bluuebunny/crossref_metadata_2025_split huggingface dataset:
Control of transmembrane charge transfer in cytochrome c oxidase by the membrane potential
Authors: Björck Markus L. , Brzezinski Peter 
Published: August 2018

AbstractThe 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

AbstractHow 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

AbstractTranscriptional 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

AbstractNatural 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

AbstractIncreases 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

AbstractDiamond 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

AbstractTargeting 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.
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

AbstractThere 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

AbstractPolyploidal 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

AbstractUrban 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

AbstractAlveolar 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

AbstractChemical 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

AbstractMetastasis 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

AbstractIn 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

AbstractPlant-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

AbstractArtificial 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.