bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential co-occurrence relationships shaping ecotype diversification within Thaumarchaeota populations in the coastal ocean water column
Authors: Reji Linta , Tolar Bradley B , Smith Jason M , Chavez Francisco P , Francis Christopher A 
Published: January 2019

Abstract
Ecological factors contributing to depth-related diversification of marine Thaumarchaeota populations remain largely unresolved. To investigate the role of potential microbial associations in shaping thaumarchaeal ecotype diversification, we examined co-occurrence relationships in a community composition dataset (16S rRNA V4-V5 region) collected as part of a 2-year time series in coastal Monterey Bay. Ecotype groups previously defined based on functional gene diversity—water column A (WCA), water column B (WCB) and Nitrosopumilus-like clusters—were recovered in the thaumarchaeal 16S rRNA gene phylogeny. Networks systematically reflected depth-related patterns in the abundances of ecotype populations, suggesting thaumarchaeal ecotypes as keystone members of the microbial community below the euphotic zone. Differential environmental controls on the ecotype populations were further evident in subnetwork modules showing preferential co-occurrence of OTUs belonging to the same ecotype cluster. Correlated abundances of Thaumarchaeota and heterotrophic bacteria (e.g., Bacteroidetes, Marinimicrobia and Gammaproteobacteria) indicated potential reciprocal interactions via dissolved organic matter transformations. Notably, the networks recovered ecotype-specific associations between thaumarchaeal and Nitrospina OTUs. Even at depths where WCB-like Thaumarchaeota dominated, Nitrospina OTUs were found to preferentially co-occur with WCA-like and Nitrosopumilus-like thaumarchaeal OTUs, highlighting the need to investigate the ecological implications of the composition of nitrifier assemblages in marine waters.
9.2%-efficient core-shell structured antimony selenide nanorod array solar cells
Authors: Li Zhiqiang , Liang Xiaoyang , Li Gang , Liu Haixu , Zhang Huiyu , Guo Jianxin , Chen Jingwei , Shen Kai , San Xingyuan , Yu Wei , Schropp Ruud E. I. , Mai Yaohua 
Published: January 2019

AbstractAntimony selenide (Sb2Se3) has a one-dimensional (1D) crystal structure comprising of covalently bonded (Sb4Se6)n ribbons stacking together through van der Waals force. This special structure results in anisotropic optical and electrical properties. Currently, the photovoltaic device performance is dominated by the grain orientation in the Sb2Se3 thin film absorbers. Effective approaches to enhance the carrier collection and overall power-conversion efficiency are urgently required. Here, we report the construction of Sb2Se3 solar cells with high-quality Sb2Se3 nanorod arrays absorber along the [001] direction, which is beneficial for sun-light absorption and charge carrier extraction. An efficiency of 9.2%, which is the highest value reported so far for this type of solar cells, is achieved by junction interface engineering. Our cell design provides an approach to further improve the efficiency of Sb2Se3-based solar cells.
Shifts in the selectivity filter dynamics cause modal gating in K+ channels
Authors: Jekhmane Shehrazade , Medeiros-Silva João , Li Jing , Kümmerer Felix , Müller-Hermes Christoph , Baldus Marc , Roux Benoît , Weingarth Markus 
Published: January 2019

AbstractSpontaneous activity shifts at constant experimental conditions represent a widespread regulatory mechanism in ion channels. The molecular origins of these modal gating shifts are poorly understood. In the K+ channel KcsA, a multitude of fast activity shifts that emulate the native modal gating behaviour can be triggered by point-mutations in the hydrogen bonding network that controls the selectivity filter. Using solid-state NMR and molecular dynamics simulations in a variety of KcsA mutants, here we show that modal gating shifts in K+ channels are associated with important changes in the channel dynamics that strongly perturb the selectivity filter equilibrium conformation. Furthermore, our study reveals a drastically different motional and conformational selectivity filter landscape in a mutant that mimics voltage-gated K+ channels, which provides a foundation for an improved understanding of eukaryotic K+ channels. Altogether, our results provide a high-resolution perspective on some of the complex functional behaviour of K+ channels.
Dickkopf-3 links HSF1 and YAP/TAZ signalling to control aggressive behaviours in cancer-associated fibroblasts
Authors: Ferrari Nicola , Ranftl Romana , Chicherova Ievgeniia , Slaven Neil D. , Moeendarbary Emad , Farrugia Aaron J. , Lam Maxine , Semiannikova Maria , Westergaard Marie C. W. , Tchou Julia , Magnani Luca , Calvo Fernando 
Published: January 2019

