julilili42/papers huggingface dataset:
High frequency of anti-PDC-E1a/E1b antibodies in sera from primary biliary cirrhosis patients: affinity purification of the mitochondrial M4 antigen predominantly enriches pyruvate dehydrogenase complex E1achains
2006-01-16

Objective: Sera from patients with primary biliary cirrhosis (PBC) contain antibodies against intracellular antigens such as denatured epitopes of the pyruvate dehydrogenase complex (PDC) derived from bovine heart mitochondria (M2). In addition, native proteins were detected within the sucrose gradient fractions derived from rat liver mitochondria (M4) only by the complement fixation test but not in Western Blot analysis. Thus, the major objective of this study was to identify these proteins. Methods: IgG fractions of M4-CFT positive (n=5) or negative (n=5) PBC marker sera were used to purify the M4 proteins by affinity chromatography. Proteins were identified by Western blotting, silver staining, and sequence analysis. Further, a cohort of 57 PBC patients was tested for the reactivity to M4 related proteins. Results: Two different AMA-pattern of the marker sera occurred: M4-CFT positive sera could be characterized by Western Blot analysis as PDC-E2+/E1+ while the M4-CFT negative sera were PDC-E2+/E1-. Using the PDC-E2+/E1+ sera for affinity chromatography, the major proteins of the mitochondrial M4 fraction could be identified as the PDC-E1a and E1b subunits. Further, we purified fragments of PDC-E2 and branched-chain 2-oxo acid dehydrogenase complex E2, and an enzyme of the b-oxidation of fatty acids, the enoyl-CoA-hydratase. A clear-cut association between anti-M4 reactivity in the CFT and the reactivity to both PDC subunits could be also documented in the cohort of 57 PBC patients showing anti-PDC-E1a and E1b antibodies in a frequency of 74% and 67%. Conclusion: CFT reactivity against M4 antigens could be preferentially identified as a reaction against PDC-E1a and E1b. In view of the high frequency of antibodies to these subunits, they must be considered as not less important as compared to PDC-E2.
Gene replacement in Staphylococcus carnosus and Staphylococcus xylosus
2006-01-17

A system for high-efficiency gene replacement in Staphylococcus carnosus and Staphylococcus xylosus has been developed, that is based on temperature-sensitive Escherichia coli-Staphylococcus shuttle vectors for fragment delivery and erythromycin resistance cassettes to facilitate selection of genomic copies of disrupted genes. The approach was tested by constructing a phosphotransferase-deficient mutant of S. carnosus and an S. xylosus mutant strain unable to utilize sucrose. Allelic replacements were observed at rather high frequencies, ranging from approximately 10% for the ptsI gene in S. carnosus up to 50% for the scrB gene in S. xylosus. These differences most likely reflect the length of homology rather than strain-specific variations in recombination efficiencies. Apart from the staphylococcal species tested in this study, the system appears to be applicable in other staphylococci.
Molecular analysis of cyp51 from fluconazole-resistant Candida albicans strains
2006-01-17

The target enzyme for fluconazole is sterol 14 alpha-demethylase, a cytochrome P450 encoded by cyp51. One mechanism of fluconazole resistance likely to occur in Candida albicans is through an altered target site. To test this hypothesis DNA sequencing of the cyp51 coding sequence from 19 fluconazole-resistant and 19 fluconazole-sensitive C. albicans was undertaken. A number of point mutations were identified in the resistant isolates which were not present in the sensitive ones: F105L (five), E266D (five), K287R (one), G448G (one), G450E (one), G464S (three) and V488I (one). These alterations are discussed in the light of a molecular model of the enzyme regarding potential roles in resistance. It was also demonstrated that sequence-specific primers can be employed to identify polymorphisms which may be associated with resistance; diagnostic tests for resistant strains will prove of value in combating this serious clinical problem.
Proapoptotic activity of Ukrain is based on Chelidonium majusL. alkaloids and mediated via a mitochondrial death pathway
2006-01-17

