bluuebunny/crossref_metadata_2025_split huggingface dataset:
p53‐Dependent subcellular proteome localization following DNA damage
Authors: Boisvert François‐Michel , Lamond Angus I. 
Published: September 2010

AbstractThe nucleolus is involved in regulating several aspects of stress responses and cell cycle arrest through the tumor suppressor p53. Under normal conditions, p53 is a short‐lived protein that is present in cells at a barely detectable level. Upon exposure of cells to various forms of exogenous stress, such as DNA damage, there is a stabilization of p53 which is then responsible for an ensuing cascade of events. To further investigate the effect of p53 activation, we used a MS‐based proteomics method to provide an unbiased, quantitative and high‐throughput approach for measuring the subcellular distribution of the proteome that is dependent on p53. The spatial proteomics method analyses a whole cell extract created by recombining differentially labeled subcellular fractions derived from cells in which proteins have been mass labeled with heavy isotopes [Boisvert, F.‐M., Lam, Y. W., Lamont, D., Lamond, A. I., Mol. Cell. Proteomics 2010, 9, 457–470]. This was used here to measure the relative distribution between cytoplasm, nucleus and nucleolus of around 2000 proteins in HCT116 cells that are either expressing wild‐type p53 or null for p53. Spatial proteomics also facilitates a proteome‐wide comparison of changes in protein localization in response to a wide range of physiological and experimental perturbations. We used this method to study differences in protein localization in HCT116 cells either with or without p53, and studied the differences in cellular response to DNA damage following treatment of HCT116 cells with etoposide in both p53 wild‐type and null genetic backgrounds.
Proteomic analysis of clathrin‐coated vesicles
Authors: McPherson Peter S. 
Published: September 2010

AbstractFor more than 50 years cell biologists have embraced the concept that biochemical and enzymatic analysis of isolated subcellular fractions provides insight into the function and machineries of cellular compartments including organelles. The utility of this approach has been significantly enhanced with the advent of mass spectrometry leading to the broad application of organelle proteomics. Clathrin‐coated vesicles (CCVs) form at the plasma membrane where they select protein and lipid cargo for endocytic entry into cells. CCVs also form at the trans‐Golgi network, where they function in protein transport from the secretory pathway to the endosomal/lysosomal system. Herein we will describe how organelle proteomics of CCVs has greatly expanded our knowledge of the machineries, mechanisms and sites of clathrin‐mediated membrane trafficking.
Synthesis of Poly(3,3‐Bis‐Azidomethyl Oxetane) via Direct Azidation of Poly(3,3‐Bis‐Bromo Oxetane)
Authors: Guo Kai , Luo Yunjun , Chen Jinzhou , Li Xinfa , Huang Lingge 
Published: September 2010

AbstractIn order to avoid using highly unstable and sensitive monomer 3,3‐bis‐azidomethyl oxetane, poly(3,3‐bis‐azidomethyl oxetane) (PBAMO) was successfully synthesized via azidation of poly(3,3‐bis‐bromo oxetane) (PBBrMO) in the aprotic and polar solvent cyclohexanone in the presence of a catalyst. It was found that the azidation proceeded very fast and almost completed in 6 h when the reaction temperature was up to 115 °C. PBAMO was characterized by gel permeation chromatography (GPC), Fourier transform infrared spectrometry (FTIR), hydrogen nuclear magnetic resonance (1H NMR), and carbon nuclear magnetic resonance (13C NMR).
A comparison of the different helices adopted by α‐ and β‐peptides suggests different reasons for their stability
Authors: Allison Jane R. , Müller Marlen , van Gunsteren Wilfred F. 
Published: September 2010

AbstractThe right‐handed α‐helix is the dominant helical fold of α‐peptides, whereas the left‐handed 314‐helix is the dominant helical fold of β‐peptides. Using molecular dynamics simulations, the properties of α‐helical α‐peptides and 314‐helical β‐peptides with different C‐terminal protonation states and in the solvents water and methanol are compared. The observed energetic and entropic differences can be traced to differences in the polarity of the solvent‐accessible surface area and, in particular, the solute dipole moments, suggesting different reasons for their stability.
Effect of using suboptimal alignments in template‐based protein structure prediction
Authors: Chen Hao , Kihara Daisuke 
Published: September 2010

