and postoperative polysomnographic variables and endothelial function-related markers were compared. Subgroup and correlation analyses were conducted to find possible indicators for better endothelial function-related markers after upper-airway surgery. In total, 44 patients with OSA were included. The mean follow-up duration was 1.72 ± 0.92 years. Serum VEGFA [−20.29 (CI: −35.27, −5.31), p < 0.05], Ang2 [−0.06 (CI: −0.16, 0.03), p < 0.05], E-selectin [−7.21 (CI: −11.01, −3.41), p < 0.001], VWF [−58.83 (CI: −103.93, −13.73), p < 0.05], VWFCP [−33.52 (CI: −66.34, −0.70), p < 0.05], and TM [−0.06 (CI: −0.09, −0.03), p < 0.05] were significantly lower after upper-airway surgery. However, other risk markers of endothelial function, such as Ang1, ICAM1, VEGFR1, and VCAM, did not change significantly. Correlations between improved endothelial function-related markers and ameliorated oxyhemoglobin saturation and glucolipid metabolism were established. Upper-airway surgery might be associated with an improvement in endothelial function in patients with OSA. These changes may be associated with improved oxygen saturation after upper-airway surgery.
Efficient production and transmission of CRISPR/Cas9-mediated mutant alleles at the IG-DMR via generation of mosaic mice using a modified 2CC method
Authors: Hara Satoshi , Terao Miho , Muramatsu Akari , Takada Shuji
Published: December 2019

Generation of mutant imprinting control region (ICR) mice using genome editing is an important approach for elucidating ICR functions. IG-DMR is an ICR in the Dlk1-Dio3 imprinted domain that contains functional regions—in both parental alleles—that are essential for embryonic development. One drawback of this approach is that embryonic lethality can occur from aberrant expression of the imprinted genes if IG-DMR gets mutated in either the paternal or maternal allele. To overcome this problem, we generated mosaic mice that contained cells with modified IG-DMR alleles and wild-type cells using the 2CC method that allowed for microinjection of the CRISPR/Cas9 constructs into a blastomere of 2-cell embryos. This method improved the birth rate of the founder pups relative to that obtained using the standard protocol. We also successfully produced mosaic mice in which the tandem repeat array sequence in the IG-DMR had been replaced by homology directed repair. Additionally, paternal transmission of the replaced allele caused aberrant expression of the imprinted genes due to hypomethylation of the IG-DMR, indicating that the replaced allele recapitulated our deletion model. Our results indicate that this method is useful for the generation of mutant mice in which a genomic locus essential for normal development has been genetically edited.
A New Artificial Urine Protocol to Better Imitate Human Urine
Authors: Sarigul Neslihan , Korkmaz Filiz , Kurultak İlhan
Published: December 2019

Artificial urine has many advantages over human urine for research and educational purposes. By closely mimicking healthy individuals’ urine, it may also be important in discovering novel biomarkers. However, up until now, there has not been any specific protocol to prove the similarity in terms of the chemical composition at the molecular level. In this study, a new artificial urine protocol is established to mimics the urine of healthy individuals. The multi-purpose artificial urine (MP-AU) presented here is compared with two other protocols most cited in literature. Furthermore, these three protocols are also compared with samples from 28 healthy young individuals. To do so, attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) is used, according to which MP-AU shows a significantly close similarity with human urine. In formulating MP-AU, the infrared spectra of nine compounds is provided, making possible the band assignment of some absorption bands to certain compounds. Given its properties, the MP-AU protocol introduced here is both economical and practical, making it useful when designing comparative-controlled experiments.
Management of soil pH promotes nitrous oxide reduction and thus mitigates soil emissions of this greenhouse gas
Authors: Hénault Catherine , Bourennane Hocine , Ayzac Adeline , Ratié Céline , Saby Nicolas P. A. , Cohan Jean-Pierre , Eglin Thomas , Gall Cécile Le
Published: December 2019

While concerns about human-induced effects on the Earth’s climate have mainly concentrated on carbon dioxide (CO2) and methane (CH4), reducing anthropogenic nitrous oxide (N2O) flux, mainly of agricultural origin, also represents an opportunity for substantial mitigation. To develop a solution that induces neither the transfer of nitrogen pollution nor decreases agricultural production, we specifically investigated the last step of the denitrification pathway, the N2O reduction path, in soils. We first observed that this path is mainly driven by soil pH and is progressively inhibited when pH is lower than 6.8. During field experiments, we observed that liming acidic soils to neutrality made N2O reduction more efficient and decreased soil N2O emissions. As we estimated acidic fertilized soils to represent 37% [27–50%] of French soils, we calculated that liming could potentially decrease France’s total N2O emissions by 15.7% [8.3–21.2%]. Nevertheless, due to the different possible other impacts of liming, we currently recommend that the deployment of this solution to mitigate N2O emission should be based on local studies that take into account agronomic, environmental and economic aspects.
Hydrodynamic stress stimulates growth of cell clusters via the ANXA1/PI3K/AKT axis in colorectal cancer
Authors: Hagihara Takeshi , Kondo Jumpei , Endo Hiroko , Ohue Masayuki , Sakai Yoshiharu , Inoue Masahiro
Published: December 2019

