bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissolved Lead in the East China Sea With Implications for Impacts of Marginal Seas on the Open Ocean Through Cross‐Shelf Exchange
Authors: Jiang Shuo , Zhang Jing , Zhang Ruifeng , Xue Yun , Zheng Wei
Published: August 2018

The distribution of lead (Pb) in the ocean is influenced by human activities. During a cruise in the East China Sea (ECS) in August 2013, we investigated six representative stations and gave the first systematic description of dissolved lead (DPb) distributions after the phasing out of leaded gasoline in China. The DPb concentration in the ECS ranged from 23.8 to 96.7 pmol/kg, with the highest concentrations observed at the surface of the middle shelf, while the lowest concentrations were determined to be in deep samples collected at the shelf break. Vertical profiles of DPb vary with geographic locations, seawater turbidity, hypoxic conditions, atmospheric deposition, and hydrographic regimes. As one of the most important western boundary currents, Kuroshio receives an additional 10–20 pmol/kg of DPb from the ECS shelf through a cross‐shelf exchange process, and approximately (1.1–1.7) × 109 g/yr of DPb was exported through the shelf break area, which will directly join the North Pacific circulation based on a preliminary box model. In addition, the ECS shelf exported another 1.4 × 109 g/yr of DPb from the Tsushima/Korea Strait, which has the potential to influence the northwestern Pacific Ocean as well as the Sea of Japan/East Sea. A residence time of 2–3 months for DPb in the ECS was inferred.
Locating Preliminary Breakdown Pulses in Positive Cloud‐to‐Ground Lightning
Authors: Wu Ting , Wang Daohong , Takagi Nobuyuki
Published: August 2018

This paper provides the first concrete evidence that preliminary breakdown (PB) pulses of either polarity in positive cloud‐to‐ground (+CG) lightning are produced by negative leaders. Three‐dimensional location results of PB pulses in 46 +CG flashes are analyzed. The majority (40) of the +CG flashes started with positive PB pulses (+PBPs), the same polarity as the positive return stroke. Location results showed that +PBPs were produced by leaders propagating upward, which were determined to be negative leaders based on PB pulse polarities. Similarly, for the negative PB pulses (−PBPs) found in six +CG flashes, location results showed that they were produced by leaders propagating downward, and we determined that these were also negative leaders. Upward negative leaders producing +PBPs in +CG lightning are very similar to those in intracloud lightning. They usually propagate upward before turning in a horizontal direction. Downward negative leaders producing −PBPs in +CG lightning are more complicated. They usually move back upward after a period of downward propagation. Positive leaders could not be detected, but their possible propagations are analyzed along with possible charge structures for different types of PB pulses. We also demonstrate that PB pulse studies based on single‐site records are potentially unreliable.
Penetrative Convection in Super‐Earth Planets: Consequences of MgSiO3 Postperovskite Dissociation Transition and Implications for Super‐Earth GJ 876 d
Authors: Shahnas M. H. , Pysklywec R. N. , Yuen D. A.
Published: August 2018

Theoretical studies suggest that MgSiO3 postperovskite dissociates into MgO and MgSi2O5 at 0.9 TPa, and MgSi2O5 dissociates into MgO and SiO2 at 2.1 TPa, both with negative Clapeyron slopes. In addition, unlike a conventional view, the viscosity in super‐Earth planets is proposed to decrease with pressure when pressure exceeds ~0.1 TPa. Employing 2‐D‐axisymmtric and 3‐D‐spherical control volume compressible models, we perform an investigation on the impact of deep mantle dissociation of postperovskite into oxides, in conjunction with variations of the mantle viscosity, on the degree of the deep mantle layering, and the consequences of this layering on cooling of the rocky planets similar to super‐Earth GJ 876 d. Small‐scale convection in a layer of thickness ~500 km from which penetrative plumes originate, develops above the core‐mantle boundary (CMB) in the models for which the viscosity at the dissociation transition depth and below is less than ~1023 Pa·s. Due to the buffering effect of this deep mantle layering, while the mean mantle temperature above the layer decreases, resulting in a viscosity increase above the layer, it increases in the layered region above the CMB. This leads to a further reduction in viscosity at the bottom of the mantle. The effect is enhanced with increasing the CMB temperature and the contrast in thermal expansivity. The cooling rate of the planet decreases in the layered models due to the buffering effect of this deep mantle transition, as well as the influence of the viscosity increase above transition depth.
A Methodology for Anomaly Coupling in Climate Simulation
Authors: Toniazzo Thomas , Koseki Shunya
Published: August 2018

