bluuebunny/crossref_metadata_2025 huggingface dataset:
Sex specific function of epithelial STAT3 signaling in pathogenesis of K-ras mutant lung cancer
Authors: Caetano Mauricio S. , Hassane Maya , Van Hieu T. , Bugarin Emmanuel , Cumpian Amber M. , McDowell Christina L. , Cavazos Carolina Gonzalez , Zhang Huiyuan , Deng Shanshan , Diao Lixia , Wang Jing , Evans Scott E. , Behrens Carmen , Wistuba Ignacio I. , Fuqua Susan A. W. , Lin Huang , Stabile Laura P. , Watowich Stephanie S. , Kadara Humam , Moghaddam Seyed Javad
Published: October 2018

Lung adenocarcinomas (LUADs) with mutations in the K-ras oncogene display dismal prognosis. Proinflammatory and immunomodulatory events that drive development of K-ras mutant LUAD are poorly understood. Here, we develop a lung epithelial specific K-ras mutant/Stat3 conditional knockout (LR/Stat3Δ/Δ) mouse model. Epithelial Stat3 deletion results in intriguing sex-associated discrepancies; K-ras mutant tumors are decreased in female LR/Stat3Δ/Δ mice whereas tumor burdens are increased in males. RNA-sequencing and tumor microenvironment (TME) analysis demonstrate increased anti-tumor immune responses following Stat3 deletion in females and, conversely, elevated pro-tumor immune pathways in males. While IL-6 blockade in male LR/Stat3Δ/Δ mice reduces lung tumorigenesis, inhibition of estrogen receptor signaling in female mice augments K-ras mutant oncogenesis and reprograms lung TME toward a pro-tumor phenotype. Our data underscore a critical sex-specific role for epithelial Stat3 signaling in K-ras mutant LUAD, thus paving the way for developing personalized (e.g. sex-based) immunotherapeutic strategies for this fatal disease.
Baleen whale cortisol levels reveal a physiological response to 20th century whaling
Authors: Trumble Stephen J. , Norman Stephanie A. , Crain Danielle D. , Mansouri Farzaneh , Winfield Zach C. , Sabin Richard , Potter Charles W. , Gabriele Christine M. , Usenko Sascha
Published: October 2018

One of the most important challenges researchers and managers confront in conservation ecology is predicting a population’s response to sub-lethal stressors. Such predictions have been particularly elusive when assessing responses of large marine mammals to past anthropogenic pressures. Recently developed techniques involving baleen whale earplugs combine age estimates with cortisol measurements to assess spatial and temporal stress/stressor relationships. Here we show a relationship between baseline-corrected cortisol levels and corresponding whaling counts of fin, humpback, and blue whales in the Northern Hemisphere spanning the 20th century. We also model the impact of alternative demographic and environmental factors and determine that increased anomalies of sea surface temperature over a 46-year mean (1970–2016) were positively associated with cortisol levels. While industrial whaling can deplete populations by direct harvest, our data underscore a widespread stress response in baleen whales that is peripheral to whaling activities or associated with other anthropogenic change.
Tissue-resident memory T cells populate the human brain
Authors: Smolders Joost , Heutinck Kirstin M. , Fransen Nina L. , Remmerswaal Ester B. M. , Hombrink Pleun , ten Berge Ineke J. M. , van Lier René A. W. , Huitinga Inge , Hamann Jörg
Published: October 2018

Most tissues are populated by tissue-resident memory T cells (TRM cells), which are adapted to their niche and appear to be indispensable for local protection against pathogens. Here we show that human white matter-derived brain CD8+ T cells can be subsetted into CD103−CD69+ and CD103+CD69+ T cells both with a phenotypic and transcription factor profile consistent with TRM cells. Specifically, CD103 expression in brain CD8+ T cells correlates with reduced expression of differentiation markers, increased expression of tissue-homing chemokine receptors, intermediate and low expression of the transcription factors T-bet and eomes, increased expression of PD-1 and CTLA-4, and low expression of cytolytic enzymes with preserved polyfunctionality upon activation. Brain CD4+ T cells also display TRM cell-associated markers but have low CD103 expression. We conclude that the human brain is surveilled by TRM cells, providing protection against neurotropic virus reactivation, whilst being under tight control of key immune checkpoint molecules.
Loss of embryonic neural crest derived cardiomyocytes causes adult onset hypertrophic cardiomyopathy in zebrafish
Authors: Abdul-Wajid Sarah , Demarest Bradley L. , Yost H. Joseph
Published: October 2018

Neural crest cells migrate to the embryonic heart and transform into a small number of cardiomyocytes, but their functions in the developing and adult heart are unknown. Here, we show that neural crest derived cardiomyocytes (NC-Cms) in the zebrafish ventricle express Notch ligand jag2b, are adjacent to Notch responding cells, and persist throughout life. Genetic ablation of NC-Cms during embryogenesis results in diminished jag2b, altered Notch signaling and aberrant trabeculation patterns, but is not detrimental to early heart function or survival to adulthood. However, embryonic NC-Cm ablation results in adult fish that show severe hypertrophic cardiomyopathy (HCM), altered cardiomyocyte size, diminished adult heart capacity and heart failure in cardiac stress tests. Adult jag2b mutants have similar cardiomyopathy. Thus, we identify a cardiomyocyte population and genetic pathway that are required to prevent adult onset HCM and provide a zebrafish model of adult-onset HCM and heart failure.
Generalized Hartmann-Shack array of dielectric metalens sub-arrays for polarimetric beam profiling
Authors: Yang Zhenyu , Wang Zhaokun , Wang Yuxi , Feng Xing , Zhao Ming , Wan Zhujun , Zhu Liangqiu , Liu Jun , Huang Yi , Xia Jinsong , Wegener Martin
Published: October 2018

