julilili42/papers huggingface dataset:
Virtual archaeology
2001-11-28

Looking at the perception of archaeology within our society, and the development of new technologies, we discover that we are faced both with new challenges and new opportunities. Ideally, our own research from excavation and documentation to analysis and publication, and a popular presentation of it, could somehow be combined within one consistent workflow, using technology tailored to meet the purpose. Given the limits of resources and know-how in academic archaeology --- even at Troy --- such ideas are mostly bound to remain science-fiction. How can we archaeologists actually be enabled to meet the challenge and make the best of new opportunities a new millenium has to offer?The general aim of the project "Virtual Archaeology" is the introduction of fundamentally changed working methods in archaeology with the aid of the most modern technologies, not only in the area of primary data acquisition but also in data processing and editing for scientific purposes and for the presentation of archaeological knowledge to a broad general public.
Biosynthesis of the Lantibiotics Epidermin and Gallidermin
2001-11-29

This chapter contains sections titled: History of lantibiotics and lantibiotic research in Tübingen Primary structure and proposed maturation of epidermin in staphylococci Genetic organization and regulation of the epidermin genes Isolation and characterization of genetically engineered gallidermin and epidermin analogues Function of the epidermin immunity genes epiFEG Inactivation and characterization of the epidermin leader peptidase EpiP The flavoenzyme EpiD and formation of peptidyl-aminoenethiolates Incorporation of d-alanine into S. aureus teichoic acids confers resistance to defensins, protegrins, and other antimicrobial peptides Conclusions References
Staphylococcal Lipases: Molecular Characterization and Use as an Expression and Secretion System
2001-11-29

This chapter contains sections titled: Introduction Molecular organization of staphylococcal lipases Biochemical characterization of staphylococcal lipases Role of the pro-peptide region The use of ShyL as expression and secretion system Concluding remarks References
The Changing Path of Hopanoid Research: From Condensing Lipids to New Membrane Enzymes
2001-11-29

This chapter contains sections titled: Introduction The cyclization reaction Purification of squalene cyclases Properties of purified cyclases Cloning of squalene-hopene cyclases Properties of SHC sequences The structure of squalene-hopene cyclase Site directed mutagenesis of squalene-hopene cyclase Hopanoid biosynthesis gene clusters Miscellaneous results Outlook Acknowledgments References
Genetic and Biochemical Analysis of the Biosynthesis of the Orange Carotenoid Staphyloxanthin of Staphylococcus aureus
2001-11-29

This chapter contains sections titled: Introduction Cloning of the carotenoid biosynthetic genes from S. aureus Newman in S. carnosus and E. coli Function of CrtM and CrtN Identification of carotenoids in S. carnosus (pOC21), E. coli (pUG1), and S. aureus Newman Identification of dehydrosqualene in E. coli (pUG1) and E. coli (UG9) Squalene is very likely no substrate for CrtN, the proposed dehydrosqualene desaturase The crt operon Homology of CrtO, CrtP, and CrtQ Construction of crtM mutants of S. aureus strain Newman σB-regulated promoter of the crt operon from S. aureus strain Newman The carotenoid biosynthesis genes Function of the pigments in S. aureus strain Newman Distribution of pigment biosynthesis genes among staphylococcal species References
Genetics of Nikkomycin Production in Streptomyces tendae Tü 901
2001-11-29

This chapter contains sections titled: Introduction: nikkomycins Isolation of nikkomycin biosynthetic genes Isolation of the nikkomycin gene cluster and expression in Streptomyces lividans Organization of the nikkomycin gene cluster Roles of the nik genes Transcriptional organization and regulation of the nik cluster References
Iron Transport in Gram‐Negative and Gram‐Positive Bacteria
2001-11-29

This chapter contains sections titled: Ferric iron transport in bacteria Ferrous-iron transport systems (Feo) of E. coli Regulation of iron transport and metabolism An [2Fe-2S] protein is involved in ferrioxamine B utilization References
Regulation of the Ferric‐Citrate Transport System by a Novel Transmembrane Transcription Control
2001-11-29

This chapter contains sections titled: Introduction Transport of Fe3+ is mediated by citrate Transcription initiation by a signaling cascade from the cell surface into the cytoplasm Iron regulation of fecIR and fecABCDE transcription Acknowledgments References
Structure, Function, Import, and Immunity of Colicins
2001-11-29

