bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico identification of AMPylating enzymes and study of their divergent evolution
Authors: Khater Shradha , Mohanty Debasisa 
Published: June 2015

AbstractAMPylation is a novel post-translational modification (PTM) involving covalent attachment of an AMP moiety to threonine/tyrosine side chains of a protein. AMPylating enzymes belonging to three different families, namely Fic/Doc, GS-ATase and DrrA have been experimentally characterized. Involvement of these novel enzymes in a myriad of biological processes makes them interesting candidates for genome-wide search. We have used SVM and HMM to develop a computational protocol for identification of AMPylation domains and their classification into various functional subfamilies catalyzing AMPylation, deAMPylation, phosphorylation and phosphocholine transfer. Our analysis has not only identified novel PTM catalyzing enzymes among unannotated proteins, but has also revealed how this novel enzyme family has evolved to generate functional diversity by subtle changes in sequence/structures of the proteins. Phylogenetic analysis of Fic/Doc has revealed three new isofunctional subfamilies, thus adding to their functional divergence. Also, frequent occurrence of Fic/Doc proteins on highly mobile and unstable genomic islands indicated their evolution via extensive horizontal gene transfers. On the other hand phylogenetic analyses indicate lateral evolution of GS-ATase family and an early duplication event responsible for AMPylation and deAMPylation activity of GS-ATase. Our analysis also reveals molecular basis of substrate specificity of DrrA proteins.
Melanophilin Stimulates Myosin-5a Motor Function by Allosterically Inhibiting the Interaction between the Head and Tail of Myosin-5a
Authors: Yao Lin-Lin , Cao Qing-Juan , Zhang Hai-Man , Zhang Jie , Cao Yang , Li Xiang-dong 
Published: June 2015

AbstractThe tail-inhibition model is generally accepted for the regulation of myosin-5a motor function. Inhibited myosin-5a is in a folded conformation in which its globular tail domain (GTD) interacts with its head and inhibits its motor function and high Ca2+ or cargo binding may reduce the interaction between the GTD and the head of myosin-5a, thus activating motor activity. Although it is well established that myosin-5a motor function is regulated by Ca2+, little is known about the effects of cargo binding. We previously reported that melanophilin (Mlph), a myosin-5a cargo-binding protein, is capable of activating myosin-5a motor function. Here, we report that Mlph-GTBDP, a 26 amino-acid-long peptide of Mlph, is sufficient for activating myosin-5a motor function. We demonstrate that Mlph-GTBDP abolishes the interaction between the head and GTD of myosin-5a, thereby inducing a folded-to-extended conformation transition for myosin-5a and activating its motor function. Mutagenesis of the GTD shows that the GTD uses two distinct, non-overlapping regions to interact with Mlph-GTBDP and the head of myosin-5a. We propose that the GTD is an allosteric protein and that Mlph allosterically inhibits the interaction between the GTD and head of myosin-5a, thereby activating myosin-5a motor function.
Surface Mn(II) oxidation actuated by a multicopper oxidase in a soil bacterium leads to the formation of manganese oxide minerals
Authors: Zhang Zhen , Zhang Zhongming , Chen Hong , Liu Jin , Liu Chang , Ni Hong , Zhao Changsong , Ali Muhammad , Liu Fan , Li Lin 
Published: June 2015

AbstractIn this manuscript, we report that a bacterial multicopper oxidase (MCO266) catalyzes Mn(II) oxidation on the cell surface, resulting in the surface deposition of Mn(III) and Mn(IV) oxides and the gradual formation of bulky oxide aggregates. These aggregates serve as nucleation centers for the formation of Mn oxide micronodules and Mn-rich sediments. A soil-borne Escherichia coli with high Mn(II)-oxidizing activity formed Mn(III)/Mn(IV) oxide deposit layers and aggregates under laboratory culture conditions. We engineered MCO266 onto the cell surfaces of both an activity-negative recipient and wild-type strains. The results confirmed that MCO266 governs Mn(II) oxidation and initiates the formation of deposits and aggregates. By contrast, a cell-free substrate, heat-killed strains and intracellularly expressed or purified MCO266 failed to catalyze Mn(II) oxidation. However, purified MCO266 exhibited Mn(II)-oxidizing activity when combined with cell outer membrane component (COMC) fractions in vitro. We demonstrated that Mn(II) oxidation and aggregate formation occurred through an oxygen-dependent biotic transformation process that requires a certain minimum Mn(II) concentration. We propose an approximate electron transfer pathway in which MCO266 transfers only one electron to convert Mn(II) to Mn(III) and then cooperates with other COMC electron transporters to transfer the other electron required to oxidize Mn(III) to Mn(IV).
Aptamer-based Sandwich Assay and its Clinical Outlooks for Detecting Lipocalin-2 in Hepatocellular Carcinoma (HCC)
Authors: Lee Kyeong-Ah , Ahn Ji-Young , Lee Sang-Hee , Singh Sekhon Simranjeet , Kim Dae-Ghon , Min Jiho , Kim Yang-Hoon 
Published: June 2015