To define and characterize optical systems, obtaining the amplitude, phase, and polarization profile of optical beams is of utmost importance. Traditional polarimetry is well established to characterize the polarization state. Recently, metasurfaces have successfully been introduced as compact optical components. Here, we take the metasurface concept to the system level by realizing arrays of metalenses, allowing the determination of the polarization profile of an optical beam. We use silicon-based metalenses with a numerical aperture of 0.32 and a mean measured focusing efficiency in transmission mode of 28% at a wavelength of 1550 nm. Our system is extremely compact and allows for real-time beam diagnostics by inspecting the foci amplitudes. By further analyzing the foci displacements in the spirit of a Hartmann-Shack wavefront sensor, we can simultaneously detect phase-gradient profiles. As application examples, we diagnose the profiles of a radially polarized beam, an azimuthally polarized beam, and of a vortex beam.
NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells
Authors: Kloet Susan L. , Karemaker Ino D. , van Voorthuijsen Lisa , Lindeboom Rik G. H. , Baltissen Marijke P. , Edupuganti Raghu R. , Poramba-Liyanage Deepani W. , Jansen Pascal W. T. C. , Vermeulen Michiel
Published: October 2018

The nucleosome remodeling and deacetylase (NuRD) complex plays an important role in gene expression regulation, stem cell self-renewal, and lineage commitment. However, little is known about the dynamics of NuRD during cellular differentiation. Here, we study these dynamics using genome-wide profiling and quantitative interaction proteomics in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). We find that the genomic targets of NuRD are highly dynamic during differentiation, with most binding occurring at cell-type specific promoters and enhancers. We identify ZFP296 as an ESC-specific NuRD interactor that also interacts with the SIN3A complex. ChIP-sequencing in Zfp296 knockout (KO) ESCs reveals decreased NuRD binding both genome-wide and at ZFP296 binding sites, although this has little effect on the transcriptome. Nevertheless, Zfp296 KO ESCs exhibit delayed induction of lineage-specific markers upon differentiation to embryoid bodies. In summary, we identify an ESC-specific NuRD-interacting protein which regulates genome-wide NuRD binding and cellular differentiation.
Global-scale control of extensional tectonics on CO2 earth degassing
Authors: Tamburello Giancarlo , Pondrelli Silvia , Chiodini Giovanni , Rouwet Dmitri
Published: October 2018

Earth degassing of CO2-rich fluids has been proven to contribute significantly to the global carbon budget. The presence of ubiquitous outgassing reveals some degree of permeability of the crust that often coincides with seismically active zones. In this study, we took advantage of the most recent global geological datasets to better understand earth degassing and how it correlates with tectonic regimes. Here we use an ad hoc point pattern analysis to show that there is a spatial correlation between CO2discharges and the presence of active fault systems, in particular with those characterized by a normal slip type. Seismic data demonstrate the existence of a positive spatial correlation between gas discharges and extensional tectonic regimes and confirms that such processes would play a key role in creating pathways for the rising gases at micro- and macro-scales, increasing the rock permeability and connecting the deep crust to the earth surface.
Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity
Authors: Chen Xingqi , Litzenburger Ulrike M. , Wei Yuning , Schep Alicia N. , LaGory Edward L. , Choudhry Hani , Giaccia Amato J. , Greenleaf William J. , Chang Howard Y.
Published: October 2018

Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry and positions in arrayed microwells, and then subject to molecular barcoding for subsequent pooled analysis. Pi-ATAC simultaneously identifies the epigenomic and proteomic heterogeneity in individual cells. Pi-ATAC reveals a casual link between transcription factor abundance and DNA motif access, and deconvolute cell types and states in the tumor microenvironment in vivo. We identify a dominant role for hypoxia, marked by HIF1α protein, in the tumor microvenvironment for shaping the regulome in a subset of epithelial tumor cells.
Effective Three-Body Interactions in Jaynes-Cummings-Hubbard Systems
Authors: Prasad Srivatsa B. , Martin Andrew M.
Published: October 2018

A generalisation of the Jaynes-Cummings-Hubbard model for coupled-cavity arrays is introduced, where the embedded two-level system in each cavity is replaced by a Ξ-type three-level system. We demonstrate that the resulting effective polariton-polariton interactions at each site are both two-body and three-body. By tuning the ratio of the two transition dipole matrix elements, we show that the strength and sign of the two-body interaction can be controlled whilst maintaining a three-body repulsion. We then proceed to demonstrate how different two-body and three-body interactions alter the mean field superfluid-Mott insulator phase diagram, with the possible emergence of a pair superfluid phase in the two-body attractive regime.
Genotyping-by-sequencing supports a genetic basis for wing reduction in an alpine New Zealand stonefly
Authors: Veale Andrew J. , Foster Brodie J. , Dearden Peter K. , Waters Jonathan M.
Published: October 2018

