bluuebunny/crossref_metadata_2025_split huggingface dataset:
K63-polyubiquitinated HAUSP deubiquitinates HIF-1α and dictates H3K56 acetylation promoting hypoxia-induced tumour progression
Authors: Wu Han-Tsang , Kuo Yi-Chih , Hung Jung-Jyh , Huang Chi-Hung , Chen Wei-Yi , Chou Teh-Ying , Chen Yeh , Chen Yi-Ju , Chen Yu-Ju , Cheng Wei-Chung , Teng Shu-Chun , Wu Kou-Juey 
Published: December 2016

AbstractIntratumoural hypoxia induces HIF-1α and promotes tumour progression, metastasis and treatment resistance. HIF-1α stability is regulated by VHL-E3 ligase-mediated ubiquitin-dependent degradation; however, the hypoxia-regulated deubiquitinase that stabilizes HIF-1α has not been identified. Here we report that HAUSP (USP7) deubiquitinase deubiquitinates HIF-1α to increase its stability, induce epithelial-mesenchymal transition and promote metastasis. Hypoxia induces K63-linked polyubiquitinated HAUSP at lysine 443 to enhance its functions. Knockdown of HAUSP decreases acetylation of histone 3 lysine 56 (H3K56Ac). K63-polyubiquitinated HAUSP interacts with a ubiquitin receptor CBP to specifically mediate H3K56 acetylation. ChIP-seq analysis of HAUSP and HIF-1α binding reveals two motifs responsive to hypoxia. HectH9 is the E3 ligase for HAUSP and a prognostic marker together with HIF-1α. This report demonstrates that hypoxia-induced K63-polyubiquitinated HAUSP deubiquitinates HIF-1α and causes CBP-mediated H3K56 acetylation on HIF-1α target gene promoters to promote EMT/metastasis, further defining HAUSP as a therapeutic target in hypoxia-induced tumour progression.
Bond selectivity in electron-induced reaction due to directed recoil on an anisotropic substrate
Authors: Anggara Kelvin , Huang Kai , Leung Lydie , Chatterjee Avisek , Cheng Fang , Polanyi John C. 
Published: December 2016

AbstractBond-selective reaction is central to heterogeneous catalysis. In heterogeneous catalysis, selectivity is found to depend on the chemical nature and morphology of the substrate. Here, however, we show a high degree of bond selectivity dependent only on adsorbate bond alignment. The system studied is the electron-induced reaction of meta-diiodobenzene physisorbed on Cu(110). Of the adsorbate’s C-I bonds, C-I aligned ‘Along’ the copper row dissociates in 99.3% of the cases giving surface reaction, whereas C-I bond aligned ‘Across’ the rows dissociates in only 0.7% of the cases. A two-electronic-state molecular dynamics model attributes reaction to an initial transition to a repulsive state of an Along C-I, followed by directed recoil of C towards a Cu atom of the same row, forming C-Cu. A similar impulse on an Across C-I gives directed C that, moving across rows, does not encounter a Cu atom and hence exhibits markedly less reaction.
Scanning superlens microscopy for non-invasive large field-of-view visible light nanoscale imaging
Authors: Wang Feifei , Liu Lianqing , Yu Haibo , Wen Yangdong , Yu Peng , Liu Zhu , Wang Yuechao , Li Wen Jung 
Published: December 2016

