bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme
Authors: Sefcikova Jana , Krasovska Maryna V. , Špačková Nad'a , Šponer Jiří , Walter Nils G. 
Published: January 2007

AbstractThe self‐cleaving hepatitis delta virus (HDV) ribozyme is essential for the replication of HDV, a liver disease causing pathogen in humans. The catalytically critical nucleotide C75 of the ribozyme is buttressed by a trefoil turn pivoting around an extruded G76. In all available crystal structures, the conformation of G76 is restricted by stacking with G76 of a neighboring molecule. To test whether this crystal contact introduces a structural perturbation into the catalytic core, we have analyzed ∼200 ns of molecular dynamics (MD) simulations. In the absence of crystal packing, the simulated G76 fluctuates between several conformations, including one wherein G76 establishes a perpendicular base quadruplet in the major groove of the adjacent P1 stem. Second‐site mutagenesis experiments suggest that the identity of the nucleotide in position 76 (N76) indeed contributes to the catalytic activity of a trans‐acting HDV ribozyme through its capacity for hydrogen bonding with P1. By contrast, in the cis‐cleaving genomic ribozyme the functional relevance of N76 is less pronounced and not correlated with the P1 sequence. Terbium(III) footprinting and additional MD show that the activity differences between N76 mutants of this ribozyme are related instead to changes in average conformation and modified cross‐correlations in the trefoil turn. © 2007 Wiley Periodicals, Inc. Biopolymers 85: 392–406, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
A method for three‐dimensional protein characterization and its application to a complex plant (corn) extract
Authors: Gu Zhengrong , Glatz Charles E. 
Published: January 2007

AbstractKnowledge of host protein properties is critical for developing purification methods for recombinant proteins from a specific host, or for choosing suitable hosts and targeted expression tissues for a specific recombinant protein. A method to obtain a three‐dimensional (3D) map (surface hydrophobicity (SH), isoelectric point (pI), and molecular weight (MW)), of a host's aqueous soluble protein properties was developed. The method consists of hydrophobic partitioning in a PEG 3350 (15.7%)‐Na2SO4 (8.9%)‐NaCl (3%) aqueous two‐phase (ATP) system followed by quantitative, 2D‐electrophoretic characterization of the proteins of each equilibrium phase and the original extract. The pI and MW of host proteins were obtained directly through 2D electrophoresis. The partition coefficients of individual proteins were obtained by quantitative matching of protein spots in the top and bottom phase gels and calculating the protein partition coefficients from this information. Correlation of the partition coefficient to a SH scale was established by partitioning several model proteins with known surface hydrophobicities in the same ATP system. The inclusion of the extract gel provided for a spot selection criterion based on satisfactory mass balance closure. The method is illustrated by application to a mixture of model proteins and to complex mixtures, that is, corn germ proteins extracted at pH 7 and pH 4. Biotechnol. Bioeng. 2007; 97: 1158–1169. © 2007 Wiley Periodicals, Inc.
Understanding signaling in yeast: Insights from network analysis
Authors: Arga K Yalçın , Önsan Z İlsen , Kırdar Betül , Ülgen Kutlu Ö , Nielsen Jens 
Published: January 2007

AbstractReconstruction of protein interaction networks that represent groups of proteins contributing to the same cellular function is a key step towards quantitative studies of signal transduction pathways. Here we present a novel approach to reconstruct a highly correlated protein interaction network and to identify previously unknown components of a signaling pathway through integration of protein–protein interaction data, gene expression data, and Gene Ontology annotations. A novel algorithm is designed to reconstruct a highly correlated protein interaction network which is composed of the candidate proteins for signal transduction mechanisms in yeast Saccharomyces cerevisiae. The high efficiency of the reconstruction process is proved by a Receiver Operating Characteristic curve analysis. Identification and scoring of the possible linear pathways enables reconstruction of specific sub‐networks for glucose‐induction signaling and high osmolarity MAPK signaling in S. cerevisiae. All of the known components of these pathways are identified together with several new “candidate” proteins, indicating the successful reconstructions of two model pathways involved in S. cerevisiae. The integrated approach is hence shown useful for (i) prediction of new signaling pathways, (ii) identification of unknown members of documented pathways, and (iii) identification of network modules consisting of a group of related components that often incorporate the same functional mechanism. Biotechnol. Bioeng. 2007; 97: 1246–1258. © 2007 Wiley Periodicals, Inc.
Mesophilic and thermophilic biotreatment of BTEX‐polluted air in reactors
Authors: Mohammad Balsam T. , Veiga María C. , Kennes Christian 
Published: January 2007

