bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-assembled amyloid fibrils with controllable conformational heterogeneity
Authors: Lee Gyudo , Lee Wonseok , Lee Hyungbeen , Lee Chang Young , Eom Kilho , Kwon Taeyun 
Published: November 2015

AbstractAmyloid fibrils are a hallmark of neurodegenerative diseases and exhibit a conformational diversity that governs their pathological functions. Despite recent findings concerning the pathological role of their conformational diversity, the way in which the heterogeneous conformations of amyloid fibrils can be formed has remained elusive. Here, we show that microwave-assisted chemistry affects the self-assembly process of amyloid fibril formation, which results in their conformational heterogeneity. In particular, microwave-assisted chemistry allows for delicate control of the thermodynamics of the self-assembly process, which enabled us to tune the molecular structure of β-lactoglobulin amyloid fibrils. The heterogeneous conformations of amyloid fibrils, which can be tuned with microwave-assisted chemistry, are attributed to the microwave-driven thermal energy affecting the electrostatic interaction during the self-assembly process. Our study demonstrates how microwave-assisted chemistry can be used to gain insight into the origin of conformational heterogeneity of amyloid fibrils as well as the design principles showing how the molecular structures of amyloid fibrils can be controlled.
Room temperature large-scale synthesis of layered frameworks as low-cost 4 V cathode materials for lithium ion batteries
Authors: Hameed A. Shahul , Reddy M. V. , Nagarathinam M. , Runčevski Tomče , Dinnebier Robert E , Adams Stefan , Chowdari B. V. R. , Vittal Jagadese J. 
Published: November 2015

AbstractLi-ion batteries (LIBs) are considered as the best available technology to push forward the production of eco-friendly electric vehicles (EVs) and for the efficient utilization of renewable energy sources. Transformation from conventional vehicles to EVs are hindered by the high upfront price of the EVs and are mainly due to the high cost of LIBs. Hence, cost reduction of LIBs is one of the major strategies to bring forth the EVs to compete in the market with their gasoline counterparts. In our attempt to produce cheaper high-performance cathode materials for LIBs, an rGO/MOPOF (reduced graphene oxide/Metal-Organic Phosphate Open Framework) nanocomposite with ~4 V of operation has been developed by a cost effective room temperature synthesis that eliminates any expensive post-synthetic treatments at high temperature under Ar/Ar-H2. Firstly, an hydrated nanocomposite, rGO/K2[(VO)2(HPO4)2(C2O4)]·4.5H2O has been prepared by simple magnetic stirring at room temperature which releases water to form the anhydrous cathode material while drying at 90 °C during routine electrode fabrication procedure. The pristine MOPOF material undergoes highly reversible lithium storage, however with capacity fading. Enhanced lithium cycling has been witnessed with rGO/MOPOF nanocomposite which exhibits minimal capacity fading thanks to increased electronic conductivity and enhanced Li diffusivity.
A highly durable fuel cell electrocatalyst based on double-polymer-coated carbon nanotubes
Authors: Berber Mohamed R. , Hafez Inas H. , Fujigaya Tsuyohiko , Nakashima Naotoshi 
Published: November 2015

AbstractDriven by the demand for the commercialization of fuel cell (FC) technology, we describe the design and fabrication of a highly durable FC electrocatalyst based on double-polymer-coated carbon nanotubes for use in polymer electrolyte membrane fuel cells. The fabricated electrocatalyst is composed of Pt-deposited polybenzimidazole-coated carbon nanotubes, which are further coated with Nafion. By using this electrocatalyst, a high FC performance with a power density of 375 mW/cm2 (at 70 ˚C, 50% relative humidity using air (cathode)/H2(anode)) was obtained and a remarkable durability of 500,000 accelerated potential cycles was recorded with only a 5% loss of the initial FC potential and 20% loss of the maximum power density, which were far superior properties compared to those of the membrane electrode assembly prepared using carbon black in place of the carbon nanotubes. The present study indicates that the prepared highly durable fuel cell electrocatalyst is a promising material for the next generation of PEMFCs.
The molecular basis of lysine 48 ubiquitin chain synthesis by Ube2K
Authors: Middleton Adam J. , Day Catherine L. 
Published: November 2015

