bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational protein design: Software implementation, parameter optimization, and performance of a simple model
Authors: Schmidt Am Busch Marcel , Lopes Anne , Mignon David , Simonson Thomas 
Published: December 2007

AbstractComputational protein design will continue to improve as new implementations and parameterizations are explored. An automated protein design procedure is implemented and applied to the full redesign of 16 globular proteins. We combine established but simple ingredients: a molecular mechanics description of the protein where nonpolar hydrogens are implicit, a simple solvent model, a folded state where the backbone is fixed, and a tripeptide model of the unfolded state. Sequences are selected to optimize the folding free energy, using a simple heuristic algorithm to explore sequence and conformational space. We show that a balanced parametrization, obtained here and in our previous work, makes this procedure effective, despite the simplicity of the ingredients. Calculations were done using our Proteins @ Home distributed computing platform, with the help of several thousand volunteers. We describe the software implementation, the optimization of selected terms in the energy function, and the performance of the method. We allowed all amino acids to mutate except glycines, prolines, and cysteines. For 15 of the 16 test proteins, the scores of the computed sequences were comparable to those of natural homologues. Using the low energy computed sequences in a BLAST search of the SWISSPROT database, we could retrieve natural sequences for all protein families considered, with no high‐ranking false‐positives. The good stability of the designed sequences was supported by molecular dynamics simulations of selected sequences, which gave structures close to the experimental native structure. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Mastoparan effects in skeletal muscle damage: An ultrastructural view until now concealed
Authors: Rocha Thalita , Leonardo Marta Beatriz , De Souza Bibiana Monson , Palma Mario Sérgio , Da Cruz‐Höfling Maria Alice 
Published: December 2007

AbstractAnimal venoms have been valuable sources for development of new drugs and important tools to understand cellular functioning in health and disease. The venom of Polybia paulista, a neotropical social wasp belonging to the subfamily Polistinae, has been sampled by headspace solid phase microextraction and analyzed by gas chromatography‐mass spectrometry. Recent study has shown that mastoparan, a major basic peptide isolated from the venom, reproduces the myotoxic effect of the whole venom. In this study, Polybia‐MPII mastoparan was synthesized and studies using transmission electron microscopy were carried out in mice tibial anterior muscle to identify the subcellular targets of its myotoxic action. The effects were followed at 3 and 24 h, 3, 7, and 21 days after mastoparan (0.25 μg/μL) intramuscular injection. The peptide caused disruption of the sarcolemma and collapse of myofibril arrangement in myofibers. As a consequence, fibers presented heteromorphic amorphous masses of agglutinated myofilaments very often intermingled with denuded sarcoplasmic areas sometimes only surrounded by a persistent basal lamina. To a lesser extent, a number of fibers apparently did not present sarcolemma rupture but instead appeared with multiple small vacuoles. The results showed that sarcolemma, sarcoplasmic reticulum (SR), and mitochondria were the main targets for mastoparan. In addition, a number of fibers showed apoptotic‐like nuclei suggesting that the peptide causes death both by necrosis and apoptosis. This study presents a hitherto unexplored view of the effects of mastoparan in skeletal muscle and contributes to discuss how the known pharmacology of the peptide is reflected in the sarcolemma, SR, mitochondria, and nucleus of muscle fibers, apparently its subcellular targets. Microsc. Res. Tech., 2008. © 2007 Wiley‐Liss, Inc.
Preservation and fluorescence of the microfossils from Neoproterozoic Doushantuo formation
Authors: Chi Huimei , Feng Man , Xiao Zhongdang , Lu Zuhong 
Published: December 2007