AbstractAggressive behaviours of solid tumours are highly influenced by the tumour microenvironment. Multiple signalling pathways can affect the normal function of stromal fibroblasts in tumours, but how these events are coordinated to generate tumour-promoting cancer-associated fibroblasts (CAFs) is not well understood. Here we show that stromal expression of Dickkopf-3 (DKK3) is associated with aggressive breast, colorectal and ovarian cancers. We demonstrate that DKK3 is a HSF1 effector that modulates the pro-tumorigenic behaviour of CAFs in vitro and in vivo. DKK3 orchestrates a concomitant activation of β-catenin and YAP/TAZ. Whereas β-catenin is dispensable for CAF-mediated ECM remodelling, cancer cell growth and invasion, DKK3-driven YAP/TAZ activation is required to induce tumour-promoting phenotypes. Mechanistically, DKK3 in CAFs acts via canonical Wnt signalling by interfering with the negative regulator Kremen and increasing cell-surface levels of LRP6. This work reveals an unpredicted link between HSF1, Wnt signalling and YAP/TAZ relevant for the generation of tumour-promoting CAFs.
RETRACTED ARTICLE: Mir20a/106a-WTX axis regulates RhoGDIa/CDC42 signaling and colon cancer progression
Authors: Zhu Gui-fang , Xu Yang-wei , Li Jian , Niu Hui-lin , Ma Wen-xia , Xu Jia , Zhou Pei-rong , Liu Xia , Ye Dan-li , Liu Xiao-rong , Yan Tao , Zhai Wei-ke , Xu Zhi-jun , Liu Chun , Wang Lei , Wang Hao , Luo Jia-mao , Liu Li , Li Xuan-qi , Guo Suiqun , Jiang Hui-ping , Shen Peng , Lin Hui-kuan , Yu Di-hua , Ding Yan-qing , Zhang Qing-ling 
Published: January 2019

AbstractWilms tumor gene on the X chromosome (WTX) is a putative tumor suppressor gene in Wilms tumor, but its expression and functions in other tumors are unclear. Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in women and the second leading cause in men in the United States. We demonstrated that WTX frequently lost in CRC which was highly correlated with cell proliferation, tumor invasion and metastasis. Mechanistically, WTX loss disrupts the interaction between RhoGDIα and CDC42 by losing of the binding with RhoGDIα and triggers the activation of CDC42 and its downstream cascades, which promotes CRC development and liver metastasis. The aberrant upregulation of miR-20a/miR-106a were identified as the reason of WTX loss in CRC both in vivo and in vitro. These study defined the mechanism how miR-20a/miR-106a-mediated WTX loss regulates CRC progression and metastasis, and provided a potential therapeutic target for preventing CRC progression.
Global phosphoproteomic analysis reveals ARMC10 as an AMPK substrate that regulates mitochondrial dynamics
Authors: Chen Zhen , Lei Caoqi , Wang Chao , Li Nan , Srivastava Mrinal , Tang Mengfan , Zhang Huimin , Choi Jong Min , Jung Sung Yun , Qin Jun , Chen Junjie 
Published: January 2019

AbstractAMP-activated protein kinase (AMPK) is a key regulator of cellular energy homeostasis. Although AMPK has been studied extensively in cellular processes, understanding of its substrates and downstream functional network, and their contributions to cell fate and disease development, remains incomplete. To elucidate the AMPK-dependent signaling pathways, we performed global quantitative phosphoproteomic analysis using wild-type and AMPKα1/α2-double knockout cells and discovered 160 AMPK-dependent phosphorylation sites. Further analysis using an AMPK consensus phosphorylation motif indicated that 32 of these sites are likely direct AMPK phosphorylation sites. We validated one uncharacterized protein, ARMC10, and demonstrated that the S45 site of ARMC10 can be phosphorylated by AMPK both in vitro and in vivo. Moreover, ARMC10 overexpression was sufficient to promote mitochondrial fission, whereas ARMC10 knockout prevented AMPK-mediated mitochondrial fission. These results demonstrate that ARMC10 is an effector of AMPK that participates in dynamic regulation of mitochondrial fission and fusion.
SREBP-dependent lipidomic reprogramming as a broad-spectrum antiviral target
Authors: Yuan Shuofeng , Chu Hin , Chan Jasper Fuk-Woo , Ye Zi-Wei , Wen Lei , Yan Bingpeng , Lai Pok-Man , Tee Kah-Meng , Huang Jingjing , Chen Dongdong , Li Cun , Zhao Xiaoyu , Yang Dong , Chiu Man Chun , Yip Cyril , Poon Vincent Kwok-Man , Chan Chris Chung-Sing , Sze Kong-Hung , Zhou Jie , Chan Ivy Hau-Yee , Kok Kin-Hang , To Kelvin Kai-Wang , Kao Richard Yi-Tsun , Lau Johnson Yiu-Nam , Jin Dong-Yan , Perlman Stanley , Yuen Kwok-Yung 
Published: January 2019

