bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissimilatory nitrate reduction by a freshwater cable bacterium
Authors: Marzocchi Ugo , Thorup Casper , Dam Ann-Sofie , Schramm Andreas , Risgaard-Petersen Nils 
Published: July 2021

Abstract
Cable bacteria (CB) are filamentous Desulfobulbaceae that split the energy-conserving reaction of sulfide oxidation into two half reactions occurring in distinct cells. CB can use nitrate, but the reduction pathway is unknown, making it difficult to assess their direct impact on the N-cycle. Here we show that the freshwater cable bacterium Ca. Electronema sp. GS performs dissimilatory nitrate reduction to ammonium (DNRA). 15NO3−-amended sediment with Ca. Electronema sp. GS showed higher rates of DNRA and nitrite production than sediment without Ca. Electronema sp. GS. Electron flux from sulfide oxidation, inferred from electric potential (EP) measurements, matched the electron flux needed to drive CB-mediated nitrate reduction to nitrite and ammonium. Ca. Electronema sp. GS expressed a complete nap operon for periplasmic nitrate reduction to nitrite, and a putative octaheme cytochrome c (pOCC), whose involvement in nitrite reduction to ammonium remains to be verified. Phylogenetic analysis suggests that the capacity for DNRA was acquired in multiple events through horizontal gene transfer from different organisms, before CB split into different salinity niches. The architecture of the nitrate reduction system suggests absence of energy conservation through oxidative phosphorylation, indicating that CB primarily conserve energy through the half reaction of sulfide oxidation.
Nrf2 activation induces mitophagy and reverses Parkin/Pink1 knock down-mediated neuronal and muscle degeneration phenotypes
Authors: Gumeni Sentiljana , Papanagnou Eleni-Dimitra , Manola Maria S. , Trougakos Ioannis P. 
Published: July 2021

AbstractThe balanced functionality of cellular proteostatic modules is central to both proteome stability and mitochondrial physiology; thus, the age-related decline of proteostasis also triggers mitochondrial dysfunction, which marks multiple degenerative disorders. Non-functional mitochondria are removed by mitophagy, including Parkin/Pink1-mediated mitophagy. A common feature of neuronal or muscle degenerative diseases, is the accumulation of damaged mitochondria due to disrupted mitophagy rates. Here, we exploit Drosophila as a model organism to investigate the functional role of Parkin/Pink1 in regulating mitophagy and proteostatic responses, as well as in suppressing degenerative phenotypes at the whole organism level. We found that Parkin or Pink1 knock down in young flies modulated proteostatic components in a tissue-dependent manner, increased cell oxidative load, and suppressed mitophagy in neuronal and muscle tissues, causing mitochondrial aggregation and neuromuscular degeneration. Concomitant to Parkin or Pink1 knock down cncC/Nrf2 overexpression, induced the proteostasis network, suppressed oxidative stress, restored mitochondrial function, and elevated mitophagy rates in flies’ tissues; it also, largely rescued Parkin or Pink1 knock down-mediated neuromuscular degenerative phenotypes. Our in vivo findings highlight the critical role of the Parkin/Pink1 pathway in mitophagy, and support the therapeutic potency of Nrf2 (a druggable pathway) activation in age-related degenerative diseases.
Growth differentiation factor 11 attenuates cardiac ischemia reperfusion injury via enhancing mitochondrial biogenesis and telomerase activity
Authors: Chen Lin , Luo Guangjin , Liu Yameng , Lin Hairuo , Zheng Cankun , Xie Dongxiao , Zhu Yingqi , Chen Lu , Huang Xiaoxia , Hu Donghong , Xie Jiahe , Chen Zhenhuan , Liao Wangjun , Bin Jianping , Wang Qiancheng , Liao Yulin 
Published: July 2021