Cancer cells are exposed to various stresses in vivo, including hydrodynamic stress (HDS). HDS on cancer cells in the blood stream can influence the metastatic potential. Recent studies revealed that circulating tumor cell clusters are more responsible for metastasis than circulating single cells. Nevertheless, most studies on HDS are based on single cells prepared from established cancer cell lines. Here, we used cancer tissue-originated spheroids (CTOS) as a patient-derived, 3D organoid model to investigate the effect of HDS on cancer cell clusters. We found that HDS induced the growth of cancer cell clusters in a population of colorectal CTOSs. Microarray analyses revealed that the multifunctional protein, Annexin 1 (ANXA1), was upregulated upon HDS exposure. Chemically-induced membrane damage also triggered the expression of ANXA1. A knockdown of ANXA1 revealed that ANXA1 regulated HDS-stimulated growth in colorectal CTOSs. Mechanistically, activating the PI3K/AKT pathway downstream of ANXA1 contributed to the phenotype. These findings demonstrate that HDS induces the growth of cancer cell clusters via ANXA1/PI3K/AKT axis, which helps to elucidate the pro-metastatic feature of circulating cancer cell clusters.
Enriched Pyridinic Nitrogen Atoms at Nanoholes of Carbon Nanohorns for Efficient Oxygen Reduction
Authors: Wee Jae-Hyung , Kim Chang Hyo , Lee Hun-Su , Choi Go Bong , Kim Doo-Won , Yang Cheol-Min , Kim Yoong Ahm
Published: December 2019

Nitrogen (N)-doped nanostructured carbons have been actively examined as promising alternatives for precious-metal catalysts in various electrochemical energy generation systems. Herein, an effective approach for synthesizing N-doped single-walled carbon nanohorns (SWNHs) with highly electrocatalytic active sites via controlled oxidation followed by N2 plasma is presented. Nanosized holes were created on the conical tips and sidewalls of SWNHs under mild oxidation, and subsequently, the edges of the holes were easily decorated with N atoms. The N atoms were present preferentially in a pyridinic configuration along the edges of the nanosized holes without significant structural change of the SWNHs. The enriched edges decorated with the pyridinic-N atoms at the atomic scale increased the number of active sites for the oxygen reduction reaction, and the inherent spherical three-dimensional feature of the SWNHs provided good electrical conductivity and excellent mass transport. We demonstrated an effective method for promoting the electrocatalytic active sites within N-doped SWNHs by combining defect engineering with the preferential formation of N atoms having a specific configuration.
Utility of Centrifugation-Controlled Convective (C3) Flow for Rapid On-chip ELISA
Authors: Espulgar Wilfred , Tadokoro Tatsuro , Tamiya Eiichi , Saito Masato
Published: December 2019

Miniaturizing the enzyme-linked immunosorbent assay (ELISA) protocols in microfluidics is sought after by researchers for a rapid, high throughput screening, on-site diagnosis, and ease in operation for detection and quantification of biomarkers. Herein, we report the use of the centrifugation-controlled convective (C3) flow as an alternative method in fluid flow control in a ring-structured channel for enhanced on-chip ELISA. A system that consists of a rotating heater stage and a microfluidic disk chip has been developed and demonstrated to detect IgA. The ring-structured channel was partially filled with microbeads (250 µm in diameter) carrying the capture antibodies and the analyte solution was driven by thermal convection flow (50 µL/min) to promote the reaction. The remaining part of the circular channel without microbeads served as the observation area to measure the absorbance value of the labeled protein. Currently, the system is capable of conducting four reactions in parallel and can be performed within 30 min at 300 G. A detection limit of 6.16 ng/mL using 24 µL of target sample (IgA) was observed. By simply changing the capture antibodies, the system is expected to be versatile for other immunoassays.
A rapid dual-channel readout approach for sensing carbendazim with 4-aminobenzenethiol-functionalized core–shell Au@Ag nanoparticles
Authors: Wang Kaiqiang , Sun Da-Wen , Pu Hongbin , Wei Qingyi
Published: December 2019

