bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vps3 and Vps8 control integrin trafficking from early to recycling endosomes and regulate integrin-dependent functions
Authors: Jonker Caspar T. H. , Galmes Romain , Veenendaal Tineke , ten Brink Corlinda , van der Welle Reini E. N. , Liv Nalan , de Rooij Johan , Peden Andrew A. , van der Sluijs Peter , Margadant Coert , Klumperman Judith 
Published: February 2018

AbstractRecycling endosomes maintain plasma membrane homeostasis and are important for cell polarity, migration, and cytokinesis. Yet, the molecular machineries that drive endocytic recycling remain largely unclear. The CORVET complex is a multi-subunit tether required for fusion between early endosomes. Here we show that the CORVET-specific subunits Vps3 and Vps8 also regulate vesicular transport from early to recycling endosomes. Vps3 and Vps8 localise to Rab4-positive recycling vesicles and co-localise with the CHEVI complex on Rab11-positive recycling endosomes. Depletion of Vps3 or Vps8 does not affect transferrin recycling, but delays the delivery of internalised integrins to recycling endosomes and their subsequent return to the plasma membrane. Consequently, Vps3/8 depletion results in defects in integrin-dependent cell adhesion and spreading, focal adhesion formation, and cell migration. These data reveal a role for Vps3 and Vps8 in a specialised recycling pathway important for integrin trafficking.
Diverse genetic error modes constrain large-scale bio-based production
Authors: Rugbjerg Peter , Myling-Petersen Nils , Porse Andreas , Sarup-Lytzen Kira , Sommer Morten O. A. 
Published: February 2018

AbstractA transition toward sustainable bio-based chemical production is important for green growth. However, productivity and yield frequently decrease as large-scale microbial fermentation progresses, commonly ascribed to phenotypic variation. Yet, given the high metabolic burden and toxicities, evolutionary processes may also constrain bio-based production. We experimentally simulate large-scale fermentation with mevalonic acid-producing Escherichia coli. By tracking growth rate and production, we uncover how populations fully sacrifice production to gain fitness within 70 generations. Using ultra-deep (>1000×) time-lapse sequencing of the pathway populations, we identify multiple recurring intra-pathway genetic error modes. This genetic heterogeneity is only detected using deep-sequencing and new population-level bioinformatics, suggesting that the problem is underestimated. A quantitative model explains the population dynamics based on enrichment of spontaneous mutant cells. We validate our model by tuning production load and escape rate of the production host and apply multiple orthogonal strategies for postponing genetically driven production declines.
Cobalt-catalyzed electrooxidative C-H/N-H [4+2] annulation with ethylene or ethyne
Authors: Tang Shan , Wang Dan , Liu Yichang , Zeng Li , Lei Aiwen 
Published: February 2018

AbstractEthylene and ethyne are among the simplest two-carbon building blocks. However, quite limited methods can be applied to incorporate ethylene or ethyne into fine chemicals. Here we demonstrate a cobalt-catalyzed dehydrogenative C–H/N–H [4+2] annulation of aryl/vinyl amides with ethylene or ethyne by using an electrochemical reaction protocol. Significantly, this work shows an example of electrochemical recycling of cobalt catalyst in oxidative C–H functionalization reactions, avoiding the use of external chemical oxidants and co-oxidants. The electrochemical method provides a reliable and safe way for incorporating gas-phase ethylene or ethyne into fine chemicals. High reaction efficiency and good functional group tolerance are observed under divided electrolytic conditions.
HMG-CoA reductase from Camphor Tulsi (Ocimum kilimandscharicum) regulated MVA dependent biosynthesis of diverse terpenoids in homologous and heterologous plant systems
Authors: Bansal Shilpi , Narnoliya Lokesh Kumar , Mishra Bhawana , Chandra Muktesh , Yadav Ritesh Kumar , Sangwan Neelam Singh 
Published: February 2018