AbstractIt has been reported that growth differentiation factor 11 (GDF11) protects against myocardial ischemia/reperfusion (IR) injury, but the underlying mechanisms have not been fully clarified. Considering that GDF11 plays a role in the aging/rejuvenation process and that aging is associated with telomere shortening and cardiac dysfunction, we hypothesized that GDF11 might protect against IR injury by activating telomerase. Human plasma GDF11 levels were significantly lower in acute coronary syndrome patients than in chronic coronary syndrome patients. IR mice with myocardial overexpression GDF11 (oe-GDF11) exhibited a significantly smaller myocardial infarct size, less cardiac remodeling and dysfunction, fewer apoptotic cardiomyocytes, higher telomerase activity, longer telomeres, and higher ATP generation than IR mice treated with an adenovirus carrying a negative control plasmid. Furthermore, mitochondrial biogenesis-related proteins and some antiapoptotic proteins were significantly upregulated by oe-GDF11. These cardioprotective effects of oe-GDF11 were significantly antagonized by BIBR1532, a specific telomerase inhibitor. Similar effects of oe-GDF11 on apoptosis and mitochondrial energy biogenesis were observed in cultured neonatal rat cardiomyocytes, whereas GDF11 silencing elicited the opposite effects to oe-GDF11 in mice. We concluded that telomerase activation by GDF11 contributes to the alleviation of myocardial IR injury through enhancing mitochondrial biogenesis and suppressing cardiomyocyte apoptosis.
Circulating mitochondrial DNA-triggered autophagy dysfunction via STING underlies sepsis-related acute lung injury
Authors: Liu Qinjie , Wu Jie , Zhang Xufei , Li Xuanheng , Wu Xiuwen , Zhao Yun , Ren Jianan 
Published: July 2021

AbstractThe STING pathway and its induction of autophagy initiate a potent immune defense response upon the recognition of pathogenic DNA. However, this protective response is minimal, as STING activation worsens organ damage, and abnormal autophagy is observed during progressive sepsis. Whether and how the STING pathway affects autophagic flux during sepsis-induced acute lung injury (sALI) are currently unknown. Here, we demonstrate that the level of circulating mtDNA and degree of STING activation are increased in sALI patients. Furthermore, STING activation was found to play a pivotal role in mtDNA-mediated lung injury by evoking an inflammatory storm and disturbing autophagy. Mechanistically, STING activation interferes with lysosomal acidification in an interferon (IFN)-dependent manner without affecting autophagosome biogenesis or fusion, aggravating sepsis. Induction of autophagy or STING deficiency alleviated lung injury. These findings provide new insights into the role of STING in the regulatory mechanisms behind extrapulmonary sALI.
Molecular-scale visualization of sarcomere contraction within native cardiomyocytes
Authors: Burbaum Laura , Schneider Jonathan , Scholze Sarah , Böttcher Ralph T. , Baumeister Wolfgang , Schwille Petra , Plitzko Jürgen M. , Jasnin Marion 
Published: July 2021

AbstractSarcomeres, the basic contractile units of striated muscle, produce the forces driving muscular contraction through cross-bridge interactions between actin-containing thin filaments and myosin II-based thick filaments. Until now, direct visualization of the molecular architecture underlying sarcomere contractility has remained elusive. Here, we use in situ cryo-electron tomography to unveil sarcomere contraction in frozen-hydrated neonatal rat cardiomyocytes. We show that the hexagonal lattice of the thick filaments is already established at the neonatal stage, with an excess of thin filaments outside the trigonal positions. Structural assessment of actin polarity by subtomogram averaging reveals that thin filaments in the fully activated state form overlapping arrays of opposite polarity in the center of the sarcomere. Our approach provides direct evidence for thin filament sliding during muscle contraction and may serve as a basis for structural understanding of thin filament activation and actomyosin interactions inside unperturbed cellular environments.
Orbital coupling of hetero-diatomic nickel-iron site for bifunctional electrocatalysis of CO2 reduction and oxygen evolution
Authors: Zeng Zhiping , Gan Li Yong , Bin Yang Hong , Su Xiaozhi , Gao Jiajian , Liu Wei , Matsumoto Hiroaki , Gong Jun , Zhang Junming , Cai Weizhen , Zhang Zheye , Yan Yibo , Liu Bin , Chen Peng 
Published: July 2021

