bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial photosynthetic cell producing energy for protein synthesis
Authors: Berhanu Samuel , Ueda Takuya , Kuruma Yutetsu 
Published: March 2019

AbstractAttempts to construct an artificial cell have widened our understanding of living organisms. Many intracellular systems have been reconstructed by assembling molecules, however the mechanism to synthesize its own constituents by self-sufficient energy has to the best of our knowledge not been developed. Here, we combine a cell-free protein synthesis system and small proteoliposomes, which consist of purified ATP synthase and bacteriorhodopsin, inside a giant unilamellar vesicle to synthesize protein by the production of ATP by light. The photo-synthesized ATP is consumed as a substrate for transcription and as an energy for translation, eventually driving the synthesis of bacteriorhodopsin or constituent proteins of ATP synthase, the original essential components of the proteoliposome. The de novo photosynthesized bacteriorhodopsin and the parts of ATP synthase integrate into the artificial photosynthetic organelle and enhance its ATP photosynthetic activity through the positive feedback of the products. Our artificial photosynthetic cell system paves the way to construct an energetically independent artificial cell.
In situ spectroscopy-guided engineering of rhodium single-atom catalysts for CO oxidation
Authors: Hülsey Max J. , Zhang Bin , Ma Zhirui , Asakura Hiroyuki , Do David A. , Chen Wei , Tanaka Tsunehiro , Zhang Peng , Wu Zili , Yan Ning 
Published: March 2019

AbstractSingle-atom catalysts have recently been applied in many applications such as CO oxidation. Experimental in situ investigations into this reaction, however, are limited. Hereby, we present a suite of operando/in situ spectroscopic experiments for structurally well-defined atomically dispersed Rh on phosphotungstic acid during CO oxidation. The identification of several key intermediates and the steady-state catalyst structure indicate that the reactions follow an unconventional Mars-van Krevelen mechanism and that the activation of O2 is rate-limiting. In situ XPS confirms the contribution of the heteropoly acid support while in situ DRIFT spectroscopy consolidates the oxidation state and CO adsorption of Rh. As such, direct observation of three key components, i.e., metal center, support and substrate, is achieved, providing a clearer picture on CO oxidation on atomically dispersed Rh sites. The obtained information are used to engineer structurally similar catalysts that exhibit T20 values up to 130 °C below the previously reported Rh1/NPTA.
Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis
Authors: Kelly Madison J. , So Joan , Rogers Amy J. , Gregory Gareth , Li Jason , Zethoven Magnus , Gearhart Micah D. , Bardwell Vivian J. , Johnstone Ricky W. , Vervoort Stephin J. , Kats Lev M. 
Published: March 2019

AbstractThe BCL6 Corepressor (BCOR) is a component of a variant Polycomb repressive complex 1 (PRC1) that is essential for normal development. Recurrent mutations in the BCOR gene have been identified in acute myeloid leukaemia and myelodysplastic syndrome among other cancers; however, its function remains poorly understood. Here we examine the role of BCOR in haematopoiesis in vivo using a conditional mouse model that mimics the mutations observed in haematological malignancies. Inactivation of Bcor in haematopoietic stem cells (HSCs) results in expansion of myeloid progenitors and co-operates with oncogenic KrasG12D in the initiation of an aggressive and fully transplantable acute leukaemia. Gene expression analysis and chromatin immunoprecipitation sequencing reveals differential regulation of a subset of PRC1-target genes including HSC-associated transcription factors such as Hoxa7/9. This study provides mechanistic understanding of how BCOR regulates cell fate decisions and how loss of function contributes to the development of leukaemia.
Aedes mosquitoes acquire and transmit Zika virus by breeding in contaminated aquatic environments
Authors: Du Senyan , Liu Yang , Liu Jianying , Zhao Jie , Champagne Clara , Tong Liangqin , Zhang Renli , Zhang Fuchun , Qin Cheng-Feng , Ma Ping , Chen Chun-Hong , Liang Guodong , Liu Qiyong , Shi Pei-Yong , Cazelles Bernard , Wang Penghua , Tian Huaiyu , Cheng Gong 
Published: March 2019