AbstractWe validated a single-stranded, DNA aptamer-based, diagnostic method capable of detecting Lipocalin-2 (LCN2), a biomarker from clinically relevant hepatocellular carcinoma (HCC) patient serum, in the sandwich assay format. Nine aptamers (LCN2_apta1 to LCN2_apta9) for LCN2 were screened with SELEX processes and a sandwich pair (LCN2_apta2 and LCN2_apta4) was finally chosen using surface plasmon resonance (SPR) and dot blotting analysis. The result of the proposed aptamer sandwich construction shows that LCN2 was sensitively detected in the concentration range of 2.5–500 ng mL−1 with a limit of detection of 0.6 ng mL−1. Quantitative measurement tests in HCC patients were run on straight serum and were compared with the performance of the conventional antibody-based ELISA kit. The aptamer sandwich assay demonstrated an excellent dynamic range for LCN2 at clinically relevant serum levels, covering sub-nanogram per mL concentrations. The new approach offers a simple and robust method for detecting serum biomarkers that have low and moderate abundance. It consists of functionalization, hybridization and signal read-out and no dilution is required. The results of the study demonstrate the capability of the aptamer sandwich assay platform for diagnosing HCC and its potential applicability to the point-of-care testing (POCT) system.
Molecular and structural analysis of Legionella DotI gives insights into an inner membrane complex essential for type IV secretion
Authors: Kuroda Takuya , Kubori Tomoko , Thanh Bui Xuan , Hyakutake Akihiro , Uchida Yumiko , Imada Katsumi , Nagai Hiroki 
Published: June 2015

AbstractThe human pathogen Legionella pneumophila delivers a large array of the effector proteins into host cells using the Dot/Icm type IVB secretion system. Among the proteins composing the Dot/Icm system, an inner membrane protein DotI is known to be crucial for the secretion function but its structure and role in type IV secretion had not been elucidated. We report here the crystal structures of the periplasmic domains of DotI and its ortholog in the conjugation system of plasmid R64, TraM. These structures reveal a striking similarity to VirB8, a component of type IVA secretion systems, suggesting that DotI/TraM is the type IVB counterpart of VirB8. We further show that DotI and its partial paralog DotJ form a stable heterocomplex. R64 TraM, encoded by the conjugative plasmid lacking DotJ ortholog, forms a homo-hexamer. The DotI-DotJ complex is distinct from the core complex, which spans both inner and outer membranes to form a substrate conduit and seems not to stably associate with the core complex. These results give insight into VirB8-family inner membrane proteins essential for type IV secretion and aid towards understanding the molecular basis of secretion systems essential for bacterial pathogenesis.
Nodal bilayer-splitting controlled by spin-orbit interactions in underdoped high-Tc cuprates
Authors: Harrison N. , Ramshaw B. J. , Shekhter A. 
Published: June 2015

AbstractThe highest superconducting transition temperatures in the cuprates are achieved in bilayer and trilayer systems, highlighting the importance of interlayer interactions for high Tc. It has been argued that interlayer hybridization vanishes along the nodal directions by way of a specific pattern of orbital overlap. Recent quantum oscillation measurements in bilayer cuprates have provided evidence for a residual bilayer-splitting at the nodes that is sufficiently small to enable magnetic breakdown tunneling at the nodes. Here we show that several key features of the experimental data can be understood in terms of weak spin-orbit interactions naturally present in bilayer systems, whose primary effect is to cause the magnetic breakdown to be accompanied by a spin flip. These features can now be understood to include the equidistant set of three quantum oscillation frequencies, the asymmetry of the quantum oscillation amplitudes in c-axis transport compared to ab-plane transport and the anomalous magnetic field angle dependence of the amplitude of the side frequencies suggestive of small effective g-factors. We suggest that spin-orbit interactions in bilayer systems can further affect the structure of the nodal quasiparticle spectrum in the superconducting phase. PACS numbers: 71.45.Lr, 71.20.Ps, 71.18.+y
Solid-state Reaction of Azolium Hydrohalogen Salts with Silver Dicyanamide – Unexpected Formation of Cyanoguanidine-azoles, Reaction Mechanism and Their Hypergolic Properties
Authors: Liu Wei , Lin Qiu-han , Li Yu-chuan , Chen Peng-wan , Fang Tao , Zhang Ru-bo , Pang Si-ping 
Published: June 2015