AbstractThe post-translational modification of proteins by ubiquitin is central to the regulation of eukaryotic cells. Substrate-bound ubiquitin chains linked by lysine 11 and 48 target proteins to the proteasome for degradation and determine protein abundance in cells, while other ubiquitin chain linkages regulate protein interactions. The specificity of chain-linkage type is usually determined by ubiquitin-conjugating enzymes (E2s). The degradative E2, Ube2K, preferentially catalyses formation of Lys48-linked chains, but like most E2s, the molecular basis for chain formation is not well understood. Here we report the crystal structure of a Ube2K~ubiquitin conjugate and demonstrate that even though it is monomeric, Ube2K can synthesize Lys48-linked ubiquitin chains. Using site-directed mutagenesis and modelling, our studies reveal a molecular understanding of the catalytic complex and identify key features required for synthesis of degradative Lys48-linked chains. The position of the acceptor ubiquitin described here is likely conserved in other E2s that catalyse Lys48-linked ubiquitin chain synthesis.
HdeB chaperone activity is coupled to its intrinsic dynamic properties
Authors: Ding Jienv , Yang Chengfeng , Niu Xiaogang , Hu Yunfei , Jin Changwen 
Published: November 2015

AbstractEnteric bacteria encounter extreme acidity when passing through hosts’ stomach. Since the bacterial periplasmic space quickly equilibrates with outer environment, an efficient acid resistance mechanism is essential in preventing irreversible protein denaturation/aggregation and maintaining bacteria viability. HdeB, along with its homolog HdeA, was identified as a periplasmic acid-resistant chaperone. Both proteins exist as homodimers and share similar monomeric structures under neutral pH, while showing different dimeric packing interfaces. Previous investigations show that HdeA functions through an acid-induced dimer-to-monomer transition and partial unfolding at low pH (pH 2–3), resulting in exposure of hydrophobic surfaces that bind substrate proteins. In contrast, HdeB appears to have a much higher optimal activation pH (pH 4–5), under which condition the protein maintains a well-folded dimer and the mechanism for its chaperone activity remains elusive. Herein, we present an NMR study of HdeB to investigate its dynamic properties. Our results reveal that HdeB undergoes significant micro- to milli-second timescale conformational exchanges at neutral to near-neutral pH, under the later condition it exhibits optimal activity. The current study indicates that HdeB activation is coupled to its intrinsic dynamics instead of structural changes and therefore its functional mechanism is apparently different from HdeA.
Flicker-assisted localization microscopy reveals altered mitochondrial architecture in hypertension
Authors: Chalmers Susan , Saunter Christopher D. , Girkin John M. , McCarron John G. 
Published: November 2015

AbstractMitochondrial morphology is central to normal physiology and disease development. However, in many live cells and tissues, complex mitochondrial structures exist and morphology has been difficult to quantify. We have measured the shape of electrically-discrete mitochondria, imaging them individually to restore detail hidden in clusters and demarcate functional boundaries. Stochastic “flickers” of mitochondrial membrane potential were visualized with a rapidly-partitioning fluorophore and the pixel-by-pixel covariance of spatio-temporal fluorescence changes analyzed. This Flicker-assisted Localization Microscopy (FaLM) requires only an epifluorescence microscope and sensitive camera. In vascular myocytes, the apparent variation in mitochondrial size was partly explained by densely-packed small mitochondria. In normotensive animals, mitochondria were small spheres or rods. In hypertension, mitochondria were larger, occupied more of the cell volume and were more densely clustered. FaLM provides a convenient tool for increased discrimination of mitochondrial architecture and has revealed mitochondrial alterations that may contribute to hypertension.
Probing the character of ultra-fast dislocations
Authors: Ruestes C. J. , Bringa E. M. , Rudd R. E. , Remington B. A. , Remington T. P. , Meyers M. A. 
Published: November 2015