We demonstrate a new methodology for anomaly coupling in general circulation models on the basis of simulations with the Norwegian Earth System Model. A correction is applied to the sea surface temperature (SST) and wind‐stress climatology of the coupled model during the integration in such a way as to match the observed climatology. The correction is found iteratively by updating the model climatology at every time step, allowing the simulation to converge toward a self‐consistent surface climatology close to that observed, with minimal impact on the simulation of variability. Our approach differs from the traditional way of anomaly coupling that employs fixed model climatologies from stand‐alone model runs to correct the model's climatological mean state. While the atmosphere and ocean components are forced by inconsistent surface fluxes in our methodology, the inconsistency becomes smaller as the simulated climatology converges toward the observations after about 30 years. Our methodology achieves a significant reduction in the systematic SST biases of the coupled model climatology, especially over the tropical and subtropical oceans. Associated with the reduction of tropical SST biases, the double‐ Inter‐tropical Convergence Zone (ITCZ) problem is mitigated, the seasonal cycle is well represented, and some aspects of coupled variability such as the El Nino Southern Oscillation are improved. The methodology can be extended in a way that ensures global energy conservation without affecting the improvements in the simulated climatology and may be thus applied for prediction purposes.
Astronomically Driven Variations in Depositional Environments in the South Atlantic During the Early Cretaceous
Authors: Behrooz L. , Naafs B. D. A. , Dickson A. J. , Love G. D. , Batenburg S. J. , Pancost R. D.
Published: August 2018

The extent and persistence of anoxia in the South Atlantic Ocean during its early opening phase in the Early Cretaceous is not well constrained, hindering a holistic understanding of the processes and mechanisms that drive past changes in water column redox conditions, as well as the impacts of such changes on marine ecosystems. Here we provide high‐resolution geochemical records from Deep Sea Drilling Project Site 364 that document variations in redox conditions, chemocline depth, marine productivity, and marine ecosystem dynamics in the northern South Atlantic during the Aptian. We show that many of these parameters varied across discrete sedimentary cycles expressed in the Deep Sea Drilling Project 364 succession. Our data indicate that during the initial stages of basin development, anoxic and euxinic conditions were prevalent and occasionally extended into the upper water column. However, strong cyclicity in sedimentological and geochemical parameters imply that the anoxia/euxinia was not a persistent state. We argue that the water column redox conditions during the Aptian were driven by changes in the hydrological cycle, induced by variations in astronomical forcing. We suggest that the episodically amplified hydrological cycle not only enhanced nutrient availability and marine productivity, but might also have caused density‐driven upper ocean stratification. The presence of black shales of similar age in other ocean basins suggests that this mechanism is broadly important for the formation of Early Cretaceous organic‐rich successions.
Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae
Authors: Morlot Cécile , Straume Daniel , Peters Katharina , Hegnar Olav A. , Simon Nolwenn , Villard Anne-Marie , Contreras-Martel Carlos , Leisico Francisco , Breukink Eefjan , Gravier-Pelletier Christine , Le Corre Laurent , Vollmer Waldemar , Pietrancosta Nicolas , Håvarstein Leiv Sigve , Zapun André
Published: August 2018

The universality of peptidoglycan in bacteria underlies the broad spectrum of many successful antibiotics. However, in our times of widespread resistance, the diversity of peptidoglycan modifications offers a variety of new antibacterials targets. In some Gram-positive species such as Streptococcus pneumoniae, Staphylococcus aureus, or Mycobacterium tuberculosis, the second residue of the peptidoglycan precursor, D-glutamate, is amidated into iso-D-glutamine by the essential amidotransferase MurT/GatD complex. Here, we present the structure of this complex at 3.0 Å resolution. MurT has central and C-terminal domains similar to Mur ligases with a cysteine-rich insertion, which probably binds zinc, contributing to the interface with GatD. The mechanism of amidation by MurT is likely similar to the condensation catalyzed by Mur ligases. GatD is a glutaminase providing ammonia that is likely channeled to the MurT active site through a cavity network. The structure and assay presented here constitute a knowledge base for future drug development studies.
Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient
Authors: Albrecht Jörg , Classen Alice , Vollstädt Maximilian G. R. , Mayr Antonia , Mollel Neduvoto P. , Schellenberger Costa David , Dulle Hamadi I. , Fischer Markus , Hemp Andreas , Howell Kim M. , Kleyer Michael , Nauss Thomas , Peters Marcell K. , Tschapka Marco , Steffan-Dewenter Ingolf , Böhning-Gaese Katrin , Schleuning Matthias
Published: August 2018

Species’ functional traits set the blueprint for pair-wise interactions in ecological networks. Yet, it is unknown to what extent the functional diversity of plant and animal communities controls network assembly along environmental gradients in real-world ecosystems. Here we address this question with a unique dataset of mutualistic bird–fruit, bird–flower and insect–flower interaction networks and associated functional traits of 200 plant and 282 animal species sampled along broad climate and land-use gradients on Mt. Kilimanjaro. We show that plant functional diversity is mainly limited by precipitation, while animal functional diversity is primarily limited by temperature. Furthermore, shifts in plant and animal functional diversity along the elevational gradient control the niche breadth and partitioning of the respective other trophic level. These findings reveal that climatic constraints on the functional diversity of either plants or animals determine the relative importance of bottom-up and top-down control in plant–animal interaction networks.
Control of transmembrane charge transfer in cytochrome c oxidase by the membrane potential
Authors: Björck Markus L. , Brzezinski Peter
Published: August 2018

