julilili42/papers huggingface dataset:
Functional Analysis of Biosynthetic Genes of Aminocoumarins and Production of Hybrid Antibiotics
2004-12-01

The aminocoumarin antibiotics novobiocin, clorobiocin and coumermycin A1 are potent inhibitors of DNA gyrase. They compete with ATP for binding to the B subunit of this enzyme and inhibit the ATP-dependent DNA supercoiling catalysed by gyrase. Cloning, sequencing and analysis of the biosynthetic gene clusters for novobiocin, clorobiocin and coumermycin A1 revealed that the structural differences and similarities of these antibiotics are perfectly reflected by the genetic organisation of the clusters. In the last four years, the function of most of the biosynthetic genes for these antibiotics could be identified by gene inactivation experiments as well as by heterologous expression in Escherichia coli or Streptomyces lividans as His6-tag or GST-tag fusion proteins. Using the information from the biosynthetic gene clusters, more than 50 new aminocoumarin derivatives have been produced by combinatorial biosynthesis, by mutasynthesis experiments or by chemoenzymatic synthesis. The biological activities of the new aminocoumarines were evaluated against E. coli gyrase and various bacterial strains. The results showed that the acyl moieties at 3-OH as well as the methyl group at 4-OH of noviose are essential for the biological activity; the methyl group and the chlorine atom at 8-position of the coumarin ring also play an important role. Aminocoumarins with a pyrrole moiety at 2-OH instead of 3-OH showed reduced biological activity. Ring A of novobiocin and clorobiocin is also involved in the interaction with gyrase. Keywords: aminocoumarin, biosynthetic genes, chemoenzymatic synthesis, gene inactivation, gyrase inhibitor, heterologous expression, hybrid antibiotic, mutasynthesis experiments, streptomyces
Effect of Two Amino Acids in TM17 of Sulfonylurea Receptor SUR1 on the Binding of ATP-Sensitive K+ Channel Modulators
2004-12-01

The sulfonylurea receptor (SUR) is the important regulatory subunit of ATP-sensitive K+ channels. It is an ATP-binding cassette protein comprising 17 transmembrane helices. SUR is endowed with binding sites for channel blockers like the antidiabetic sulfonylurea glibenclamide and for the chemically very heterogeneous channel openers. SUR1, the typical pancreatic SUR isoform, shows much higher affinity for glibenclamide but considerably lower affinity for most openers than SUR2. In radioligand binding assays, we investigated the role of two amino acids, T1285 and M1289, located in transmembrane helix (TM)-17, in opener binding to SUR1. These amino acids were exchanged for the corresponding amino acids of SUR2. In competition experiments using [3H]glibenclamide as radioligand, SUR1(T1285L, M1289T) showed much higher affinity toward the cyanoguanidine openers pinacidil and P1075 than SUR1 wild type. The affinity for the thioformamide aprikalim was also markedly increased. In contrast, the affinity for the benzopyrans rilmakalim and levcromakalim was unaffected; however, the amount of displaced [3H]glibenclamide binding was nearly doubled. The binding properties of the opener diazoxide and the blocker glibenclamide were unchanged. In conclusion, mutation of two amino acids in TM17 of SUR1, especially of M1289, leads to class-specific effects on opener binding by increasing opener affinity or by changing allosteric coupling between opener and glibenclamide binding.
Retinol has specific effects on binding of thyrotrophin to cultured porcine thyrocytes
2004-12-01