In this study, a 4-aminobenzenethiol-functionalized silver-coated gold nanoparticle (Au@Ag-4ABT NP) system was designed for the rapid sensing of carbendazim (CBZ) using a combination of naked-eye colorimetry and SERS dual-channel approach.
Hydrothermally self-templated synthesis of rectangular polyimide submicrotubes and promising potentials in electrochemical energy storage
Authors: Lei Sheng , Cui Xun , Liu Xufei , Zhang Xiaofang , Han Xiaoyan , Yang Yingkui
Published: December 2019

An unconventional hydrothermally self-templated polycondensation of monomer salt crystals to produce rectangular polyimide submicrotubes for promising electrochemical energy storage materials.
Magnetic and electrical properties of LuFe2O4 epitaxial thin films with a self-assembled interface structure
Authors: Kim You Jin , Konishi Shinya , Hayasaka Yuichiro , Kakeya Itsuhiro , Tanaka Katsuhisa
Published: December 2019

Thin film of LuFe2O4, one of multiferroics, deposited on an yttria-stabilized zirconia substrate shows a unique interface structure, leading to an exchange bias effect. The thin film itself undergoes spin glass or cluster glass transition.
Thermal deformation of gold nanostructures and its influence on surface plasmon resonance sensing
Authors: Kim Hyun-Tae , Pathak Mayank , Rajasekaran Keshav , Gupta Ashwani K. , Yu Miao
Published: December 2019

The deformation of lithographic planar gold nanostructures under cyclic thermal loading and its influence on surface plasmon resonance sensing are investigated.
A tri-responsive and fast self-healing organogel with stretchability based on multiple dynamic covalent bonds
Authors: Ren Shujing , Liang Huiqin , Sun Panpan , Gao Yanan , Zheng Liqiang
Published: December 2019

An organogel based on multiple dynamic covalent chemistry can respond to pH, redox and glucose, as well as self-heal quickly.
Study on the internal electric field in the Cu2O/g-C3N4p–n heterojunction structure for enhancing visible light photocatalytic activity
Authors: Liu Hao , Zhu Xiaodong , Han Rui , Dai Yuxue , Sun Yuanling , Lin Yanna , Gao Dandan , Wang Xueying , Luo Chuannan
Published: December 2019

A Cu2O/g-C3N4p–n heterojunction efficiently removes tetracycline in the presence of a built-in electric field.
Sustainable nitrogen-doped carbon electrodes for use in high-performance supercapacitors and Li-ion capacitors
Authors: Zheng Yulong , Wang Huanlei , Sun Shijiao , Lu Gaofei , Liu Haolin , Huang Minghua , Shi Jing , Liu Wei , Li Haiyan
Published: December 2019

Supercapacitor and Li-ion capacitor assembled by well-matched carbon anode and cathode obtained from ginger straw, both exhibiting remarkable energy and power combinations.
The multi-thermal chromosphere
Authors: da Silva Santos J. M. , de la Cruz Rodríguez J. , Leenaarts J. , Chintzoglou G. , De Pontieu B. , Wedemeyer S. , Szydlarski M.
Published: December 2019

Context. Numerical simulations of the solar chromosphere predict a diverse thermal structure with both hot and cool regions. Observations of plage regions in particular typically feature broader and brighter chromospheric lines, which suggests that they are formed in hotter and denser conditions than in the quiet Sun, but also implies a nonthermal component whose source is unclear.

Aims. We revisit the problem of the stratification of temperature and microturbulence in plage and the quiet Sun, now adding millimeter (mm) continuum observations provided by the Atacama Large Millimiter Array (ALMA) to inversions of near-ultraviolet Interface Region Imaging Spectrograph (IRIS) spectra as a powerful new diagnostic to disentangle the two parameters. We fit cool chromospheric holes and track the fast evolution of compact mm brightenings in the plage region.

Methods. We use the STiC nonlocal thermodynamic equilibrium (NLTE) inversion code to simultaneously fit real ultraviolet and mm spectra in order to infer the thermodynamic parameters of the plasma.

Results. We confirm the anticipated constraining potential of ALMA in NLTE inversions of the solar chromosphere. We find significant differences between the inversion results of IRIS data alone compared to the results of a combination with the mm data: the IRIS+ALMA inversions have increased contrast and temperature range, and tend to favor lower values of microturbulence (∼3−6 km s−1 in plage compared to ∼4−7 km s−1 from IRIS alone) in the chromosphere. The average brightness temperature of the plage region at 1.25 mm is 8500 K, but the ALMA maps also show much cooler (∼3000 K) and hotter (∼11 000 K) evolving features partially seen in other diagnostics. To explain the former, the inversions require the existence of localized low-temperature regions in the chromosphere where molecules such as CO could form. The hot features could sustain such high temperatures due to non-equilibrium hydrogen ionization effects in a shocked chromosphere – a scenario that is supported by low-frequency shock wave patterns found in the Mg II lines probed by IRIS.