AbstractZika virus (ZIKV) is a mosquito-borne flavivirus that predominantly circulates between humans and Aedes mosquitoes. Clinical studies have shown that Zika viruria in patients persists for an extended period, and results in infectious virions being excreted. Here, we demonstrate that Aedes mosquitoes are permissive to ZIKV infection when breeding in urine or sewage containing low concentrations of ZIKV. Mosquito larvae and pupae, including from field Aedes aegypti can acquire ZIKV from contaminated aquatic systems, resulting in ZIKV infection of adult females. Adult mosquitoes can transmit infectious virions to susceptible type I/II interferon receptor-deficient (ifnagr-/-) C57BL/6 (AG6) mice. Furthermore, ZIKV viruria from infected AG6 mice can causes mosquito infection during the aquatic life stages. Our studies suggest that infectious urine could be a natural ZIKV source, which is potentially transmissible to mosquitoes when breeding in an aquatic environment.
Bromodomain and extraterminal proteins foster the core transcriptional regulatory programs and confer vulnerability in liposarcoma
Authors: Chen Ye , Xu Liang , Mayakonda Anand , Huang Mo-Li , Kanojia Deepika , Tan Tuan Zea , Dakle Pushkar , Lin Ruby Yu-Tong , Ke Xin-Yu , Said Jonathan W. , Chen Jianxiang , Gery Sigal , Ding Ling-Wen , Jiang Yan-Yi , Pang Angela , Puhaindran Mark Edward , Goh Boon Cher , Koeffler H. Phillip 
Published: March 2019

AbstractLiposarcomas (LPSs) are a group of malignant mesenchymal tumors showing adipocytic differentiation. Here, to gain insight into the enhancer dysregulation and transcriptional addiction in this disease, we chart super-enhancer structures in both LPS tissues and cell lines. We identify a bromodomain and extraterminal (BET) protein-cooperated FUS-DDIT3 function in myxoid LPS and a BET protein-dependent core transcriptional regulatory circuitry consisting of FOSL2, MYC, and RUNX1 in de-differentiated LPS. Additionally, SNAI2 is identified as a crucial downstream target that enforces both proliferative and metastatic potentials to de-differentiated LPS cells. Genetic depletion of BET genes, core transcriptional factors, or SNAI2 mitigates consistently LPS malignancy. We also reveal a compelling susceptibility of LPS cells to BET protein degrader ARV-825. BET protein depletion confers additional advantages to circumvent acquired resistance to Trabectedin, a chemotherapy drug for LPS. Moreover, this study provides a framework for discovering and targeting of core oncogenic transcriptional programs in human cancers.
Boundary activated hydrogen evolution reaction on monolayer MoS2
Authors: Zhu Jianqi , Wang Zhi-Chang , Dai Huijia , Wang Qinqin , Yang Rong , Yu Hua , Liao Mengzhou , Zhang Jing , Chen Wei , Wei Zheng , Li Na , Du Luojun , Shi Dongxia , Wang Wenlong , Zhang Lixin , Jiang Ying , Zhang Guangyu 
Published: March 2019

AbstractRecently, monolayer molybdenum disulphide (MoS2) has emerged as a promising and non–precious electrocatalyst for hydrogen evolution reaction. However, its performance is largely limited by the low density and poor reactivity of active sites within its basal plane. Here, we report that domain boundaries in the basal plane of monolayer MoS2 can greatly enhance its hydrogen evolution reaction performance by serving as active sites. Two types of effective domain boundaries, the 2H-2H domain boundaries and the 2H-1T phase boundaries, were investigated. Superior hydrogen evolution reaction catalytic activity, long-term stability and universality in both acidic and alkaline conditions were achieved based on a multi-hierarchy design of these two types of domain boundaries. We further demonstrate that such superior catalysts are feasible at a large scale by applying this multi-hierarchy design of domain boundaries to wafer-scale monolayer MoS2 films.
Microbial recognition by GEF-H1 controls IKKε mediated activation of IRF5
Authors: Zhao Yun , Zagani Rachid , Park Sung-Moo , Yoshida Naohiro , Shah Pankaj , Reinecker Hans-Christian 
Published: March 2019

AbstractDuring infection, transcription factor interferon regulatory factor 5 (IRF5) is essential for the control of host defense. Here we show that the microtubule-associated guanine nucleotide exchange factor (GEF)-H1, is required for the phosphorylation of IRF5 by microbial muramyl-dipeptides (MDP), the minimal structural motif of peptidoglycan of both Gram-positive and Gram-negative bacteria. Specifically, GEF-H1 functions in a microtubule based recognition system for microbial peptidoglycans that mediates the activation of IKKε which we identify as a new upstream IKKα/β and IRF5 kinase. The deletion of GEF-H1 or dominant-negative variants of GEF-H1 prevent activation of IKKε and phosphorylation of IRF5. The GEF-H1-IKKε-IRF5 signaling axis functions independent of NOD-like receptors and is critically required for the recognition of intracellular peptidoglycans and host defenses against Listeria monocytogenes.
Overcoming the thermodynamic equilibrium of an isomerization reaction through oxidoreductive reactions for biotransformation
Authors: Liu Jing-Jing , Zhang Guo-Chang , Kwak Suryang , Oh Eun Joong , Yun Eun Ju , Chomvong Kulika , Cate Jamie H. D. , Jin Yong-Su 
Published: March 2019

