bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus
Authors: Naas A.E. , MacKenzie A.K. , Dalhus B. , Eijsink V.G.H. , Pope P.B. 
Published: July 2015

AbstractPrevious gene-centric analysis of a cow rumen metagenome revealed the first potentially cellulolytic polysaccharide utilization locus, of which the main catalytic enzyme (AC2aCel5A) was identified as a glycoside hydrolase (GH) family 5 endo-cellulase. Here we present the 1.8 Å three-dimensional structure of AC2aCel5A and characterization of its enzymatic activities. The enzyme possesses the archetypical (β/α)8-barrel found throughout the GH5 family and contains the two strictly conserved catalytic glutamates located at the C-terminal ends of β-strands 4 and 7. The enzyme is active on insoluble cellulose and acts exclusively on linear β-(1,4)-linked glucans. Co-crystallization of a catalytically inactive mutant with substrate yielded a 2.4 Å structure showing cellotriose bound in the −3 to −1 subsites. Additional electron density was observed between Trp178 and Trp254, two residues that form a hydrophobic “clamp”, potentially interacting with sugars at the +1 and +2 subsites. The enzyme’s active-site cleft was narrower compared to the closest structural relatives, which in contrast to AC2aCel5A, are also active on xylans, mannans and/or xyloglucans. Interestingly, the structure and function of this enzyme seem adapted to less-substituted substrates such as cellulose, presumably due to the insufficient space to accommodate the side-chains of branched glucans in the active-site cleft.
Nano-sized Superlattice Clusters Created by Oxygen Ordering in Mechanically Alloyed Fe Alloys
Authors: Hu Yong-Jie , Li Jing , Darling Kristopher A. , Wang William Y. , VanLeeuwen Brian K. , Liu Xuan L. , Kecskes Laszlo J. , Dickey Elizabeth C. , Liu Zi-Kui 
Published: July 2015

AbstractCreating and maintaining precipitates coherent with the host matrix, under service conditions is one of the most effective approaches for successful development of alloys for high temperature applications; prominent examples include Ni- and Co-based superalloys and Al alloys. While ferritic alloys are among the most important structural engineering alloys in our society, no reliable coherent precipitates stable at high temperatures have been found for these alloys. Here we report discovery of a new, nano-sized superlattice (NSS) phase in ball-milled Fe alloys, which maintains coherency with the BCC matrix up to at least 913 °C. Different from other precipitates in ferritic alloys, this NSS phase is created by oxygen-ordering in the BCC Fe matrix. It is proposed that this phase has a chemistry of Fe3O and a D03 crystal structure and becomes more stable with the addition of Zr. These nano-sized coherent precipitates effectively double the strength of the BCC matrix above that provided by grain size reduction alone. This discovery provides a new opportunity for developing high-strength ferritic alloys for high temperature applications.
Detoxification mechanisms of honey bees (Apis mellifera) resulting in tolerance of dietary nicotine
Authors: Rand Esther E. du , Smit Salome , Beukes Mervyn , Apostolides Zeno , Pirk Christian W.W. , Nicolson Susan W. 
Published: July 2015

AbstractInsecticides are thought to be among the major factors contributing to current declines in bee populations. However, detoxification mechanisms in healthy, unstressed honey bees are poorly characterised. Alkaloids are naturally encountered in pollen and nectar and we used nicotine as a model compound to identify the mechanisms involved in detoxification processes in honey bees. Nicotine and neonicotinoids have similar modes of action in insects. Our metabolomic and proteomic analyses show active detoxification of nicotine in bees, associated with increased energetic investment and also antioxidant and heat shock responses. The increased energetic investment is significant in view of the interactions of pesticides with diseases such as Nosema spp which cause energetic stress and possible malnutrition. Understanding how healthy honey bees process dietary toxins under unstressed conditions will help clarify how pesticides, alone or in synergy with other stress factors, lead to declines in bee vitality.
Acyl-CoA N-acyltransferase influences fertility by regulating lipid metabolism and jasmonic acid biogenesis in cotton
Authors: Fu Wenfeng , Shen Ying , Hao Juan , Wu Jianyong , Ke Liping , Wu Caiyun , Huang Kai , Luo Binglun , Xu Mingfeng , Cheng Xiaofei , Zhou Xueping , Sun Jie , Xing Chaozhu , Sun Yuqiang 
Published: July 2015