Wing polymorphism is a prominent feature of numerous insect groups, but the genomic basis for this diversity remains poorly understood. Wing reduction is a commonly observed trait in many species of stoneflies, particularly in cold or alpine environments. The widespread New Zealand stoneflyZelandoperla fenestrataspecies group (Z.fenestrata,Z.tillyardi,Z.pennulata) contains populations ranging from fully winged (macropterous) to vestigial-winged (micropterous), with the latter phenotype typically associated with high altitudes. The presence of flightless forms on numerous mountain ranges, separated by lowland fully winged populations, suggests wing reduction has occurred multiple times. We use Genotyping by Sequencing (GBS) to test for genetic differentiation between fully winged (n = 62) and vestigial-winged (n = 34) individuals, sampled from a sympatric population of distinct wing morphotypes, to test for a genetic basis for wing morphology. While we found no population genetic differentiation between these two morphotypes across 6,843 SNP loci, we did detect several outlier loci that strongly differentiated morphotypes across independent tests. These findings indicate that small regions of the genome are likely to be highly differentiated between morphotypes, suggesting a genetic basis for wing reduction. Our results provide a clear basis for ongoing genomic analysis to elucidate critical regulatory pathways for wing development in Pterygota.
Fast, Cost-effective and Energy Efficient Mercury Removal-Recycling Technology
Authors: Ganguly Mainak , Dib Simon , Ariya Parisa A.
Published: October 2018

We herein present a novel and sustainable technology for mercury recycling, with the maximum observed uptake capacity. Facile synthesis of the most efficient (~1.9 gg−1) nano-trap, made of montmorillonite-Fe-iron oxides, was performed to instantaneously remove mercury(II) ions from water. Elemental Hg was recovered from the adduct, by employing Fe granules, at ambient conditions. Varied pHs and elevated temperatures further enhanced this already highly efficient recycling process. The reduction of Hg(II) to Hg(I) by the nano trap and Hg(I) to Hg(0) by Fe granules are the main driving forces behind the recycling process. Facile sustainable recycling of the nano-trap and Fe granules require no additional energy. We have further developed a recyclable model for Hg nano-trap, which is inexpensive (<$5 CAD), and can remove mercury in a few seconds. This technology has multiple applications, including in the communities exposed to mercury contamination.
Measurement of mean subcutaneous fat thickness: eight standardised ultrasound sites compared to 216 randomly selected sites
Authors: Störchle Paul , Müller Wolfram , Sengeis Marietta , Lackner Sonja , Holasek Sandra , Fürhapter-Rieger Alfred
Published: October 2018

Ultrasound (US) provides the most accurate technique for thickness measurements of subcutaneous adipose tissue (SAT) layers. This US method was recently standardised using eight sites to capture SAT patterning and allows distinguishing between fat and embedded fibrous structures. These eight sites chosen for fat patterning studies do not represent the mean SAT thickness measured all over the body that is necessary for determining subcutaneous fat mass. This was obtained by SAT measurements at 216 sites distributed randomly all over the body. Ten participants with BMI below 28.5kgm−2and SAT means (from eight sites) ranging from 3 mm to 10 mm were selected. The means from eight sites overestimated the means obtained from 216 sites (i.e. 2160 US measurements in the ten participants); the calibration factor of 0.65 corrects this; standard deviation (SD) was 0.05, i.e. 8%. The SD of the calibration factor transforms linearly when estimating the error range of the whole body’s SAT volume (body surface area times the calibrated mean SAT thickness). The SAT masses ranged from 3.2 to 12.4 kg in this group. The standard deviations resulting from solely the calibration factor uncertainty were ±0.3 and ±1.0 kg, respectively. For these examples, the SAT percentages were 4.9(±0.4)% and 13.3(±1.0)%.
X-linked ADGRG2 mutation and obstructive azoospermia in a large Pakistani family
Authors: Khan Muhammad Jaseem , Pollock Nijole , Jiang Huaiyang , Castro Carlos , Nazli Rubina , Ahmed Jawad , Basit Sulman , Rajkovic Aleksandar , Yatsenko Alexander N.
Published: October 2018

We performed whole exome sequencing to identify an unknown genetic cause of azoospermia and male infertility in a large Pakistani family. Three infertile males were subjected to semen analysis, hormone testing, testicular histology, ultrasonography, karyotyping, Y-chromosome microdeletion and CFTR testing. The clinical testing suggested a diagnosis of obstructive azoospermia (OA). To identify the cause, we performed whole exome sequencing (WES) for 2 infertile brothers and 2 fertile family members. For segregation analysis and variant confirmation, we performed Sanger sequencing. WES data analysis of the family revealed segregated variants in 3 candidate genes. We considered novel nonsense variant c.2440C > T(p.Arg814*) in X-linked gene ADGRG2 as biologically most plausible. It is predicted to truncate the protein by 204 amino acids (aa) at a key transmembrane domain. Adgrg2-knockout male mice show sperm loss due to obstructive fluid stasis, while ADGRG2 mutations cause OA in the infertile male patients. Our analysis of testicular histology reveals secondary severe reduction of spermatogenesis, consistent with human and knockout mouse phenotypes. The ADGRG2 nonsense mutation is absent in the largest population databases, ExAC and gnomAD. Analysis of the novel nonsense mutation in extended family members confirmed co-segregation of the mutation with OA in all affected males. The likely pathogenic nature of the mutation is supported by its truncation effect on the transmembrane domain and distinctive ultrasound results. The study demonstrates effectiveness of WES in discovering a genetic cause of azoospermia.
Human Defensin-5 Blocks Ethanol and Colitis-Induced Dysbiosis, Tight Junction Disruption and Inflammation in Mouse Intestine
Authors: Shukla Pradeep K. , Meena Avtar S. , Rao Vaishnavi , Rao Roshan G. , Balazs Louisa , Rao RadhaKrishna
Published: October 2018