AbstractThe phosphatized microfossils from Doushantuo Formation, Southeast China show us the biodiversity about 600 million years ago, which is a unique window for the evolution of the early life on earth. However, the process of phosphatic fossilization in detail still remains unknown. Here we report our study on the preservation state of the fossils by using confocal laser scanning microscopy. We found that fluorescent signal of the fossil could reflect the preservation state when compared with the transmission light microscopy. First, we found the fluorescent signal of the decayed cells of the fossil was weaker than that of the nondecayed part. Second, we found that the three‐dimensional reconstruction of the fluorescent signals could help to judge the degree of mineralization of the fossil cells, compared with the observation by transmission light microscope. Third, we found that almost all of the fossil specimens we observed could fluoresce more or less when excited by laser light. Therefore, the fluorescent microscopy provides a useful method for the study of the preservation state of the phosphatic fossil cells. Microsc. Res. Tech., 2008. © 2007 Wiley‐Liss, Inc.
Colocalization of MCM8 and MCM7 with proteins involved in distinct aspects of DNA replication
Authors: Kinoshita Yayoi , Johnson Edward M. , Gordon Ronald E. , Negri‐Bell Heather , Evans Mark T. , Coolbaugh Jennifer , Rosario‐Peralta Yaseris , Samet Joseph , Slusser Evelyn , Birkenbach Mark P. , Daniel Dianne C. 
Published: December 2007

AbstractMinichromosome maintenance (MCM) proteins are essential for DNA replication in eukaryotes. A subcomplex of the MCM2‐7 family members, initially characterized in yeast, is thought to serve as a eukaryotic DNA replicative helicase. MCM8 is a new family member, not present in yeast, which may function alone or with other family members in aspects of DNA metabolism, including replication initiation and elongation. Through the use of chromatin immunoprecipitation, we find that MCM8, like MCM7, colocalizes on a specific DNA segment of the c‐MYC replication initiation zone (c‐MYC replicator) with Cdc6, a protein potentially involved in loading MCM proteins onto DNA. The association between MCM8 and MCM7 peaks in mid G1, at the time of assembly of the prereplication complex. The association of both MCM proteins with Cdc6, however, continues even after DNA replication is complete. We also find that MCM8 colocalizes at the c‐MYC replicator with chromatin‐bound Cdk2. Our data indicate that any role MCM8 may play in elongation is likely to be discontinuous, in its association with DNA, from a potential role in initiation. Using immunogold electron microscopy we show that MCM8 and MCM7 differ in spatial relation to RPA70 during S phase. Our data strongly suggest that MCM8 functions with other known replication proteins in processes which accompany DNA replication, especially initiation, and which are specifically adapted to suit higher eukaryotes. Microsc. Res. Tech, 2008. © 2007 Wiley‐Liss, Inc.
Automated recognition system to classify subcellular protein localizations in images of different cell lines acquired by different imaging systems
Authors: Tsai Yuh‐Show , Chung I‐Fang , Simpson Jeremy C. , Lee Mei‐I , Hsiung Chia‐Cheng , Chiu Tai‐Yu , Kao Lung‐Sen , Chiu Te‐Cheng , Lin Chin‐Teng , Lin Wen‐Chieh , Liang Sheng‐Fu , Lin Chung‐Chih 
Published: December 2007

AbstractSystemic analysis of subcellular protein localization (location proteomics) provides clues for understanding gene functions and physiological condition of the cells. However, recognition of cell images of subcellular structures highly depends on experience and becomes the rate‐limiting step when classifying subcellular protein localization. Several research groups have extracted specific numerical features for the recognition of subcellular protein localization, but these recognition systems are restricted to images of single particular cell line acquired by one specific imaging system and not applied to recognize a range of cell image sources. In this study, we establish a single system for automated subcellular structure recognition to identify cell images from various sources. Two different sources of cell images, 317 Vero (http://gfp‐cdna.embl.de) and 875 CHO cell images of subcellular structures, were used to train and test the system. When the system was trained by a single source of images, the recognition rate is high and specific to the trained source. The system trained by the CHO cell images gave high average recognition accuracy for CHO cells of 96%, but this was reduced to 46% with Vero images. When we trained the system using a mixture of CHO and Vero cell images, an average accuracy of recognition reached 86.6% for both CHO and Vero cell images. The system can reject images with low confidence and identify the cell images correctly recognized to avoid manual reconfirmation. In summary, we have established a single system that can recognize subcellular protein localizations from two different sources for location‐proteomic studies. studies. Microsc. Res. Tech., 2008. © 2007 Wiley‐Liss, Inc.
Gene delivery to the vasculature mediated by low‐titre adeno‐associated virus serotypes 1 and 5
Authors: Sen S. , Conroy S. , Hynes S. O. , McMahon J. , O'Doherty A. , Bartlett J. S. , Akhtar Y. , Adegbola T. , Connolly C. E. , Sultan S. , Barry F. , Katusic Z. S. , O'Brien T. 
Published: December 2007