AbstractNanoscale correlation of structural information acquisition with specific-molecule identification provides new insight for studying rare subcellular events. To achieve this correlation, scanning electron microscopy has been combined with super-resolution fluorescent microscopy, despite its destructivity when acquiring biological structure information. Here we propose time-efficient non-invasive microsphere-based scanning superlens microscopy that enables the large-area observation of live-cell morphology or sub-membrane structures with sub-diffraction-limited resolution and is demonstrated by observing biological and non-biological objects. This microscopy operates in both non-invasive and contact modes with ∼200 times the acquisition efficiency of atomic force microscopy, which is achieved by replacing the point of an atomic force microscope tip with an imaging area of microspheres and stitching the areas recorded during scanning, enabling sub-diffraction-limited resolution. Our method marks a possible path to non-invasive cell imaging and simultaneous tracking of specific molecules with nanoscale resolution, facilitating the study of subcellular events over a total cell period.
Covalency and vibronic couplings make a nonmagnetic j=3/2 ion magnetic
Authors: Xu Lei , Bogdanov Nikolay A , Princep Andrew , Fulde Peter , van den Brink Jeroen , Hozoi Liviu 
Published: December 2016

AbstractFor 4d1 and 5d1 spin–orbit-coupled electron configurations, the notion of nonmagnetic j=3/2 quartet ground state discussed in classical textbooks is at odds with the observed variety of magnetic properties. Here we throw fresh light on the electronic structure of 4d1 and 5d1 ions in molybdenum- and osmium-based double-perovskite systems and reveal different kinds of on-site many-body physics in the two families of compounds: although the sizable magnetic moments and g-factors measured experimentally are due to both metal d–ligand p hybridisation and dynamic Jahn–Teller interactions for 4d electrons, it is essentially d−p covalency for the 5d1 configuration. These results highlight the subtle interplay of spin–orbit interactions, covalency and electron–lattice couplings as the major factor in deciding the nature of the magnetic ground states of 4d and 5d quantum materials. Cation charge imbalance in the double-perovskite structure is further shown to allow a fine tuning of the gap between the t2g and eg levels, an effect of much potential in the context of orbital engineering in oxide electronics.
High-density Association Mapping and Interaction Analysis of PLA2R1 and HLA Regions with Idiopathic Membranous Nephropathy in Japanese
Authors: Thiri Myo , Honda Kenjiro , Kashiwase Koichi , Mabuchi Akihiko , Suzuki Hodaka , Watanabe Kimio , Nakayama Masaaki , Watanabe Tsuyoshi , Doi Kent , Tokunaga Katsushi , Noiri Eisei 
Published: December 2016

AbstractAlthough recent studies showed anti-PLA2R antibody plays a crucial role in idiopathic membranous nephropathy (IMN), detailed HLA mapping and interaction between the HLA genes and PLA2R1 have not been investigated in IMN. We genotyped across the PLA2R1 gene and the HLA region, using 183 IMN patients and 811 healthy controls. Five SNPs around the PLA2R1 gene were significantly associated with IMN. In addition to the two SNPs previously reported to be strongly associated with IMN, rs3749119 and rs35771982 (OR 3.02 and 2.93, P = 3.24E-14 and 4.64E-14, respectively), two novel intronic SNPs (rs2715928 and rs16844715) were also identified as IMN-associated SNPs (OR = 2.30 and 2.51, P = 3.15E-10 and 5.66E-13, respectively). In the HLA gene analysis, DRB1*1501 and DQB1*0602 were strongly associated with IMN (P = 1.14E-11 and 1.25E-11, respectively). The interaction was strongest between HLA-DRB1*15:01 - HLA-DQB1*06:02 and the intronic SNP rs2715928 (OR = 17.53, P = 4.26E-26). Furthermore, positive interaction was also observed between HLA-DRB1*15:01 - HLA-DQB1*06:02 and the missense SNP rs35771982 (OR = 15.91, P = 2.76E-29), which is in strong linkage disequilibrium with 5′UTR SNP rs3749119, and intronic SNP rs16844715 (OR = 15.91, P = 2.30E-26) for IMN. Neither HLA-DRB1*15:01 nor HLA-DQB1*06:02 was associated with steroid responsiveness, overall survival and renal survival during the observation period of mean 11 years though limited number of analysis.
Rapid, Affordable and Portable Medium-Throughput Molecular Device for Zika Virus
Authors: Chan Kamfai , Weaver Scott C. , Wong Pui-Yan , Lie Sherly , Wang Eryu , Guerbois Mathilde , Vayugundla Siva Praneeth , Wong Season 
Published: December 2016