AbstractViruses are obligate intracellular microbes that exploit the host metabolic machineries to meet their biosynthetic demands, making these host pathways potential therapeutic targets. Here, by exploring a lipid library, we show that AM580, a retinoid derivative and RAR-α agonist, is highly potent in interrupting the life cycle of diverse viruses including Middle East respiratory syndrome coronavirus and influenza A virus. Using click chemistry, the overexpressed sterol regulatory element binding protein (SREBP) is shown to interact with AM580, which accounts for its broad-spectrum antiviral activity. Mechanistic studies pinpoint multiple SREBP proteolytic processes and SREBP-regulated lipid biosynthesis pathways, including the downstream viral protein palmitoylation and double-membrane vesicles formation, that are indispensable for virus replication. Collectively, our study identifies a basic lipogenic transactivation event with broad relevance to human viral infections and represents SREBP as a potential target for the development of broad-spectrum antiviral strategies.
Olefin-accelerated solid-state C–N cross-coupling reactions using mechanochemistry
Authors: Kubota Koji , Seo Tamae , Koide Katsumasa , Hasegawa Yasuchika , Ito Hajime 
Published: January 2019

AbstractPalladium-catalyzed cross-coupling reactions are one of the most powerful and versatile methods to synthesize a wide range of complex functionalized molecules. However, the development of solid-state cross-coupling reactions remains extremely limited. Here, we report a rational strategy that provides a general entry to palladium-catalyzed Buchwald-Hartwig cross-coupling reactions in the solid state. The key finding of this study is that olefin additives can act as efficient molecular dispersants for the palladium-based catalyst in solid-state media to facilitate the challenging solid-state cross-coupling. Beyond the immediate utility of this protocol, our strategy could inspire the development of industrially attractive solvent-free palladium-catalyzed cross-coupling processes for other valuable synthetic targets.
Spin-Orbit induced phase-shift in Bi2Se3 Josephson junctions
Authors: Assouline Alexandre , Feuillet-Palma Cheryl , Bergeal Nicolas , Zhang Tianzhen , Mottaghizadeh Alireza , Zimmers Alexandre , Lhuillier Emmanuel , Eddrie Mahmoud , Atkinson Paola , Aprili Marco , Aubin Hervé 
Published: January 2019

AbstractThe transmission of Cooper pairs between two weakly coupled superconductors produces a superfluid current and a phase difference; the celebrated Josephson effect. Because of time-reversal and parity symmetries, there is no Josephson current without a phase difference between two superconductors. Reciprocally, when those two symmetries are broken, an anomalous supercurrent can exist in the absence of phase bias or, equivalently, an anomalous phase shift φ0 can exist in the absence of a superfluid current. We report on the observation of an anomalous phase shift φ0 in hybrid Josephson junctions fabricated with the topological insulator Bi2Se3 submitted to an in-plane magnetic field. This anomalous phase shift φ0 is observed directly through measurements of the current-phase relationship in a Josephson interferometer. This result provides a direct measurement of the spin-orbit coupling strength and open new possibilities for phase-controlled Josephson devices made from materials with strong spin-orbit coupling.
Differential PROTAC substrate specificity dictated by orientation of recruited E3 ligase
Authors: Smith Blake E. , Wang Stephen L. , Jaime-Figueroa Saul , Harbin Alicia , Wang Jing , Hamman Brian D. , Crews Craig M. 
Published: January 2019