AbstractBackgroundVascular gene therapy requires safe and efficient gene transfer in vivo. Recombinant adeno‐associated virus (AAV) is a promising viral vector but its use in the vasculature has produced conflicting results and serotypes other than AAV2 have not been intensively studied. We investigated the efficiency of alternative AAV serotypes for vascular gene delivery in vitro and in vivo.MethodsVascular cell lines were transduced in vitro with AAV vectors. Rabbit carotid arteries were transduced with AAV1, 2 and 5 encoding enhanced green fluorescent protein (eGFP) (∼1.4 × 109 DNAse‐resistant particles (drp)). Gene transfer in vivo was assessed at 14 and 28 days. High‐titre doses of AAV2 encoding β‐galactosidase in vivo were also studied.ResultsIn vitro, transgene expression was not observed in endothelial cells using AAV2 whereas the use of serotypes 1 and 5 resulted in detectable levels of transgene expression. Coronary artery smooth muscle cells (CASMCs) transduced with AAV2 demonstrated higher levels of GFP expression than AAV1 or 5. Transgene expression in vivo was noted using low‐titre AAV1 and AAV5 (∼1.4 × 109 drp) in the media and adventitia. Only delivery of AAV1eGFP resulted in neointimal formation (3/7 vessels examined), with transgene expression noted in the neointima. Transgene expression with AAV2 was not detected in any layer of the blood vessel wall using low titre (∼109 drp). However, high‐titre (∼1011 drp) AAV2 resulted in transduction of cells in the media and adventitia but not the endothelium.ConclusionsAAV1 and AAV5 have advantages over AAV2 for vascular gene delivery at low titres. Copyright © 2007 John Wiley & Sons, Ltd.
Microbial diversity of mine water at Zhong Tiaoshan copper mine, China
Authors: He Zhiguo , Xie Xuehui , Xiao Shengmu , Liu Jianshe , Qiu Guanzhou 
Published: December 2007

AbstractMicrobial diversity of mine water at Zhong Tiaoshan copper mine, Shanxi province, China, was analyzed using a culture‐independent 16S rRNA gene (rDNA) based on cloning approach. A total of 59 Operational Taxonomic Units (OTUs) were obtained from 226 clones from all three samples (8 OTUs from sample SX1, 25 from SX2 and 26 from SX3). 46 of them were representative OTUs and were sequenced. 93.5% of the total clones had sequences that were less than 5% difference from those in the nucleic acids database. The percentage of overlapping OTUs among samples was from 12.1% to 35.3%. Phylogenetic analysis indicated that 60.62% of the clones were affiliated with members of the Proteobacteria (α ‐3.10%, β ‐24.78%, γ ‐31.41%, δ ‐1.33%), whereas 29.20% of the clones were closely related to the Nitrospira (Leptospirillum ferrooxidans 20.80%, Leptospirillum ferriphilum 0.88% and Leptospirillum group III 7.52%, respectively). The rest clones were affiliated with the Firmicutes (2.65%) and the Bacteroidetes (7.52%). The results of Principal Component Analysis (PCA) based on the percentages of OTUs and biogeochemical data revealed that biogeochemical properties affected the diversity of microbial communities in mine water. Especially, the pH value, temperature and different concentrations of elements such as lead, zinc, sulfur, iron and copper seemed to be key factors affecting the composition and structure of microbial communities in this study. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Chromate reducing and plant growth promoting activies of psychrotrophic Rhodococcus erythropolis MtCC 7905
Authors: Trivedi Pankaj , Pandey Anita , Sa Tongmin 
Published: December 2007

AbstractA psychrotrophic bacterial strain resistant to 300 mg l–1 of Cr6+ was isolated from metal contaminated soil samples from a site situated in the Indian Himalayan Region. Based on 16 S rRNA analysis the isolate showed maximum similarity to Rhodococcus erythropolis. Rhodococcus erythropolis MTCC 7905 reduced substantial amounts of Cr6+ to Cr3+ at 10 °C and showed plant growth promotion. The isolate offer promise as inoculant to promote plant growth of pea (Pisum sativum) in the presence of toxic Cr6+ concentration. To the best of our knowledge this is the first report on a psychrotrophic strain belonging to species R. erythropolis and its functional characterization to reduce Cr6+ and promote plant growth at low temperature. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Roles of larger conductance mechanosensitive channels (MscL) in sporulation and Act secretion in Streptomyces coelicolor
Authors: Wang Chun‐Xia , Ge Huan‐Xi , Hou Xiao‐Ping , Li Yong‐Quan 
Published: December 2007