Retinoids are potential candidates for the treatment of thyroid cancer. However, one of the disadvantages of these substances is their dedifferentiating effect on normal non-transformed thyrocytes. To identify conditions under which no dedifferentiating effect of retinol on normal thyrocytes can be observed, we determined iodide uptake, protein iodination, expression of sodium–iodide symporter (NIS) mRNA and protein, and the binding of iodine-125-labelled bTSH in cultured porcine thyrocytes. Combination of TSH and ≤6.5 μM retinol increased iodide uptake and protein iodination compared with TSH alone over the entire incubation time, whereas TSH plus ≥13 μM retinol increased the uptake of iodine-125 only during the first 12 h but decreased it after 30 h and longer. After ≥30 h incubation times with ≥13 μM retinol, the fraction of apoptotic cells was enhanced and proliferation decreased. The incubation with retinol enhanced the binding of [ 125 I]bTSH to thyrocytes, but did not influence expression of the NIS. With low retinol concentrations, the effect on the binding of TSH apparently predominated and retinol increased thyroid function; with higher concentrations the pro-apoptotic effect of retinol overlapped and a two-phased time course resulted. It can be concluded that low concentrations of retinol also exert differentiating effects in normal thyrocytes.
The Randomized Sample Tree: A Data Structure for Interactive Walk-Throughs in Externally Stored Virtual Environments
2004-12-01

We present a new data structure for rendering highly complex virtual environments of arbitrary topology. The special feature of our approach is that it allows an interactive navigation in very large scenes (30 GB/400 million polygons in our benchmark scenes) that cannot be stored in main memory, but only on a local or remote hard disk. Furthermore, it allows interactive rendering of substantially more complex scenes by instantiating objects. The sampling process is done in the preprocessing. There, the polygons are randomly distributed in our hierarchical data structure, the randomized sample tree. This tree uses only space that is linear in the number of polygons. In order to produce an approximate image of the scene, the tree is traversed and polygons stored in the visited nodes are rendered. During the interactive walk-through, parts of the sample tree are loaded from a local or remote hard disk. We implement our algorithm in a prototypical walk-through system. Analysis and experiments show that the quality of our images is comparable to images computed by the conventional z-buffer algorithm regardless of the scene topology.
The World of the Living and the World of the Dead
2004-12-01

Abstract Archaeologists discovered Syria's first untouched royal tomb during excavations of the palace complex of Qatna. The burial chambers allow new insights into the ancestral cult and burial practices of the ancient Near East
Characterization of some chemically modified acidic alumina T samples for TLC
2004-12-01

Chemically modified acidic alumina T stationary phases have been prepared by organosilylation with the trifunctional organosilicon compounds n -octadecyltrichlorosilane, 3-mercaptopropyltri-methoxysilane, and N -(2-aminoethyl)-3-aminopropyltrimethoxysilane. These chemically modified phases were characterized by elemental analysis, measurement of specific surface area, FTIR spectroscopy, 13 C CP/MAS NMR spectroscopy, mass spectrometry, and thermal analysis. The TLC behavior of unmodified and chemically modified acidic alumina T has been tested by separation and identification of some dyes and benzo[ a ]pyrene derivatives.
The Cytosolic Domains of Ca2+-sensitive Adenylyl Cyclases Dictate Their Targeting to Plasma Membrane Lipid Rafts
2004-12-02

Lipid rafts are specialized, cholesterol-rich domains of the plasma membrane that are enriched in certain signaling proteins, including Ca(2+)-sensitive adenylyl cyclases. This restrictive localization plays a key role in the regulation of the Ca(2+)-stimulable AC8 and the Ca(2+)-inhibitable AC6 by capacitative calcium entry. Interestingly, AC7, a Ca(2+)-insensitive AC, is found in the plasma membrane but is excluded from lipid rafts (Smith, K. E., Gu, C., Fagan, K. A., Hu, B., and Cooper, D. M. F. (2002) J. Biol. Chem. 277, 6025-6031). The mechanisms governing the specific membrane targeting of adenylyl cyclase isoforms remain unknown. To address this issue, a series of chimeras were produced between the raft-targeted AC5 and the non-raft-targeted AC7, involving switching of their major domains. The AC5-AC7 chimeras were expressed in HEK 293 cells and lipid rafts were isolated from the bulk plasma membrane by either detergent-based or non-detergent-based fractionation methods. Additionally, confocal imaging was used to investigate the precise cellular targeting of the chimeras. Surprisingly, the two tandem six-transmembrane domains of AC5 were not required for localization to lipid rafts. Rather, AC5 localization depended on the complete cytoplasmic loops (C1 and C2); constructs with mixed domains were either retained in the endoplasmic reticulum or degraded. Similar conclusions are drawn for the lipid raft localization of the Ca(2+)/calmodulin-stimulable AC8; again, the C1 and C2 domains are critical. Thus, protein-protein interactions may be more important than protein-lipid interactions in targeting these calcium-sensitive enzymes to lipid rafts.
Anionic Phosphane − A New Ligand with a Phosphane and a Weakly Coordinating Heteroborate Moiety
2004-12-02