AbstractThis study compares the removal of a mixture of benzene, toluene, ethylbenzene, and all three xylene isomers (BTEX) in mesophilic and thermophilic (50°C) bioreactors. In the mesophilic reactor fungi became dominant after long‐term operation, while bacteria dominated in the thermophilic unit. Microbial acclimation was achieved by exposing the biofilters to initial BTEX loads of 2–15 g m−3 h−1, at an empty bed residence time of 96 s. After adaptation, the elimination capacities ranged from 3 to 188 g m−3 h−1, depending on the inlet load, for the mesophilic biofilter with removal efficiencies reaching 96%. On the other hand, in the thermophilic reactor the average removal efficiency was 83% with a maximum elimination capacity of 218 g m−3 h−1. There was a clear positive relationship between temperature gradients as well as CO2 production and elimination capacities across the biofilters. The gas phase was sampled at different depths along the reactors observing that the percentage pollutant removal in each section was strongly dependant on the load applied. The fate of individual alkylbenzene compounds was checked, showing the unusually high biodegradation rate of benzene at high loads under thermophilic conditions (100%) compared to its very low removal in the mesophilic reactor at such load (<10%). Such difference was less pronounced for the other pollutants. After 210 days of operation, the dry biomass content for the mesophilic and thermophilic reactors were 0.300 and 0.114 g g−1support, respectively, reaching higher removals under thermophilic conditions with a lower biomass accumulation, that is, lower pressure drop. Biotechnol. Bioeng. 2007;97:1423–1438. © 2007 Wiley Periodicals, Inc.
Submerged monoxenic culture of the entomopathogenic nematode Steinernema carpocapsae in an internal‐loop airlift bioreactor using two configurations of the inner tube
Authors: Chavarría‐Hernández Norberto , Sanjuan‐Galindo René , Rodríguez‐Pastrana Blanca‐Rosa , Medina‐Torres Luis , Rodríguez‐Hernández Adriana‐Inés 
Published: January 2007

AbstractThis article reports the submerged culture of the entomopathogenic nematode Steinernema carpocapsae and its symbiotic bacterium, Xenorhabdus nematophila, within an internal‐loop airlift bioreactor. Two configurations of the inner cylinder were tested: a standard draft tube (SDT) and a static mixer (SM), as well as two production media: MP1 (500 mL/L whey, among other ingredients) and MP2 (82 mL/L agave‐juice from Agave spp., among other ingredients). Three fermentations were carried out: F1 → SDT‐MP1, F2 → SM‐MP1 and F3 → SM‐MP2. The operating conditions were expressed on the basis of dimensionless Reynolds number (Re) and volumetric oxygen transfer coefficient (kLa), both of them determined on riser and downcomer sections within the bioreactor. The experiments began with fewer than 1,000 infective juvenile nematode stages (IJ) per mL and at t = 20 d, they achieved (nematodes/mL‐%IJ) 222,000‐87%, 62,200‐23% and 114,600‐80%, within F1, F2 and F3 experiments, respectively. Nonetheless, the achieved maximum nematode biomass concentrations (g/L) were F1 → 408, F2 → 557 and F3 → 613, and occurred at t = 16, 10 and 12 d, respectively. The fermentation operating conditions involved 0.042 (−) < Re < 647 (−) and 2.8× 10−4 s−1 < kLa < 0.0447 s−1, as functions of 0.004 m/s < superficial gas velocity (within the riser) < 0.079 m/s, 0.001 m/s < mean downcomer velocity < 0.014 m/s, and culture broth rheological properties which evolved from nearly the Newtonian behaviour to the pseudoplastic one. The maximum IJ concentration was achieved within F1 experiment (193,406 IJ/mL). Also, fermentation conditions involving higher riser‐Re and lower downcomer‐Re as well as higher nutriment concentrations in culture medium, promote higher nematode biomass concentrations but lower %IJ, maybe as a result of better conditions for the nematode population development. Biotechnol. Bioeng. 2007; 98: 167–176. © 2007 Wiley Periodicals, Inc.
Coronary septal collaterals as an access for the retrograde approach in the percutaneous treatment of coronary chronic total occlusions
Authors: Surmely Jean‐François , Katoh Osamu , Tsuchikane Etsuo , Nasu Kenya , Suzuki Takahiko 
Published: January 2007