Alcohol consumption has been shown to cause dysbiosis, but the mechanism involved in it is unknown. Recurrent colitis is known to induce expression of α-defensins in the colon, but the effect of alcohol consumption on it is not known. We investigated the effect of ethanol on α-defensin expression in the small intestine and colitis-induced expression in colon in mice. Furthermore, we evaluated the effect of human defensin-5 (HD5) on ethanol and colitis-induced gut barrier dysfunction and mucosal damage. Recurrent colitis was induced by feeding dextran sulfate sodium (DSS), 3 cycles of 5-days each with 15 days intervals, followed by 30-days remission. Ethanol was fed during the intervals and recovery in a liquid diet with or without HD5. Expression of α-defensins, tight junction (TJ) integrity and cytokine/chemokine expression were analyzed. Chronic ethanol feeding reduced α-defensin expression in the small intestine and colitis-induced defensin expression in the colon. HD5 attenuated the growth of enterotoxigenic Bacteriodes fragilis and E. coli, but had no effect on non-toxigenic Bacteriodes fragilis or probiotics, the Lactobacilli. Ethanol and colitis elevated Enterobacteriaceae, Firmicutes and Firmicutes to Bacteriodetes ratio in colonic mucosa. HD5 feeding attenuated ethanol and colitis-induced dysbiosis, disruption of intestinal epithelial TJ, mucosal inflammation, expression of pro-inflammatory cytokines and chemokines in the small intestine and colon, and endotoxemia. These results demonstrate that ethanol suppresses intestinal α-defensin expression, leading to dysbiosis, barrier dysfunction, inflammation and endotoxemia. HD5 feeding attenuates intestinal injury caused by ethanol and colitis, indicating that defensin expression is a potential target for treatment of alcoholic tissue injury and colitis.
Omega-3 polyunsaturated fatty acids do not fluidify bilayers in the liquid-crystalline state
Authors: De Santis Augusta , Varela Yaiza , Sot Jesús , D’Errico Gerardino , Goñi Félix M. , Alonso Alicia
Published: October 2018

This work reports on the effects of two omega-3 fatty acids, namely docosahexaenoic (C22:64,7,10,13,16,19) acid (DHA), and eicosapentaenoic (C20:55,8,11,14,17) acid (EPA), with oleic (C18:19) acid (OA) as a control, on the gel-liquid crystalline phase transition of dipalmitoyl phosphatidylcholine (DPPC). Mainly differential scanning calorimetry has been used, together with Laurdan fluorescence, and confocal fluorescence microscopy. All three fatty acids DHA, EPA and OA exhibited fluidifying properties when added to the DPPC bilayers, decreasing the main transition temperature. DHA and EPA were somewhat more effective than OA in this respect, but the effects of all three were of the same order of magnitude, thus the long-chain omega-3 fatty acids failed to exhibit any peculiar fluidifying potency. The same was true when the omega-3 fatty acids were esterified in the sn-2 position of a phosphatidylcholine. Moreover the omega-3 fatty acids had very small or no effects on the fluidity of bilayers in the liquid-crystalline, or fluid disordered state (egg phosphatidylcholine and others), or in the fluid ordered state (phospholipid: cholesterol mixtures). The hypothesis that some physiological effects of long-chain omega-3 fatty acids could be related to their special fluidifying properties is not supported by these data.
Flexural phonons in supported graphene: from pinning to localization
Authors: Zhao Wei L. Z. , Tikhonov Konstantin S. , Finkel’stein Alexander M.
Published: October 2018

We identify graphene layer on a disordered substrate as a system where localization of phonons can be observed. Generally, observation of localization for scattering waves is not simple, because the Rayleigh scattering is inversely proportional to a high power of wavelength. The situation is radically different for the out of plane vibrations, so-called flexural phonons, scattered by pinning centers induced by a substrate. In this case, the scattering time for vanishing wave vector tends to a finite limit. One may, therefore, expect that physics of the flexural phonons exhibits features characteristic for electron localization in two dimensions, albeit without complications caused by the electron-electron interactions. We confirm this idea by calculating statistical properties of the Anderson localization of flexural phonons for a model of elastic sheet in the presence of the pinning centers. Finally, we discuss possible manifestations of the flexural phonons, including the localized ones, in the electronic thermal conductance.
Anatomy of the Campi Flegrei caldera using Enhanced Seismic Tomography Models
Authors: Calò Marco , Tramelli Anna
Published: October 2018

Campi Flegrei caldera (Southern Italy) is a densely inhabited area and suffered several unrest episodes in the last centuries. The dynamic of the caldera is highly debated because of conflicting interpretations. Here we present a detailed reconstruction of the Campi Flegrei structure obtained using the microseismicity recorded during the 1984 unrest. Enhanced Seismic Tomography models obtained with these data allow us describing seismic velocities, attenuation, and scattering patterns. Results show: (1) a plumbing system with a diameter of 1 km located between 2.3 km and 4 km depth (2) a 0.5 km thick caprock located at 2 km depth interpreted as the main structure regulating the fluid interchange between deep and shallow sectors of the caldera, (3) the shape and volume of a shallow reservoir beneath the city of Pozzuoli; this reservoir played a key role during the 1982–1984 unrest, (4) several small reservoirs beneath the main craters of the caldera. All these features fit into the debated question on magmatic or hydrothermal mechanism driving the caldera deformation resulting of crucial importance to allow a better assessment of the hazard.
Dopamine release in mushroom bodies of the honey bee (Apis mellifera L.) in response to aversive stimulation
Authors: Jarriault David , Fuller Justine , Hyland Brian I. , Mercer Alison R.
Published: October 2018