This chapter contains sections titled: Introduction Colicin M inhibits murein biosynthesis and thus displays a unique activity among the colicins Colicins 5 and 10 are taken up by a novel mechanism Colicins evolved by the exchange of DNA fragments which precisely defined functional domains Pore-forming colicins are inactivated by the cognate immunity proteins shortly before the formation of the transmembrane pores Pesticin is a muramidase which is inactivated by the immunity protein in the periplasm Acknowledgments References
Regulated Transport and Signal Transfer Channels Involved in Bacterial Iron Supply
2001-11-29

This chapter contains sections titled: Introduction The Fhu proteins catalyze active transport of ferrichrome and the antibiotic albomycin across the outer membrane and the cytoplasmic membrane of E. coli Transduction of energy from the cytoplasmic membrane into the outer membrane for the activation of FhuA as a transporter and phage receptor Transport of ferrichrome across the cytoplasmic membrane Ferric-carboxylate transport system of Morganella morganii Transport of ferric iron ions by the Sfu system of Serratia marcescens Acknowledgments References
Second Messenger Systems in Paramecium
2001-11-29

This chapter contains sections titled: Introduction Identification and characterization of cGMP and cAMP second messenger signaling systems in Paramecium Biochemical properties of an adenylyl cyclase A guanylyl cyclase disguised as an adenylyl cyclase On the way to an adenylyl cyclase with an intrinsic ion conductance Downstream of second messengers In vivo screening of bacterial secondary metabolites Acknowledgments References
Introduction
2001-11-29

This chapter contains sections titled: Antibiotic research The unique features of microbial iron transport Transport of bacterial proteins Membrane components and membrane polarization Chemistry of microbial peptides and proteins Summary of short-term projects of the collaborative research center
Aminopeptidase N mediates the utilization of the GSH precursor CysGly by cultured neurons
2001-11-30

Abstract Neurons in culture rely on the supply of exogenous cysteine for their glutathione synthesis. After application of cysteine to neuron‐rich primary cultures, the glutathione content was doubled after a 4‐hr incubation. The dipeptide cysteinylglycine (CysGly) was able to substitute for cysteine as exogenous glutathione precursor. In kidneys, the ectopeptidase aminopeptidase N (ApN) has been reported to hydrolyze CysGly. Expression of mRNA of ApN in rat brain and cultured rat neurons was demonstrated by reverse transcriptase polymerase chain reaction and sequencing of the cDNA fragment obtained. In addition, the presence of ApN protein in cultured neurons was demonstrated by its immunocytochemical localization. In the presence of an activity‐inhibiting antiserum against ApN the utilization of CysGly as neuronal glutathione precursor was completely prevented, whereas that of cysteine plus glycine was not affected. The data presented demonstrates that cultured rat neurons express ApN and that this ectopeptidase participates in the utilization of CysGly as precursor for neuronal glutathione. © 2001 Wiley‐Liss, Inc.
AMP deaminase in rat brain: Localization in neurons and ependymal cells
2001-11-30

Abstract The purine nucleotide cycle enzyme AMP deaminase (AMPD) catalyzes the irreversible hydrolytic deamination of AMP. The physiological function of the purine nucleotide cycle in the brain is unknown. In situ hybridization and immunocytochemical studies were performed to identify the regional and cellular expression of AMPD in rat brain with the goal of elucidating the neural function of the purine nucleotide cycle. AMPD messenger RNA was detected in ventricular ependymal cells and cells of the choroid plexus and in neurons of distinct brain areas. Although only low antibody titers were obtained by immunization with the purified sheep brain AMPD, immunization of mice with synthetic lipopeptide vaccines containing oligopeptides derived from a known partial complementary DNA sequence of the enzyme yielded an antiserum suitable for immunocytochemistry. Immunostaining of cells in culture showed that neurons but not astroglial cells express appreciable amounts of the enzyme. Results of immunocytochemical staining performed on rat brain slices were in accord with the localization of AMPD messenger RNA, thus confirming the expression of AMPD in neurons of the brain stem, hippocampus, cerebellar nuclei and mesencephalic nuclei, as well as in ventricular ependymal cells and their cilia. © 2001 Wiley‐Liss, Inc.
Diabetes-Associated Sustained Activation of the Transcription Factor Nuclear Factor-κB
2001-12-01