AbstractCotton (Gossypium spp.) is an important economic crop and there is obvious heterosis in cotton, fertility has played an important role in this heterosis. However, the genes that exhibit critical roles in anther development and fertility are not well understood. Here, we report an acyl-CoA N-acyltransferase (EC2.3; GhACNAT) that plays a key role in anther development and fertility. Suppression of GhACNAT by virus-induced gene silencing in transgenic cotton (G. hirsutum L. cv. C312) resulted in indehiscent anthers that were full of pollen, diminished filaments and stamens and plant sterility. We found GhACNAT was involved in lipid metabolism and jasmonic acid (JA) biosynthesis. The genes differentially expressed in GhACNAT-silenced plants and C312 were mainly involved in catalytic activity and transcription regulator activity in lipid metabolism. In GhACNAT-silenced plants, the expression levels of genes involved in lipid metabolism and jasmonic acid biosynthesis were significantly changed, the amount of JA in leaves and reproductive organs was significantly decreased compared with the amounts in C312. Treatments with exogenous methyl jasmonate rescued anther dehiscence and pollen release in GhACNAT-silenced plants and caused self-fertility. The GhACNAT gene may play an important role in controlling cotton fertility by regulating the pathways of lipid synthesis and JA biogenesis.
Ionic liquid flow along the carbon nanotube with DC electric field
Authors: Hwal Shin Jung , Hwee Kim Geon , Kim Intae , Jeon Hyungkook , An Taechang , Lim Geunbae 
Published: July 2015

AbstractLiquid pumping can occur along the outer surface of an electrode under a DC electric field. For biological applications, a better understanding of the ionic solution pumping mechanism is required. Here, we fabricated CNT wire electrodes (CWEs) and tungsten wire electrodes (TWEs) of various diameters to assess an ionic solution pumping. A DC electric field created by a bias of several volts pumped the ionic solution in the direction of the negatively biased electrode. The resulting electro-osmotic flow was attributed to the movement of an electric double layer near the electrode and the flow rates along the CWEs were on the order of picoliters per minute. According to electric field analysis, the z-directional electric field around the meniscus of the small electrode was more concentrated than that of the larger electrode. Thus, the pumping effect increased as the electrode diameter decreased. Interestingly in CWEs, the initiating voltage for liquid pumping did not change with increasing diameter, up to 20 μm. We classified into three pumping zones, according to the initiating voltage and faradaic reaction. Liquid pumping using the CWEs could provide a new method for biological studies with adoptable flow rates and a larger ‘Recommended pumping zone’.
Controlled electromechanical cell stimulation on-a-chip
Authors: Pavesi Andrea , Adriani Giulia , Rasponi Marco , Zervantonakis Ioannis K. , Fiore Gianfranco B. , Kamm Roger D. 
Published: July 2015

AbstractStem cell research has yielded promising advances in regenerative medicine, but standard assays generally lack the ability to combine different cell stimulations with rapid sample processing and precise fluid control. In this work, we describe the design and fabrication of a micro-scale cell stimulator capable of simultaneously providing mechanical, electrical and biochemical stimulation and subsequently extracting detailed morphological and gene-expression analysis on the cellular response. This micro-device offers the opportunity to overcome previous limitations and recreate critical elements of the in vivo microenvironment in order to investigate cellular responses to three different stimulations. The platform was validated in experiments using human bone marrow mesenchymal stem cells. These experiments demonstrated the ability for inducing changes in cell morphology, cytoskeletal fiber orientation and changes in gene expression under physiological stimuli. This novel bioengineering approach can be readily applied to various studies, especially in the fields of stem cell biology and regenerative medicine.
Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics
Authors: Goto Noriko , Bazar Gyorgy , Kovacs Zoltan , Kunisada Makoto , Morita Hiroyuki , Kizaki Seiichiro , Sugiyama Hiroshi , Tsenkova Roumiana , Nishigori Chikako 
Published: July 2015