InDrosophila melanogaster, aversive (electric shock) stimuli have been shown to activate subpopulations of dopaminergic neurons with terminals in the mushroom bodies (MBs) of the brain. While there is compelling evidence that dopamine (DA)-induced synaptic plasticity underpins the formation of aversive memories in insects, the mechanisms involved have yet to be fully resolved. Here we take advantage of the accessibility of MBs in the brain of the honey bee to examine, using fast scan cyclic voltammetry, the kinetics of DA release and reuptakein vivoin response to electric shock, and to investigate factors that modulate the release of this amine. DA increased transiently in the MBs in response to electric shock stimuli. The magnitude of release varied depending on stimulus duration and intensity, and a strong correlation was identified between DA release and the intensity of behavioural responses to shock. With repeated stimulation, peak DA levels increased. However, the amount of DA released on the first stimulation pulse typically exceeded that evoked by subsequent pulses. No signal was detected in response to odour alone. Interestingly, however, if odour presentation was paired with electric shock, DA release was enhanced. These results set the stage for analysing the mechanisms that modulate DA release in the MBs of the bee.
Engineering Lineage Potency and Plasticity of Stem Cells using Epigenetic Molecules
Authors: Dhaliwal Anandika , Pelka Sandra , Gray David S. , Moghe Prabhas V.
Published: October 2018

Stem cells are considered as a multipotent regenerative source for diseased and dysfunctional tissues. Despite the promise of stem cells, the inherent capacity of stem cells to convert to tissue-specific lineages can present a major challenge to the use of stem cells for regenerative medicine. We hypothesized that epigenetic regulating molecules can modulate the stem cell’s developmental program, and thus potentially overcome the limited lineage differentiation that human stem cells exhibit based on the source and processing of stem cells. In this study, we screened a library of 84 small molecule pharmacological agents indicated in nucleosomal modification and identified a sub-set of specific molecules that influenced osteogenesis in human mesenchymal stem cells (hMSCs) while maintaining cell viability in-vitro. Pre-treatment with five candidate hits, Gemcitabine, Decitabine, I-CBP112, Chidamide, and SIRT1/2 inhibitor IV, maximally enhanced osteogenesis in-vitro. In contrast, five distinct molecules, 4-Iodo-SAHA, Scriptaid, AGK2, CI-amidine and Delphidine Chloride maximally inhibited osteogenesis. We then tested the role of these molecules on hMSCs derived from aged human donors and report that small epigenetic molecules, namely Gemcitabine and Chidamide, can significantly promote osteogenic differentiation by 5.9- and 2.3-fold, respectively. Taken together, this study demonstrates new applications of identified small molecule drugs for sensitively regulating the lineage plasticity fates of bone-marrow derived mesenchymal stem cells through modulating the epigenetic profile of the cells.
An immune cell spray (ICS) formulation allows for the delivery of functional monocyte/macrophages
Authors: Beneke Valerie , Küster Fennja , Neehus Anna-Lena , Hesse Christina , Lopez-Rodriguez Elena , Haake Kathrin , Rafiei Hashtchin Anna , Schott Juliane Wilhelmine , Walter Dorothee , Braun Armin , Wolkers Willem F. , Ackermann Mania , Lachmann Nico
Published: October 2018

Macrophages are key cells of the innate immune system and act as tissue resident macrophages (TRMs) in the homeostasis of various tissues. Given their unique functions and therapeutic use as well as the feasibility to derive macrophages in vitro from hematopoietic stem cell (HSC) sources, we propose an “easy-to-use” immune cell spray (ICS) formulation to effectively deliver HSC-derived macrophages. To achieve this aim, we used classical pump spray devices to spray either the human myeloid cell line U937 or primary murine HSC-derived macrophages. For both cell types used, one puff could deliver cells with maintained morphology and functionality. Of note, cells tolerated the spraying process very well with a recovery of more than 90%. In addition, we used osmotic preconditioning to reduce the overall cell size of macrophages. While a 800 mosm hyperosmolar sucrose solution was able to reduce the cell size by 27%, we identified 600 mosm to be effective to reduce the cell size by 15% while maintaining macrophage morphology and functionality. Using an isolated perfused rat lung preparation, the combinatorial use of the ICS with preconditioned and genetically labeled U937 cells allowed the intra-pulmonary delivery of cells, thus paving the way for a new cell delivery platform.
Two fluid model in low energy excited states within spin-ice systems
Authors: López-Bara F. I. , López-Aguilar F.
Published: October 2018

Excitations in magnetic structures of the so-called spin-ice materials generate two different peaks in the specific heat and anomalies in entropy in the temperature interval between 0 and 1 K. These points are due to the existence of two low-energy excited global states which seem to transit from a bosonic condensate towards a magnetic neutral plasma in a narrow temperature interval between 0.05 ≤ T ≤ 1 K. In this paper, we determine the characteristic features of two states and we analyze the possibilities of existence of a BEC state and its phase transition to the magnetic plasma state from a model of two magnetic charge fluids. From the structural analysis of the many-body excitation states, we obtain theoretical results about entropy and specific heat since these two key physical magnitudes announce the phase transitions. We give criteria for distinguishing if some of these phase transitions is of either first or second order.
Structure of bacterial oligosaccharyltransferase PglB bound to a reactive LLO and an inhibitory peptide
Authors: Napiórkowska Maja , Boilevin Jérémy , Darbre Tamis , Reymond Jean-Louis , Locher Kaspar P.
Published: October 2018