Activation of the transcription factor nuclear factor-κB (NF-κB) has been suggested to participate in chronic disorders, such as diabetes and its complications. In contrast to the short and transient activation of NF-κB in vitro, we observed a long-lasting sustained activation of NF-κB in the absence of decreased IκBα in mononuclear cells from patients with type 1 diabetes. This was associated with increased transcription of NF-κBp65. A comparable increase in NF-κBp65 antigen and mRNA was also observed in vascular endothelial cells of diabetic rats. As a mechanism, we propose that binding of ligands such as advanced glycosylation end products (AGEs), members of the S100 family, or amyloid-β peptide (Aβ) to the transmembrane receptor for AGE (RAGE) results in protein synthesis–dependent sustained activation of NF-κB both in vitro and in vivo. Infusion of AGE-albumin into mice bearing a β-globin reporter transgene under control of NF-κB also resulted in prolonged expression of the reporter transgene. In vitro studies showed that RAGE-expressing cells induced sustained translocation of NF-κB (p50/p65) from the cytoplasm into the nucleus for &amp;gt;1 week. Sustained NF-κB activation by ligands of RAGE was mediated by initial degradation of IκB proteins followed by new synthesis of NF-κBp65 mRNA and protein in the presence of newly synthesized IκBα and IκBβ. These data demonstrate that ligands of RAGE can induce sustained activation of NF-κB as a result of increased levels of de novo synthesized NF-κBp65 overriding endogenous negative feedback mechanisms and thus might contribute to the persistent NF-κB activation observed in hyperglycemia and possibly other chronic diseases.
High expression of the chemokine receptor CXCR4 predicts extramedullary organ infiltration in childhood acute lymphoblastic leukaemia
2001-12-01

Childhood acute lymphoblastic leukaemia (ALL) is a malignancy with the potential to infiltrate the liver, spleen, lymph nodes and brain. Such extramedullary presentation is important for understanding the biology of childhood ALL and also for developing new prognostic parameters. A potential mechanism in the trafficking of leukaemia cells is the interaction of the chemokine receptor CXCR4, which is expressed on ALL cells, and its ligand stromal cell‐derived factor‐1 (SDF‐1), produced by stromal cells in bone marrow and extramedullary organs. Functionality of CXCR4 was demonstrated by a high correlation between cell surface density of CXCR4 and transendothelial migration of leukaemia blasts towards a gradient of SDF‐1 ( r = 0·73, P = 0·001). Inhibition of SDF‐1‐induced migration by an anti‐CXCR4 monoclonal antibody (78·33 ± 23·86% inhibition) evidenced the specificity of CXCR4 to SDF‐1. In order to evaluate clinical significance of CXCR4 expression, lymphoblasts from the bone marrow of 73 patients with and without extramedullary organ infiltration were compared. Multiparameter flow cytometry revealed that lymphoblasts from patients with high extramedullary organ infiltration, defined as ultrasonographically measured enlargement of liver or spleen, expressed the CXCR4 receptor at higher fluorescence intensity (median 66·12 ± 66·17) than patients without extramedullary organ infiltration (median 17·56 ± 19·29; P &lt; 0·001). Consequently, high expression of CXCR4 was strongly predictive for extramedullary organ involvement, independently of the peripheral lymphoblast count. Highest CXCR4 expression was seen in mature B ALL (median 102·74 ± 92·13; P &lt; 0·003), a disease characterized by a high incidence of extramedullary bulky disease. As high expression of the chemokine receptor CXCR4 predicts extramedullary organ infiltration in childhood ALL, we suggest that CXCR4 and its ligand play an essential role in extramedullary invasion.
XMM-EPIC observation of MCG-6-30-15: direct evidence for the extraction of energy from a spinning black hole?
2001-12-01

X-ray spectra of Seyfert 1 galaxies commonly show an iron Kα emission line at ∼6keV. The line is often extremely broad, with a velocity width of&amp;gt; 70000 km s −1. Furthermore, the asymmetries in the line profiles are well explained
Boron and Oxygen Isotope Composition of Certified Reference Materials NIST SRM 610/612 and Reference Materials JB‐2 and JR‐2
2001-12-01