The respiratory chain in mitochondria is composed of membrane-bound proteins that couple electron transfer to proton translocation across the inner membrane. These charge-transfer reactions are regulated by the proton electrochemical gradient that is generated and maintained by the transmembrane charge transfer. Here, we investigate this feedback mechanism in cytochromecoxidase in intact inner mitochondrial membranes upon generation of an electrochemical potential by hydrolysis of ATP. The data indicate that a reaction step that involves proton uptake to the catalytic site and presumably proton translocation is impaired by the potential, but electron transfer is not affected. These results define the order of electron and proton-transfer reactions and suggest that the proton pump is regulated by the transmembrane electrochemical gradient through control of internal proton transfer rather than by control of electron transfer.
Holocene reconfiguration and readvance of the East Antarctic Ice Sheet
Authors: Greenwood Sarah L. , Simkins Lauren M. , Halberstadt Anna Ruth W. , Prothro Lindsay O. , Anderson John B.
Published: August 2018

How ice sheets respond to changes in their grounding line is important in understanding ice sheet vulnerability to climate and ocean changes. The interplay between regional grounding line change and potentially diverse ice flow behaviour of contributing catchments is relevant to an ice sheet’s stability and resilience to change. At the last glacial maximum, marine-based ice streams in the western Ross Sea were fed by numerous catchments draining the East Antarctic Ice Sheet. Here we present geomorphological and acoustic stratigraphic evidence of ice sheet reorganisation in the South Victoria Land (SVL) sector of the western Ross Sea. The opening of a grounding line embayment unzipped ice sheet sub-sectors, enabled an ice flow direction change and triggered enhanced flow from SVL outlet glaciers. These relatively small catchments behaved independently of regional grounding line retreat, instead driving an ice sheet readvance that delivered a significant volume of ice to the ocean and was sustained for centuries.
Structural basis for reactivating the mutant TERT promoter by cooperative binding of p52 and ETS1
Authors: Xu Xueyong , Li Yinghui , Bharath Sakshibeedu R. , Ozturk Mert Burak , Bowler Matthew W. , Loo Bryan Zong Lin , Tergaonkar Vinay , Song Haiwei
Published: August 2018

Transcriptional factors ETS1/2 and p52 synergize downstream of non-canonical NF-κB signaling to drive reactivation of the −146C>T mutant TERT promoter in multiple cancer types, but the mechanism underlying this cooperativity remains unknown. Here we report the crystal structure of a ternary p52/ETS1/−146C>T TERT promoter complex. While p52 needs to associate with consensus κB sites on the DNA to function during non-canonical NF-κB signaling, we show that p52 can activate the −146C>T TERT promoter without binding DNA. Instead, p52 interacts with ETS1 to form a heterotetramer, counteracting autoinhibition of ETS1. Analogous to observations with the GABPA/GABPB heterotetramer, the native flanking ETS motifs are required for sustained activation of the −146C>T TERT promoter by the p52/ETS1 heterotetramer. These observations provide a unifying mechanism for transcriptional activation by GABP and ETS1, and suggest that genome-wide targets of non-canonical NF-κB signaling are not limited to those driven by consensus κB sequences.
Universal molecular structures in natural dissolved organic matter
Authors: Zark Maren , Dittmar Thorsten
Published: August 2018

Natural dissolved organic matter (DOM) comprises a broad range of dissolved organic molecules in aquatic systems and is among the most complex molecular mixtures known. Here we show, by comparing detailed structural fingerprints of individual molecular formulae in DOM from a set of four marine and one freshwater environments, that a major component of DOM is molecularly indistinguishable in these diverse samples. Molecular conformity was not only apparent by the co-occurrence of thousands of identical molecular formulae, but also by identical structural features of those isomers that collectively represent a molecular formula. The presence of a large pool of compounds with identical structural features in DOM is likely the result of a cascade of degradation processes or common synthetic pathways that ultimately lead to the formation of a universal background, regardless of origin and history of the organic material. This novel insight impacts our understanding of long-term turnover of DOM as the underlying mechanisms are possibly universal.
More replenishment than priming loss of soil organic carbon with additional carbon input
Authors: Liang Junyi , Zhou Zhenghu , Huo Changfu , Shi Zheng , Cole James R. , Huang Lei , Konstantinidis Konstantinos T. , Li Xiaoming , Liu Bo , Luo Zhongkui , Penton C. Ryan , Schuur Edward A. G. , Tiedje James M. , Wang Ying-Ping , Wu Liyou , Xia Jianyang , Zhou Jizhong , Luo Yiqi
Published: August 2018

Increases in carbon (C) inputs to soil can replenish soil organic C (SOC) through various mechanisms. However, recent studies have suggested that the increased C input can also stimulate the decomposition of old SOC via priming. Whether the loss of old SOC by priming can override C replenishment has not been rigorously examined. Here we show, through data–model synthesis, that the magnitude of replenishment is greater than that of priming, resulting in a net increase in SOC by a mean of 32% of the added new C. The magnitude of the net increase in SOC is positively correlated with the nitrogen-to-C ratio of the added substrates. Additionally, model evaluation indicates that a two-pool interactive model is a parsimonious model to represent the SOC decomposition with priming and replenishment. Our findings suggest that increasing C input to soils likely promote SOC accumulation despite the enhanced decomposition of old C via priming.
Hybrid nanodiamond quantum sensors enabled by volume phase transitions of hydrogels
Authors: Zhang Ting , Liu Gang-Qin , Leong Weng-Hang , Liu Chu-Feng , Kwok Man-Hin , Ngai To , Liu Ren-Bao , Li Quan
Published: August 2018