AbstractObjectives: To investigate the feasibility and safety of the percutaneous dilatation of coronary septal collaterals and to allow its use as an access for retrograde approach to percutaneous coronary intervention (PCI) of coronary chronic total occlusions (CTOs). Background: Despite improvements in percutaneous techniques and materials, CTO recanalization success rate is still suboptimal. The retrograde approach allows to significantly increase this success rate. However, its application via a bypass graft or epicardial collateral can potentially result in severe complications. A safer retrograde access is desired and would allow broadening the application of the retrograde approach in the percutaneous treatment of CTOs. Methods: After a failed antegrade CTO recanalization attempt, a retrograde approach via septal collaterals was tried in 21 patients (19 males, 2 females). The septal collateral was accessed via the contralateral patent coronary artery and was crossed with a hydrophilic floppy wire. After successful wire crossing of the septal collateral, sequential low pressure dilatation was performed with a 1.25 or 1.5 mm balloon to allow the delivery of a balloon catheter up to the distal CTO site. Results: Successful wire crossing and balloon dilatation of septal collaterals was achieved in 19 cases and in 17 cases, respectively. Postdilatation septal collateral diameter increased significantly reaching a mean diameter of 1.46 ± 0.38 mm. Retrograde CTO recanalization was successfully performed in 71% of the cases. No major complications occurred. Conclusions: Coronary septal collaterals can be used as an access for the retrograde approach in the percutaneous treatment of CTOs. © 2007 Wiley‐Liss, Inc.
Patent foramen ovale closure: A new therapy for migraine
Authors: Schwerzmann Markus , Nedeltchev Krassen , Meier Bernhard 
Published: January 2007

AbstractMigraine is a recurrent disabling disorder predominantly affecting middle‐aged women. Migraine occurs with or without aura symptoms. Several studies have shown an increased prevalence of right‐to‐left shunts (RLSs) in migraine with aura. The overwhelming majority of these shunts were due to a patent foramen ovale (PFO). Furthermore, migraine with aura is more prevalent in clinical entities associated with a RLS, e.g. cryptogenic stroke, decompression illness in divers, or in patients with hereditary hemorrhagic teleangiectasia and pulmonary arteriovenous fistulas. Retrospective studies have consistently shown that shunt closure was associated with a significant reduction in migraine frequency. Its beneficial effect seemed to exceed the efficacy of conventional migraine therapy. Several randomized clinical trials to prospectively assess the benefit of shunt closure in migraine patients have been initiated. The only one completed, the MIST trial (Migraine Intervention with STARFLEX Technology), showed a significant reduction of migraine with aura after device implantation, compared with controls. However, the benefit of PFO closure was more modest than expected. This review recapitulates the current data regarding PFO closure and migraine with aura and summarizes in brief the current knowledge regarding migraine pathophysiology and the link to a RLS. © 2006 Wiley‐Liss, Inc.
New Predictive Correlations for the Drop Size in a Rotating Disc Contactor Liquid‐Liquid Extraction Column
Authors: Ismail Al‐Rahawi A. M. 
Published: January 2007

AbstractSauter mean drop sizes (d32) generated from a hole distributor in liquid extraction RDC columns were studied under various conditions. Experiments were designed to generate data required to determine the main variables that control the drop sizes in RDCs. Two precise correlations were proposed for predicting d32 in a RDC extraction column. The first was based on operating variables, hole‐distributor diameter, disc speed, column geometry, and system physical properties. The second one considered the same variables, except the column geometry. This model can be used for design purposes. The two correlations are the first of their type to consider the distributor hole inlet diameter in a RDC column. This diameter has been neglected by previous investigators. The maximum standard deviation for all data is 0.75 %, with a maximum absolute error of 6.8 %.
Leuchtdioden in der Chemie – Eine Hochzeit verschiedener Technologien
Authors: Kreisel G. , Meyer S. , Tietze D. , Fidler T. , Gorges R. , Kirsch A. , Schäfer B. , Rau S. 
Published: January 2007