AbstractUltraviolet (UV) radiation causes cellular DNA damage, among which cyclobutane pyrimidine dimers (CPDs) are responsible for a variety of genetic mutations. Although several approaches have been developed for detection of CPDs, conventional methods require time-consuming steps. Aquaphotomics, a new approach based on near-infrared spectroscopy (NIRS) and multivariate analysis that determines interactions between water and other components of the solution, has become an effective method for qualitative and quantitative parameters measurement in the solutions. NIR spectral patterns of UVC-irradiated and nonirradiated DNA solutions were evaluated using aquaphotomics for detection of UV-induced CPDs. Groups of UV-irradiated and nonirradiated DNA samples were classified (87.5% accuracy) by soft independent modeling of class analogy (SIMCA). A precise regression model calculated from NIR water spectral patterns based on UVC doses (r Val = 0.9457) and the concentration of cis-syn cyclobutane thymine dimers (cis-syn T<>Ts; r Val = 0.9993) was developed using partial least squares regression (PLSR), while taking advantage of water spectral patterns, particularly around 1400–1500 nm. Our results suggested that, in contrast to DNA, the formation of cis-syn T<>Ts increased the strongly hydrogen bonded water. Additionally, NIRS could qualitatively and quantitatively detect cis-syn T<>Ts in isolated DNA aqueous solutions upon UVC exposure.
Host Responses and Regulation by NFκB Signaling in the Liver and Liver Epithelial Cells Infected with A Novel Tick-borne Bunyavirus
Authors: Sun Qiyu , Jin Cong , Zhu Lili , Liang Mifang , Li Chuan , Cardona Carol J. , Li Dexin , Xing Zheng 
Published: July 2015

AbstractInfection in humans by severe fever with thrombocytopenia syndrome virus (SFTSV), a novel bunyavirus transmitted by ticks, is often associated with pronounced liver damage, especially in fatal cases. Little has been known, however, about how liver cells respond to SFTSV and how the response is regulated. In this study we report that proinflammatory cytokines were induced in liver tissues of C57/BL6 mice infected with SFTSV, which may cause tissue necrosis in mice. Human liver epithelial cells were susceptible to SFTSV and antiviral interferon (IFN) and IFN-inducible proteins were induced upon infection. We observed that infection of liver epithelial cells led to significant increases in proinflammatory cytokines and chemokines, including IL-6, RANTES, IP-10 and MIP-3a, which were regulated by NFκB signaling and the activation of NFκB signaling during infection promoted viral replication in liver epithelial cells. Viral nonstructural protein NSs was inhibitory to the induction of IFN-β, but interestingly, NFκB activation was enhanced in the presence of NSs. Therefore, NSs plays dual roles in the suppression of antiviral IFN-β induction as well as the promotion of proinflammatory responses. Our findings provide the first evidence for elucidating host responses and regulation in liver epithelial cells infected by an emerging bunyavirus.
Heat-Denatured Lysozyme Inactivates Murine Norovirus as a Surrogate Human Norovirus
Authors: Takahashi Hajime , Nakazawa Moemi , Ohshima Chihiro , Sato Miki , Tsuchiya Tomoki , Takeuchi Akira , Kunou Masaaki , Kuda Takashi , Kimura Bon 
Published: July 2015