AbstractZika virus (ZIKV) has gained global attention as an etiologic agent of fetal microcephaly and Guillain-Barré syndrome. Existing immuno-based rapid tests often fail to distinguish between Zika and related flaviviruses that are common in affected regions of Central and South Americas and the Caribbean. The US CDC and qualified state health department laboratories can perform the reverse transcription polymerase chain reaction (RT-PCR) ZIKV test using highly sophisticated instruments with long turnaround times. The preliminary results of a portable and low-cost molecular diagnostics system for ZIKV infection are reported here. In less than 15 minutes, this low-cost platform can automatically perform high quality RNA extraction from up to 12 ZIKV-spiked urine samples simultaneously. It can also perform reverse transcription recombinase polymerase amplification reaction (RT-RPA) in ≤15 minutes. The fluorescent signal produced from probe-based RT-RPA or RT-PCR assays can be monitored using LEDs and a smartphone camera. In addition, the RT-RPA and RT-PCR assays do not cross-react with dengue and chikungunya viral RNA. This low-cost system lacks complicated, sensitive and high cost components, making it suitable for resource-limited settings. It has the potential to offer simple sample-to-answer molecular diagnostics and can inform healthcare workers of patients’ diagnosis promptly.
Quantitative HDL Proteomics Identifies Peroxiredoxin-6 as a Biomarker of Human Abdominal Aortic Aneurysm
Authors: Burillo Elena , Jorge Inmaculada , Martínez-López Diego , Camafeita Emilio , Blanco-Colio Luis Miguel , Trevisan-Herraz Marco , Ezkurdia Iakes , Egido Jesús , Michel Jean-Baptiste , Meilhac Olivier , Vázquez Jesús , Martin-Ventura Jose Luis 
Published: December 2016

AbstractHigh-density lipoproteins (HDLs) are complex protein and lipid assemblies whose composition is known to change in diverse pathological situations. Analysis of the HDL proteome can thus provide insight into the main mechanisms underlying abdominal aortic aneurysm (AAA) and potentially detect novel systemic biomarkers. We performed a multiplexed quantitative proteomics analysis of HDLs isolated from plasma of AAA patients (N = 14) and control study participants (N = 7). Validation was performed by western-blot (HDL), immunohistochemistry (tissue), and ELISA (plasma). HDL from AAA patients showed elevated expression of peroxiredoxin-6 (PRDX6), HLA class I histocompatibility antigen (HLA-I), retinol-binding protein 4, and paraoxonase/arylesterase 1 (PON1), whereas α-2 macroglobulin and C4b-binding protein were decreased. The main pathways associated with HDL alterations in AAA were oxidative stress and immune-inflammatory responses. In AAA tissue, PRDX6 colocalized with neutrophils, vascular smooth muscle cells, and lipid oxidation. Moreover, plasma PRDX6 was higher in AAA (N = 47) than in controls (N = 27), reflecting increased systemic oxidative stress. Finally, a positive correlation was recorded between PRDX6 and AAA diameter. The analysis of the HDL proteome demonstrates that redox imbalance is a major mechanism in AAA, identifying the antioxidant PRDX6 as a novel systemic biomarker of AAA.
Genome maintenance and bioenergetics of the long-lived hypoxia-tolerant and cancer-resistant blind mole rat, Spalax: a cross-species analysis of brain transcriptome
Authors: Malik Assaf , Domankevich Vered , Lijuan Han , Xiaodong Fang , Korol Abraham , Avivi Aaron , Shams Imad 
Published: December 2016