Diamond nitrogen-vacancy (NV) center-based magnetometry provides a unique opportunity for quantum bio-sensing. However, NV centers are not sensitive to parameters such as temperature and pressure, and immune to many biochemical parameters such as pH and non-magnetic biomolecules. Here, we propose a scheme that can potentially enable the measurement of various biochemical parameters using diamond quantum sensing, by employing stimulus-responsive hydrogels as a spacing transducer in-between a nanodiamond (ND, with NV centers) and magnetic nanoparticles (MNPs). The volume phase transition of hydrogel upon stimulation leads to sharp variation in the separation distance between the MNPs and the ND. This in turn changes the magnetic field that the NV centers can detect sensitively. We construct a temperature sensor under this hybrid scheme and show the proof-of-the-principle demonstration of reversible temperature sensing. Applications in the detection of other bio-relevant parameters are envisioned if appropriate types of hydrogels can be engineered.
Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment
Authors: Quevedo Camilo E. , Cruz-Migoni Abimael , Bery Nicolas , Miller Ami , Tanaka Tomoyuki , Petch Donna , Bataille Carole J. R. , Lee Lydia Y. W. , Fallon Phillip S. , Tulmin Hanna , Ehebauer Matthias T. , Fernandez-Fuentes Narcis , Russell Angela J. , Carr Stephen B. , Phillips Simon E. V. , Rabbitts Terence H.
Published: August 2018

Targeting specific protein–protein interactions (PPIs) is an attractive concept for drug development, but hard to implement since intracellular antibodies do not penetrate cells and most small-molecule drugs are considered unsuitable for PPI inhibition. A potential solution to these problems is to select intracellular antibody fragments to block PPIs, use these antibody fragments for target validation in disease models and finally derive small molecules overlapping the antibody-binding site. Here, we explore this strategy using an anti-mutant RAS antibody fragment as a competitor in a small-molecule library screen for identifying RAS-binding compounds. The initial hits are optimized by structure-based design, resulting in potent RAS-binding compounds that interact with RAS inside the cells, prevent RAS-effector interactions and inhibit endogenous RAS-dependent signalling. Our results may aid RAS-dependent cancer drug development and demonstrate a general concept for developing small compounds to replace intracellular antibody fragments, enabling rational drug development to target validated PPIs.
Author Correction: Periodical reactivation under the effect of caffeine attenuates fear memory expression in rats
Authors: Pedraza Lizeth K. , Sierra Rodrigo O. , Lotz Fernanda N. , De Oliveira Alvares Lucas
Published: August 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Virtual Recovery of Content from X-Ray Micro-Tomography Scans of Damaged Historic Scrolls
Authors: Rosin Paul L. , Lai Yu-Kun , Liu Chang , Davis Graham R. , Mills David , Tuson Gary , Russell Yuki
Published: August 2018

There is a large body of historical documents that are too fragile to be opened or unrolled, making their contents inaccessible. Recent improvements in X-ray scanning technology and computer vision techniques make it possible to perform a “virtual” unrolling of such documents. We describe a novel technique to process a stack of 3D X-ray images to identify the surface of parchment scrolls, unroll them, and create a visualization of their written contents. Unlike existing techniques, we can handle even challenging cases with minimal manual interaction. Our novel approach was deployed on two 15th and 16th century damaged historic scrolls from the manors of Bressingham and Diss Heywood. The former has become fused, probably due to exposure to moisture, and cannot be fully unrolled. The latter was severely burnt several hundred years ago, becoming thoroughly charred, heat-shrunken, and distorted, with all the sheets now brittle and fused together. Our virtual unrolling revealed text that has been hidden for centuries.
Dysregulation in Actin Cytoskeletal Organization Drives Increased Stiffness and Migratory Persistence in Polyploidal Giant Cancer Cells
Authors: Xuan Botai , Ghosh Deepraj , Cheney Emily M. , Clifton Elizabeth M. , Dawson Michelle R.
Published: August 2018

Polyploidal giant cancer cells (PGCCs) have been observed by pathologists in patient tumor samples and are especially prominent in late stage, high grade disease or after chemotherapy. However, they are often overlooked due to their apparent dormancy. Recent research has shown PGCCs to be chemoresistant and express stem-like features, traits associated with disease progression and relapse. Here, we show the preferential survival of PGCCs during Paclitaxel (PTX) treatment and used multiple particle tracking analysis to probe their unique biophysical phenotype. We show that PGCCs have higher inherent cytoplasmic and nuclear stiffness in order to withstand the mechanical stress associated with their increased size and the chemical stress from PTX treatment. Inhibitor studies show the involvement of a dysregulated RhoA-Rock1 pathway and overall actin cytoskeletal network as the underlying mechanism for the altered biophysical phenotype of PGCCs. Furthermore, PGCCs exhibit a slow but persistent migratory phenotype, a trait commonly associated with metastatic dissemination and invasiveness. This work demonstrates the clinical relevance and the need to study this subpopulation, in order to devise therapeutic strategies to combat disease relapse. By highlighting the unique biophysical phenotype of PGCCs, we hope to provide unique avenues for therapeutic targeting of these cells in disease treatment.
Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems
Authors: Hu Yue O. O. , Ndegwa Nelson , Alneberg Johannes , Johansson Sebastian , Logue Jürg Brendan , Huss Mikael , Käller Max , Lundeberg Joakim , Fagerberg Jens , Andersson Anders F.
Published: August 2018

Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli; E. coli) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E. coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E. coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E. coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.
Isolation and characterisation of alveolar type II pneumocytes from adult bovine lung
Authors: Lee Diane Frances , Salguero Francisco Javier , Grainger Duncan , Francis Robert James , MacLellan-Gibson Kirsty , Chambers Mark Andrew
Published: August 2018

Alveolar type II (ATII) cells play a key role as part of the distal lung epithelium, including roles in the innate immune response and as self-renewing progenitors to replace alveolar type I (ATI) cells during regeneration of the alveolar epithelium. Their secretion of surfactant protein helps to maintain homeostasis in the distal lung and exert protective, antimicrobial properties. Despite the cell’s crucial roles, they remain difficult to study, in part due to inefficient and expensive isolation methods, a propensity to differentiate into alveolar type I cells in culture and susceptibility to fibroblast overgrowth from primary isolations. Published methods of isolation often require specialist technology, negatively impacting the development of in vitro models of disease, including bovine tuberculosis (BTB), a serious re-emerging disease in both animals and humans worldwide. We present here a simple and cost-effective method that may be utilised in the generation of bovine primary ATII cells. These exhibit an ATII phenotype in 2D and 3D culture in our studies and are conducive to further study of the role of ATII cells in bovine respiratory diseases.
A simple and inexpensive quantitative technique for determining chemical sensitivity in Saccharomyces cerevisiae
Authors: Hung Chao-Wei , Martínez-Márquez Jorge Y. , Javed Fatima T. , Duncan Mara C.
Published: August 2018

Chemical sensitivity, growth inhibition in response to a chemical, is a powerful phenotype that can reveal insight into diverse cellular processes. Chemical sensitivity assays are used in nearly every model system, however the yeast Saccharomyces cerevisiae provides a particularly powerful platform for discovery and mechanistic insight from chemical sensitivity assays. Here we describe a simple and inexpensive approach to determine chemical sensitivity quantitatively in yeast in the form of half maximal inhibitory concentration (IC50) using common laboratory equipment. We demonstrate the utility of this method using chemicals commonly used to monitor changes in membrane traffic. When compared to traditional agar-based plating methods, this method is more sensitive and can detect defects not apparent using other protocols. Additionally, this method reduces the experimental protocol from five days to 18 hours for the toxic amino acid canavanine. Furthermore, this method provides reliable results using lower amounts of chemicals. Finally, this method is easily adapted to additional chemicals as demonstrated with an engineered system that activates the spindle assembly checkpoint in response to rapamycin with differing efficiencies. This approach provides researchers with a cost-effective method to perform chemical genetic profiling without specialized equipment.
Lysyl hydroxylases are transcription targets for GATA3 driving lung cancer cell metastasis
Authors: Liu Wei , Zhang Ting , Guo Lixia , Wang Yuanyuan , Yang Yanan
Published: August 2018

Metastasis associates with late stages of lung cancer progression and remains the main cause of patient death due to the lack of clinically effective therapeutics. Here we report that the transcription factor GATA3 and its co-factor FOG2 commonly promote the expression of the lysyl hydroxylase (LH) family members, including LH2 and LH3, which in turn drive lung adenocarcinoma cell migration, invasion, and metastasis. We show evidence that both LH2 and LH3 are direct transcription targets for GATA3. Knockdown of either LH2 or LH3 suppresses migration and invasion; on the contrary, forced expression of LH2 or LH3 promotes growth and migration, suggesting that the two LHs exert redundant oncogenic functions. Importantly, re-expression of LH2 is sufficient to restore the metastatic capacity of GATA3-depleted cells, suggesting a role for LHs as the downstream mediators of GATA3. Collectively, our data reveal a pro-metastatic GATA3-LHs axis for lung cancer, supporting the notion that targeting LHs may be useful for treating lung cancer.
Silkworms suppress the release of green leaf volatiles by mulberry leaves with an enzyme from their spinnerets
Authors: Takai Hiroki , Ozawa Rika , Takabayashi Junji , Fujii Saki , Arai Kiriko , Ichiki Ryoko T. , Koeduka Takao , Dohra Hideo , Ohnishi Toshiyuki , Taketazu Sakura , Kobayashi Jun , Kainoh Yooichi , Nakamura Satoshi , Fujii Takeshi , Ishikawa Yukio , Kiuchi Takashi , Katsuma Susumu , Uefune Masayoshi , Shimada Toru , Matsui Kenji
Published: August 2018