AbstractIsomerases perform biotransformations without cofactors but often cause an undesirable mixture of substrate and product due to unfavorable thermodynamic equilibria. We demonstrate the feasibility of using an engineered yeast strain harboring oxidoreductase reactions to overcome the thermodynamic limit of an isomerization reaction. Specifically, a yeast strain capable of consuming lactose intracellularly is engineered to produce tagatose from lactose through three layers of manipulations. First, GAL1 coding for galactose kinase is deleted to eliminate galactose utilization. Second, heterologous xylose reductase (XR) and galactitol dehydrogenase (GDH) are introduced into the ∆gal1 strain. Third, the expression levels of XR and GDH are adjusted to maximize tagatose production. The resulting engineered yeast produces 37.69 g/L of tagatose from lactose with a tagatose and galactose ratio of 9:1 in the reaction broth. These results suggest that in vivo oxidoreaductase reactions can be employed to replace isomerases in vitro for biotransformation.
Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA
Authors: Yang Ei-Wen , Bahn Jae Hoon , Hsiao Esther Yun-Hua , Tan Boon Xin , Sun Yiwei , Fu Ting , Zhou Bo , Van Nostrand Eric L. , Pratt Gabriel A. , Freese Peter , Wei Xintao , Quinones-Valdez Giovanni , Urban Alexander E. , Graveley Brenton R. , Burge Christopher B. , Yeo Gene W. , Xiao Xinshu 
Published: March 2019

AbstractAllele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo binding of RNA-binding proteins is greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed a new computational approach, called BEAPR, to identify allele-specific binding (ASB) events in eCLIP-Seq data. BEAPR takes into account crosslinking-induced sequence propensity and variations between replicated experiments. Using simulated and actual data, we show that BEAPR largely outperforms often-used count analysis methods. Importantly, BEAPR overcomes the inherent overdispersion problem of these methods. Complemented by experimental validations, we demonstrate that the application of BEAPR to ENCODE eCLIP-Seq data of 154 proteins helps to predict functional GVs that alter splicing or mRNA abundance. Moreover, many GVs with ASB patterns have known disease relevance. Overall, BEAPR is an effective method that helps to address the outstanding challenge of functional interpretation of GVs.
Coherent quantum control of nitrogen-vacancy center spins near 1000 kelvin
Authors: Liu Gang-Qin , Feng Xi , Wang Ning , Li Quan , Liu Ren-Bao 
Published: March 2019

AbstractQuantum coherence control usually requires low temperature environments. Even for nitrogen-vacancy center spins in diamond, a remarkable exception, the coherence signal is limited to about 700 K due to the quench of the spin-dependent fluorescence at a higher temperature. Here we overcome this limit and demonstrate quantum coherence control of the electron spins of nitrogen-vacancy centers in nanodiamonds at temperatures near 1000 K. The scheme is based on initialization and readout of the spins at room temperature and control at high temperature, which is enabled by pulse laser heating and rapid diffusion cooling of nanodiamonds on amorphous carbon films. Using the diamond magnetometry based on optically detected magnetic resonance up to 800 K, we observe the magnetic phase transition of a single nickel nanoparticle at about 615 K. This work enables nano-thermometry and nano-magnetometry in the high-temperature regime.
Selective binding of a toxin and phosphatidylinositides to a mammalian potassium channel
Authors: Liu Yang , LoCaste Catherine E. , Liu Wen , Poltash Michael L. , Russell David H. , Laganowsky Arthur 
Published: March 2019

AbstractG-protein-gated inward rectifying potassium channels (GIRKs) require Gβγ subunits and phosphorylated phosphatidylinositides (PIPs) for gating. Although studies have provided insight into these interactions, the mechanism of how these events are modulated by Gβγ and the binding affinity between PIPs and GIRKs remains poorly understood. Here, native ion mobility mass spectrometry is employed to directly monitor small molecule binding events to mouse GIRK2. GIRK2 binds the toxin tertiapin Q and PIPs selectively and with significantly higher affinity than other phospholipids. A mutation in GIRK2 that causes a rotation in the cytoplasmic domain, similarly to Gβγ-binding to the wild-type channel, revealed differences in the selectivity towards PIPs. More specifically, PIP isoforms known to weakly activate GIRKs have decreased binding affinity. Taken together, our results reveal selective small molecule binding and uncover a mechanism by which rotation of the cytoplasmic domain can modulate GIRK•PIP interactions.
A green metal-free fused-ring initiating substance
Authors: Deng Mucong , Feng Yongan , Zhang Wenquan , Qi Xiujuan , Zhang Qinghua 
Published: March 2019