We present data on the concentration, the isotope composition and the homogeneity of boron in NIST silicate glass reference materials SRM 610 and SRM 612, and in powders and glasses of geological reference materials JB‐2 (basalt) and JR‐2 (rhyolite). Our data are intended to serve as references for both microanalytical and wet‐chemical techniques. The δ 11 B compositions determined by N‐TIMS and P‐TIMS agree within 0.5% and compare with SIMS data within 2.5%. SIMS profiles demonstrate boron isotope homogeneity to better than δ 11 B = 2% for both NIST glasses, however a slight boron depletion was detected towards the outermost 200 μm of the rim of each sample wafer. The boron isotope compositions of SRM 610 and SRM 612 were indistinguishable. Glasses produced in this study by fusing JB‐2 and JR‐2 powder also showed good boron isotope homogeneity, both within and between different glass fragments. Their major element abundance as well as boron isotope compositions and concentrations were identical to those of the starting composition. Hence, reference materials (glasses) for the in situ measurement of boron isotopes can be produced from already well‐studied volcanic samples without significant isotope fractionation. Oxygen isotope ratios, both within and between wafers, of NIST reference glasses SRM 610 and SRM 612 are uniform. In contrast to boron, significant differences in oxygen isotope compositions were found between the two glasses, which may be due to the different amounts of trace element oxides added at ten‐fold different concentration levels to the silicate matrix.
Anti‐inflammatory antioxidants attenuate the expression of inducible nitric oxide synthase mediated by advanced glycation endproducts in murine microglia
2001-12-01

Abstract Advanced glycation endproducts (AGEs) accumulate on long‐lived protein deposits including β‐amyloid plaques in Alzheimer's disease (AD). AGE‐modified amyloid deposits contain oxidized and nitrated proteins as markers of a chronic neuroinflammatory condition and are surrounded by activated microglial and astroglial cells. We show in this study that AGEs increase nitric oxide production by induction of the inducible nitric oxide synthase (iNOS) on the mRNA and protein level in the murine microglial cell line N‐11. Membrane permeable antioxidants including oestrogen derivatives (e.g. 17β‐oestradiol) thiol antioxidants (e.g. (R+)‐α‐lipoic acid) and Gingko biloba extract EGb 761, but not phosphodiesterase inhibitors such as propentophylline, prevent the up‐regulation of AGE‐induced iNOS expression and NO production. These results indicate that oxygen free radicals serve as second messengers in AGE‐induced pro‐inflammatory signal transduction pathways. As this pharmacological mechanism is not only relevant for Alzheimer's disease, but also for many chronic inflammatory conditions, such membrane‐permeable antioxidants could be regarded not only as antioxidant, but also as potent therapeutic anti‐inflammatory drugs.
HS 0705+6700: A new eclipsing sdB binary
2001-12-01

We report the discovery of an eclipsing binary - HS 0705+6700 - being an sdB star with a faint companion. From its light curve the orbital period of 8263.87 s, the mass ratio of the system q = 0.28, the inclination of 84.4 deg and other system parameters are derived. The companion does not contribute to the optical light of the system except through a strong reflection effect. The semi-amplitude of the radial velocity curve K1 = 85.8 km/s and a mass function of f(m) = 0.00626 Msun are determined. A spectroscopic analysis of the blue spectra results in Teff = 28800K, log g = 5.40, and log n(He)/n(H) = -2.68. These characteristics are typical for sdB stars, as is its mass of 0.48 Msun. According to its mass (0.13 Msun) and radius (0.19 Rsun), the companion is an M dwarf. The primary is in a core helium burning phase of evolution, and the system must have gone through a common envelope stage when the primary was near the tip of the red giant branch.
Human Cofilin Forms Oligomers Exhibiting Actin Bundling Activity
2001-12-01

Human cofilin possesses the tendency for self-association, as indicated by the rapid formation of dimers and oligomers when reacted with water-soluble carbodiimide, Ellman's reagent, or glutathione disulfide. Intermolecular disulfide bonds involve Cys(39) and probably Cys(147) of two adjacent cofilin units. The disulfide-linked dimers and oligomers exhibit a biological activity distinct from the monomer. While monomeric cofilin decreased viscosity and light-scattering of F-actin solutions, dimers and oligomers caused an increase in viscosity and light scattering. Electron microscopy revealed that cofilin oligomers induce the formation of highly ordered actin bundles with occasionally blunt ends similar to actin-cofilin rods observed in cells under oxidative stress. Bundling activity of the disulfide-linked oligomers could be completely reversed into severing activity by dithiothreitol. Formation of cofilin oligomers occurred also in the presence of actin at pH 8, but not at pH 6.6, and was significantly enhanced in the presence of phosphatidylinositol 4,5-bisphosphate. Our data are consistent with the idea that cofilin exists in two forms in vivo also: as monomers exhibiting the known severing activity and as oligomers exhibiting actin bundling activity. However, stabilization of cofilin oligomers in cytoplasm is probably achieved not by disulfide bonds but by a local increase in cofilin concentration and/or binding of regulatory proteins.
Coronary Arteries: Retrospectively ECG-gated Multi–Detector Row CT Angiography with Selective Optimization of the Image Reconstruction Window
2001-12-01