AbstractThe subterranean blind mole rat,Spalax,experiences acute hypoxia-reoxygenation cycles in its natural subterranean habitat. At the cellular level, these conditions are known to promote genomic instability, which underlies both cancer and aging. However,Spalaxis a long-lived animal and is resistant to both spontaneous and induced cancers. To study this apparent paradox we utilized a computational procedure that allows detecting differences in transcript abundance betweenSpalaxand the closely related above-groundRattus norvegicusin individuals of different ages. Functional enrichment analysis showed thatSpalaxwhole brain tissues maintain significantly higher normoxic mRNA levels of genes associated with DNA damage repair and DNA metabolism, yet keep significantly lower mRNA levels of genes involved in bioenergetics. Many of the genes that showed higher transcript abundance inSpalaxare involved in DNA repair and metabolic pathways that, in other species, were shown to be downregulated under hypoxia, yet are required for overcoming replication- and oxidative-stress during the subsequent reoxygenation. We suggest that these differentially expressed genes may prevent the accumulation of DNA damage in mitotic and post-mitotic cells and defective resumption of replication in mitotic cells, thus maintaining genome integrity as an adaptation to acute hypoxia-reoxygenation cycles.
Transient appearance of circulating tumor DNA associated with de novo treatment
Authors: Kato Kikuya , Uchida Junji , Kukita Yoji , Kumagai Toru , Nishino Kazumi , Inoue Takako , Kimura Madoka , Imamura Fumio 
Published: December 2016

AbstractThe limitation of circulating tumor DNA (ctDNA) is its inability to detect cancer cell subpopulations with few or no dying cells. Lung cancer patients subjected to the EGFR tyrosine kinase inhibitor (EGFR-TKI) treatment were prospectively collected, and ctDNA levels represented by the activating and T790M mutations were measured. The first data set (21 patients) consisting of samples collected in the period from before initiation of EGFR-TKI to at least 2 weeks after initiation: the ctDNA dynamics generally exhibited a rapid decrease and/or a transient increase. In 4 patients, we detected a transient increase of ctDNA bearing activating mutations not identified in biopsy samples. ctDNA with the same genotypical pattern was identified in 7 out of the 39 patients of the second data set intended to include samples until the onset of disease progression. In 6 of the 7 patients, this unique ctDNA appeared in the early period after treatment initiation, and did not reappear even after disease progression or chemotherapy. In another patient, similar ctDNA appeared upon radiation therapy. The identification of ctDNA with a unique genotype indicates the presence of cancer cell subpopulations that normally contain few or no dying cells, but generate dead cells because of the treatment.
Two-dimensional Fibonacci grating for far-field super-resolution imaging
Authors: Wu Kedi , Wang Guo Ping 
Published: December 2016

AbstractA two-dimensional (2D) Fibonacci grating is used to transform evanescent waves into propagating waves for far-field super-resolution imaging. By detecting far-field intensity distributions of light field through objects in front of the 2D Fibonacci grating in free space at once, we can retrieve the image of objects with beyond λ/7 spatial resolution. We also find that the coherent illumination case can give a better resolution than incoherent illumination case by such 2D grating-assisted imaging system. The analytical results are verified by numerical simulation.
Structure determination of molecules in an alignment laser field by femtosecond photoelectron diffraction using an X-ray free-electron laser
Authors: Minemoto Shinichirou , Teramoto Takahiro , Akagi Hiroshi , Fujikawa Takashi , Majima Takuya , Nakajima Kyo , Niki Kaori , Owada Shigeki , Sakai Hirofumi , Togashi Tadashi , Tono Kensuke , Tsuru Shota , Wada Ken , Yabashi Makina , Yoshida Shintaro , Yagishita Akira 
Published: December 2016