AbstractOver the past century, the search for lead-free, environmentally friendly initiating substances has been a highly challenging task in the field of energetic materials. Here, an organic primary explosive featuring a fused-ring structure, 6-nitro-7-azido-pyrazol[3,4-d][1,2,3]triazine-2-oxide, was designed and synthesized through a facile two-step reaction from commercially available reagents. This organic initiating substance meets nearly all of the stringent criteria of environmentally friendly primary explosives for commercial applications: it is free of toxic metals and perchlorate, has a high density, high priming ability, unusual sensitivities towards non-explosive stimuli, excellent environmental resistance, decent thermal stability, high detonation performance, satisfactory flowability and pressure durability, and is low-cost and easy to scale-up. These combined properties and performance measures surpass the current and widely used organic primary explosive, DDNP. The fused-ring organic primary explosive reported herein may find real-world application as an initiating explosive device in the near future.
Spatial-fluxomics provides a subcellular-compartmentalized view of reductive glutamine metabolism in cancer cells
Authors: Lee Won Dong , Mukha Dzmitry , Aizenshtein Elina , Shlomi Tomer 
Published: March 2019

AbstractThe inability to inspect metabolic activities within subcellular compartments has been a major barrier to our understanding of eukaryotic cell metabolism. Here, we describe a spatial-fluxomics approach for inferring metabolic fluxes in mitochondria and cytosol under physiological conditions, combining isotope tracing, rapid subcellular fractionation, LC-MS-based metabolomics, computational deconvolution, and metabolic network modeling. Applied to study reductive glutamine metabolism in cancer cells, shown to mediate fatty acid biosynthesis under hypoxia and defective mitochondria, we find a previously unappreciated role of reductive IDH1 as the sole net contributor of carbons to fatty acid biosynthesis under standard normoxic conditions in HeLa cells. In murine cells with defective SDH, we find that reductive biosynthesis of citrate in mitochondria is followed by a reversed CS activity, suggesting a new route for supporting pyrimidine biosynthesis. We expect this spatial-fluxomics approach to be a highly useful tool for elucidating the role of metabolic dysfunction in human disease.
Etiology of 305 cases of refractory hematospermia and therapeutic options by emerging endoscopic technology
Authors: Liao Liang-Gong , Li Yan-Feng , Zhang Yong , Li Ke , Zhu Tong , Li Bo-Jun , Wang Qi , Liu Xu-Dong , Luo Yong , Zhou Bo , Jiang Jun 
Published: March 2019

AbstractTo investigate the surgical outcomes of vesiculoscopy on refractory hematospermia and ejaculatory duct obstruction (EDO), the clinical data (including pelvic magnetic resonance imaging (MRI) examinations and the long-term effects of endoscopic treatment) from 305 patients were analyzed. Four main etiologic groups were found on MRI. We found that 62.0% (189/305) of patients showed abnormal signal intensity in MRI investigations in the seminal vesicle (SV) area. Cystic lesions were observed in 36.7% (112/305) of the patients. The third sign was dilatation or enlargement of unilateral or bilateral SV, which were observed in 32.1% (98/305) of the patients. The fourth sign was stone formation in SV or in an adjacent cyst, which was present in 8.5% (26/305) of the patients. The transurethral endoscopy or seminal vesiculoscopy and the related procedures, including fenestration in prostatic utricle (PU), irrigation, lithotripsy, stone removal, biopsy, electroexcision, fulguration, or transurethral resection/incision of the ejaculatory duct (TURED/TUIED), chosen according to the different situations of individual patients were successfully performed in 296 patients. Fenestrations in PU+ seminal vesiculoscopy were performed in 66.6% (197/296) of cases. Seminal vesiculoscopy via the pathological opening in PU was performed in 10.8% (32/296) of cases. TURED/TUIED + seminal vesiculoscopy was performed in 12.8% (38/296) of cases, and seminal vesiculoscopy by the natural orifices of the ejaculatory duct (ED) was performed in 2.4% (7/296) of cases. Electroexcision and fulguration to the abnormal blood vessels or cavernous hemangioma at posterior urethra were performed in 7.4% (22/296) of cases. Two hundred and seventy-one patients were followed up for 6–72 months. The hematospermia of all the patients disappeared within 2–6 weeks, and 93.0% of the patients showed no further hematospermia during follow-up. No obvious postoperative complications were observed. The transurethral seminal vesiculoscopy technique and related procedures are safe and effective approaches for refractory hematospermia and EDO.
Predicting the behavioural tendency of loss aversion
Authors: Zeng Jianmin , Wang Yujiao , Zeng Jing , Cao Zhipeng , Chen Hong , Liu Yijun , Zhang Qinglin , Su Li 
Published: March 2019