AbstractPlasticity is often controlled by dislocation motion, which was first measured for low pressure, low strain rate conditions decades ago. However, many applications require knowledge of dislocation motion at high stress conditions where the data are sparse and come from indirect measurements dominated by the effect of dislocation density rather than velocity. Here we make predictions based on atomistic simulations that form the basis for a new approach to measure dislocation velocities directly at extreme conditions using three steps: create prismatic dislocation loops in a near-surface region using nanoindentation, drive the dislocations with a shockwave and use electron microscopy to determine how far the dislocations moved and thus their velocity at extreme stress and strain rate conditions. We report on atomistic simulations of tantalum that make detailed predictions of dislocation flow and find that the approach is feasible and can uncover an exciting range of phenomena, such as transonic dislocations and a novel form of loop stretching. The simulated configuration enables a new class of experiments to probe average dislocation velocity at very high applied shear stress.
Multiple Sources of Infection and Potential Endemic Characteristics of the Large Outbreak of Dengue in Guangdong in 2014
Authors: Shen Shu-Qun , Wei Hai-Xia , Fu Yong-Hang , Zhang Hao , Mo Qing-Yi , Wang Xiao-Jun , Deng Sheng-Qun , Zhao Wei , Liu Yu , Feng Xiao-Shuang , Chen Wei , Peng Hong-Juan 
Published: November 2015

AbstractA large outbreak of dengue, with the most documented cases, occurred in Guangdong China in 2014. Epidemiological studies and phylogenetic analysis of the isolated dengue virus (DENV) showed this outbreak was attributed to multiple sources and caused by at least two genotypes of DENV-1 (Genotypes I and III) and two genotypes of DENV-2 (Cosmopolitan and Asian I Genotypes). A retrospective review and phylogenetic analysis of DENV isolated in Guangdong showed that DENV-1 Genotype I strains were reported continuously during 2004–2014, Genotype III strains were reported during 2009–2014 ; DENV-2 Cosmopolitan and Asian I Genotype strains were reported continuously during 2012–2014. At least 45,171 cases were reported in this outbreak, with 65.9% of the patients in the 21–55-year-old group. A trend toward a decrease in the daily newly emerged cases lagged by approximately 20 days compared with the mosquito density curve. Several epidemiological characteristics of this outbreak and the stably sustained serotypes and genotypes of DENV isolated in Guangdong suggest that Guangdong has been facing a threat of transforming from a dengue epidemic area to an endemic area. The high temperature, drenching rain, rapid urbanization and pandemic of dengue in Southeast Asia may have contributed to this large outbreak of dengue.
Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis
Authors: de Cima Sergio , Polo Luis M. , Díez-Fernández Carmen , Martínez Ana I. , Cervera Javier , Fita Ignacio , Rubio Vicente 
Published: November 2015

AbstractHuman carbamoyl phosphate synthetase (CPS1), a 1500-residue multidomain enzyme, catalyzes the first step of ammonia detoxification to urea requiring N-acetyl-L-glutamate (NAG) as essential activator to prevent ammonia/amino acids depletion. Here we present the crystal structures of CPS1 in the absence and in the presence of NAG, clarifying the on/off-switching of the urea cycle by NAG. By binding at the C-terminal domain of CPS1, NAG triggers long-range conformational changes affecting the two distant phosphorylation domains. These changes, concerted with the binding of nucleotides, result in a dramatic remodeling that stabilizes the catalytically competent conformation and the building of the ~35 Å-long tunnel that allows migration of the carbamate intermediate from its site of formation to the second phosphorylation site, where carbamoyl phosphate is produced. These structures allow rationalizing the effects of mutations found in patients with CPS1 deficiency (presenting hyperammonemia, mental retardation and even death), as exemplified here for some mutations.
Intrahaplotypic Variants Differentiate Complex Linkage Disequilibrium within Human MHC Haplotypes
Authors: Lam Tze Hau , Tay Matthew Zirui , Wang Bei , Xiao Ziwei , Ren Ee Chee 
Published: November 2015