AbstractDie Miniaturisierung von Reaktoren hat eine bemerkenswerte Eigendynamik entwickelt. Die Schwierigkeit besteht dabei oft darin, in das Konzept analytische Komponenten oder Einrichtungen zum Energieeintrag etc. zu integrieren. Für den Fall der Photomikrostrukturreaktoren ist es nun gelungen, Leuchtdioden (LEDs) als Lichtquellen mit dieser Reaktortechnik zu kombinieren. Darüber hinaus wird die Eignung von LEDs als monochromatische Lichtquelle im chemischen Labor gezeigt.
Modellierung und experimentelle Untersuchung der Wirbelschicht‐Sprühgranulation im überhitzen Wasserdampf
Authors: Hampel R. , Peglow M. , Heinrich S. , Mörl L. 
Published: January 2007

AbstractDie Wirbelschichttechnik bietet die Möglichkeit, feindisperse Produkte durch Granulation in grobkörnige Produkte umzuwandeln und diesen dadurch veränderte Partikeleigenschaften aufzuprägen. Die Wirbelschicht‐Sprühgranulation in Luft wird in vielen Bereichen der Industrie angewendet. Die Verwendung von Dampf als Fluidisationsmedium hat demgegenüber für bestimmte Stoffsysteme Vorteile. Der Prozess der Granulation im überhitzten Wasserdampf wird in diesem Beitrag theoretisch und experimentell untersucht.
Implications of Molecular Orbital Symmetries and Energies for the Electron Delocalization of Inorganic Clusters
Authors: Corminboeuf Clémence , King R. Bruce , Schleyer Paul von Rague 
Published: January 2007

AbstractIsostructural clusters exhibit contrasting magnetic properties when the number of electrons differs. Surprisingly, the same is true even for isoelectronic cages (e.g. Oh B6H62− is diatropic, whereas Oh Si62− is paratropic) or for those with different substitutents (e.g. Td B4H4 is paratropic, whereas Td B4F4 is diatropic). Indeed, the total nucleus‐independent chemical shift (NICS) values, based on shieldings computed at cluster centers, may range considerably in magnitude and even change from diatropic (up‐field shifted) to paratropic (down‐field shifted). Similarly, individual dissected canonical molecular orbital contributions to the total NICS values computed at the “gauge‐including atomic orbitals” (GIAO) level vary greatly. This contrasting behavior arises from molecular orbital energy differences, from the extent of orbital overlap, as well as from symmetry‐based selection rules derived from group theory. Differences in magnetic properties may originate from the symmetry of the orbitals; specifically from the forbidden nature of the highest occupied molecular orbital→lowest unoccupied molecular orbital (HOMO→LUMO) electronic excitation weighted by the occupied‐unoccupied orbital energy difference. Thus, HOMO‐NICS values are generally highly paratropic if the HOMO→LUMO rotational transition is allowed by symmetry selection rules.
Discontinuous fragmentation of nuclear DNA during apoptosis revealed by discrete “sub‐G1” peaks on DNA content histograms
Authors: Kajstura Malgorzata , Halicka H. Dorota , Pryjma Juliusz , Darzynkiewicz Zbigniew 
Published: January 2007