Abstract Background The anticancer drug Ukrain (NSC-631570) which has been specified by the manufacturer as semisynthetic derivative of the Chelidonium majus L. alkaloid chelidonine and the alkylans thiotepa was reported to exert selective cytotoxic effects on human tumour cell lines in vitro . Few clinical trials suggest beneficial effects in the treatment of human cancer. Aim of the present study was to elucidate the importance of apoptosis induction for the antineoplastic activity of Ukrain, to define the molecular mechanism of its cytotoxic effects and to identify its active constituents by mass spectrometry. Methods Apoptosis induction was analysed in a Jurkat T-lymphoma cell model by fluorescence microscopy (chromatin condensation and nuclear fragmentation), flow cytometry (cellular shrinkage, depolarisation of the mitochondrial membrane potential, caspase-activation) and Western blot analysis (caspase-activation). Composition of Ukrain was analysed by mass spectrometry and LC-MS coupling. Results Ukrain turned out to be a potent inducer of apoptosis. Mechanistic analyses revealed that Ukrain induced depolarisation of the mitochondrial membrane potential and activation of caspases. Lack of caspase-8, expression of cFLIP-L and resistance to death receptor ligand-induced apoptosis failed to inhibit Ukrain-induced apoptosis while lack of FADD caused a delay but not abrogation of Ukrain-induced apoptosis pointing to a death receptor independent signalling pathway. In contrast, the broad spectrum caspase-inhibitor zVAD-fmk blocked Ukrain-induced cell death. Moreover, over-expression of Bcl-2 or Bcl-x L and expression of dominant negative caspase-9 partially reduced Ukrain-induced apoptosis pointing to Bcl-2 controlled mitochondrial signalling events. However, mass spectrometric analysis of Ukrain failed to detect the suggested trimeric chelidonine thiophosphortriamide or putative dimeric or monomeric chelidonine thiophosphortriamide intermediates from chemical synthesis. Instead, the Chelidonium majus L. alkaloids chelidonine, sanguinarine, chelerythrine, protopine and allocryptopine were identified as major components of Ukrain. Apart from sanguinarine and chelerythrine, chelidonine turned out to be a potent inducer of apoptosis triggering cell death at concentrations of 0.001 mM, while protopine and allocryptopine were less effective. Similar to Ukrain, apoptosis signalling of chelidonine involved Bcl-2 controlled mitochondrial alterations and caspase-activation. Conclusion The potent proapoptotic effects of Ukrain are not due to the suggested "Ukrain-molecule" but to the cytotoxic efficacy of Chelidonium majus L. alkaloids including chelidonine.
Effect of leader peptide mutations on biosynthesis of the lantibiotic Pep5
2006-01-17

Lantibiotics are lanthionine-containing antibiotic peptides which are synthesized from ribosomal prepeptides by post-translational modification. In order to elucidate the function of a conserved motif in the N-terminal leader sequence of lantibiotic prepeptides, three amino acids were exchanged in the leader peptide sequence of the lantibiotic Pep5. Exchanging Phe-19 for Ser and Glu-16 for Lys in the FDLEI-motif, reduced Pep5 production to 35 and 38% of the control whereas, after exchanging Asp-6 for Ser and Glu-16 for Lys in the FDLEI-motif, reduced Pep5 production to 35 and 38% of the control whereas, after exchanging ASp-6 for Lys, the production was decreased only to 82%. Proteolytic fragments of Pep5 or incorrectly modified Pep5 molecules, indicative of incorrect modifications, were not found in the culture supernatant. Thus, in contrast to the biosynthesis of the lantibiotic nisin, the FDLEI-motif is not essential for biosynthesis of Pep5 and has no influence on correct ring formation or processing, but seems to be important for optimal biosynthesis rates.
Identification of the serine acetyltransferase gene of Staphylococcus xylosus
2006-01-17