AbstractCyanoguanidines as well as azoles are important bioactive groups, which play an important role in the medical application; meanwhile, the high nitrogen content makes them excellent backbones for energetic materials. A Novel and simple method that combined these two fragments into one molecular compound was developed through the transformation of dicyanamide ionic salts. In return, compounds 4–11 were synthesized and fully characterized by IR, MS, NMR and elemental analysis. Meanwhile, the structures of compounds 4, 8 and 11 were confirmed by X-ray crystal diffraction. Detailed reaction mechanisms were studied through accurate calculations on the reaction energy profiles of the azolium cations and DCA anion, which revealed the essence of the transformation proceeding. Meanwhile, compound 8 exhibits excellent hypergolic property, which could be potentially novel molecular hypergolic fuel.
Three-dimensional patterns from the thin-film drying of amino acid solutions
Authors: Zhang Xuehua , Crivoi Alexandru , Duan Fei 
Published: June 2015

AbstractExperimental atomic force microscopy (AFM) images show the dried-in patterns from amino acid solutions which can be in the form of dots or networks. The three-dimensional lattice-gas Kinetic Monte Carlo (KMC) model is applied to simulate the formation of dot-like and network-like particle structures from the evaporating thin films of solutions. A sigmoidal jump in the chemical potential value is implemented to obtain dual-scale structures with the grain size distribution peaking at two distinctive values. The simulated and experimental results are qualitatively comparable.
Mechanisms linking metabolism of Helicobacter pylori to 18O and 13C-isotopes of human breath CO2
Authors: Som Suman , De Anulekha , Banik Gourab Dutta , Maity Abhijit , Ghosh Chiranjit , Pal Mithun , Daschakraborty Sunil B. , Chaudhuri Sujit , Jana Subhra , Pradhan Manik 
Published: June 2015

AbstractThe gastric pathogen Helicobacter pylori utilize glucose during metabolism, but the underlying mechanisms linking to oxygen-18 (18O) and carbon-13 (13C)-isotopic fractionations of breath CO2 during glucose metabolism are poorly understood. Using the excretion dynamics of 18O/16O and 13C/12C-isotope ratios of breath CO2, we found that individuals with Helicobacter pylori infections exhibited significantly higher isotopic enrichments of 18O in breath CO2 during the 2h-glucose metabolism regardless of the isotopic nature of the substrate, while no significant enrichments of 18O in breath CO2 were manifested in individuals without the infections. In contrast, the 13C-isotopic enrichments of breath CO2 were significantly higher in individuals with Helicobacter pylori compared to individuals without infections in response to 13C-enriched glucose uptake, whereas a distinguishable change of breath 13C/12C-isotope ratios was also evident when Helicobacter pylori utilize natural glucose. Moreover, monitoring the 18O and 13C-isotopic exchange in breath CO2 successfully diagnosed the eradications of Helicobacter pylori infections following a standard therapy. Our findings suggest that breath 12C18O16O and 13C16O16O can be used as potential molecular biomarkers to distinctively track the pathogenesis of Helicobacter pylori and also for eradication purposes and thus may open new perspectives into the pathogen’s physiology along with isotope-specific non-invasive diagnosis of the infection.
Extrachromosomal circular DNA is common in yeast
Authors: Møller Henrik D. , Parsons Lance , Jørgensen Tue S. , Botstein David , Regenberg Birgitte 
Published: June 2015

Significance
We performed a screen for extrachromosomal circular DNAs containing segments of genomic yeast DNA. We found 1,756 such extrachromosomal circular DNAs containing about 23% of the total yeast genomic information. The abundance of these circular forms of genomic DNA suggests that eccDNA formation might be a common mutation that can arise in any part of the genome, and not in only a few special loci. We propose that eccDNAs may be precursors to the copy number variation in eukaryotic genomes characteristic of both the evolutionary process and cancer progression.
Effect of Predator Size and Prey Characteristics on Piscivory of Juvenile Largemouth Bass
Authors: Einfalt Lisa M. , Parkos Joseph J. , Wahl David H. 
Published: June 2015