AbstractLarger conductance mechanosensitive channels (MscL) is a conserved channel existing in eukarya, bacteria and archaea. The gene SCO3190 in Streptomyces coelicolor encodes an MscL homolog of Escherichia coli. To elucidate the physiological roles of MscL in S. coelicolor (Sc‐MscL), deletion mutant was constructed. The Sc‐MscL deletion brought sporulation ahead, and had no significant influence to antibiotic synthesis in S. coelicolor. When Sc‐MscL was overexpressed in S. coelicolor, the colony of S. coelicolor was small and sleek with abundant blue pigment corresponding to actinorhodin (Act). Furthermore, abundant blue pigment displayed on hypoosmotic LB plates comparing to hyperosmotic R5 plates. These results suggested that Sc‐MscL was involved into Act secretion and sporulation relating to osmotic stress response in S. coelicolor. Moreover, Sc‐MscL showed possible functional pentamer by cross‐linking in vitro. It is first report about biochemical and functional characterization of MscL in S. coelicolor. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Temperature and pH effect on lindane removal by Streptomyces sp. M7 in soil extract
Authors: Benimeli C. S. , González A. J. , Chaile A. P. , Amoroso M. J. 
Published: December 2007

AbstractThis work was conduced to study the removal of γ‐hexachlorocyclohexane (lindane) in a soil extract liquid medium (SE) by Streptomyces sp. M7 and to determine the influence of pH and temperature on bacterial growth and pesticide removal in this medium. When Streptomyces sp. M7 was cultured in SE supplemented with lindane 100 μg l–1 at different initial pH, the maximum growth was observed at pH 7 and the microorganism was not able to grow at pH 5 and 9; the highest pesticide removal (70.4%) by Streptomyces sp. M7 was noted at an initial pH of 7 at 4 weeks of incubation. The maximum removal (70% approximately) was observed when the microorganism was incubated in SE at 30 °C; although the optimal temperature for Streptomyces sp. M7 growth, with and without lindane, was 25 °C, and for the pesticide removal was 30 °C. The results of this study suggest that this actinomycete strain appears as an effective alternative in the remediation of lindane polluted sites. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Microbial diversity analysis of former salterns in southern Taiwan by 16S rRNA‐based methods
Authors: Wang Chung‐Yi , Ng Chang‐Chai , Chen Tseng‐Wei , Wu Sz‐Jie , Shyu Yuan‐Tay 
Published: December 2007

AbstractThe microbiota diversity of the former salterns in southern Taiwan was investigated by denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH). Soil samples from three salterns were analyzed using DGGE and 16S rRNA from 502 colonies representing 5 archaea and 18 bacteria taxonomic groups. Each representative taxonomic group was further identified, whereas 8.7% of clones were unclassified microorganisms. Chromohalobacter, Halomonas and Virgibacillus are dominant in the Biemen saltern, Chiguensis saltern and Szutsau saltern, respectively. During FISH analysis, several taxonomic‐specific probes were used. The DAPI‐stained‐cell count in the Szutsao saltern had a higher number of microorganisms (4.58 × 107 cell/cm3) than the other salterns. Archaea occupied 2.7–6.6% whereas bacteria accounted for 37.2–52.9% of total microbial population at the three sites. Among these three sampling sites, the Szutsao saltern had the highest diversity in halophilic microbial composition, as indicated by DGGE and FISH. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Biosorption of metal and salt tolerant microbial isolates from a former uranium mining area. Their impact on changes in rare earth element patterns in acid mine drainage
Authors: Haferburg Götz , Merten Dirk , Büchel Georg , Kothe Erika 
Published: December 2007