AbstractOcimum kilimandscharicum is unique in possessing terpenoids whereas other Ocimum species are renowned for phenylpropanoids as major constituents of essential oil. The key enzyme of MVA/terpenoid metabolic pathway viz 3-hydroxy-3-methylglutaryl Co-A reductase (OkHMGR) of 1.7-Kb ORF encoding ~60-kDa protein was cloned from O. kilimandscharicum and its kinetic characteristics revealed the availability of HMG-CoA as a control point of MVA-pathway. Transcript profiling of the OkHMGR elucidated tissue-specific functions of the gene in flower and leaf tissues in accumulation of terpenoidal essential oil. OkHMGR was differentially regulated in response to exposure to methyl-jasmonate, salicylic-acid, and stress conditions such-as salt and temperature stress, demonstrating its key role in managing signaling and stress-responses. To elucidate its functional role, OkHMGR was transiently over-expressed in homologous and heterologous plants such as O. sanctum, O. basilicum, O. gratissimum, Withania somnifera and Artemisia annua. The over-expression and inhibition dual strategy revealed that the additional OkHMGR in-planta could afford endogenous flow of isoprenoid units towards synthesis of terpenoids. The present study provides in-depth insight of OkHMGR in regulation of biosynthesis of non-plastidal isoprenoids. This is first report on any gene of MVA/isoprenoid pathway from under-explored Camphor Tulsi belonging to genus Ocimum. Studies also suggested that OkHMGR could be a potential tool for attempting metabolic engineering for enhancing medicinally important terpenoidal metabolites in plants.
STAT3 regulates cytotoxicity of human CD57+ CD4+ T cells in blood and lymphoid follicles
Authors: Alshekaili Jalila , Chand Rochna , Lee Cindy Eunhee , Corley Susan , Kwong Kristy , Papa Ilenia , Fulcher David A. , Randall Katrina L. , Leiding Jennifer W. , Ma Cindy S. , Wilkins Marc R. , Uzel Gulbu , Goodnow Chris C. , Vinuesa Carola G. , Tangye Stuart G. , Cook Matthew C. 
Published: February 2018

AbstractA subset of human follicular helper T cells (TFH) cells expresses CD57 for which no distinct function has been identified. We show that CD57+ TFH cells are universally PD-1hi, but compared to their CD57− PD-1hicounterparts, express little IL-21 or IL-10 among others. Instead, CD57 expression on TFH cells marks cytotoxicity transcriptional signatures that translate into only a weak cytotoxic phenotype. Similarly, circulating PD-1+ CD57+ CD4+ T cells make less cytokine than their CD57− PD-1+ counterparts, but have a prominent cytotoxic phenotype. By analysis of responses to STAT3-dependent cytokines and cells from patients with gain- or loss-of-functionSTAT3mutations, we show that CD4+ T cell cytotoxicity is STAT3-dependent. TFH formation also requires STAT3, but paradoxically, once formed, PD-1hicells become unresponsive to STAT3. These findings suggest that changes in blood and germinal center cytotoxicity might be affected by changes in STAT3 signaling, or modulation of PD-1 by therapy.
Validity of Weyl fermion picture for transition metals monopnictides TaAs, TaP, NbAs, and NbP from ab initio studies
Authors: Grassano Davide , Pulci Olivia , Mosca Conte Adriano , Bechstedt Friedhelm 
Published: February 2018

AbstractWe investigate electronic and optical properties of the topological Weyl semimetals TaAs, TaP, NbAs and NbP crystallizing in bct geometry by means of theab initiodensity functional theory with spin-orbit interaction within the independent-particle approximation. The small energetical overlap of Ta5dor Nb4dderived conduction and valence bands leads to electron and/or hole pockets near the Fermi energy at the 24 Weyl nodes. The nodes give rise to two-(three-)dimensional Dirac cones for theW1(W2) Weyl type. The band dispersion and occupation near the Weyl nodes determine the infrared optical properties. They are dominated by interband transitions, which lead to a deviation from the expected constant values of the imaginary part of the dielectric function. The resulting polarization anisotropy is also visible in the real part of the optical conductivity, whose lineshape deviates from the expected linearity. The details of the Weyl nodes are discussed in relation to recent ARPES results for TaAs and NbP, and compared with measured optical spectra for TaAs. The spectral features of the anisotropic and tilted Weyl fermions are restricted to low excitation energies above absorption onsets due to the band occupation.
A genetic variant in SLC30A2 causes breast dysfunction during lactation by inducing ER stress, oxidative stress and epithelial barrier defects
Authors: Lee Sooyeon , Zhou Yandong , Gill Donald L. , Kelleher Shannon L. 
Published: February 2018