Oligosaccharyltransferase (OST) is a key enzyme of the N-glycosylation pathway, where it catalyzes the transfer of a glycan from a lipid-linked oligosaccharide (LLO) to an acceptor asparagine within the conserved sequon N-X-T/S. A previous structure of a ternary complex of bacterial single subunit OST, PglB, bound to a non-hydrolyzable LLO analog and a wild type acceptor peptide showed how both substrates bind and how an external loop (EL5) of the enzyme provided specific substrate-binding contacts. However, there was a relatively large separation of the substrates at the active site. Here we present the X-ray structure of PglB bound to a reactive LLO analog and an inhibitory peptide, revealing previously unobserved interactions in the active site. We found that the atoms forming the N-glycosidic bond (C-1 of the GlcNAc moiety of LLO and the –NH2 group of the peptide) are closer than in the previous structure, suggesting that we have captured a conformation closer to the transition state of the reaction. We find that the distance between the divalent metal ion and the glycosidic oxygen of LLO is now 4 Å, suggesting that the metal stabilizes the leaving group of the nucleophilic substitution reaction. Further, the carboxylate group of a conserved aspartate of PglB mediates an interaction network between the reducing-end sugar of the LLO, the asparagine side chain of the acceptor peptide, and a bound divalent metal ion. The interactions identified in this novel state are likely to be relevant in the catalytic mechanisms of all OSTs.
Single molecule localisation microscopy reveals how HIV-1 Gag proteins sense membrane virus assembly sites in living host CD4 T cells
Authors: Floderer Charlotte , Masson Jean-Baptiste , Boilley Elise , Georgeault Sonia , Merida Peggy , El Beheiry Mohamed , Dahan Maxime , Roingeard Philippe , Sibarita Jean-Baptiste , Favard Cyril , Muriaux Delphine
Published: October 2018

Monitoring virus assembly at the nanoscale in host cells remains a major challenge. Human immunodeficiency virus type 1 (HIV-1) components are addressed to the plasma membrane where they assemble to form spherical particles of 100 nm in diameter. Interestingly, HIV-1 Gag protein expression alone is sufficient to produce virus-like particles (VLPs) that resemble the immature virus. Here, we monitored VLP formation at the plasma membrane of host CD4+ T cells using a newly developed workflow allowing the analysis of long duration recordings of single-molecule Gag protein localisation and movement. Comparison of Gag assembling platforms in CD4+ T cells expressing wild type or assembly-defective Gag mutant proteins showed that VLP formation lasts roughly 15 minutes with an assembly time of 5 minutes. Trapping energy maps, built from membrane associated Gag protein movements, showed that one third of the assembling energy is due to direct Gag capsid-capsid interaction while the remaining two thirds require the nucleocapsid-RNA interactions. Finally, we show that the viral RNA genome does not increase the attraction of Gag at the membrane towards the assembling site but rather acts as a spatiotemporal coordinator of the membrane assembly process.
Mining latent information in PTSD psychometrics with fuzziness for effective diagnoses
Authors: Li Yuanyuan , Xiong Xi , Qiu Changjian , Wang Qiang , Xu Jiajun
Published: October 2018

The options of traditional self-report rating-scale, like the PTSD Checklist Civilian (PCL-C) scale, have no clear boundaries which might cause considerable biases and low effectiveness. This research aimed to explore the feasibility of using fuzzy set in the data processing to promote the screening effectiveness of PCL-C in real-life practical settings. The sensitivity, specificity, Youden’s index etc., of PCL-C at different cutoff lines (38, 44 and 50 respectively) were analyzed and compared with those of fuzzy set approach processing. In practice, no matter the cutoff line of the PCL-C was set at 50, 44 or 38, the PCL-C showed good specificity, but failed to exhibit good sensitivity and screening effectiveness. The highest sensitivity was at 65.22%, with Youden’s index being 0.64. After fuzzy processing, the fuzzy-PCL-C’s sensitivity increased to 91.30%, Youden’s index rose to 0.91, having seen marked augmentation. In conclusion, this study indicates that fuzzy set can be used in the data processing of psychiatric scales which have no clear definition standard of the options to improve the effectiveness of the scales.
Brassica yellows virus’ movement protein upregulates anthocyanin accumulation, leading to the development of purple leaf symptoms on Arabidopsis thaliana
Authors: Chen Xiang-Ru , Wang Ying , Zhao Hang-Hai , Zhang Xiao-Yan , Wang Xian-Bing , Li Da-Wei , Yu Jia-Lin , Han Cheng-Gui
Published: October 2018

Poleroviruses are widely distributed and often of great economic importance because they cause a variety of symptoms, such as the rolling of young leaves, leaf color changes, and plant decline, in infected plants. However, the molecular mechanism behind these viral-induced symptoms is still unknown. Here, we verified the pathogenicity of the polerovirus Brassica yellows virus (BrYV) by transforming its full-length amplicon intoArabidopsis thaliana, which resulted in many abnormal phenotypes. To better understand the interactions between BrYV and its host, global transcriptome profiles of the transgenic plants were compared with that of non-transgenic Arabidopsis plants. An association between the BrYV- induced purple leaf symptoms and the activation of anthocyanin biosynthesis was noted. Using the transgenic approach, we found that movement protein of BrYV was responsible for the induction of these coloration symptoms. Collectively, our findings demonstrate the BrYV’ pathogenicity and show that the BrYV-induced purple leaf symptom resulted from its movement protein stimulating anthocyanin accumulation.
TRIAMF: A New Method for Delivery of Cas9 Ribonucleoprotein Complex to Human Hematopoietic Stem Cells
Authors: Yen Jonathan , Fiorino Michael , Liu Yi , Paula Steve , Clarkson Scott , Quinn Lisa , Tschantz William R. , Klock Heath , Guo Ning , Russ Carsten , Yu Vionnie W. C. , Mickanin Craig , Stevenson Susan C. , Lee Cameron , Yang Yi
Published: October 2018