Abstract Reaction of chloropropyl‐substituted stanna‐ closo ‐dodecaborate [Cl(CH 2 ) 3 SnB 11 H 11 ] − with the nucleophile Li[CH 2 PPh 2 ] provided a straightforward synthesis of an anionic phosphane [Ph 2 PCH 2 SnB 11 H 11 ] − . Derivatization of the phosphane was carried out in reaction with sulfur and hydrochloric acid to give [Bu 3 MeN][Ph 2 P(S)CH 2 SnB 11 H 11 ] and the zwitterion [Ph 2 P(H)CH 2 SnB 11 H 11 ]. In reaction with various transition metal electrophiles, complexation reactions were accomplished resulting in the isolation of trans ‐substituted palladium and platinum complexes [Bu 3 MeN] 2 [ trans ‐(Ph 2 PCH 2 SnB 11 H 11 ) 2 MCl 2 ] (M = Pd, Pt), a neutral silver adduct [(acetone)Ag(Ph 2 PCH 2 SnB 11 H 11 )], and a linearly coordinated bisphosphane of gold [Bu 3 MeN][Au(Ph 2 PCH 2 SnB 11 H 11 ) 2 ]. The solid state structures of the ligand salt, the palladium and gold coordination compounds were determined and discussed. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Toll‐like receptor 6‐independent signaling by diacylated lipopeptides
2004-12-03

Abstract Bacterial lipopeptides are strong immune modulators that activate early host responses after infection as well as initiating adjuvant effects on the adaptive immune system. These lipopeptides induce signaling in cells of the immune system through Toll‐like receptor 2 (TLR2)–TLR1 or TLR2–TLR6 heteromers. So far it has been thought that triacylated lipopeptides, such as the synthetic N‐palmitoyl‐S‐[2,3‐bis(palmitoyloxy)‐(2 RS )‐propyl]‐( R )‐cysteine (Pam3)‐CSK4, signal through TLR2–TLR1 heteromers, whereas diacylated lipopeptides, like the macrophage‐activating lipopeptide from Mycoplasma fermentans (MALP2) or S‐[2,3‐bis(palmitoyloxy)‐(2 RS )‐propyl]‐( R )‐cysteine (Pam2)‐CGNNDESNISFKEK, induce signaling through TLR2–TLR6 heteromers. Using new synthetic lipopeptide derivatives we addressed the contribution of the lipid and, in particular, the peptide moieties with respect to TLR2 heteromer usage. In contrast to the current model of receptor usage, not only triacylated lipopeptides, but also diacylated lipopeptides like Pam2CSK4 and the elongated MALP2 analog Pam2CGNNDESNISFKEK‐SK4 (MALP2‐SK4) induced B lymphocyte proliferation and TNF‐α secretion in macrophages in a TLR6‐independent manner as determined with cells from TLR6‐deficient mice. Our results indicate that both the lipid and the N‐terminal peptides of lipoproteins contribute to the specificity of recognition by TLR2 heteromers and are responsible for the ligand–receptor interaction on host cells.
Exploitation of KESTREL to identify NDRG family members as physiological substrates for SGK1 and GSK3
2004-12-07