In response to herbivory, plants emit a blend of volatile organic compounds that includes green leaf volatiles (GLVs) and terpenoids. These volatiles are known to attract natural enemies of herbivores and are therefore considered to function as an indirect defense. Selection should favor herbivores that are able to suppress these volatile emissions, and thereby make themselves less conspicuous to natural enemies. We tested this possibility for silkworms, which were observed to leave secretions from their spinnerets while feeding on mulberry leaves. When we ablated the spinnerets of silkworms, no secretions were observed. Leaves infested by intact silkworms released smaller amounts of GLVs than leaves infested by ablated silkworms, indicating that the spinneret secretion suppressed GLV production. This difference in GLV emissions was also reflected in the behavioral response of Zenillia dolosa (Tachinidae), a parasitoid fly of silkworms. The flies laid fewer eggs when exposed to the volatiles from intact silkworm-infested leaves than when exposed to the volatiles from ablated silkworm-infested leaves. We identified a novel enzyme in the secretion from the spinneret that is responsible for the GLV suppression. The enzyme converted 13(S)-hydroperoxy-(9Z,11E,15Z)-octadecatrienoic acid, an intermediate in the biosynthetic pathway of GLVs, into its keto-derivative in a stereospecific manner. Taken together, this study shows that silkworms are able to feed on mulberry in a stealthy manner by suppressing GLV production with an enzyme in secretions of their spinnerets, which might be a countermeasure against induced indirect defense by mulberry plants.
Soil microarthropods alter the outcome of plant-soil feedback experiments
Authors: Kuťáková Eliška , Cesarz Simone , Münzbergová Zuzana , Eisenhauer Nico
Published: August 2018

Plant-soil feedback (PSF) effects are studied as plant growth responses to soil previously conditioned by another plant. These studies usually exclude effects of soil fauna, such as nematodes, soil arthropods, and earthworms, although these organisms are known to influence plant performance. Here, we aimed to explore effects of a model microarthropod community on PSFs. We performed a PSF experiment in microcosms with two plant species,Phleum pratenseandPoa pratensis. We added a model microarthropod community consisting of three fungivorous springtail species (Proisotoma minuta,Folsomia candida, andSinella curviseta) and a predatory mite (Hypoaspis aculeifer) to half of the microcosms. We measured seedling establishment and plant biomass, nematode and microbial community composition, microbial biomass, and mycorrhizal colonization of roots. Microarthropods caused changes in the composition of nematode and microbial communities. Their effect was particularly strong inPhleumplants where they altered the composition of bacterial communities. Microarthropods also generally influenced plant performance, and their effects depended on previous soil conditioning and the identity of plant species. Microarthropods did not affect soil microbial biomass and mycorrhizal colonization of roots. We conclude that the role of soil microarthropods should be considered in future PSF experiments, especially as their effects are plant species-specific.
Incubation and water temperatures influence the performances of loggerhead sea turtle hatchlings during the dispersal phase
Authors: Kobayashi Shohei , Aokura Nanamo , Fujimoto Ryohei , Mori Keisuke , Kumazawa Yoshinori , Ando Yusuke , Matsuda Tsuyoshi , Nitto Hiroshi , Arai Katsuhiko , Watanabe Gen , Saito Tomomi
Published: August 2018

Artificial manipulation of incubation temperature has been proposed as a potential strategy for mitigating the effects of climate change on sea turtles for which sex determination is temperature-dependent, but thermal manipulation may also affect hatchling survival. Here, we demonstrated that incubation and water temperatures influenced several performance traits that contribute to the survival of loggerhead sea turtles (Caretta caretta) during the post-hatchling dispersal phase. Hatchlings from warm incubation temperatures (31 °C) had significantly shorter incubation periods, higher initial swimming performance, lower sustained swimming performance, and lower growth rates during the first three weeks post-hatching, as well as higher blood glucose concentrations, than those from cool incubation temperatures (27.5 °C). Hatchlings in warm water temperatures (30 °C) exhibited significantly greater swimming performance than those in cool water temperatures (27 °C). Our results indicated that altering incubation temperatures indirectly influences the survival of loggerhead hatchlings by modifying their swimming performance and growth rates, which may affect hatchling predator-avoidance capability. Moreover, thermal manipulation may alter the incubation period, exposing hatchling to water temperatures that they would not otherwise normally experience, which may affect swimming performance. Our results suggest that such conservation strategies may influence their survival, and thus should be carefully considered.
MLL1 is essential for retinal neurogenesis and horizontal inner neuron integrity
Authors: Brightman Diana S. , Grant Rachel L. , Ruzycki Philip A. , Suzuki Ray , Hennig Anne K. , Chen Shiming
Published: August 2018

Development of retinal structure and function is controlled by cell type-specific transcription factors and widely expressed co-regulators. The latter includes the mixed-lineage leukemia (MLL) family of histone methyltransferases that catalyze histone H3 lysine 4 di- and tri-methylation associated with gene activation. One such member, MLL1, is widely expressed in the central nervous system including the retina. However, its role in retinal development is unknown. To address this question, we knocked out Mll1 in mouse retinal progenitors, and discovered that MLL1 plays multiple roles in retinal development by regulating progenitor cell proliferation, cell type composition and neuron-glia balance, maintenance of horizontal neurons, and formation of functional synapses between neuronal layers required for visual signal transmission and processing. Altogether, our results suggest that MLL1 is indispensable for retinal neurogenesis and function development, providing a new paradigm for cell type-specific roles of known histone modifying enzymes during CNS tissue development.
Low temperature a/b nanotwins in Ni50Mn25+xGa25−x Heusler alloys
Authors: Straka L. , Drahokoupil J. , Veřtát P. , Zelený M. , Kopeček J. , Sozinov A. , Heczko O.
Published: August 2018