CRISPR/Cas9 mediated gene editing of patient-derived hematopoietic stem and progenitor cells (HSPCs) ex vivo followed by autologous transplantation of the edited HSPCs back to the patient can provide a potential cure for monogenic blood disorders such as β-hemoglobinopathies. One challenge for this strategy is efficient delivery of the ribonucleoprotein (RNP) complex, consisting of purified Cas9 protein and guide RNA, into HSPCs. Because β-hemoglobinopathies are most prevalent in developing countries, it is desirable to have a reliable, efficient, easy-to-use and cost effective delivery method. With this goal in mind, we developed TRansmembrane Internalization Assisted by Membrane Filtration (TRIAMF), a new method to quickly and effectively deliver RNPs into HSPCs by passing a RNP and cell mixture through a filter membrane. We achieved robust gene editing in HSPCs using TRIAMF and demonstrated that the multilineage colony forming capacities and the competence for engraftment in immunocompromised mice of HSPCs were preserved post TRIAMF treatment. TRIAMF is a custom designed system using inexpensive components and has the capacity to process HSPCs at clinical scale.
Effect of Statins on Renal Function in Chronic Kidney Disease Patients
Authors: Hu Ping-Jen , Wu Mei-Yi , Lin Tsu-Chen , Chen Tzu-Ting , Wu Yun-Chun , Su Sui-Lung , Lu Kuo-Cheng , Chen Jin-Shuen , Sung Fung-Chang , Lee Chien-Te , Yang Yu , Hwang Shang-Jyh , Wang Ming-Cheng , Hsu Yung-Ho , Chiou Hung-Yi , Wong Chung-Shun , Lin Yuh-Feng
Published: October 2018

Dyslipidemia is associated with glomerular injury. However, the effect of statins on chronic kidney disease (CKD) progression remains controversial. We aimed to investigate the efficacy of statins for renal protection in patients with CKD. The retrospective cohort study comprised 3441 patients diagnosed with CKD in multiple medical centers. We divided the patients into two cohorts based on statin prescription, and compared proportions and risks of CKD progression events between the two groups. CKD progression event was defined as an average annual decline of eGFR >5 mL/min/1.73 m2 or advancement to the dialysis stage. The result revealed that among all incident patients with CKD, 28.7% and 30.3% of the users and nonusers demonstrated CKD progression, respectively. The crude odds ratio (OR) of CKD progression was 0.93 [95% confidence interval (CI) 0.78–1.10]. After adjustment for baseline characteristics, the adjusted OR was 0.80 (95% CI 0.63–1.01). The sensitivity analysis results showed consistent OR for CKD progression, stratification by age, sex, Charlson score, and statins use within 1 year before index date. The effect of statins was significant in patients with CKD stage 3B-5 (OR 0.68, 95% CI 0.48–0.95), but not statistically significant in those with CKD stage 1–3A (OR 0.97, 95% CI 0.68–1.38). The effect of statins was significant in patients with proteinuria ≥1000 mg/day (OR 0.63, 95% CI 0.43–0.92), but not statistically significant in those with proteinuria <1000 mg/day (OR 1.02, 95% CI 0.74–1.41).
Evolution of Glassy Carbon Microstructure: In Situ Transmission Electron Microscopy of the Pyrolysis Process
Authors: Sharma Swati , Shyam Kumar C. N. , Korvink Jan G. , Kübel Christian
Published: October 2018

Glassy carbon is a graphene-rich form of elemental carbon obtained from pyrolysis of polymers, which is composed of three-dimensionally arranged, curved graphene fragments alongside fractions of disordered carbon and voids. Pyrolysis encompasses gradual heating of polymers at ≥ 900 °C under inert atmosphere, followed by cooling to room temperature. Here we report on an experimental method to perform in situ high-resolution transmission electron microscopy (HR-TEM) for the direct visualization of microstructural evolution in a pyrolyzing polymer in the 500–1200 °C temperature range. The results are compared with the existing microstructural models of glassy carbon. Reported experiments are performed at 80 kV acceleration voltage using MEMS-based heating chips as sample substrates to minimize any undesired beam-damage or sample preparation induced transformations. The outcome suggests that the geometry, expansion and atomic arrangement within the resulting graphene fragments constantly change, and that the intermediate structures provide important cues on the evolution of glassy carbon. A complete understanding of the pyrolysis process will allow for a general process tuning specific to the precursor polymer for obtaining glassy carbon with pre-defined properties.
Genetic diversity of submergence stress response in cytoplasms of the Triticum-Aegilops complex
Authors: Takenaka Shotaro , Yamamoto Ryohei , Nakamura Chiharu
Published: October 2018

Genetic diversity in cytoplasmic and nuclear genomes and their interaction affecting adaptive traits is an attractive research subject in plants. We addressed submergence stress response of wheat that has become increasingly important but remained largely uninvestigated. Our primary aim was to disclose cytoplasmic diversity using nucleus-cytoplasm (NC) hybrids possessing a series of heterologous cytoplasms in a common nuclear background. Effects of submergence on seedling emergence and growth from imbibed seeds were studied and compared with euplasmic lines. Marked phenotypic variabilities were observed among both lines, demonstrating divergent cytoplasmic and nuclear effects on submergence response. NC hybrids with cytoplasm of Aegilops mutica showed a less inhibition, indicative of their positive contribution to submergence tolerance, whereas cytoplasms of Aegilops umbellulata and related species caused a greater inhibition. Superoxide dismutase (SOD) activity showed a marked increase accompanied by retardation of seedling growth in a susceptible NC hybrid. The observation suggested that the elevated SOD activity was resulted from a high level of reactive oxygen species accumulated and remained in susceptible seedlings. Taken together, our results point to the usefulness of NC hybrids in further studies needed to clarify molecular mechanisms underlying the nucleus-cytoplasm interaction regulating submergence stress response in wheat.
Proteomics based analysis of the nicotine catabolism in Paenarthrobacter nicotinovorans pAO1
Authors: Mihăşan Marius , Babii Cornelia , Aslebagh Roshanak , Channaveerappa Devika , Dupree Emmalyn , Darie Costel C.
Published: October 2018