We detected a protein in rabbit skeletal muscle extracts that was phosphorylated rapidly by SGK1 (serum- and glucocorticoid-induced kinase 1), but not by protein kinase Bα, and identified it as NDRG2 (N-myc downstream-regulated gene 2). SGK1 phosphorylated NDRG2 at Thr330, Ser332 and Thr348in vitro. All three residues were phosphorylated in skeletal muscle from wild-type mice, but not from mice that do not express SGK1. SGK1 also phosphorylated the related NDRG1 isoform at Thr328, Ser330 and Thr346 (equivalent to Thr330, Ser332 and Thr348 of NDRG2), as well as Thr356 and Thr366. Residues Thr346, Thr356 and Thr366 are located within identical decapeptide sequences GTRSRSHTSE, repeated three times in NDRG1. These threonines were phosphorylated in NDRG1 in the liver, lung, spleen and skeletal muscle of wild-type mice, but not in SGK1−/− mice. Knock-down of SGK1 in HeLa cells using small interfering RNA also suppressed phosphorylation of the threonine residues in the repeat region of NDRG1. The phosphorylation of NDRG1 by SGK1 transformed it into an excellent substrate for GSK3 (glycogen synthase kinase 3), which could then phosphorylate Ser342, Ser352 and Ser362 in the repeat region. Incubation of HeLa cells with the specific GSK3 inhibitor CT 99021 increased the electrophoretic mobility of NDRG1 in HeLa cells, demonstrating that this protein is phosphorylated by GSK3 in cells. Our results identify NDRG1 and NDRG2 as physiological substrates for SGK1, and demonstrate that phosphorylation of NDRG1 by SGK1 primes it for phosphorylation by GSK3.
Shadow on the Wall Cast by an Abrikosov Vortex
2004-12-07

At the surface of a d-wave superconductor, a zero-energy peak in the quasiparticle spectrum can be observed. This peak appears due to Andreev bound states and is maximal if the nodal direction of the d-wave pairing potential is perpendicular to the boundary. We examine the effect of a single Abrikosov vortex in front of a reflecting boundary on the zero-energy density of states. We can clearly see a splitting of the low-energy peak and therefore a suppression of the zero-energy density of states in a shadowlike region extending from the vortex to the boundary. This effect is stable for different models of the single Abrikosov vortex, for different mean free paths and also for different distances between the vortex center and the boundary. This observation promises to have also a substantial influence on the differential conductance and the tunneling characteristics for low excitation energies.
RNA Transfection of Dendritic Cells
2004-12-07

Dendritic cells (DC) are the most powerful antigen-presenting cells that induce and maintain primary immune responses in vitro and in vivo. The development of protocols for the ex vivo generation of DC provided a rationale to design and develop DC-based vaccination studies for the treatment of infectious and malignant diseases. The efficacy of antigen loading and delivery into DC is pivotal for the optimal induction of T-cell-mediated immune responses. Recently it was shown that DC transfected with RNA coding for a tumor-associated antigen (TAA) or whole-tumor RNA are able to induce potent antigen- and tumor-specific T-cell responses directed against multiple epitopes. The latter technique does not require the definition of the TAA or HLA haplotype of the patients and has the potential of broad clinical application. Such a polyvalent vaccine might be able to reduce the probability of clonal tumor escape and to elicit CTL responses directed against naturally processed and presented immuno-dominant tumor antigens. Additional targeting of HLA class II restricted epitopes may further amplify and prolong the induced T-cell responses.
Dendritic Cells in Clinical Trials for Multiple Myeloma
2004-12-07

Due to the existence of the truly specific tumor antigen idiotype in multiple myeloma and based on encouraging data from dendritic cell vaccinated B-cell non-Hodgkin's lymphoma (NHL) patients, dendritic cell-based vaccination was first initiated in myeloma patients in 1995. This overview will summarize published and ongoing clinical trials in patients with multiple myeloma who are treated with idiotype-based dendritic cell (Id/DC) vaccination. All groups of investigators have found that Id/DC vaccination of multiple-myeloma patients is feasible and that myeloma-specific immunity can be induced in heavily pretreated individuals. In future trials, new dendritic cell-based immunization strategies will be investigated based on techniques like RNA transfection of DC.
Atomic Interferometer with Amplitude Gratings of Light and Its Applications to Atom Based Tests of the Equivalence Principle
2004-12-08