AbstractLoss aversion manifests itself in rejecting a gamble of gaining or losing the same amount of money with equal chance. Although loss aversion is a well-known and intensively studied phenomenon, whether individual differences in behavioural loss aversion can be predicted using scalp potentials (EEG) remains unclear. The current study measured scalp potential when subjects played a series of fair coin-toss games in three situations (high, medium and low loss conditions). We found that most people chose to bet in the low loss condition and avoided to bet in the high loss condition. However, their betting behaviour in the medium loss condition was variable, reflecting their different behavioural tendency of loss aversion. We found that late positive complex (LPC) significantly increased when subjects accepted gambles in the low loss condition (implying potential loss), relative to when they rejected gambles in the high loss condition (implying no gain and no loss), which is consistent with the previous finding that emotional stimuli can induce enhanced LPC. We further found that the difference in the scalp potentials from the above two conditions could predict behavioural tendency of loss aversion in the medium loss condition across subjects. This result demonstrated how behavioural tendency in a situation can be predicted using EEG from other situations.
Evidence of mitochondrial DNA in the chloroplast genome of Convallaria keiskei and its subsequent evolution in the Asparagales
Authors: Raman Gurusamy , Park Seongjun , Lee Eun Mi , Park SeonJoo 
Published: March 2019

AbstractDNA transfer between internal organelles such as the nucleus, mitochondrion, and plastid is a well-known phenomenon in plant evolution, and DNA transfer from the plastid and mitochondrion to the nucleus, from the plastid to the mitochondrion, and from the nucleus to the mitochondrion has been well-documented in angiosperms. However, evidence of the transfer of mitochondrial DNA (mtDNA) to the plastid has only been found in three dicotyledons and one monocotyledon. In the present study, we characterised and analysed two chloroplast (cp) genome sequences of Convallaria keiskei and Liriope spicata, and found that C. keiskei has the largest cp genome (162,109 bp) in the Asparagaceae. Interestingly, C. keiskei had a ~3.3-kb segment of mtDNA in its cp genome and showed similarity with the mt gene rpl10 as a pseudogene. Further analyses revealed that mtDNA transfer only occurred in C. keiskei in the Nolinoideae, which diverged very recently (7.68 million years ago (mya); 95% highest posterior density (HPD): 14.55–2.97 mya). These findings indicate that the C. keiskei cp genome is unique amongst monocotyledon land plants, but further work is necessary to understand the direction and mechanism involved in the uptake of mtDNA by the plastid genome of C. keiskei.
Cyclin D1 protein affecting global women’s health by regulating HPV mediated adenocarcinoma of the uterine cervix
Authors: Tripathi Richa , Rath Gayatri , Jawanjal Poonam , Bharadwaj Mausumi , Mehrotra Ravi 
Published: March 2019

AbstractAdenocarcinoma (ADC) of the uterine cervix (UC) is a rare form of cervical cancer (CC) caused due to the infection of Human Papilloma Virus (HPV). Cyclin D1 is one of the downstream targets of aberrantly activated Notch signaling, contribute to the etiology of CC. However, little is known about the role of Cyclin D1 in the modulation of cervical ADC and is controversial. The purpose of this study is to determine the role of Cyclin D1 protein and to elucidate the combined analysis with Notch signaling proteins in HPV associated ADCs of CC. A total of 60 biopsy samples (40 normal and 20 ADCs of CC) were analyzed for the expression of Cyclin D1 in HPV associated ADCs via immunohistochemistry and by immunoblotting. HPV-16 positive ADC patients showed a strong association with the Cyclin D1 expression (p = 0.007). The significant mean difference (p = 0.0001) and the pairwise comparison between Cyclin D1/JAG1 (p = 0.0001), and Cyclin D1/Notch-3 (p = 0.0001) were observed. The above Notch signaling proteins showed their synergistic role in modulating Cyclin D1 which in-turn regulates HPV-16 associated ADC of the uterine cervix (UC), affecting women’s global health.