AbstractWe have successfully determined the internuclear distance of I2 molecules in an alignment laser field by applying our molecular structure determination methodology to an I 2p X-ray photoelectron diffraction profile observed with femtosecond X-ray free electron laser pulses. Using this methodology, we have found that the internuclear distance of the sample I2 molecules in an alignment Nd:YAG laser field of 6 × 1011 W/cm2 is elongated by from 0.18 to 0.30 Å “in average” relatively to the equilibrium internuclear distance of 2.666 Å. Thus, the present experiment constitutes a critical step towards the goal of femtosecond imaging of chemical reactions and opens a new direction for the study of ultrafast chemical reaction in the gas phase.
Gestational age-dependency of height and body mass index trajectories during the first 3 years in Japanese small-for-gestational age children
Authors: Maeyama Kaori , Morioka Ichiro , Iwatani Sota , Fukushima Sachiyo , Kurokawa Daisuke , Yamana Keiji , Nishida Kosuke , Ohyama Shohei , Fujioka Kazumichi , Awano Hiroyuki , Taniguchi-Ikeda Mariko , Nozu Kandai , Nagase Hiroaki , Nishimura Noriyuki , Shirai Chika , Iijima Kazumoto 
Published: December 2016

AbstractGestational age (GA) is thought to affect height growth in small-for-gestational age (SGA) children. However, the GA-specific trajectories in body mass index (BMI) and early appearances of adiposity rebound (AR) have not been fully investigated in a cohort of Japanese SGA children. A longitudinal cohort study was conducted with 1063 SGA children born in Kobe, Japan, with sufficient records from birth to 3 years of age. Subjects were divided into subgroups based on GA: 39–41 weeks GA (n = 723), 37–38 weeks GA (n = 256), 34–36 weeks GA (n = 62), and <34 weeks GA (n = 22). Height and BMI were assessed at 4 months, 9 months, 1.5 years, and 3 years of age. The catch-up rate for height was GA-dependent. Most children with 39–41 weeks GA (91%) caught up by 4 months of age; however, lower GA was associated with a slower elevation in the catch-up rate. The BMI trajectory during the first 3 years was also GA-dependent, with a change in GA dependency at a boundary of 37 weeks GA. Approximately 7% of SGA children had already developed AR before 3 years of age. In conclusion, growth patterns during infancy and early childhood in SGA children differ depending on GA.
Improving the photovoltaic performance of perovskite solar cells with acetate
Authors: Zhao Qian , Li G. R. , Song Jian , Zhao Yulong , Qiang Yinghuai , Gao X. P. 
Published: December 2016

AbstractIn an all-solid-state perovskite solar cell, methylammonium lead halide film is in charge of generating photo-excited electrons, thus its quality can directly influence the final photovoltaic performance of the solar cell. This paper accentuates a very simple chemical approach to improving the quality of a perovskite film with a suitable amount of acetic acid. With introduction of acetate ions, a homogeneous, continual and hole-free perovskite film comprised of high-crystallinity grains is obtained. UV-visible spectra, steady-state and time-resolved photoluminescence (PL) spectra reveal that the obtained perovskite film under the optimized conditions shows a higher light absorption, more efficient electron transport, and faster electron extraction to the adjoining electron transport layer. The features result in the optimized perovskite film can provide an improved short-circuit current. The corresponding solar cells with a planar configuration achieves an improved power conversion efficiency of 13.80%, and the highest power conversion efficiency in the photovoltaic measurements is up to 14.71%. The results not only provide a simple approach to optimizing perovskite films but also present a novel angle of view on fabricating high-performance perovskite solar cells.
Effect of Kelp Waste Extracts on the Growth and Development of Pakchoi (Brassica chinensis L.)
Authors: Zheng Shiyan , Jiang Jie , He Meilin , Zou Shanmei , Wang Changhai 
Published: December 2016