AbstractSLC30A2 encodes a zinc (Zn) transporter (ZnT2) that imports Zn into vesicles in highly-specialized secretory cells. Numerous mutations and non-synonymous variants in ZnT2 have been reported in humans and in breastfeeding women; ZnT2 variants are associated with abnormally low milk Zn levels and can lead to severe infantile Zn deficiency. However, ZnT2-null mice have profound defects in mammary epithelial cell (MEC) polarity and vesicle secretion, indicating that normal ZnT2 function is critical for MEC function. Here we report that women who harbor a common ZnT2 variant (T288S) present with elevated levels of several oxidative and endoplasmic reticulum (ER) stress markers in their breast milk. Functional studies in vitro suggest that substitution of threonine for serine at amino acid 288 leads to hyperphosphorylation retaining ZnT2 in the ER and lysosomes, increasing ER and lysosomal Zn accumulation, ER stress, the generation of reactive oxygen species, and STAT3 activation. These changes were associated with decreased abundance of zona occludens-1 and increased tight junction permeability. This study confirms that ZnT2 is important for normal breast function in women during lactation, and suggests that women who harbor defective variants in ZnT2 may be at-risk for poor lactation performance.
Low-level Gestational Lead Exposure Alters Dendritic Spine Plasticity in the Hippocampus and Reduces Learning and Memory in Rats
Authors: Zhao Zai-Hua , Zheng Gang , Wang Tao , Du Ke-jun , Han Xiao , Luo Wen-Jing , Shen Xue-Feng , Chen Jing-Yuan 
Published: February 2018

AbstractLead (Pb) is known to impair children’s cognitive function. It has been previously shown that developmental Pb exposure alters dendritic spine formation in hippocampal pyramidal neurons. However, the underlying mechanism has not yet been defined. In this study, a low-level gestational Pb exposure (GLE) rat model was employed to investigate the impact of Pb on the spine density of the hippocampal pyramidal neurons and its regulatory mechanism. Pb exposure resulted in impaired performance of the rats in the Morris water maze tasks, and in decreased EPSC amplitudes in hippocampal CA3-CA1 regions. With a 3D reconstruction by the Imaris software, the results from Golgi staining showed that the spine density in the CA1 region was reduced in the Pb-exposed rats in a dose-dependent manner. Decreased spine density was also observed in cultured hippocampal neurons following the Pb treatment. Furthermore, the expression level of NLGN1, a postsynaptic protein that mediates synaptogenesis, was significantly decreased following the Pb exposure bothin vivoandin vitro. Up-regulation of NLGN1 in cultured primary neurons partially attenuated the impact of Pb on the spine density. Taken together, our resultssuggest that Pb exposure alters spine plasticity in the developing hippocampus by down-regulating NLGN1 protein levels.
Functionally distinct smiles elicit different physiological responses in an evaluative context
Authors: Martin Jared D. , Abercrombie Heather C. , Gilboa-Schechtman Eva , Niedenthal Paula M. 
Published: February 2018

AbstractWhen people are being evaluated, their whole body responds. Verbal feedback causes robust activation in the hypothalamic-pituitary-adrenal (HPA) axis. What about nonverbal evaluative feedback? Recent discoveries about the social functions of facial expression have documented three morphologically distinct smiles, which serve the functions of reinforcement, social smoothing, and social challenge. In the present study, participants saw instances of one of three smile types from an evaluator during a modified social stress test. We find evidence in support of the claim that functionally different smiles are sufficient to augment or dampen HPA axis activity. We also find that responses to the meanings of smiles as evaluative feedback are more differentiated in individuals with higher baseline high-frequency heart rate variability (HF-HRV), which is associated with facial expression recognition accuracy. The differentiation is especially evident in response to smiles that are more ambiguous in context. Findings suggest that facial expressions have deep physiological implications and that smiles regulate the social world in a highly nuanced fashion.
Reduced graphene oxide (rGO) based wideband optical sensor and the role of Temperature, Defect States and Quantum Efficiency
Authors: Abid  , Sehrawat Poonam , Islam S. S. , Mishra Prabhash , Ahmad Shahab 
Published: February 2018