AbstractWhile inheriting the exceptional merits of single atom catalysts, diatomic site catalysts (DASCs) utilize two adjacent atomic metal species for their complementary functionalities and synergistic actions. Herein, a DASC consisting of nickel-iron hetero-diatomic pairs anchored on nitrogen-doped graphene is synthesized. It exhibits extraordinary electrocatalytic activities and stability for both CO2 reduction reaction (CO2RR) and oxygen evolution reaction (OER). Furthermore, the rechargeable Zn-CO2 battery equipped with such bifunctional catalyst shows high Faradaic efficiency and outstanding rechargeability. The in-depth experimental and theoretical analyses reveal the orbital coupling between the catalytic iron center and the adjacent nickel atom, which leads to alteration in orbital energy level, unique electronic states, higher oxidation state of iron, and weakened binding strength to the reaction intermediates, thus boosted CO2RR and OER performance. This work provides critical insights to rational design, working mechanism, and application of hetero-DASCs.
Liquid flow reversibly creates a macroscopic surface charge gradient
Authors: Ober Patrick , Boon Willem Q. , Dijkstra Marjolein , Backus Ellen H. G. , van Roij René , Bonn Mischa 
Published: July 2021

AbstractThe charging and dissolution of mineral surfaces in contact with flowing liquids are ubiquitous in nature, as most minerals in water spontaneously acquire charge and dissolve. Mineral dissolution has been studied extensively under equilibrium conditions, even though non-equilibrium phenomena are pervasive and substantially affect the mineral-water interface. Here we demonstrate using interface-specific spectroscopy that liquid flow along a calcium fluoride surface creates a reversible spatial charge gradient, with decreasing surface charge downstream of the flow. The surface charge gradient can be quantitatively accounted for by a reaction-diffusion-advection model, which reveals that the charge gradient results from a delicate interplay between diffusion, advection, dissolution, and desorption/adsorption. The underlying mechanism is expected to be valid for a wide variety of systems, including groundwater flows in nature and microfluidic systems.
Direct and selective access to amino-poly(phenylene vinylenes)s with switchable properties by dimerizing polymerization of aminoaryl carbenes
Authors: Sobczak Quentin , Kunche Aravindu , Magis Damien , Carrizo Daiann Sosa , Miqueu Karinne , Sotiropoulos Jean-Marc , Cloutet Eric , Brochon Cyril , Landais Yannick , Taton Daniel , Vignolle Joan 
Published: July 2021

AbstractDespite the ubiquity of singlet carbenes in chemistry, their utility as true monomeric building blocks for the synthesis of functional organic polymers has been underexplored. In this work, we exploit the capability of purposely designed mono- and bis-acyclic amino(aryl)carbenes to selectively dimerize as a general strategy to access diaminoalkenes and hitherto unknown amino-containing poly(p-phenylene vinylene)s (N-PPV’s). The unique selectivity of the dimerization of singlet amino(aryl)carbenes, relative to putative C-H insertion pathways, is rationalized by DFT calculations. Of particular interest, unlike classical PPV’s, the presence of amino groups in α-position of C=C double bonds in N-PPV’s allows their physico-chemical properties to be manipulated in different ways by a simple protonation reaction. Hence, depending on the nature of the amino group (iPr2N vs. piperidine), either a complete loss of conjugation or a blue-shift of the maximum of absorption is observed, as a result of the protonation at different sites (nitrogen vs. carbon). Overall, this study highlights that singlet bis-amino(aryl)carbenes hold great promise to access functional polymeric materials with switchable properties, through a proper selection of their substitution pattern.
Reduction of corpus callosum activity during whisking leads to interhemispheric decorrelation
Authors: Oran Yael , Katz Yonatan , Sokoletsky Michael , Malina Katayun Cohen-Kashi , Lampl Ilan 
Published: July 2021