AbstractComputational protein structure prediction remains a challenging task in protein bioinformatics. In the recent years, the importance of template‐based structure prediction is increasing because of the growing number of protein structures solved by the structural genomics projects. To capitalize the significant efforts and investments paid on the structural genomics projects, it is urgent to establish effective ways to use the solved structures as templates by developing methods for exploiting remotely related proteins that cannot be simply identified by homology. In this work, we examine the effect of using suboptimal alignments in template‐based protein structure prediction. We showed that suboptimal alignments are often more accurate than the optimal one, and such accurate suboptimal alignments can occur even at a very low rank of the alignment score. Suboptimal alignments contain a significant number of correct amino acid residue contacts. Moreover, suboptimal alignments can improve template‐based models when used as input to Modeller. Finally, we use suboptimal alignments for handling a contact potential in a probabilistic way in a threading program, SUPRB. The probabilistic contacts strategy outperforms the partly thawed approach, which only uses the optimal alignment in defining residue contacts, and also the re‐ranking strategy, which uses the contact potential in re‐ranking alignments. The comparison with existing methods in the template‐recognition test shows that SUPRB is very competitive and outperforms existing methods. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Intrinsic disorder of Drosophila melanogaster hormone receptor 38 N‐terminal domain
Authors: Dziedzic‐Letka Agnieszka , Rymarczyk Grzegorz , Kapłon Tomasz M. , Górecki Andrzej , Szamborska‐Gbur Agnieszka , Wojtas Magdalena , Dobryszycki Piotr , Ożyhar Andrzej 
Published: September 2010

AbstractDrosophila hormone receptor 38 (dHR38), an ortholog of the vertebrate NR4A subclass of nuclear receptors, responds to ecdysteroids, which mediate developmental transitions during the Drosophila life cycle. However, this response is independent of the ecdysteroid receptor, and it does not involve binding of ecdysteroids to dHR38. It has been suggested that ecdysteroids may indirectly activate dHR38, perhaps by recruiting specific proteins. There have been recent reports pointing out the decisive role that nuclear receptor N‐terminal domains (NTDs) have in protein–protein interactions that are important for regulation of gene expression. It is reasonable to assume that dHR38‐NTD may also be involved in some protein–protein interactions that are critical for the ecdysteroid signaling pathway. To facilitate the exploration of the molecular basis of these interactions, we developed and optimized a protocol for the efficient expression and purification of the recombinant dHR38‐NTD. Using a diverse array of biochemical and biophysical methods, we carried out the first structural characterization of dHR38‐NTD. The results of our study indicate that dHR38‐NTD exhibits a characteristic reminiscent of pre‐molten globule‐like intrinsically disordered proteins existing in a partially unfolded conformation with regions of secondary structures. The dHR38‐NTD structure, which apparently comprises some local, ordered, tertiary structure clusters, is pliable and can adopt more ordered conformations in response to changes in environmental conditions. Thus, dHR38‐NTD, which exhibits the structural and functional characteristic of a pre‐molten globule‐like intrinsically disordered protein, could serve as a platform for multiple protein–protein interactions, possibly including interactions with proteins involved in an unusual ecdysteroid signaling pathway. Proteins 2011.© 2010 Wiley‐Liss, Inc.
The biological role of pituitary adenylate cyclase‐activating polypeptide (PACAP) in growth and feeding behavior in juvenile fish
Authors: Lugo Juana Maria , Oliva Aymé , Morales Antonio , Reyes Osvaldo , Garay Hilda Elisa , Herrera Fidel , Cabrales Ania , Pérez Ever , Estrada Mario Pablo 
Published: September 2010