A transposon Tn917-induced mutant strain of Staphylococcus xylosus was isolated that required exogenous cysteine for growth. The transposon was found to reside within a gene, designated cysE, encoding a protein of 216 amino acids with a high level of similarity to bacterial serine acetyltransferases. The cysE::Tn917 mutant completely lost serine acetyltransferase activity, which is easily detectable in the wild-type strain. In addition, the mutant strain could no longer grow in minimal medium without cysteine. Therefore, the cysE gene product is essential for the de novo synthesis of cysteine via O-acetyl-L-serine in S. xylosus. The cysE gene is surrounded by genes encoding glutamyl-tRNA synthetase (gltX) and cysteinyl-tRNA synthetase (cysS), as deduced from sequence comparisons. The genetic organisation in S. xylosus, gltX-cysE-cysS, is identical to that found in Bacillus subtilis and Bacillus stearothermophilus.
Quantum deformation of the Dirac bracket
2006-01-17

The quantum deformation of the Poisson bracket is the Moyal bracket. We construct quantum deformation of the Dirac bracket for systems which admit global symplectic basis for constraint functions. Equivalently, it can be considered as an extension of the Moyal bracket to second-class constraints systems and to gauge-invariant systems which become second class when gauge-fixing conditions are imposed.
In vivo reaction of affinity-tag-labelled epidermin precursor peptide with flavoenzyme EpiD
2006-01-17

The Staphylococcus epidermidis genes encoding the His-tag-labelled epidermin precursor peptide EpiA and the flavoenzyme EpiD or the mutant protein EpiD-G93D, which lacks the coenzyme, were co-expressed and the proteins were synthesized in vivo in Escherichia coli. Only in the presence of EpiD was the precursor peptide converted to a reaction product with a decrease in mass of 44-46 Da. This result confirms the in vitro experiments carried out with purified EpiA and purified EpiD from Staphylococcus epidermidis [Kupke et al. (1994) J. Biol. Chem. 269, 5653-5659]. EpiD catalyzes the oxidative decarboxylation of the C-terminal cysteine residue of EpiA to a [Z]-enethiol structure. In the presence of EpiD, the amount of purified (modified) peptide EpiA was several-fold higher than in the presence of EpiD-G93D, indicating that the stabilization of EpiA against proteolysis is due to an interaction with EpiD or to the presence of the C-terminal modification. The presented experimental approach will be valuable for the analysis of enzymes that catalyze posttranslational modification reaction of peptides and proteins.
Specific in vivo thiol-labeling of the FhuA outer membrane ferrichrome transport protein of Escherichia coli K-12: evidence for a disulfide bridge in the predicted gating loop
2006-01-17

The multifunctional FhuA protein of Escherichia coli K-12 forms a channel that is closed by a loop, tentatively designated the 'gating loop', which is also the principal binding site for all FhuA ligands. In this report, it is shown by in vivo labeling that the two cysteines in the gating loop form a disulfide bridge, and they react weakly after reduction with biotin-maleimide, as determined by streptavidin-beta-galactosidase bound to biotin. The two cysteines close to the C-terminus of FhuA also form a disulfide bridge and react with the thiol reagents only after heat denaturation of FhuA in SDS. Replacement of the existing cysteines by serine did not alter the sensitivity of cells to the FhuA ligands tested (T5, phi 80, T1, colicin M, and albomycin) and supported growth on ferrichrome as sole iron source. The cysteines in the gating loop play no specific functional role; they are largely buried in the interior of the loop, and the disulfide bridges are not essential for maintaining the conformation of FhuA. The C-terminal cysteines are in the interior of FhuA and are also not important for the structure of FhuA. The method used allows the identification of free cysteines and disulfides in surface exposed protein regions.
Combining signals from spotted cDNA microarrays obtained at different scanning intensities
2006-01-17

Abstract Motivation: The analysis of spotted cDNA microarrays involves scanning of color signals from fluorescent dyes. A common problem is that a given scanning intensity is not usually optimal for all spotted cDNAs. Specifically, some spots may be at the saturation limit, resulting in poor separation of signals from different tissues or conditions. The problem may be addressed by multiple scans with varying scanning intensities. Multiple scanning intensities raise the question of how to combine different signals from the same spot, particularly when measurement error is not negligible. Results: This paper suggests a non-linear latent regression model for this purpose. It corrects for biases caused by the saturation limit and efficiently combines data from multiple scans. Combining multiple scans also allows reduction of technical error particularly for cDNA spots with low signal. The procedure is exemplified using cDNA expression data from maize. Availability: All methods were implemented using standard procedures available in the SAS/STAT module of the SAS System. Programming statements are available from the first author upon request. Contact: piepho@uni-hohenheim.de Supplementary information: The supplementary data are available at Bioinformatics online.
Direct Cross-talk of Interleukin-6 and Insulin Signal Transduction via Insulin Receptor Substrate-1 in Skeletal Muscle Cells
2006-01-18