AbstractInterhemispheric correlation between homotopic areas is a major hallmark of cortical physiology and is believed to emerge through the corpus callosum. However, how interhemispheric correlations and corpus callosum activity are affected by behavioral states remains unknown. We performed laminar extracellular and intracellular recordings simultaneously from both barrel cortices in awake mice. We find robust interhemispheric correlations of both spiking and synaptic activities that are reduced during whisking compared to quiet wakefulness. Accordingly, optogenetic inactivation of one hemisphere reveals that interhemispheric coupling occurs only during quiet wakefulness, and chemogenetic inactivation of callosal terminals reduces interhemispheric correlation especially during quiet wakefulness. Moreover, in contrast to the generally elevated firing rate observed during whisking epochs, we find a marked decrease in the activity of imaged callosal fibers. Our results indicate that the reduction in interhemispheric coupling and correlations during active behavior reflects the specific reduction in the activity of callosal neurons.
The T cell receptor repertoire of tumor infiltrating T cells is predictive and prognostic for cancer survival
Authors: Valpione Sara , Mundra Piyushkumar A. , Galvani Elena , Campana Luca G. , Lorigan Paul , De Rosa Francesco , Gupta Avinash , Weightman John , Mills Sarah , Dhomen Nathalie , Marais Richard 
Published: July 2021

AbstractTumor infiltration by T cells is paramount for effective anti-cancer immune responses. We hypothesized that the T cell receptor (TCR) repertoire of tumor infiltrating T lymphocytes could therefore be indicative of the functional state of these cells and determine disease course at different stages in cancer progression. Here we show that the diversity of the TCR of tumor infiltrating T cell at baseline is prognostic in various cancers, whereas the TCR clonality of T cell infiltrating metastatic melanoma pre-treatment is predictive for activity and efficacy of PD1 blockade immunotherapy.
Reduced efficacy of a Src kinase inhibitor in crowded protein solution
Authors: Kasahara Kento , Re Suyong , Nawrocki Grzegorz , Oshima Hiraku , Mishima-Tsumagari Chiemi , Miyata-Yabuki Yukako , Kukimoto-Niino Mutsuko , Yu Isseki , Shirouzu Mikako , Feig Michael , Sugita Yuji 
Published: July 2021

AbstractThe inside of a cell is highly crowded with proteins and other biomolecules. How proteins express their specific functions together with many off-target proteins in crowded cellular environments is largely unknown. Here, we investigate an inhibitor binding with c-Src kinase using atomistic molecular dynamics (MD) simulations in dilute as well as crowded protein solution. The populations of the inhibitor, 4-amino-5-(4-methylphenyl)−7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP1), in bulk solution and on the surface of c-Src kinase are reduced as the concentration of crowder bovine serum albumins (BSAs) increases. This observation is consistent with the reduced PP1 inhibitor efficacy in experimental c-Src kinase assays in addition with BSAs. The crowded environment changes the major binding pathway of PP1 toward c-Src kinase compared to that in dilute solution. This change is explained based on the population shift mechanism of local conformations near the inhibitor binding site in c-Src kinase.
SS18 regulates pluripotent-somatic transition through phase separation
Authors: Kuang Junqi , Zhai Ziwei , Li Pengli , Shi Ruona , Guo Wenjing , Yao Yuxiang , Guo Jing , Zhao Guoqing , He Jiangpin , Xu Shuyang , Wu Chuman , Yu Shengyong , Zhou Chunhua , Wu Linlin , Qin Yue , Cai Baomei , Li Wei , Wu Zichao , Li Xiaoxi , Chu Shilong , Yang Tingting , Wang Bo , Cao Shangtao , Li Dongwei , Zhang Xiaofei , Chen Jiekai , Liu Jing , Pei Duanqing 
Published: July 2021