AbstractBackground:Internucleosomal DNA fragmentation is one of the hallmarks of apoptosis. Because the low molecular weight DNA fragments are extracted during cell staining in aqueous solutions, apoptotic cells can be identified on DNA content frequency histograms as cells with fractional (“sub‐G1”) DNA content. The aim of the present study was to explore whether in situ DNA fragmentation during apoptosis is discontinuous or progresses incessantly and if it is discontinuous, to define the resistant to cleavage fraction of DNA that remains stainable with the fluorochrome.Materials and Methods:The model of activation‐induced apoptosis of human lymphocytes was chosen as it provides uniform cell population with identical DNA content (DI = 1.00) that undergo apoptosis. Their apoptosis was induced by multivalent mitogen phytohemagglutinin (PHA) in the absence and presence of geldanamycin (GA), the benzoquinone ansamycin antibiotic which binds to Hsp90 (Heat Shock Protein 90) and alters its function. The cells were stained with acridine orange, the metachromatic fluorochrome that differentially stains cellular DNA and RNA.Results:A sharp, discrete peak representing the subpopulation of “sub‐G1” cells with highly reproducible DI = 0.42 ± 0.02 (CV = 5.5 ± 1.2) was observed on DNA content histograms of lymphocytes whose apoptosis was induced by PHA alone. Two distinct peaks, one representing cell subpopulations with DI = 0.42 (as above) and another, with DI = 0.79 ± 0.04 (CV = 5.8 ± 0.4), respectively, were seen in apoptotic cells from cultures stimulated with PHA in the presence of GA. The frequency of cells represented by the sub‐G1 peaks varied depending on time of induction of apoptosis and GA concentration.Conclusions:Apoptosis‐induced DNA fragmentation is discontinuous; approximately 42% of DNA is relatively stable and remains within the cell. The data suggest that the stable DNA is associated with nuclear matrix while the degradable fraction represents DNA in loop domains. A transient DNA stabilization is apparent in the presence of GA as evidenced by the presence of cell subpopulations with 79% of DNA retained in the cell. The observed discontinuity of DNA fragmentation appears to reflect sequential involvement of different nucleases and may also be modulated by chromatin structure. © 2007 International Society for Analytical Cytology.
Greater hippocampal neuronal recruitment in food‐storing than in non‐food‐storing birds
Authors: Hoshooley Jennifer S. , Sherry David F. 
Published: January 2007

AbstractPrevious research has shown heightened recruitment of new neurons to the chickadee hippocampus in the fall. The present study was conducted to determine whether heightened fall recruitment is associated with the seasonal onset of food‐storing by comparing neurogenesis in chickadees and a non‐food‐storing species, the house sparrow. Chickadees and house sparrows were captured in the wild in fall and spring and received multiple injections of the cell birth marker bromodeoxyuridine (BrdU). Birds were held in captivity and the level of hippocampal neuron recruitment was assessed after 6 weeks. Chickadees showed significantly more hippocampal neuronal recruitment than house sparrows. We found no seasonal differences in hippocampal neuronal recruitment in either species. In chickadees and in house sparrows, one‐third of new cells labeled for BrdU also expressed the mature neuronal protein, NeuN. In a region adjacent to the hippocampus, the hyperpallium apicale, we observed no significant differences in neuronal recruitment between species or between seasons. Hippocampal volume and total neuron number both were greater in spring than in fall in chickadees, but no seasonal differences were observed in house sparrows. Enhanced neuronal recruitment in the hippocampus of food‐storing chickadees suggests a degree of neurogenic specialization that may be associated with the spatial memory requirements of food‐storing behavior. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007.
Cyclic fatty acids in sunflower oils during frying of frozen foods with oil replenishment
Authors: Romero Antonio , Bastida Sara , Sánchez‐Muniz Francisco J. 
Published: January 2007

AbstractFrying of frozen foods has become popular because it considerably reduces cooking time. Polymers and cyclic fatty acid monomers (CFAM) formed during frying are potentially toxic and therefore their production should be minimized. Twenty discontinuous fryings of different frozen foods were carried out over ten consecutive days, in sunflower oil (SO) and in high‐oleic acid sunflower oil (HOSO), by adding fresh oil after each frying to bring the volume of the fryer oil back to 3 L. CFAM methyl ester derivates were hydrogenated, isolated, concentrated and quantified by HPLC using a reverse‐phase column, followed by gas chromatography. After 20 fryings, significantly higher contents of polar material, polymers and CFAM (all p <0.001) were found in SO than in HOSO. Bicyclic compound formation was four times higher in SO (p <0.001). The fat from the fried potatoes presented a polymer content very similar to that of their corresponding oils. The 100‐g rations of the SO‐fried potatoes from the 20th frying supply 49 or 15%, respectively, more polymers and CFAM and 1 mg more bicyclic fatty acids than the 100‐g rations of HOSO‐fried potatoes. Because digestion and absorption of polar material, polymers and CFAM occur, the data clearly show the advantageousness and advisability of frying with HOSO rather than SO.