AbstractDistinct regions of long-range genetic fixation in the human MHC region, known as conserved extended haplotypes (CEHs), possess unique genomic characteristics and are strongly associated with numerous diseases. While CEHs appear to be homogeneous by SNP analysis, the nature of fine variations within their genomic structure is unknown. Using multiple, MHC-homozygous cell lines, we demonstrate extensive sequence conservation in two common Asian MHC haplotypes: A33-B58-DR3 and A2-B46-DR9. However, characterization of phase-resolved MHC haplotypes revealed unique intra-CEH patterns of variation and uncovered 127 single nucleotide variants (SNVs) which are missing from public databases. We further show that the strong linkage disequilibrium structure within the human MHC that typically confounds precise identification of genetic features can be resolved using intra-CEH variants, as evidenced by rs3129063 and rs448489, which affect expression of ZFP57, a gene important in methylation and epigenetic regulation. This study demonstrates an improved strategy that can be used towards genetic dissection of diseases.
Lipidomic Profiling of Liver Tissue from Obesity-Prone and Obesity-Resistant Mice Fed a High Fat Diet
Authors: Nam Miso , Choi Myung-Sook , Jung Sunhee , Jung Youngae , Choi Ji-Young , Ryu Do Hyun , Hwang Geum-Sook 
Published: November 2015

AbstractObesity is a multifactorial health problem resulting from genetic, environmental and behavioral factors. A particularly interesting aspect of obesity is the differences observed in response to the same high-fat diet (HFD). In this study, we performed lipidomic profiling on livers from HFD-fed C57BL/6J mice using ultra-performance liquid chromatography–quadrupole time-of-flight mass spectrometry. Mice were divided into three groups: normal diet (ND), HFD-obesity prone (HFD-OP) and HFD-obesity resistant (HFD-OR). Principal components analyses showed a difference between the HFD-OP and HFD-OR groups. Individuals in the HFD-OR group were closer to those in the ND group compared with those in the HFD-OP group. In particular, phosphocholine (PC) and triglyceride (TG) levels differed significantly depending on the length of the acyl chain and degree of unsaturation, respectively. PC species were either positively or negatively correlated with concentrations of glucose, insulin, leptin and hepatic cholesterol according to the length of the acyl chain. Decreased expression of the scavenger receptor B1 and ATP-binding cassette A1 in HFD-OP mice indicated that the acyl chain length of PC species may be related to high-density lipoprotein cholesterol metabolism. This study demonstrates that lipidomic profiling is an effective approach to analyzing global lipid alterations as they pertain to obesity.
Identification of Bacillus strains by MALDI TOF MS using geometric approach
Authors: Starostin Konstantin V. , Demidov Evgeny A. , Bryanskaya Alla V. , Efimov Vadim M. , Rozanov Alexey S. , Peltek Sergey E. 
Published: November 2015

AbstractMicroorganism identification by MALDI TOF mass-spectrometry is based on the comparison of the mass spectrum of the studied organism with those of reference strains. It is a rapid and reliable method. However, commercial databases and programs are mostly designed for identification of clinically important strains and can be used only for particular mass spectrometer models. The need for open platforms and reference databases is obvious. In this study we describe a geometric approach for microorganism identification by mass spectra and demonstrate its capabilities by analyzing 24 strains belonging to theBacillus pumilusgroup. This method is based on representing mass spectra as points on a multidimensional space, which allows us to use geometric distances to compare the spectra. Delimitation of microorganisms performed by geometric approach correlates well with the results of molecular phylogenetic analysis and clustering using Biotyper 3.1. All three methods used allowed us to reliably divide the strains into two groups corresponding to closely related species,Bacillus pumilusandBacillus altitudinis. The method developed by us will be implemented in a Web interface designed for using open reference databases for microorganism identification. The data is available athttp://www.bionet.nsc.ru/mbl/database/database.html.
A high-density immunoblotting methodology for quantification of total protein levels and phosphorylation modifications
Authors: Mazet F. , Dunster J. L. , Jones C. I. , Vaiyapuri S. , Tindall M. J. , Fry M. J. , Gibbins J. M. 
Published: November 2015