AbstractTo date, many technologies have been developed to increase efficiency in aquaculture, but very few successful biotechnology molecules have arrived on the market. In this context, marine biotechnology has an opportunity to develop products to improve the output of fish in aquaculture. Published in vivo studies on the action of the pituitary adenylate cyclase‐activating polypeptide (PACAP) in fish are scarce. Recently, our group, for the first time, demonstrated the biological role of this neuropeptide administrated by immersion baths in the growth and development of larval fish. In this work, we have evaluated the effects of recombinant Clarias gariepinus PACAP administration by intraperitoneal injection on growth performance and feeding behavior in juvenile fish. Our results showed the physiological role of this peptide for growth control in fish, including the juvenile stage, and confirm that its biological functions are well conserved in fish, since C. gariepinus PACAP stimulated growth in juvenile tilapia Oreochromis niloticus. In addition, we have observed that the growth‐promoting effect of PACAP in juvenile tilapia was correlated with higher GH concentration in serum. With regard to the neuroendocrine regulation of growth control by PACAP, it was demonstrated that PACAP stimulates food intake in juvenile tilapia. In general, PACAP appears to act in the regulation of the growth control in juvenile fish. These findings propose that PACAP is a prominent target with the potential to stimulate fish growth in aquaculture. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
ChemMatrix® for complex peptides and combinatorial chemistry
Authors: García‐Ramos Yésica , Paradís‐Bas Marta , Tulla‐Puche Judit , Albericio Fernando 
Published: September 2010

AbstractCM resin is a totally PEG‐based resin, made exclusively from primary ether bonds and therefore highly chemically stable. Compared to other PEG resins, it exhibits good loading and is user friendly because of its free‐flowing form upon drying. It shows improved performance over PS resins for the preparation of hydrophobic, highly structured poly‐Arg peptides. In combination with ψPros, it allows the synthesis of small proteins such as the chemokine RANTES. Like other PEG‐based resins, CM resin swells well in biocompatible solvents such as water, thereby allowing on‐bead screening. Furthermore, the high loading of this resin permits the use of a tiny quarter of a bead as a microreactor for HPLC and MALDI‐TOF analysis, thus further extending its applications in the field of combinatorial chemistry. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
Improved Fmoc‐based solid‐phase synthesis of homologous peptide fragments of human and mouse prion proteins
Authors: Grillo‐Bosch Dolors , Rabanal Francesc , Giralt Ernest 
Published: September 2010

AbstractThe synthesis of difficult peptide sequences has been a challenge since the very beginning of SPPS. The self‐assembly of the growing peptide chains has been proposed as one of the causes of this synthetic problem. However, there is an increasing need to obtain peptides and proteins that are prone to aggregate. These peptides and proteins are generally associated with diseases known as amyloidoses. We present an efficient SPPS of two homologous peptide fragments of HuPrP (106–126) and MoPrP105–125 based on the use of the PEGA resin combined with proper coupling approaches. These peptide fragments were also studied by CD and TEM to determine their ability to aggregate. On the basis of these results, we support PEG‐based resins as an efficient synthetic tool to prepare peptide sequences prone to aggregate on‐resin. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
Time‐dependent density functional study on the excitation spectrum of point defects in semiconductors
Authors: Gali Adam 
Published: September 2010

AbstractA common fingerprint of the electrically active point defects in semiconductors is the transition between their localized defect states upon excitation, which may result in characteristic absorption or photoluminescence spectrum. While density functional calculations have been very successful in exploring the ground‐state properties like formation energies or hyperfine tensors the density functional theory (DFT), in principle, is not capable of providing reliable excitation spectrum. Time‐dependent (TD)‐DFT, however, addresses this issue which makes possible to study the properties of point defects associated with their excited states. In this paper, we apply the TD‐DFT on two characteristic examples: the well‐known nitrogen‐vacancy defect in diamond and the less known divacancy in silicon carbide. The former defect is a leading candidate in solid state quantum bit applications where detailed knowledge about the excitation spectrum is extremely important. The excitation property of divacancy will be also studied and its relevance in different applications will be discussed.
Preparation and specific properties of single crystalline metallic nanowires
Authors: Hassel Achim Walter , Bello‐Rodriguez Belen , Smith Andrew Jonathan , Chen Ying , Milenkovic Srdjan 
Published: September 2010