AbstractWe report a facile and cost-effective approach to develop self-standing reduced Graphene Oxide (rGO) film based optical sensor and its low-temperature performance analysis where midgap defect states play a key role in tuning the crucial sensor parameters. Graphite oxide (GO) is produced by modified Hummers’ method and reduced thermally at 250 °C for 1 h in Argon atmosphere to obtain rGO. Self-standing rGO film is prepared via vacuum filtration. The developed film is characterized by HRTEM, FESEM, Raman, and XRD techniques. The developed sensor exhibits highest sensitivity towards 635 nm illumination wavelength, irrespective of the operating temperature. For a given excitation wavelength, photoresponse study at low temperature (123K–303K) reveals inverse relationship between sensitivity and operating temperature. Highest sensitivity of 49.2% is obtained at 123 K for 635 nm laser at power density of 1.4 mW/mm2. Unlike sensitivity, response- and recovery-time demonstrate directly proportional dependence with operating temperature. Power dependent studies establish linear relation between power-density and sensitivity, and a safe limit beyond which sample heating prolongs the recovery time. Wavelength-dependent studies shows that proposed sensor can efficiently operate from visible to near NIR region. To the best of our knowledge such rGO based optical sensor performance at low temperature had not been reported earlier.
Sub-cellular In-situ Characterization of Ferritin(iron) in a Rodent Model of Spinal Cord Injury
Authors: Blissett A. R. , Deng B. , Wei P. , Walsh K. J. , Ollander B. , Sifford J. , Sauerbeck A. D. , McComb D. W. , McTigue D. M. , Agarwal G. 
Published: February 2018

AbstractIron (Fe) is an essential metal involved in a wide spectrum of physiological functions. Sub-cellular characterization of the size, composition, and distribution of ferritin(iron) can provide valuable information on iron storage and transport in health and disease. In this study we employ magnetic force microscopy (MFM), transmission electron microscopy (TEM), and electron energy loss spectroscopy (EELS) to characterize differences in ferritin(iron) distribution and composition across injured and non-injured tissues by employing a rodent model of spinal cord injury (SCI). Our biophysical and ultrastructural analyses provide novel insights into iron distribution which are not obtained by routine biochemical stains. In particular, ferritin(iron) rich lysosomes revealed increased heterogeneity in MFM signal from tissues of SCI animals. Ultrastructural analysis using TEM elucidated that both cytosolic and lysosomal ferritin(iron) density was increased in the injured (spinal cord) and non-injured (spleen) tissues of SCI as compared to naïve animals. In-situ EELs analysis revealed that ferritin(iron) was primarily in Fe3+ oxidation state in both naïve and SCI animal tissues. The insights provided by this study and the approaches utilized here can be applied broadly to other systemic problems involving iron regulation or to understand the fate of exogenously delivered iron-oxide nanoparticles.
A combinatorial framework to quantify peak/pit asymmetries in complex dynamics
Authors: Hasson Uri , Iacovacci Jacopo , Davis Ben , Flanagan Ryan , Tagliazucchi Enzo , Laufs Helmut , Lacasa Lucas 
Published: February 2018

AbstractWe explore a combinatorial framework which efficiently quantifies the asymmetries between minima and maxima in local fluctuations of time series. We first showcase its performance by applying it to a battery of synthetic cases. We find rigorous results on some canonical dynamical models (stochastic processes with and without correlations, chaotic processes) complemented by extensive numerical simulations for a range of processes which indicate that the methodology correctly distinguishes different complex dynamics and outperforms state of the art metrics in several cases. Subsequently, we apply this methodology to real-world problems emerging across several disciplines including cases in neurobiology, finance and climate science. We conclude that differences between the statistics of local maxima and local minima in time series are highly informative of the complex underlying dynamics and a graph-theoretic extraction procedure allows to use these features for statistical learning purposes.
Comparative transcriptomics of multidrug-resistant Acinetobacter baumannii in response to antibiotic treatments
Authors: Qin Hao , Lo Norman Wai-Sing , Loo Jacky , Lin Xiao , Yim Aldrin Kay-Yuen , Tsui Stephen Kwok-Wing , Lau Terrence Chi-Kong , Ip Margaret , Chan Ting-Fung 
Published: February 2018

AbstractMultidrug-resistant Acinetobacter baumannii, a major hospital-acquired pathogen, is a serious health threat and poses a great challenge to healthcare providers. Although there have been many genomic studies on the evolution and antibiotic resistance of this species, there have been very limited transcriptome studies on its responses to antibiotics. We conducted a comparative transcriptomic study on 12 strains with different growth rates and antibiotic resistance profiles, including 3 fast-growing pan-drug-resistant strains, under separate treatment with 3 antibiotics, namely amikacin, imipenem, and meropenem. We performed deep sequencing using a strand-specific RNA-sequencing protocol, and used de novo transcriptome assembly to analyze gene expression in the form of polycistronic transcripts. Our results indicated that genes associated with transposable elements generally showed higher levels of expression under antibiotic-treated conditions, and many of these transposon-associated genes have previously been linked to drug resistance. Using co-expressed transposon genes as markers, we further identified and experimentally validated two novel genes of which overexpression conferred significant increases in amikacin resistance. To the best of our knowledge, this study represents the first comparative transcriptomic analysis of multidrug-resistant A. baumannii under different antibiotic treatments, and revealed a new relationship between transposons and antibiotic resistance.
Indian Summer Monsoon Simulations: Usefulness of Increasing Horizontal Resolution, Manual Tuning, and Semi-Automatic Tuning in Reducing Present-Day Model Biases
Authors: Anand Abhishek , Mishra Saroj K. , Sahany Sandeep , Bhowmick Mansi , Rawat Janmejai Singh , Dash S. K. 
Published: February 2018