The exercise-induced interleukin (IL)-6 production and secretion within skeletal muscle fibers has raised the question of a putative tissue-specific function of IL-6 in the energy metabolism of the muscle during and after the exercise. In the present study, we followed the hypothesis that IL-6 signaling may directly interact with insulin receptor substrate (IRS)-1, a keystone in the insulin signaling cascade. We showed that IL-6 induces a rapid recruitment of IRS-1 to the IL-6 receptor complex in cultured skeletal muscle cells. Moreover, IL-6 induced a rapid and transient phosphorylation of Ser-318 of IRS-1 in muscle cells and in muscle tissue, but not in the liver of IL-6-treated mice, probably via the IL-6-induced co-recruitment of protein kinase C-delta. This Ser-318 phosphorylation improved insulin-stimulated Akt phosphorylation and glucose uptake in myotubes since transfection with an IRS-1/Glu-318 mutant simulating a permanent phospho-Ser-318 modification increased Akt phosphorylation and glucose uptake. Noteworthily, two inhibitory mechanisms of IL-6 on insulin action, phosphorylation of the inhibitory Ser-307 residue of IRS-1 and induction of SOCS-3 expression, were only found in liver but not in muscle of IL-6-treated mice. Thus, the data provided evidence for a possible molecular mechanism of the physiological metabolic effects of IL-6 in skeletal muscle, thereby exerting short term beneficial effects on insulin action.
A WNK kinase binds and phosphorylates V‐ATPase subunit C
2006-01-18

WNK (with no lysine (K)) protein kinases are found in many eukaryotes and share a unique active site. Here, we report that a member of the Arabidopsis WNK family (AtWNK8) interacts with subunit C of the vacuolar H + ‐ATPase (V‐ATPase) via a short C‐terminal domain. AtWNK8 is shown to autophosphorylate intermolecularly and to phosphorylate Arabidopsis subunit C (AtVHA‐C) at multiple sites as determined by MALDI‐TOF MS analysis. Furthermore, we show that AtVHA‐C and other V‐ATPase subunits are phosphorylated when V 1 ‐complexes are used as substrates for AtWNK8. Taken together, our results provide evidence that V‐ATPases are potential targets of WNK kinases and their associated signaling pathways.
Localization for Mobile Robots using Panoramic Vision, Local Features and Particle Filter
2006-01-18

Abstract — In this paper we present a vision-based approach to self-localization that uses a novel scheme to integrate featurebased matching of panoramic images with Monte Carlo localization. A specially modified version of Lowe’s SIFT algorithm is used to match features extracted from local interest points in the image, rather than using global features calculated from the whole image. Experiments conducted in a large, populated indoor environment (up to 5 persons visible) over a period of several months demonstrate the robustness of the approach, including kidnapping and occlusion of up to 90 % of the robot’s field of view. I.
Melanoma of the ear: prognostic factors and surgical strategies
2006-01-18

This is the largest series of ear melanomas reported so far. The overall survival depended only on the tumour thickness and Clark level of invasion. Local recurrence was more frequent with smaller excision margins, but this did not influence the overall survival. Smaller excision margins under 3D-histological control did not carry an increased risk of local recurrence. Our results do not permit conclusions regarding the prognostic impact of SLNB for patients with melanoma of the ear.
Omnidirectional 3D Modeling on a Mobile Robot using Graph Cuts
2006-01-18