AbstractPROteolysis-TArgeting Chimeras (PROTACs) are hetero-bifunctional molecules that recruit an E3 ubiquitin ligase to a given substrate protein resulting in its targeted degradation. Many potent PROTACs with specificity for dissimilar targets have been developed; however, the factors governing degradation selectivity within closely-related protein families remain elusive. Here, we generate isoform-selective PROTACs for the p38 MAPK family using a single warhead (foretinib) and recruited E3 ligase (von Hippel-Lindau). Based on their distinct linker attachments and lengths, these two PROTACs differentially recruit VHL, resulting in degradation of p38α or p38δ. We characterize the role of ternary complex formation in driving selectivity, showing that it is necessary, but insufficient, for PROTAC-induced substrate ubiquitination. Lastly, we explore the p38δ:PROTAC:VHL complex to explain the different selectivity profiles of these PROTACs. Our work attributes the selective degradation of two closely-related proteins using the same warhead and E3 ligase to heretofore underappreciated aspects of the ternary complex model.
RNA inhibitors of nuclear proteins responsible for multiple organ dysfunction syndrome
Authors: Urak Kevin T. , Blanco Giselle N. , Shubham Shambhavi , Lin Li-Hsien , Dassie Justin P. , Thiel William H. , Chen Yani , Sonkar Vijay Kumar , Lei Beilei , Murthy Shubha , Gutierrez Wade R. , Wilson Mary E. , Stiber Jonathan A. , Klesney-Tait Julia , Dayal Sanjana , Miller Francis J. , Giangrande Paloma H. 
Published: January 2019

AbstractThe development of multiple organ dysfunction syndrome (MODS) following infection or tissue injury is associated with increased patient morbidity and mortality. Extensive cellular injury results in the release of nuclear proteins, of which histones are the most abundant, into the circulation. Circulating histones are implicated as essential mediators of MODS. Available anti-histone therapies have failed in clinical trials due to off-target effects such as bleeding and toxicity. Here, we describe a therapeutic strategy for MODS based on the neutralization of histones by chemically stabilized nucleic acid bio-drugs (aptamers). Systematic evolution of ligands by exponential enrichment technology identified aptamers that selectively bind those histones responsible for MODS and do not bind to serum proteins. We demonstrate the efficacy of histone-specific aptamers in human cells and in a murine model of MODS. These aptamers could have a significant therapeutic benefit in the treatment of multiple diverse clinical conditions associated with MODS.
A metamaterial-enabled design enhancing decades-old short backfire antenna technology for space applications
Authors: Binion J. Daniel , Lier Erik , Hand Thomas H. , Jiang Zhi Hao , Werner Douglas H. 
Published: January 2019

AbstractNearly two decades of intense study have passed since the term metamaterials was first introduced in 1999. In spite of their great promise, however, metamaterials have been slow to find their way into practical devices, and examples of real-world applications remain rare. In this paper, an Advanced Short Backfire Antenna (A-SBFA), augmented with anisotropic metamaterial surfaces (metasurfaces), has been designed to achieve a very high aperture efficiency across two frequency bands. This performance is unprecedented for an antenna that has seen widespread use, but few design changes over its more than 50 year existence. The reduced weight, compact design, hexagonal aperture, high dual-band efficiency, high cross-polarization isolation, as well as low multipaction and passive intermodulation (PIM) risk make the A-SBFA ideal for spaceborne applications. This transformative design demonstrates how practical metamaterials, when applied to conventional antenna technology, can provide significant performance enhancements.
GORAB scaffolds COPI at the trans-Golgi for efficient enzyme recycling and correct protein glycosylation
Authors: Witkos Tomasz M. , Chan Wing Lee , Joensuu Merja , Rhiel Manuel , Pallister Ed , Thomas-Oates Jane , Mould A. Paul , Mironov Alex A. , Biot Christophe , Guerardel Yann , Morelle Willy , Ungar Daniel , Wieland Felix T. , Jokitalo Eija , Tassabehji May , Kornak Uwe , Lowe Martin 
Published: January 2019

AbstractCOPI is a key mediator of protein trafficking within the secretory pathway. COPI is recruited to the membrane primarily through binding to Arf GTPases, upon which it undergoes assembly to form coated transport intermediates responsible for trafficking numerous proteins, including Golgi-resident enzymes. Here, we identify GORAB, the protein mutated in the skin and bone disorder gerodermia osteodysplastica, as a component of the COPI machinery. GORAB forms stable domains at the trans-Golgi that, via interactions with the COPI-binding protein Scyl1, promote COPI recruitment to these domains. Pathogenic GORAB mutations perturb Scyl1 binding or GORAB assembly into domains, indicating the importance of these interactions. Loss of GORAB causes impairment of COPI-mediated retrieval of trans-Golgi enzymes, resulting in a deficit in glycosylation of secretory cargo proteins. Our results therefore identify GORAB as a COPI scaffolding factor, and support the view that defective protein glycosylation is a major disease mechanism in gerodermia osteodysplastica.
Thermal radiation control from hot graphene electrons coupled to a photonic crystal nanocavity
Authors: Shiue Ren-Jye , Gao Yuanda , Tan Cheng , Peng Cheng , Zheng Jiabao , Efetov Dmitri K. , Kim Young Duck , Hone James , Englund Dirk 
Published: January 2019