AbstractLargemouth Bass Micropterus salmoides undergo a diet shift to fish prey during the juvenile stage, but mechanisms influencing piscivorous behavior are largely unknown. In laboratory experiments, we examined ontogenetic effects of predator and prey size on piscivory of juvenile Largemouth Bass. Prey size preferences were determined in aquaria experiments by introducing multiple size ranges of either Bluegill Lepomis macrochirus, Gizzard Shad Dorosoma cepedianum, or Fathead Minnow Pimephales promelas with a Largemouth Bass from one of three length‐classes (30, 50, and 75 mm TL). For Gizzard Shad, Largemouth Bass most often selected larger sizes (33–65% of Largemouth Bass length) than in experiments with either Fathead Minnow or Bluegill (25–48%). Although an optimal foraging model (handling time/prey dry mass) predicted most prey sizes chosen, Largemouth Bass, with their large gape, chose slightly larger prey than predicted for all three prey species. Using optimal‐sized prey, we further investigated differential prey vulnerability and development of foraging behavior of juvenile Largemouth Bass (30–75 mm) in experiments conducted in a 750‐L tank. Prey increased schooling and distance maintained from predators as they grew, but all sizes of Largemouth Bass foraged similarly, suggesting differences in predation success were due to prey morphology and species‐specific behavioral responses of prey. Results of our study can provide better predictions for prey consumption patterns of piscivorous juvenile Largemouth Bass in field settings.
Influence of Postcapture Ventilation Assistance on Migration Success of Adult Sockeye Salmon following Capture and Release
Authors: Robinson Kendra A. , Hinch Scott G. , Raby Graham D. , Donaldson Michael R. , Robichaud Dave , Patterson David A. , Cooke Steven J. 
Published: June 2015

AbstractCatch and release is a tactic employed in recreational fisheries to help conserve and sustain fish populations, but postrelease mortality can occur when fish fail to recover from the stress and exhaustion of capture. Depending on factors like the duration of the stressor and whether air exposure occurs, fish can be lethargic or have negative equilibrium upon release; some anglers are motivated to attempt to manually revive fish upon release by assisting with water flow across the gills. Indeed, some management agencies and angling groups recommend different recovery techniques, but very little scientifically defensible evidence exists about the utility of assisted ventilation. We conducted two separate field experiments on Sockeye Salmon Oncorhynchus nerka in the lower Fraser River basin in which fish were (1) exposed to a standardized exercise stressor with air exposure or (2) angled by volunteer anglers and air exposed, with a subset of fish in each experiment then being provided with 1 min of assisted ventilation before release with a radio transmitter. Assisted ventilation took the form of simply holding the fish below the water surface, facing into a flow of ∼0.5 m/s. Postrelease behavior and migration success were examined in both experiments by radio‐tracking fish, using a combination of fixed stations and manual tracking. Our results from both experiments provide no support for the utility of this revival technique in benefiting the migration success of Sockeye Salmon exhausted from a capture‐and‐release event. Future experiments should test the survival and physiological benefits of different revival techniques and durations for fish at different levels of postcapture impairment.
Characterization of Isolates of Streptococcus agalactiae from Diseased Farmed and Wild Marine Fish from the U.S. Gulf Coast, Latin America, and Thailand
Authors: Soto Esteban , Wang Rui , Wiles Judy , Baumgartner Wes , Green Christopher , Plumb John , Hawke John 
Published: June 2015