The image reconstruction window for CT angiography of the coronary arteries should be adapted to each coronary artery. The use of one fixed time point in the cardiac cycle for image reconstruction does not provide optimal image quality.
Wild-type, mitochondrial and ER-restricted Bcl-2 inhibit DNA damage-induced apoptosis but do not affect death receptor-induced apoptosis
2001-12-01

The proto-oncogene Bcl-2 is expressed in membranes of mitochondria and endoplasmic reticulum and mediates resistance against a broad range of apoptotic stimuli. Although several mechanisms of Bcl-2 action have been proposed, its role in different cellular organelles remains elusive. Here, we analyzed the function of Bcl-2 targeted specifically to certain subcellular compartments in Jurkat cells. Bcl-2 expression was restricted to the outer mitochondrial membrane by replacing its membrane anchor with the mitochondrial insertion sequence of ActA (Bcl-2/MT) or the ER-specific sequence of cytochrome b5 (Bcl-2/ER). Additionally, cells expressing wild-type Bcl-2 (Bcl-2/WT) or a transmembrane domain-lacking mutant (Bcl-2/ΔTM) were employed. Apoptosis induced by ionizing radiation or by the death receptors for CD95L or TRAIL was analyzed by determination of the mitochondrial membrane potential (ΔΨm) and activation of different caspases. Bcl-2/WT and Bcl-2/MT strongly inhibited radiation-induced apoptosis and caspase activation, whereas Bcl-2/ΔTM had completely lost its anti-apoptotic effect. Interestingly, Bcl-2/ER conferred protection against radiation-induced mitochondrial damage and apoptosis similarly to Bcl-2/MT. The finding that ER-targeted Bcl-2 interfered with mitochondrial ΔΨm breakdown and caspase-9 activation indicates the presence of a crosstalk between both organelles in radiation-induced apoptosis. By contrast, Bcl-2 in either subcellular position did not influence CD95- or TRAIL-mediated apoptosis.
Cathepsin S and an asparagine-specific endoprotease dominate the proteolytic processing of human myelin basic proteinin vitro
2001-12-01

The biochemical characterization of antigen degradation is an important basis for a better understanding of both the immune response and autoimmune diseases mediated by MHC class II molecules. In this study we used high-performance liquid chromatography and mass spectrometry to analyze the processing of myelin basic protein (MBP), a potential autoantigen implicated in the pathogenesis of multiple sclerosis. We resolved the kinetics of MBP processing by lysosomal extracts or purified endocytic proteases, identified the major cleavage sites during this process and assigned them to the activity of proteolytic enzymes. Proteolytic processing of MBP is mostly guided along the hydrophobic regions of the protein. It is initiated by two proteolytic steps (after N(92) and S(110)) that are performed by an asparagine-specific endopeptidase (AEP) and by cathepsin (Cat) S, respectively. The resulting processing intermediates are converted into more than 60 different species of 20-40-mers due to the activity of endopeptidases including CatS, D and L. The fragments thus generated are subsequently degraded by C- or N-terminal trimming. Strikingly, the initial cleavages during MBP processing affect two immunodominant regions of the potential autoantigen [MBP(85-99) and MBP(111-129)] in an inverse manner. CatS directly generates the N terminus of the epitope MBP(111-129) in large quantities during the initial phase of processing, which might explain the immunogenicity of this region in spite of its relatively poor binding to HLA-DR4. In contrast, the dominant cleavage by AEP mediates the destruction of MBP(85-99) unless the epitope is protected, e.g. by binding to HLA-DR. Our results thus characterize the proteolytic events during processing of MBP on a molecular level and suggest a biochemical basis for the immunogenicity of the immunodominant epitopes, which could serve as a guideline for future therapeutic strategies.