AbstractHuman norovirus infects humans through the consumption of contaminated food, contact with the excrement or vomit of an infected person and through airborne droplets that scatter the virus through the air. Being highly infectious and highly viable in the environment, inactivation of the norovirus requires a highly effective inactivating agent. In this study, we have discovered the thermal denaturing capacity of a lysozyme with known antimicrobial activity against gram-positive bacteria, as well as its inactivating effect on murine norovirus. This study is the first report on the norovirus-inactivating effects of a thermally denatured lysozyme. We observed that lysozymes heat-treated for 40 min at 100 °C caused a 4.5 log reduction in infectivity of norovirus. Transmission electron microscope analysis showed that virus particles exposed to thermally denatured lysozymes were expanded, compared to the virus before exposure. The amino acid sequence of the lysozyme was divided into three sections and the peptides of each artificially synthesised, in order to determine the region responsible for the inactivating effect. These results suggest that thermal denaturation of the lysozyme changes the protein structure, activating the region responsible for imparting an inactivating effect against the virus.
Pros and cons of methylation-based enrichment methods for ancient DNA
Authors: Seguin-Orlando Andaine , Gamba Cristina , Sarkissian Clio Der , Ermini Luca , Louvel Guillaume , Boulygina Eugenia , Sokolov Alexey , Nedoluzhko Artem , Lorenzen Eline D. , Lopez Patricio , McDonald H. Gregory , Scott Eric , Tikhonov Alexei , Stafford, Thomas W. , Alfarhan Ahmed H. , Alquraishi Saleh A. , Al-Rasheid Khaled A. S. , Shapiro Beth , Willerslev Eske , Prokhortchouk Egor , Orlando Ludovic 
Published: July 2015

AbstractThe recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.
Systematic characterization of the peroxidase gene family provides new insights into fungal pathogenicity in Magnaporthe oryzae
Authors: Mir Albely Afifa , Park Sook-Young , Sadat Md. Abu , Kim Seongbeom , Choi Jaeyoung , Jeon Junhyun , Lee Yong-Hwan 
Published: July 2015

AbstractFungal pathogens have evolved antioxidant defense against reactive oxygen species produced as a part of host innate immunity. Recent studies proposed peroxidases as components of antioxidant defense system. However, the role of fungal peroxidases during interaction with host plants has not been explored at the genomic level. Here, we systematically identified peroxidase genes and analyzed their impact on fungal pathogenesis in a model plant pathogenic fungus, Magnaporthe oryzae. Phylogeny reconstruction placed 27 putative peroxidase genes into 15 clades. Expression profiles showed that majority of them are responsive to in planta condition and in vitro H2O2. Our analysis of individual deletion mutants for seven selected genes including MoPRX1 revealed that these genes contribute to fungal development and/or pathogenesis. We identified significant and positive correlations among sensitivity to H2O2, peroxidase activity and fungal pathogenicity. In-depth analysis of MoPRX1 demonstrated that it is a functional ortholog of thioredoxin peroxidase in Saccharomyces cerevisiae and is required for detoxification of the oxidative burst within host cells. Transcriptional profiling of other peroxidases in ΔMoprx1 suggested interwoven nature of the peroxidase-mediated antioxidant defense system. The results from this study provide insight into the infection strategy built on evolutionarily conserved peroxidases in the rice blast fungus.
Directional radiation of Babinet-inverted optical nanoantenna integrated with plasmonic waveguide
Authors: Kim Jineun , Roh Young-Geun , Cheon Sangmo , Jeong Kim Un , Hwang Sung Woo , Park Yeonsang , Lee Chang-Won 
Published: July 2015

AbstractWe present a Babinet-inverted optical nanoantenna integrated with a plasmonic waveguide. Using an integrated nanoantenna, we can couple the plasmon guide mode in a metal-insulator-metal (MIM) structure into the resonant antenna feed directly. The resonantly excited feed slot then radiates to free space and generates a magnetic dipole-like far-field pattern. The coupling efficiency of the integrated nanoantenna is calculated as being approximately 19% using a three-dimensional finite-difference time-domain (3D FDTD) simulation. By adding an auxiliary groove structure along with the feed, the radiation direction can be controlled similar to an optical Yagi-Uda antenna. We also determine, both theoretically and experimentally, that groove depth plays a significant role to function groove structure as a reflector or a director. The demonstrated Babinet-inverted optical nanoantenna integrated with a plasmonic waveguide can be used as a “plasmonic via” in plasmonic nanocircuits.
Innate cellular sources of interleukin-17A regulate macrophage accumulation in cigarette- smoke-induced lung inflammation in mice
Authors: Bozinovski Steven , Seow Huei Jiunn , Chan Sheau Pyng Jamie , Anthony Desiree , McQualter Jonathan , Hansen Michelle , Jenkins Brendan J. , Anderson Gary P. , Vlahos Ross 
Published: July 2015