AbstractThe concentration of metals in microbial habitats influenced by mining operations can reach enormous values. Worldwide, much emphasis is placed on the research of resistance and biosorptive capacities of microorganisms suitable for bioremediation purposes. Using a collection of isolates from a former uranium mining area in Eastern Thuringia, Germany, this study presents three Gram‐positive bacterial strains with distinct metal tolerances. These strains were identified as members of the genera Bacillus, Micrococcus and Streptomyces. Acid mine drainage (AMD) originating from the same mining area is characterized by high metal concentrations of a broad range of elements and a very low pH. AMD was analyzed and used as incubation solution. The sorption of rare earth elements (REE), aluminum, cobalt, copper, manganese, nickel, strontium, and uranium through selected strains was studied during a time course of four weeks. Biosorption was investigated after one hour, one week and four weeks by analyzing the concentrations of metals in supernatant and biomass. Additionally, dead biomass was investigated after four weeks of incubation. The maximum of metal removal was reached after one week. Up to 80% of both Al and Cu, and more than 60% of U was shown to be removed from the solution. High concentrations of metals could be bound to the biomass, as for example 2.2 mg/g U. The strains could survive four weeks of incubation. Distinct and different patterns of rare earth elements of the inoculated and non‐inoculated AMD water were observed. Changes in REE patterns hint at different binding types of heavy metals regarding incubation time and metabolic activity of the cells. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Microbes and metals: interactions in the environment
Authors: Haferburg Götz , Kothe Erika 
Published: December 2007

AbstractResearch on the behaviour of microorganisms in geogenic or anthropogenic metallomorphic environments is an integral part of geomicrobiology. The investigation of microbial impact on the fate of minerals and geologically significant compounds of mining areas can lead to an understanding of biogeochemical cycles. Metabolic processes of microorganisms are the cause for the dissolution of minerals, and especially pyrite oxidation results in the generation of acid mine drainage which, in turn, leads to heavy metal contamination as a result of mining activities. On the other hand, microbial metabolism can also contribute to the formation of certain ore deposits over geological time.The adaptation to heavy metal rich environments is resulting in microorgansims which show activities for biosorption, bioprecipitation, extracellular sequestration, transport mechanisms, and/or chelation. Such resistance mechanisms are the basis for the use of microorganisms in bioremediation approaches. As only a small part of the worldwide occurring prokaryotes has been described yet, the understanding of the role bacteria play in a geogenic and pedogenic context is very likely to change deeply as soon as more habitat relevant microbial functions can be described. Examples for the identification of microbial processes from case studies may help to advance this field. The strongly interdisciplinary field of bio‐geo‐interactions spanning from the microorganism to the mineral holds much promise for future developments in both basic research as well as applied sciences. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hydrocarbon degradation by thermophilic Nocardia otitidiscaviarum strain TSH1: physiological aspects
Authors: Zeinali Majid , Vossoughi Manouchehr , Ardestani Sussan K. , Babanezhad Esmaeil , Masoumian Mohamadreza 
Published: December 2007

AbstractIndigenous thermophilic hydrocarbon degraders are of special significance for the bioremediation of oil‐contaminated desert soils with ambient temperature of 45–50 °C. The first objective of this study was to demonstrate the hydrocarbon‐degrading capability of Nocardia otitidiscaviarum TSH1 (DSM 45036) which grows optimally at 50 °C. Analysis of the metabolic profile of the strain TSH1 showed that it could metabolize phenol, intermediate‐chain‐length n ‐alkanes and some polycyclic aromatic hydrocarbons (PAHs) ranging in size from two to four fused rings efficiently, but not toluene and xylene. N. otitidiscaviarum TSH1 was able to survive and grow at phenol concentrations up to 875 mg l–1. For the first time, the physiological response of a thermophilic Nocardia strain to poorly available hydrophobic compounds was also investigated. When grown on a mineral salt medium with hexadecane, N. otitidiscaviarum TSH1 showed very high affinity for the organic phase. Additionally, PAH‐grown cells were considerably hydrophobic. The capacity of PAH‐utilizing N. otitidiscaviarum TSH1 isolate to produce biosurfactants was also investigated. Fatty acids (C14–C18) were detected by GC‐MS analysis during bacterial growth in PAH supplemented mineral media. High cell surface hydrophobicity and capability of N. otitidiscaviarum TSH1 to degrade different hydrocarbons at 50 °C may make it an ideal candidate to treat oil‐contaminated desert soils. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)