Abstract
We examined Lancefield serogroup B Streptococcus isolates recovered from diseased, cultured hybrid Striped Bass (Striped Bass Morone saxatilis × White Bass M. chrysops) and wild and cultured Gulf Killifish Fundulus grandis from coastal waters of the U.S. Gulf of Mexico (Gulf coast) and compared those isolates to strains from tilapias Oreochromis spp. reared in Mississippi, Thailand, Ecuador, and Honduras and to the original Gulf coast strain identified by Plumb et al. (1974). The isolates were subjected to phylogenetic, biochemical, and antibiotic susceptibility analyses. Genetic analysis was performed using partial sequence comparison of (1) the 16S ribosomal RNA (rRNA) gene; (2) the sipA gene, which encodes a surface immunogenic protein; (3) the cspA gene, which encodes a cell surface-associated protein; and (4) the secY gene, which encodes components of a general protein secretion pathway. Phylogenies inferred from sipA, secY, and cspA gene sequence comparisons were more discriminating than that inferred from the 16S rRNA gene sequence comparison. The U.S. Gulf coast strains showed a high degree of similarity to strains from South America and Central America and belonged to a unique group that can be distinguished from other group B streptococci. In agreement with the molecular findings, biochemical and antimicrobial resistance analyses demonstrated that the isolates recovered from the U.S. Gulf coast and Latin America were more similar to each other than to isolates from Thailand. Three laboratory challenge methods for inducing streptococcosis in Gulf Killifish were evaluated—intraperitoneal (IP) injection, immersion (IMM), and immersion plus abrasion (IMMA)—using serial dilutions of S. agalactiae isolate LADL 97-151, a representative U.S. Gulf coast strain. The dose that was lethal to 50% of test fish by 14 d postchallenge was approximately 2 CFU/fish via IP injection. In contrast, the fish that were challenged via IMM or IMMA presented cumulative mortality less than 40% by 14 d postchallenge.
Received July 31, 2014; accepted March 11, 2015
The Concept of Opera
Authors: Goehr Lydia 
Published: June 2015

AbstractChapter 5 investigates opera’s concept historically, given a context in which the terms of the individual arts—music, painting, poetry, sculpture, architecture, dance, or ballet—have been contested, often by contests being staged within the artworks themselves. This context is best described as agonisticand paragonal. Connecting opera’s concept to the ancient Greek notion of agôn—contest/debate—and to the Renaissance idea of the paragone—comparison/contest—opens up a two-fold path. It leads the concept, via a “fatherly” hand, to its claimed origins in Classical Athens and, via a “maternal” hand, to its claimed birth in Italy. The ancestral discourse of origin and birth begs for serious deconstruction. Yet, its impact on opera’s history is pervasive and undeniable. This chapter thus investigates the discourse critically, to reveal its use and its abuse in the many histories written—pro and contra opera as an art.
Meaning
Authors: Kramer Lawrence 
Published: June 2015

AbstractThe distinguishing resource of meaning in opera is operatic voice—not only opera’s most obvious feature but also the source of its generic identity. To a large extent this voice defines itself as a force of rupture, something nearly impossible for other vocal modalities to assimilate or appropriate. Opera as a genre depends on the difference between its own mode of vocalization and any other. For that reason, the self-reflexive staging of opera’s dependence on this singular voice is also a primary generic feature. Opera recurrently gazes at itself through the mirror of its voice. The potentials and perplexities of this self-marking, or “re-marking,” take exemplary form in scenes from Mozart’s Don Giovanni, Wagner’s Tannhäuser, and John Adams’s Doctor Atomic.
Castrato Acts
Authors: Feldman Martha 
Published: June 2015

AbstractChapter 18 delineates issues surrounding castrati as performative beings. It explores the intersubjective dimensions of castrato performance onstage and off, including the perspectives of tourists who followed castrato appearances at opera houses while on the grand tour or encountered them in salons and churches, with special attention drawn to early modern issues of cultural tourism, celebrity culture, and singing. The chapter then explores scholars’ preoccupations with castrati since about 1980, when they began to read castrato voices through the thickly psychoanalytic lenses of Freud and Lacan and the post-structural views of Barthes, Foucault, Bakhtin, and Derrida. Finally, it examines a more recent “machine turn” in castrato studies, manifest in (1) collaborations between musicians, sound engineers, and film/TV producers who have attempted to reconstruct the castrato voice; and (2) a scholarly move toward thinking about mechanism in historical connection with ways that early modern castrati were produced and staged.
Regietheater/Director’s Theater
Authors: Müller Ulrich 
Published: June 2015

Abstract
This chapter discusses the meaning and history of the German term for “Director’s Theater,” which, since the 1950s, has been a favorite term of the German-speaking feuilleton and later was adopted by the international press. For the audience, not for the reviewers, it has in many cases a negative, even an aggressive meaning. The first well-known protagonists were the opera directors Wieland Wagner (Bayreuth/Stuttgart) and Walter Felsenstein (Komische Oper Berlin). The social and artistic context is presented with many details and important examples; the chapter also defines modern Regietheater as a visualization of different subtexts, including even the individual personal problems of the director. A final case study is dedicated to Joachim Herz, one of the most influential German opera directors, who “invented” several methods of interpretation that are very common today but also fiercely polemicized against opera productions that deconstructed plot and action.