AbstractControlling thermal radiation is central in a range of applications including sensing, energy harvesting, and lighting. The thermal emission spectrum can be strongly modified through the electromagnetic local density of states (EM LDOS) in nanoscale-patterned metals and semiconductors. However, these materials become unstable at high temperature, preventing improvements in radiative efficiency and applications such as thermophotovoltaics. Here, we report stable high-temperature thermal emission based on hot electrons (>2000 K) in graphene coupled to a photonic crystal nanocavity, which strongly modifies the EM LDOS. The electron bath in graphene is highly decoupled from lattice phonons, allowing a comparatively cool temperature (700 K) of the photonic crystal nanocavity. This thermal decoupling of hot electrons from the LDOS-engineered substrate opens a broad design space for thermal emission control that would be challenging or impossible with heated nanoscale-patterned metals or semiconductor materials.
Ultrafast data mining of molecular assemblies in multiplexed high-density super-resolution images
Authors: Yin Yandong , Lee Wei Ting Chelsea , Rothenberg Eli 
Published: January 2019

AbstractMulticolor single-molecule localization super-resolution microscopy has enabled visualization of ultrafine spatial organizations of molecular assemblies within cells. Despite many efforts, current approaches for distinguishing and quantifying such organizations remain limited, especially when these are contained within densely distributed super-resolution data. In theory, higher-order correlation such as the Triple-Correlation function is capable of obtaining the spatial configuration of individual molecular assemblies masked within seemingly discorded dense distributions. However, due to their enormous computational cost such analyses are impractical, even for high-end computers. Here, we developed a fast algorithm for Triple-Correlation analyses of high-content multiplexed super-resolution data. This algorithm computes the probability density of all geometric configurations formed by every triple-wise single-molecule localization from three different channels, circumventing impractical 4D Fourier Transforms of the entire megapixel image. This algorithm achieves 102-folds enhancement in computational speed, allowing for high-throughput Triple-Correlation analyses and robust quantification of molecular complexes in multiplexed super-resolution microscopy.
Integrating all-optical switching with spintronics
Authors: Lalieu M. L. M. , Lavrijsen R. , Koopmans B. 
Published: January 2019

AbstractAll-optical switching (AOS) of magnetic materials describes the reversal of the magnetization using short (femtosecond) laser pulses, and received extensive attention in the past decade due to its high potential for fast and energy-efficient data writing in future spintronic memory applications. Unfortunately, the AOS mechanism in the ferromagnetic multilayers commonly used in spintronics needs multiple pulses for the magnetization reversal, losing its speed and energy efficiency. Here, we experimentally demonstrate on-the-fly single-pulse AOS in combination with spin Hall effect (SHE) driven motion of magnetic domains in Pt/Co/Gd synthetic-ferrimagnetic racetracks. Moreover, using field-driven-SHE-assisted domain wall (DW) motion measurements, both the SHE efficiency in the racetrack is determined and the chirality of the optically written DW’s is verified. Our experiments demonstrate that Pt/Co/Gd racetracks facilitate both single-pulse AOS as well as efficient SHE-induced domain wall motion, which might ultimately pave the way towards integrated photonic memory devices.
Live imaging of leukocyte recruitment in a zebrafish model of chemical liver injury
Authors: Stoddard Michelina , Huang Cong , Enyedi Balázs , Niethammer Philipp 
Published: January 2019

AbstractStudying early immune responses to organ damage in situ requires animal models amenable to intravital imaging. Here, we used transparent zebrafish larvae, a powerful animal model for innate immunity, to measure leukocyte recruitment to damaged livers. Bath application of metronidazole (Mtz) to fish expressing nitroreductase (NTR) under a liver-specific promoter damaged the organ within 24 hours causing oxidative stress, distorted liver morphology, accumulation of TUNEL-positive cells, and transcriptional upregulation of apoptotic and antioxidant genes. Inflammatory gene transcription in damaged hepatocytes was attenuated. In line with predominant apoptosis, macrophages were massively recruited into Mtz/NTR-damaged livers. By contrast, neutrophil infiltration was more variable and delayed, consistent with less abundant necrosis and an attenuated inflammatory capacity of damaged hepatocytes.