AbstractCoupled Global Climate Models (CGCMs) of the Coupled Model Intercomparison Project Phase 5 (CMIP5) are unable to resolve the spatial and temporal characteristics of the South Asian Monsoon satisfactorily. A CGCM with the capability to reliably project the global as well as the regional climatic features would be a valuable tool for scientists and policymakers. Analysis of 28 CMIP5 models highlights varying degree of biases in precipitation and 2 m surface air temperature (T2m) over south Asia, and the Community Earth System Model (CESM) developed at the National Center for Atmospheric Research is found to be one of the best performing models. However, like all other CMIP5 models, CESM also has some inherent model biases. Using CESM, it is found that the precipitation and T2M biases reduce with increase in the model horizontal resolution from 2° to 0.5°. Further, a few deep convective parameters in the Zhang-McFarlane convection scheme are tuned for 2° and 1° model resolutions using both manual and semi-automatic model tuning methods. Comparing results from the two tuning methods we find that the performance of the manually tuned model is better than that of the semi-automated one.
Profiling Atlantic salmon B cell populations: CpG-mediated TLR-ligation enhances IgM secretion and modulates immune gene expression
Authors: Jenberie Shiferaw , Thim Hanna L. , Sunyer J. Oriol , Skjødt Karsten , Jensen Ingvill , Jørgensen Jorunn B. 
Published: February 2018

AbstractWhile TLR-activated pathways are key regulators of B cell responses in mammals, their impact on teleost B cells are scarcely addressed. Here, the potential of Atlantic salmon B cells to respond to TLR ligands was shown by demonstrating a constitutive expression of nucleic-acid sensing TLRs in magnetic sorted IgM+ cells. Of the two receptors recognizing CpG in teleosts, tlr9 was the dominating receptor with over ten-fold higher expression than tlr21. Upon CpG-stimulation, IgM secretion increased for head kidney (HK) and splenic IgM+ cells, while blood B cells were marginally affected. The results suggest that CpG directly affects salmon B cells to differentiate into antibody secreting cells (ASCs). IgM secretion was also detected in the non-treated controls, again with the highest levels in the HK derived population, signifying that persisting ASCs are present in this tissue. In all tissues, the IgM+ cells expressed high MHCII levels, suggesting antigen-presenting functions. Upon CpG-treatment the co-stimulatory molecules cd83 and cd40 were upregulated, while cd86 was down-regulated under the same conditions. Finally, ifna1 was upregulated upon CpG-stimulation in all tissues, while a restricted upregulation was evident for ifnb, proposing that salmon IgM+ B cells exhibit a type I IFN-response.
Wrinkled Nitrogen-doped Carbon Belts
Authors: Fajardo-Díaz Juan L. , López-Urías Florentino , Muñoz-Sandoval Emilio 
Published: February 2018

AbstractGraphene, carbon nanotubes, and fullerenes are nanomaterials with outstanding properties such as electrical, thermal, mechanical strength, flexibility, and high surface area. These nanomaterials are used as building blocks for the construction of novel and astonishing 3D-dimensional networks. In the present work, nitrogen-doped carbon belt (N-CB) structures containing wrinkled carbon fibres as building blocks were synthesized under unstable conditions in a chemical vapour deposition experiment. N-CB structures with 0.2–3.0 microns of wide and 350 nm thick were assembled from complex individual wrinkled carbon fibres grown on Co/Cu films. These complex structures have a tubular appearance, showing holed and wrinkled graphite layers. Sulphur and copper atoms drastically affect the catalytic role of cobalt, changing the conventional growth of carbon nanotubes. Chemical functional groups, N-doping, and carbons hybridizations involved in the winkled carbon fibres are investigated. These findings provides a novel material that can be used as an excellent oxygen-reduction reaction catalyst or nano-electronics component.