We have found low temperature a/b nanotwins having (110) twinning plane in a five-layered modulated martensite phase of Ni50Mn25+xGa25−x (at. %) Heusler alloys and identified the particular region in phase diagram where the nanotwinning occurs. Evolution of the structure with decreasing temperature was studied by X-ray diffraction using single crystals exhibiting magnetic shape memory effect. The merging of (400) and (040) lines upon cooling for 2.6 < x < 3.5 indicated a/b nanotwinning originating from the refinement of initially coarse a/b twins. Refinement of the twins with decreasing temperature was observed directly using scanning electron microscopy. The prerequisite for nanotwinning is an extremely low twin boundary energy, which we estimated using first-principles calculations to be 0.16 meV/Å2. As the nanotwinning distorts the relation between the crystal lattice and the X-ray diffraction pattern, it should be taken into consideration in structural studies of Ni-Mn-Ga Heusler alloys.
The impacts of delivery mode on infant’s oral microflora
Authors: Li Hongping , Wang Jun , Wu Lijuan , Luo Jun , Liang Xia , Xiao Bin , Zhu Yuanfang
Published: August 2018

This study investigated the effects of different delivery modes on oral microflora in healthy newborns immediately post-partum, and provided evidence for microbial colonization disruption induced by medical procedures. Eighteen infants delivered by cesarean section and 74 by vaginal delivery were included in the study. High-throughput sequencing of 16S bacterial rRNA was performed on oral samples collected immediately after birth. All data were analyzed using bioinformatics approaches. Our results indicated that different oral bacteria were found between infants delivered by cesarean section compared to vaginal delivery group. Lactobacillus, Prevotella and Gardnerella were the most abundant genera in the vaginal group, while Petrimonas, Bacteroides, Desulfovibrio, Pseudomonas, Staphylococcus, Tepidmicrobium, VadinCA02, and Bifidobacterium were dominant bacteria in the cesarean section (C-section) group. Furthermore, bacteria isolated from 27 vaginally-delivered infants were not clustered into the vaginal group. Most of them spent more than 24 hours in the delivery room and this led to repeated sterilization procedures. We hypothesized that repeated sterilization might have influenced oral microflora in those cases. To conclude, this study suggested that different modes of birth delivery affect oral microflora in healthy infants. In addition, attention shall be paid to the clinical practice of repeated sterilization of the vulva that possibly obstructs the colonization of vaginal bacterial.
Gauss’s law for networks directly reveals community boundaries
Authors: Sinha Ayan , Gleich David F. , Ramani Karthik
Published: August 2018

The study of network topology provides insight into the function and behavior of physical, social, and biological systems. A natural step towards discovering the organizing principles of these complex topologies is to identify a reduced network representation using cohesive subgroups or communities. This procedure often uncovers the underlying mechanisms governing the functional assembly of complex networks. A community is usually defined as a subgraph or a set of nodes that has more edges than would be expected from a simple, null distribution of edges over the graph. This view drives objective such as modularity. Another perspective, corresponding to objectives like conductance or density, is that communities are groups of nodes that have extremal properties with respect to the number of internal edges and cut edges. Here we show that identifying community boundaries rather than communities results in a more accurate decomposition of the network into informative components. We derive a network analog of Gauss’s law that relates a measure of flux through a subgraph’s boundary to the connectivity among the subgraph’s nodes. Our Gauss’s law for networks naturally characterizes a community as a subgraph with high flux through its boundary. Aggregating flux over these boundaries gives rise to a Laplacian and forms the basis of our “Laplacian modularity” quality function for community detection that is applicable to general network types. This technique allows us to determine communities that are both overlapping and hierarchically organized.
A cis-eQTL of HLA-DPB1 Affects Susceptibility to Type 1 Autoimmune Hepatitis
Authors: Yamazaki Tomoo , Umemura Takeji , Joshita Satoru , Yoshizawa Kaname , Tanaka Eiji , Ota Masao
Published: August 2018

Autoimmune hepatitis (AIH) is a chronic inflammatory liver disease characterized by an autoimmune reaction to hepatocytes. A single nucleotide polymorphism in the 3′ untranslated region of HLA-DPB1, rs9277534, is associated with HLA-DPB1 expression. rs9277534 has been linked to hepatitis B virus recovery/persistence and the risk of graft-versus-host disease with HLA-DPB1 mismatching transplantation of hematopoietic cells, but its role along with that of HLA-DP expression in AIH have not been fully clarified. We genotyped rs9277534 in 146 Japanese patients with AIH and 326 healthy subjects. HLA-DPB1 expression was determined by quantitative PCR. HLA-DPB1 expression was significantly higher for rs9277534G than for rs9277534A (P < 0.05). rs9277534 genotype was in strong linkage disequilibrium with the HLA-DPB1 allele (pairwise D′ = 0.82–1.00). Although HLA-DP alleles were not significantly associated with AIH, the frequency of the rs9277534G allele was significantly higher in AIH patients compared with healthy subjects (P = 0.002, odds ratio [OR] = 1.56). Logistic regression analysis revealed that the HLA-DRB1*04:05 allele (P < 0.001, OR = 4.61) and rs9277534 (P = 0.004, OR = 1.67) were independently associated with AIH susceptibility. rs9277534G in the HLA-DP gene is an eQTL that affects gene expression and may contribute to AIH susceptibility.
Inhibiting the CD8+ T cell infiltration in the tumor microenvironment after radiotherapy is an important mechanism of radioresistance
Authors: Chen Hai-yan , Xu Lei , Li Lin-feng , Liu Xiao-xing , Gao Jian-xin , Bai Yong-rui
Published: August 2018