AbstractDirectional solidification of eutectics is a route to produce iso‐oriented metallic single crystalline nanowires (NWs). Etching or electrochemical oxidation allows selective dissolution of either of the phases to produce NW arrays, isolated NWs, nanopore arrays and also derived structures by combining various process steps.A good understanding of the thermodynamics and the kinetics of the phase transformation and chemical reactions including electrodissolution, passivation, selective etching, complexing of reaction products and electrodeposition in the systems NiAl–X (X = Re, W, Mo), Ag–Cu and Fe–Au was reached. Functional devices based on these NWs, like high aspect ratio NW based STM tips, nanoelectromechanical systems (NEMS), NW pH sensors and sensor arrays were constructed.
magnified imageArray of rhenium single crystalline NWs embedded in the NiAl matrix after partial dissolution of the matrix.
Robotic surgery in gynecologic oncology fellowship programs in the USA: a survey of fellows and fellowship directors
Authors: Sfakianos Gregory P. , Frederick Peter J. , Kendrick James E. , Straughn J. Michael , Kilgore Larry C. , Huh Warner K. 
Published: September 2010

AbstractBackgroundIn order to understand how robotic surgery impacts gynecologic oncology fellowship training and surgical practices, a survey of fellows and fellowship directors was conducted.MethodsQuestionnaires designed to determine the prevalence, application, and acceptance of robotics were sent to fellows and fellowship directors in approved U.S. programs.ResultsOf the respondents, 95% have a robot at their institution and 95% utilize it. Most responding fellowship directors (70%) reported that fellow education is enhanced by robotic surgery. Most fellows (65%) who responded feel comfortable using the robot, and 94% plan on performing robotic surgery upon completion of fellowship training.ConclusionsThis survey demonstrates that robotic surgery is utilized in the majority of responding gynecologic oncology fellowship programs for a wide array of indications. Fellowship directors and fellows‐in‐training generally have a favorable view of this evolving technology. Based on these responses, robotic surgery will play an increasingly important role in the future. Copyright © 2010 John Wiley & Sons, Ltd.
Pericyclic reactions in an aqueous molecular flask
Authors: Murase Takashi , Fujita Makoto 
Published: September 2010

AbstractA self‐assembled molecular flask with a nanometer‐sized restricted cavity offers a new reaction environment that is quite different from the bulk solution. The self‐assembled cage accommodates a pair of hydrophobic molecules to perform unusual Diels‐Alder reactions and [2+2] photoadditions of otherwise unreactive aromatic molecules. In this cage, for example, the Diels‐Alder reaction of naphthalene proceeds smoothly under mild conditions, and aceanthrylene shows reactivity for both [2+2] and [2+4] cycloadditions via the identical ternary host–guest complex. The observed greatly enhanced reactivity stems from the increased local concentration and pre‐organization of the substrate pair within the cage, which reduces the entropic cost and switches the reaction profile from a bimolecular to a pseudo‐intramolecular reaction pathway. The reinforced orientation and arrangement of substrate pairs specify regio‐ and stereo‐selectivities of the subsequent reactions in the cavity. Chiral auxiliaries outside the cage create the inner chiral environment and induce asymmetric reactions inside the cage (up to 50% ee). © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.201000027
The role of New Directions for Teaching and Learning in documenting changes in postsecondary education
Authors: Svinicki Marilla D. 
Published: September 2010

AbstractNew Directions for Teaching and Learning was first published in 1980. Since that time, there have been some changes, but many aspects have remained. NDTL issues are designed for faculty across the disciplines and are written in a way that they can be read easily and widely. This provides an important and distinctive variety of perspectives.
The promise of technology for college instruction: From drill and practice to avatars
Authors: Kuhlenschmidt Sally , Kacer Barbara 
Published: September 2010

AbstractTechnology and its uses have undergone significant change in the past several decades. Technology has many benefits and it has impacted many of the ways that teaching and learning occur. However, the role of thoughtful consideration, selection, implementation, and assessment of the technology remains the ultimate responsibility of the teacher.
Passive structural control of offshore wind turbines
Authors: Lackner Matthew A. , Rotea Mario A. 
Published: September 2010