Paenarthrobacter nicotinovorans is a nicotine-degrading microorganism that shows a promising biotechnological potential for the production of compounds with industrial and pharmaceutical importance. Its ability to use nicotine was linked to the presence of the catabolic megaplasmid pAO1. Although extensive work has been performed on the molecular biology of nicotine degradation in this bacterium, only half of the genes putatively involved have been experimentally linked to nicotine. In the current approach, we used nanoLC–MS/MS to identify a total of 801 proteins grouped in 511 non-redundant protein clusters when P. nicotinovorans was grown on citrate, nicotine and nicotine and citrate as the only carbon sources. The differences in protein abundance showed that deamination is preferred when citrate is present. Several putative genes from the pAO1 megaplasmid have been shown to have a nicotine-dependent expression, including a hypothetical polyketide cyclase. We hypothesize that the enzyme would hydrolyze the N1-C6 bond from the pyridine ring with the formation of α-keto- glutaramate. Two chromosomally-encoded proteins, a malate dehydrogenase, and a D-3-phosphoglycerate dehydrogenase were shown to be strongly up-regulated when nicotine was the sole carbon source and could be related to the production the α-keto-glutarate. The data have been deposited to the ProteomeXchange with identifier PXD008756.
Second-harmonic patterned polarization-analyzed reflection confocal microscopy of stromal collagen in benign and malignant breast tissues
Authors: Okoro Chukwuemeka , Kelkar Varun , Sivaguru Mayandi , Emmadi Rajyasree , Toussaint Kimani C.
Published: October 2018

We present the results of polarimetric analysis of collagen on varying pathologies of breast tissues using second-harmonic patterned polarization-analyzed reflection confocal (SPPARC) microscopy. Experiments are conducted on a breast tissue microarray having benign tissues (BT), malignant invasive lobular carcinoma (ILC), and benign stroma adjacent to the malignant tissues (called the benign adjacent tissue, or BAT). Stroma in BAT and ILC exhibit the largest parameter differences. We observe that stromal collagen readings in ILC show lower depolarization, lower diattenuation and higher linear degree-of-polarization values than stromal collagen in BAT. This suggests that the optical properties of collagen change most in the vicinity of tumors. A similar trend is also exhibited in the non-collagenous extrafibrillar matrix plus cells (EFMC) region. The three highlighted parameters show greatest sensitivity to changes in the polarization response of collagen between pathologies.
CpG-DNA exerts antibacterial effects by protecting immune cells and producing bacteria-reactive antibodies
Authors: Kim Te Ha , Kim Dongbum , Gautam Avishekh , Lee Heesu , Kwak Min Hyung , Park Min Chul , Park Sangkyu , Wu Guang , Lee Bok Luel , Lee Younghee , Kwon Hyung-Joo
Published: October 2018

CpG-DNA activates various immune cells, contributing to the host defense against bacteria. Here, we examined the biological function of CpG-DNA in the production of bacteria-reactive antibodies. The administration of CpG-DNA increased survival in mice following infection with methicillin-resistantS. aureusand protected immune cell populations in the peritoneal cavity, bone marrow, and spleen. CpG-DNA injection likewise increased bacteria-reactive antibodies in the mouse peritoneal fluid and serum, which was dependent on TLR9. B cells isolated from the peritoneal cavity produced bacteria-reactive antibodiesin vitrofollowing CpG-DNA administration that enhanced the phagocytic activity of the peritoneal cells. The bacteria-reactive monoclonal antibody enhanced phagocytosisin vitroand protected mice afterS. aureusinfection. Therefore, we suggest that CpG-DNA enhances the antibacterial activity of the immune system by protecting immune cells and triggering the production of bacteria-reactive antibodies. Consequently, we believe that monoclonal antibodies could aid in the treatment of antibiotic-resistant bacterial infections.
Spatially controlled electrostatic doping in graphene p-i-n junction for hybrid silicon photodiode
Authors: Li Tiantian , Mao Dun , Petrone Nick W. , Grassi Robert , Hu Hao , Ding Yunhong , Huang Zhihong , Lo Guo-Qiang , Hone James C. , Low Tony , Wong Chee Wei , Gu Tingyi
Published: October 2018

Sufficiently large depletion region for photocarrier generation and separation is a key factor for two-dimensional material optoelectronic devices, but only a few device configurations have been explored for a deterministic control over the space charge region area in graphene with convincing scalability. Here we investigate a graphene-silicon p-i-n photodiode defined in a foundry processed planar photonic crystal waveguide structure, achieving visible—near-infrared, zero-bias, and ultrafast photodetection. Graphene is electrically contacting to the wide intrinsic region of silicon and extended to the p an n doped region, functioning as the primary photocarrier conducting channel for electronic gain. Graphene significantly improves the device speed through ultrafast out-of-plane interfacial carrier transfer and the following in-plane built-in electric field assisted carrier collection. More than 50 dB converted signal-to-noise ratio at 40 GHz has been demonstrated under zero bias voltage, the quantum efficiency could be further amplified by hot carrier gain on graphene-i Si interface and avalanche process on graphene-doped Si interface. With the device architecture fully defined by nanomanufactured substrate, this work demonstrates post-fabrication-free two-dimensional material active silicon photonic devices.