Cigarette smoke (CS) is the major cause of chronic obstructive pulmonary disease (COPD). Interleukin-17A (IL-17A) is a pivotal cytokine that regulates lung immunity and inflammation. The aim of the present study was to investigate how IL-17A regulates CS-induced lung inflammation in vivo. IL-17A knockout (KO) mice and neutralization of IL-17A in wild-type (WT) mice reduced macrophage and neutrophil recruitment and chemokine (C-C motif) ligand 2 (CCL2), CCL3 and matrix metalloproteinase (MMP)-12 mRNA expression in response to acute CS exposure. IL-17A expression was increased in non-obese diabetic (NOD) severe combined immunodeficiency SCID) mice with non-functional B- and T-cells over a 4-week CS exposure period, where macrophages accumulated to the same extent as in WT mice. Gene expression analysis by QPCR (quantitative real-time PCR) of isolated immune cell subsets detected increased levels of IL-17A transcript in macrophages, neutrophils and NK/NKT cells in the lungs of CS-exposed mice. In order to further explore the relative contribution of innate immune cellular sources, intracellular IL-17A staining was performed. In the present study, we demonstrate that CS exposure primes natural killer (NK), natural killer T (NKT) and γδ T-cells to produce more IL-17A protein and CS alone increased the frequency of IL17+ γδ T-cells in the lung, whereas IL-17A protein was not detected in macrophages and neutrophils. Our data suggest that activation of innate cellular sources of IL-17A is an essential mediator of macrophage accumulation in CS-exposed lungs. Targeting non-conventional T-cell sources of IL-17A may offer an alternative strategy to reduce pathogenic macrophages in COPD.
Sound Production Treatment: Synthesis and Quantification of Outcomes
Authors: Bailey Dallin J. , Eatchel Kelly , Wambaugh Julie 
Published: July 2015

Purpose
This investigation was designed to provide a quantification and synthesis of a series of single-case experimental design investigations into the effects of sound production treatment, an articulatory-kinematic treatment for acquired apraxia of speech (AOS). The main purpose was to perform a meta-analysis of aggregated sound production treatment data in order to provide benchmarks to serve as indicators of magnitude of change. Additional analyses explored various factors influencing effect sizes and level of performance.

Method
Effect sizes were calculated for treated and untreated items for 24 participants across 10 investigations. Benchmarks were calculated as the quartiles of the distributions of the effect sizes. Correlational analyses were performed to examine (a) end-of-treatment performance relative to follow-up performance, (b) response of trained items relative to untrained items, and (c) effect size relative to participant variables.

Results
Effect sizes were predominantly large and positive; benchmarks for treated items were larger than those for untreated items. End of treatment and follow-up performance were positively correlated, and response generalization was positively correlated with AOS severity.

Conclusion
These benchmarks may assist in evaluating the effects of interventions for individuals with AOS utilizing similar outcome measures in both clinical and research settings.
Family Ratings of Communication Largely Reflect Expressive Language and Conversation-Level Ability in People With Aphasia
Authors: Fucetola Robert , Tabor Connor Lisa 
Published: July 2015

Purpose
Family ratings of communication and social interactions represent an important source of information about people with aphasia. Because of the reliance on family/partner ratings as an outcome measure in many aphasia treatment studies and in the clinic, there is a great need for the validation of commonly used family/partner rating measures, and a better understanding of predictors of family ratings of communication.

Method
The communication ability of 130 individuals with aphasia due to neurologic illness was rated by family members/partners on the Communicative Effectiveness Index (CETI; Lomas et al., 1989). Information on aphasia severity, mood, quality of life, nonverbal cognitive functioning, and various demographic factors was collected.

Results
Principal component analysis confirmed a 2-factor model best represents the relationships among CETI rating items, and this model largely consists of a conversation-level ability factor. Family ratings were largely predicted by the patient's expressive (not receptive) language but also patient self-perceived quality of communication life.

Conclusions
Family/partners typically rate the effectiveness of communication based largely on expressive language, despite the fact that other aspects of the aphasia (e.g., listening comprehension) are as important for everyday communication.