AbstractThe application of control techniques to offshore wind turbines has the potential to significantly improve the structural response of these systems. A new simulation tool is developed that can be utilized to model passive, semi‐active and active structural control systems in wind turbines. Two independent, single degree of freedom (DOF) tuned mass‐
damper (TMD) devices are incorporated into a modified version of the aero‐elastic code FAST (Fatigue, Aerodynamics, Structures and Turbulence). The TMDs are located in the nacelle of the turbine model, with one TMD translating in the fore‐aft direction, and the other in the side‐side direction. The equations of motion of the TMDs are incorporated into the source code of FAST, yielding a more realistic system for modeling structural control in wind turbines than has previously been modeled. The stiffness, damping and commanded force of each TMD are controllable through the FAST‐Simulink interface, and so idealizations of semi‐active and active control approaches can be implemented. A parametric study is performed to determine the optimal parameters of a passive single DOF, fore‐aft, TMD system in both a barge‐type and monopile support structure. The wind turbine models equipped with TMDs are then simulated and the performance of these new systems is evaluated. The results indicate that passive control approaches can be used to improve the structural response of offshore wind turbines. The results also demonstrate the potential for active control approaches. Copyright © 2010 John Wiley & Sons, Ltd.
Die historische Entwicklung der Farbstofftheorien Teil I
Authors: Dähne Siegfried 
Published: September 2010

Abstract„Tief ist der Brunnen der Vergangenheit. Sollte man ihn nicht unergründlich nennen? ……denn mit unserer Forscherangelegentlichkeit treibt das Unerforschliche eine Art von foppendem Spiel: es bietet ihr Scheinhalte und Wegesziele, hinter denen, wenn sie erreicht sind, neue Vergangenheitsstrecken sich auftun, wie es dem Küstengänger ergeht, der des Wanderns kein Ende findet, weil hinter jeder lehmigen Dünenkulisse, die er erstrebte, neue Weiten zu neuen Vorgebirgen vorwärtslocken.”︁
Blood groups in the species survival plan®, European endangered species program, and managed in situ populations of bonobo (Pan paniscus), common chimpanzee (Pan troglodytes), gorilla (Gorilla ssp.), and orangutan (Pongo pygmaeus ssp.)
Authors: Gamble Kathryn C. , Moyse Jill A. , Lovstad Jessica N. , Ober Carole B. , Thompson Emma E. 
Published: September 2010

AbstractBlood groups of humans and great apes have long been considered similar, although they are not interchangeable between species. In this study, human monoclonal antibody technology was used to assign human ABO blood groups to whole blood samples from great apes housed in North American and European zoos and in situ managed populations, as a practical means to assist blood transfusion situations for these species. From a subset of each of the species (bonobo, common chimpanzee, gorilla, and orangutans), DNA sequence analysis was performed to determine blood group genotype. Bonobo and common chimpanzee populations were predominantly group A, which concurred with historic literature and was confirmed by genotyping. In agreement with historic literature, a smaller number of the common chimpanzees sampled were group O, although this O blood group was more often present in wild‐origin animals as compared with zoo‐born animals. Gorilla blood groups were inconclusive by monoclonal antibody techniques, and genetic studies were inconsistent with any known human blood group. As the genus and, specifically, the Bornean species, orangutans were identified with all human blood groups, including O, which had not been reported previously. Following this study, it was concluded that blood groups of bonobo, common chimpanzees, and some orangutans can be reliably assessed by human monoclonal antibody technology. However, this technique was not reliable for gorilla or orangutans other than those with blood group A. Even in those species with reliable blood group detection, blood transfusion preparation must include cross‐matching to minimize adverse reactions for the patient. Zoo Biol 30:427–444, 2011. © 2010 Wiley‐Liss, Inc.
How access to exhibit space impacts the behavior of female tigers (Panthera tigris)
Authors: Miller Angela , Leighty Katherine A. , Maloney Margaret A. , Kuhar Christopher W. , Bettinger Tamara L. 
Published: September 2010

AbstractLittle is known about how socially housed captive carnivores respond to temporary reductions in available space. We documented rates of aggression and affiliation in our group of six female tigers, under their normal housing conditions and during a period of exhibit renovations which resulted in a 50% reduction in time spent in an outdoor enclosure. During the period of reduced availability of space, significant declines in aggression and affiliation were observed indicating that these tigers responded in a manner consistent with a strategy of conflict avoidance. These reductions in rates of social behavior remained in place during the year following the return to their original housing conditions. Thus, even temporary alterations to housing practices have the potential to have lasting impacts on the social behavior of this species. Zoo Biol 30:479–486, 2011. © 2010 Wiley Periodicals, Inc.