Endogenous immune response participates in tumor control, and radiotherapy has immune modulatory capacity, but the role of immune modulation in the tumor microenvironment invoked by radiotherapy in radiosensitivity is poorly defined. In the present study, a radio-resistant melanoma cell line was obtained after repeated irradiation to the parental tumor in C57BL/6 mice. Radiotherapy resulted in aggregation of CD8+ and CD3+ T cells, and decrease of myeloid-derived suppressor cells and dendritic cells in the parental tumor, but not in the resistant tumors. CD4+ T cells and B cells did not change significantly. The CD8+ T cell infiltration after radiotherapy is important for tumor response, because in the nude mice and CD8+ T cell-depleted C57BL/6 mice, the parental and resistant tumor has similar radiosensitivity. Patients with good radiation response had more CD8+ T cells aggregation after radiotherapy. Radiotherapy resulted in robust transcription of T cell chemoattractant in the parental cells, and the expression of CCL5 was much higher. These results reveal a novel mechanism of radioresistance, tumor cells inhibit the infiltration of CD8+ T cell after radiotherapy and become radioresistant. Increasing CD8+ T cell infiltration after RT may be an effective way to improve tumor radiosensitivity.
Quantum phases for moving charges and dipoles in an electromagnetic field and fundamental equations of quantum mechanics
Authors: Kholmetskii A. L. , Yarman T. , Missevitch O. V. , Arik M.
Published: August 2018

We analyze the quantum phase effects for point-like charges and electric (magnetic) dipoles under a natural assumption that the observed phase for a dipole represents the sum of corresponding phases for charges composing this dipole. This way we disclose two novel quantum phases for charged particles, which we named as complementary electric Aharonov-Bohm (A-B) phase and complementary magnetic A-B phase, respectively. We reveal that these phases are derived from the Schrödinger equation only in the case, where the operator of momentum is re-defined via the replacement of the canonical momentum of particle by the sum of its mechanical momentum and interactional field momentum for a system of charged particles. The related alteration should be introduced to Klein-Gordon and Dirac equations, too, and implications of this modification are discussed.
Diabetes induces fibrotic changes in the lung through the activation of TGF-β signaling pathways
Authors: Talakatta Girish , Sarikhani Mohsen , Muhamed Jaseer , Dhanya K. , Somashekar Bagganahalli S. , Mahesh Padukudru Anand , Sundaresan Nagalingam , Ravindra P. V.
Published: August 2018

In the long term, diabetes profoundly affects multiple organs, such as the kidney, heart, brain, liver, and eyes. The gradual loss of function in these vital organs contributes to mortality. Nonetheless, the effects of diabetes on the lung tissue are not well understood. Clinical and experimental data from our studies revealed that diabetes induces inflammatory and fibrotic changes in the lung. These changes were mediated by TGF-β-activated epithelial-to-mesenchymal transition (EMT) signaling pathways. Our studies also found that glucose restriction promoted mesenchymal-to-epithelial transition (MET) and substantially reversed inflammatory and fibrotic changes, suggesting that diabetes-induced EMT was mediated in part by the effects of hyperglycemia. Additionally, the persistent exposure of diabetic cells to high glucose concentrations (25 mM) promoted the upregulation of caveolin-1, N-cadherin, SIRT3, SIRT7 and lactate levels, suggesting that long-term diabetes may promote cell proliferation. Taken together, our results demonstrate for the first time that diabetes induces fibrotic changes in the lung via TGF-β1-activated EMT pathways and that elevated SMAD7 partially protects the lung during the initial stages of diabetes. These findings have implications for the management of patients with diabetes.
Functional Nano-Coating Materials by Michael Addition and Ring-opening Polymerization: Reactivity, Molecular Architecture and Refractive index
Authors: Jena Kishore K. , Alhassan Saeed M. , Tiwari Atul , Hihara L. H.
Published: August 2018

Understanding the molecular interaction and morphology of organic-inorganic hybrid materials is an important and fundamental assignment to develop novel high-performance materials. In this work, we developed two types of hybrid coating materials by using different silane coupling agents via Michael addition reaction and ring-opening polymerization. The changes in molecular interaction and morphology of the hybrid coatings due to chemical composition and curing temperature were studied by electron microscopy, spectroscopy and solid state 29Si nuclear magnetic resonance analysis. Fundamental differences were observed in HYBRID I and HYBRID II coatings during the nucleation stage that was dependent on the curing temperature. Higher curing temperature of the hybrid coatings resulted in improved uniformity and greater crystallinity of dispersed phases, and better control of the morphology compared with coatings cured at lower temperatures. The higher curing temperature provided more consistent nucleation sites for the growth of larger nanostructures of desired characteristics (e.g., size and surface features). There is great flexibility in synthesizingg these hybrid materials where different structure and morphology can be achieved to produce materials whose applications can range from adhesives to protective coatings. Refractive index results revealed that HYBRID I (90 °C) coating showed higher refractive index than HYBRID II (90 °C) coating.