AbstractThe components of many signaling pathways have been identified and there is now a need to conduct quantitative data-rich temporal experiments for systems biology and modeling approaches to better understand pathway dynamics and regulation. Here we present a modified Western blotting method that allows the rapid and reproducible quantification and analysis of hundreds of data points per day on proteins and their phosphorylation state at individual sites. The approach is of particular use where samples show a high degree of sample-to-sample variability such as primary cells from multiple donors. We present a case study on the analysis of >800 phosphorylation data points from three phosphorylation sites in three signaling proteins over multiple time points from platelets isolated from ten donors, demonstrating the technique’s potential to determine kinetic and regulatory information from limited cell numbers and to investigate signaling variation within a population. We envisage the approach being of use in the analysis of many cellular processes such as signaling pathway dynamics to identify regulatory feedback loops and the investigation of potential drug/inhibitor responses, using primary cells and tissues, to generate information about how a cell’s physiological state changes over time.
Scaling of decoherence for a system of uncoupled spin qubits
Authors: Jing Jun , Hu Xuedong 
Published: November 2015

AbstractSignificant experimental progresses in recent years have generated continued interest in quantum computation. A practical quantum computer would employ thousands if not millions of coherent qubits and maintaining coherence in such a large system would be imperative for its utility. As an attempt at understanding the quantum coherence of multiple qubits, here we study decoherence of a multi-spin-qubit state under the influence of hyperfine interaction and clearly demonstrate that the state structure is crucial to the scaling behavior of n-spin decoherence. Specifically, we find that coherence times of a multi-spin state at most scale with the number of qubits n as "Equation missing", while some states with higher symmetries have scale-free coherence with respect to n. Statistically, convergence to these scaling behavior is generally determined by the size of the Hilbert space m, which is usually much larger than n (up to an exponential function of n), so that convergence rate is very fast as we increase the number of qubits. Our results can be extended to other decoherence mechanisms, including in the presence of dynamical decoupling, which allow meaningful discussions on the scalability of spin-based quantum coherent technology.
Exploring comprehensive within-motif dependence of transcription factor binding in Escherichia coli
Authors: Yang Chi , Chang Chuan-Hsiung 
Published: November 2015

AbstractModeling the binding of transcription factors helps to decipher the control logic behind transcriptional regulatory networks. Position weight matrix is commonly used to describe a binding motif but assumes statistical independence between positions. Although current approaches take within-motif dependence into account for better predictive performance, these models usually rely on prior knowledge and incorporate simple positional dependence to describe binding motifs. The inability to take complex within-motif dependence into account may result in an incomplete representation of binding motifs. In this work, we applied association rule mining techniques and constructed models to explore within-motif dependence for transcription factors in Escherichia coli. Our models can reflect transcription factor-DNA recognition where the explored dependence correlates with the binding specificity. We also propose a graphical representation of the explored within-motif dependence to illustrate the final binding configurations. Understanding the binding configurations also enables us to fine-tune or design transcription factor binding sites and we attempt to present the configurations through exploring within-motif dependence.
Evaluation of Reference Genes for RT-qPCR Studies in the Seagrass Zostera muelleri Exposed to Light Limitation
Authors: Schliep M. , Pernice M. , Sinutok S. , Bryant C. V. , York P. H. , Rasheed M. A. , Ralph P. J. 
Published: November 2015

AbstractSeagrass meadows are threatened by coastal development and global change. In the face of these pressures, molecular techniques such as reverse transcription quantitative real-time PCR (RT-qPCR) have great potential to improve management of these ecosystems by allowing early detection of chronic stress. In RT-qPCR, the expression levels of target genes are estimated on the basis of reference genes, in order to control for RNA variations. Although determination of suitable reference genes is critical for RT-qPCR studies, reports on the evaluation of reference genes are still absent for the major Australian speciesZostera muellerisubsp.capricorni(Z. muelleri). Here, we used three different software (geNorm, NormFinder and Bestkeeper) to evaluate ten widely used reference genes according to their expression stability inZ. muelleriexposed to light limitation. We then combined results from different software and used a consensus rank of four best reference genes to validate regulation in Photosystem I reaction center subunit IV B and Heat Stress Transcription factor A- gene expression inZ. muelleriunder light limitation. This study provides the first comprehensive list of reference genes inZ. muelleriand demonstrates RT-qPCR as an effective tool to identify early responses to light limitation in seagrass.