AbstractTo explore the effects of kelp waste extracts (KWE) on the growth and development of Brassia chinensis L., germination and greenhouse experiments were carried out under different concentrations of KWE. The results showed that a higher germination percentage (95%), associated with high germination index (8.70), germination energy (71.67%) and seedling vigor index (734.67), was obtained under a lower KWE concentration (2%) compared with the control. The radicle length (4.97 cm), fresh weight (0.32 g/10 seedlings) and dry weight (0.015 g/10 seedlings) were significantly increased in the treatment of 2% KWE. KWE also could enhance the root growth, the maximum leaf length × width and the fresh weight of plants, the optimal value of which increased by 8.37 cm, 58.14 cm2 and 7.76 g under the treatment of 10% KWE compared with the control respectively. Meanwhile, the contents of vitamin C and soluble sugars in pakchoi leaf were improved by 19.6 mg/100 g and 1.44 mg/g compared with the control, and the nitrate content was decreased by 212.27 mg/kg. Briefly, KWE could markedly stimulate the pakchoi seeds germination at a lower concentration (2%) and enhance the plant growth and quality at a higher concentration (10%).
Effect of arginine on oligomerization and stability of N-acetylglutamate synthase
Authors: Haskins N. , Mumo A. , Brown P. H. , Tuchman M. , Morizono H. , Caldovic L. 
Published: December 2016

AbstractN-acetylglutamate synthase (NAGS; E.C.2.3.1.1) catalyzes the formation of N-acetylglutamate (NAG) from acetyl coenzyme A and glutamate. In microorganisms and plants, NAG is the first intermediate of the L-arginine biosynthesis; in animals, NAG is an allosteric activator of carbamylphosphate synthetase I and III. In some bacteria bifunctional N-acetylglutamate synthase-kinase (NAGS-K) catalyzes the first two steps of L-arginine biosynthesis. L-arginine inhibits NAGS in bacteria, fungi, and plants and activates NAGS in mammals. L-arginine increased thermal stability of the NAGS-K from Maricaulis maris (MmNAGS-K) while it destabilized the NAGS-K from Xanthomonas campestris (XcNAGS-K). Analytical gel chromatography and ultracentrifugation indicated tetrameric structure of the MmMNAGS-K in the presence and absence of L-arginine and a tetramer-octamer equilibrium that shifted towards tetramers upon binding of L-arginine for the XcNAGS-K. Analytical gel chromatography of mouse NAGS (mNAGS) indicated either different oligomerization states that are in moderate to slow exchange with each other or deviation from the spherical shape of the mNAGS protein. The partition coefficient of the mNAGS increased in the presence of L-arginine suggesting smaller hydrodynamic radius due to change in either conformation or oligomerization. Different effects of L-arginine on oligomerization of NAGS may have implications for efforts to determine the three-dimensional structure of mammalian NAGS.
The impact of environmental parameters on microcystin production in dialysis bag experiments
Authors: Xie Liqiang , Rediske Richard R. , Gillett Nadia D. , O’Keefe James P. , Scull Brian , Xue Qingju 
Published: December 2016

AbstractIt is important to understand what environmental parameters may regulate microcystin (MC) production and congener type. To determine if environmental conditions in two hydraulically connected lakes can influence MC production and congener ratios, we incubated dialysis bags containing phytoplankton from mesotrophic/eutrophic Muskegon Lake into hypereutrophic Bear Lake (Michigan, USA) and vice versa. Strong cyanobacteria growth was observed in all dialysis bags with Bear Lake phytoplankton in July and August. Phytoplankton communities were dominated by Aphanizomenon aphanizomenoides, Microcystis wesenbergii, Limnothrix redekei. MC concentrations were correlated with M. wesenbergii and A. aphanizomenoides biovolume. MC concentrations in bags incubated in the Muskegon Lake with Bear Lake water were significantly higher than the other bags. The higher light intensity and total nitrogen concentration may have caused the increase of MC production. The MC-LR/MC-RR ratios varied with sample origin but not with lake of incubation, indicating that physical environmental factors (water temperature and turbidity) were not the reasons for different toxin production ratios. Differences in total phosphorus concentrations might be one reason for the dissimilarity of the MC-LR/MC-RR ratio between the two lakes. The higher light intensity and NO3-N concentration in Muskegon Lake are two factors contributing to an increase of MC production.