For a mobile robot it is a natural task to build a 3D model of its environment. Such a model is not only useful for planning robot actions but also to provide a remote human surveillant a realistic visualization of the robot's state with respect to the environment. Acquiring 3D models of environments is also an important task on its own with many possible applications like creating virtual interactive walkthroughs or as basis for 3D-TV. In this paper we present our method to acquire a 3D model using a mobile robot that is equipped with a laser scanner and a panoramic camera. The method is based on calculating dense depth maps for panoramic images using pairs of panoramic images taken from different positions using stereo matching. Traditional 2D-SLAM using laser-scan-matching is used to determine the needed camera poses. To receive high-quality results we use a high-quality stereo matching algorithm – the graph cut method. We describe the necessary modifications to handle panoramic images and specialized post-processing methods.
Model-based Shape Analysis of Gas Concentration Gridmaps for Improved Gas Source Localisation
2006-01-18

This work addresses the capability to use concentration gridmaps to locate a static gas source. In previous works it was found that depending on the shape of the mapped gas distribution (corresponding to different airflow conditions) the gas source location can be sometimes approximated with high accuracy by the maximum in the concentration map while this is not possible in other cases. This paper introduces a method to distinguish both cases by analysing the shape of the obtained concentration map in terms of a model of the time-averaged gas distribution known from physics. The parameters of the model that approximates the concentration map most closely are determined by nonlinear least squares fitting using evolution strategies (ES). The best fit also provides a better estimate of the gas source position in situations where the concentration maximum estimate fails. Different methods to select the most truthful estimate are introduced in this work and a comparison regarding their accuracy is presented, based on a total of 34h of concentration mapping experiments.
Multi-level design validation in a secure embedded system
2006-01-18

We present a simulation-based methodology to support secure embedded design. The methodology is explained through a case study, the Thumbpod-2 portable embedded fingerprint authenticator. By using multi-level validation, we can observe the flow of sensitive information through the system as it takes on multiple forms, from software variables to hardware bus-signals. This allows shielding off of unwanted side-channel information leaks at the protocol, software, or hardware level. We discuss how the ThumbPod-2 design is partitioned into a side-channel-free implementation, and how a codesign environment called GEZEL is used to validate this partitioning process at each abstraction level. © 2005 IEEE.
Overlap reduction in symbolic system traversal
2006-01-18

A divide-and-conquer approach in BDD-based verification to handle larger designs is to partition BDDs exceeding a threshold size and to deal with the partitions separately. Crossover transitions to the same state cause the main problem of this methodology, because they result in overlap of the partitions and thus introduce redundant computations when dealing with the partitions. In this paper we describe an algorithm for splitting Boolean functions representing state sets of synchronous systems such that in subsequent symbolic traversal of the resulting subsets the state set overlap is reduced. We demonstrate the effectiveness of our splitting algorithm by applying it in sequential and distributed versions of a bounded property checking algorithm. Also, a dynamic extension to static overlap reduction is sketched.
A Molecular Framework for Plant Regeneration
2006-01-19

Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin—a cell-fate–instructive plant hormone—in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription factors regulate the expression and polar position of PIN auxin efflux–facilitating membrane proteins to reconstitute auxin transport in renewed root tips. Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution.
Cathemerality and Lunar Periodicity of Activity Rhythms in Owl Monkeys of the Argentinian Chaco
2006-01-19

Although most South American owl monkeys are mainly nocturnal, Aotus azarai azarai of the Argentinean Chaco regularly shows diurnal activity. In this study we examined the strong influence of moonlight on its diurnal and nocturnal activity, as well as the interaction of moonlight effects with other exogenous factors. We analyzed long-term automated activity recordings obtained with accelerometer collars from 7 owl monkeys during 2003 and 2004. Our data show marked lunar periodic and seasonal modulations of the owl monkeys’ activity pattern. On full moon days they were active throughout the whole night and displayed reduced activity during the day. With a new moon, activity decreased during the dark portion of the night, peaked during dawn and dusk and extended over the bright morning hours. Waxing and waning moons induced a significant increase in activity during the first and the second half of the night, respectively. During the cold winter months the monkeys displayed twice as much activity throughout the warmer bright part of the day than during the rest of the year. These findings indicate that A. a. azarai is mainly a dark-active species, but is still able to shift a considerable portion of activity into the bright part of the day if unfavourable lighting and/or temperature conditions prevail during the night.