AbstractThe transition from pluripotent to somatic states marks a critical event in mammalian development, but remains largely unresolved. Here we report the identification of SS18 as a regulator for pluripotent to somatic transition or PST by CRISPR-based whole genome screens. Mechanistically, SS18 forms microscopic condensates in nuclei through a C-terminal intrinsically disordered region (IDR) rich in tyrosine, which, once mutated, no longer form condensates nor rescue SS18−/− defect in PST. Yet, the IDR alone is not sufficient to rescue the defect even though it can form condensates indistinguishable from the wild type protein. We further show that its N-terminal 70aa is required for PST by interacting with the Brg/Brahma-associated factor (BAF) complex, and remains functional even swapped onto unrelated IDRs or even an artificial 24 tyrosine polypeptide. Finally, we show that SS18 mediates BAF assembly through phase separation to regulate PST. These studies suggest that SS18 plays a role in the pluripotent to somatic interface and undergoes liquid-liquid phase separation through a unique tyrosine-based mechanism.
Dissecting spatial heterogeneity and the immune-evasion mechanism of CTCs by single-cell RNA-seq in hepatocellular carcinoma
Authors: Sun Yun-Fan , Wu Liang , Liu Shi-Ping , Jiang Miao-Miao , Hu Bo , Zhou Kai-Qian , Guo Wei , Xu Yang , Zhong Yu , Zhou Xiao-Rui , Zhang Ze-Fan , Liu Geng , Liu Sheng , Shi Ying-Hong , Ji Yuan , Du Min , Li Nan-Nan , Li Gui-Bo , Zhao Zhi-Kun , Huang Xiao-Yun , Xu Li-Qin , Yu Qi-Chao , Peng David H. , Qiu Shuang-Jian , Sun Hui-Chuan , Dean Michael , Wang Xiang-Dong , Chung Wen-Yuan , Dennison Ashley R. , Zhou Jian , Hou Yong , Fan Jia , Yang Xin-Rong 
Published: July 2021

AbstractLittle is known about the transcriptomic plasticity and adaptive mechanisms of circulating tumor cells (CTCs) during hematogeneous dissemination. Here we interrogate the transcriptome of 113 single CTCs from 4 different vascular sites, including hepatic vein (HV), peripheral artery (PA), peripheral vein (PV) and portal vein (PoV) using single-cell full-length RNA sequencing in hepatocellular carcinoma (HCC) patients. We reveal that the transcriptional dynamics of CTCs were associated with stress response, cell cycle and immune-evasion signaling during hematogeneous transportation. Besides, we identify chemokine CCL5 as an important mediator for CTC immune evasion. Mechanistically, overexpression of CCL5 in CTCs is transcriptionally regulated by p38-MAX signaling, which recruites regulatory T cells (Tregs) to facilitate immune escape and metastatic seeding of CTCs. Collectively, our results reveal a previously unappreciated spatial heterogeneity and an immune-escape mechanism of CTC, which may aid in designing new anti-metastasis therapeutic strategies in HCC.
Super-elasticity at 4 K of covalently crosslinked polyimide aerogels with negative Poisson’s ratio
Authors: Cheng Yang , Zhang Xiang , Qin Yixiu , Dong Pei , Yao Wei , Matz John , Ajayan Pulickel M. , Shen Jianfeng , Ye Mingxin 
Published: July 2021

AbstractThe deep cryogenic temperatures encountered in aerospace present significant challenges for the performance of elastic materials in spacecraft and related apparatus. Reported elastic carbon or ceramic aerogels overcome the low-temperature brittleness in conventional elastic polymers. However, complicated fabrication process and high costs greatly limited their applications. In this work, super-elasticity at a deep cryogenic temperature of covalently crosslinked polyimide (PI) aerogels is achieved based on scalable and low-cost directional dimethyl sulfoxide crystals assisted freeze gelation and freeze-drying strategy. The covalently crosslinked chemical structure, cellular architecture, negative Poisson’s ratio (−0.2), low volume shrinkage (3.1%), and ultralow density (6.1 mg/cm3) endow the PI aerogels with an elastic compressive strain up to 99% even in liquid helium (4 K), almost zero loss of resilience after dramatic thermal shocks (∆T = 569 K), and fatigue resistance over 5000 times compressive cycles. This work provides a new pathway for constructing polymer-based materials with super-elasticity at deep cryogenic temperature, demonstrating much promise for extensive applications in ongoing and near-future aerospace exploration.
Cellphone enabled point-of-care assessment of breast tumor cytology and molecular HER2 expression from fine-needle aspirates
Authors: Joh Daniel Y. , Heggestad Jacob T. , Zhang Shengwei , Anderson Gray R. , Bhattacharyya Jayanta , Wardell Suzanne E. , Wall Simone A. , Cheng Amy B. , Albarghouthi Faris , Liu Jason , Oshima Sachi , Hucknall Angus M. , Hyslop Terry , Hall Allison H. S. , Wood Kris C. , Shelley Hwang E. , Strickland Kyle C. , Wei Qingshan , Chilkoti Ashutosh 
Published: July 2021

AbstractManagement of breast cancer in limited-resource settings is hindered by a lack of low-cost, logistically sustainable approaches toward molecular and cellular diagnostic pathology services that are needed to guide therapy. To address these limitations, we have developed a multimodal cellphone-based platform—the EpiView-D4—that can evaluate both cellular morphology and molecular expression of clinically relevant biomarkers directly from fine-needle aspiration (FNA) of breast tissue specimens within 1 h. The EpiView-D4 is comprised of two components: (1) an immunodiagnostic chip built upon a “non-fouling” polymer brush-coating (the “D4”) which quantifies expression of protein biomarkers directly from crude cell lysates, and (2) a custom cellphone-based optical microscope (“EpiView”) designed for imaging cytology preparations and D4 assay readout. As a proof-of-concept, we used the EpiView-D4 for assessment of human epidermal growth factor receptor-2 (HER2) expression and validated the performance using cancer cell lines, animal models, and human tissue specimens. We found that FNA cytology specimens (prepared in less than 5 min with rapid staining kits) imaged by the EpiView-D4 were adequate for assessment of lesional cellularity and tumor content. We also found our device could reliably distinguish between HER2 expression levels across multiple different cell lines and animal xenografts. In a pilot study with human tissue (n = 19), we were able to accurately categorize HER2-negative and HER2-positve tumors from FNA specimens. Taken together, the EpiView-D4 offers a promising alternative to invasive—and often unavailable—pathology services and may enable the democratization of effective breast cancer management in limited-resource settings.
The Rayleigh–Lorentz invariant for superconducting resonators and optimal adiabatic qubit-information detection
Authors: Choi Jeong Ryeol 
Published: July 2021

AbstractDynamical properties of a resonator can be analyzed using the Rayleigh–Lorentz invariant which is not an exact constant but varies more or less over time depending on variations of parameters. We investigate the time behavior of this invariant for a superconducting nano-resonator in order for better understanding of qubit-information detection with the resonator. Superconducting resonators which uses parametric resonance in a Josephson junction circuit can be utilized in implementing diverse next generation nano-optic and nano-electronic devices such as quantum computing systems. Through the analyses of the temporal evolution of the invariant, we derive a condition for optimal adiabatic qubit-information detection with the resonator. This condition is helpful for controlling the dynamics of the resonators over long periods of time. It is necessary to consider it when designing a nano-resonator used for quantum nondemolition readouts of qubit states, crucial in quantum computation.