We have developed a matter wave interferometer based on the diffraction of atoms from effective absorption gratings of light. In a setup with cold rubidium atoms in an atomic fountain the interferometer has been used to carry out tests of the equivalence principle on an atomic basis. The gravitational acceleration of the two isotopes 85Rb and 87Rb was compared, yielding a difference Deltag/g=(1.2+/-1.7)x10(-7). We also perform a differential free fall measurement of atoms in two different hyperfine states, and obtained a result of Deltag/g=(0.4+/-1.2)x10(-7).
Fetal and neonatal murine skin harbors Langerhans cell precursors
2004-12-08

Abstract Resident epidermal Langerhans cells (LC) in adult mice express ADPase, major histocompatibility complex (MHC) class II, and CD205 and CD207 molecules, while the first dendritic leukocytes that colonize the fetal and newborn epidermis are only ADPase+. In this study, we tested whether dendritic epidermal leukocytes (DEL) are end-stage cells or represent LC precursors. In epidermal sheets of fetal and neonatal mice, we found no apoptotic leukocytes, suggesting that these cells do not die in situ. To address whether DEL can give rise to LC, sorted DEL from murine newborn skin were cultured with cytokines used to generate LC from human CD34+ precursors. After 7–14 days, DEL proliferated and acquired the morphology and phenotype of cells reminiscent of LC. In concordance with this finding, we show that neonatal epidermis harbors 10–20 times the number of cycling MHC class II+ leukocytes as adult tissue. To test whether LC can differentiate from skin precursors in vivo, we developed a transplantation model. As it was impossible to transplant fetal epidermis, whole fetal skin was grafted onto adult severe combined immunodeficient mice. As opposed to the uniform absence of donor LC at the time of transplantation, examination of the epidermis from the grafts after 2–4 weeks revealed MHC class II+ donor cells, which had acquired CD205 and CD207, thus qualifying them as LC. Finally, we present evidence that endogenous LC persist in skin grafts for the observation period of 45 days. These studies show that hematopoietic precursors seed the skin during embryonic life and can give rise to LC.
Why are pathogenic staphylococci so lysozyme resistant? The peptidoglycan O‐acetyltransferase OatA is the major determinant for lysozyme resistance of Staphylococcus aureus
2004-12-09

Summary Staphylococcus species belong to one of the few bacterial genera that are completely lysozyme resistant, which greatly contributes to their persistence and success in colonizing the skin and mucosal areas of humans and animals. In an attempt to discover the cause of lysozyme resistance, we identified a gene, oatA , in Staphylococcus aureus . The corresponding oatA deletion mutant had an increased sensitivity to lysozyme. HPLC and electrospray ionization tandem mass spectrometry analyses of the cell wall revealed that the muramic acid of peptidoglycan of the wild‐type strain was O‐acetylated at C6‐OH, whereas the muramic acid of the oatA mutant lacked this modification. The complemented oatA mutant was lysozyme resistant. We identified the first bacterial peptidoglycan‐specific O ‐acetyltransferase in S. aureus and showed that OatA, an integral membrane protein, is the molecular basis for the high lysozyme resistance in staphylococci.
The intercellular biotrophic leaf pathogen Cymadothea trifolii locally degrades pectins, but not cellulose or xyloglucan in cell walls of Trifolium repens
2004-12-09

The intercellular ascomycetous pathogen Cymadothea trifolii, causing sooty blotch of clover, proliferates within leaves of Trifolium spp. and produces a complex structure called interaction apparatus (IA) in its own hyphae. Opposite the IA the plant plasmalemma invaginates to form a bubble. Both structures are connected by a tube with an electron-dense sheath. Using immunocytochemistry on high-pressure frozen and freeze-substituted samples, we examined several plant and fungal cell wall components, including those in new host wall appositions at the interaction site, as well as a fungal polygalacturonase. Within the tube linking IA and host bubble, labelling was obtained for cellulose and xyloglucan but not for rhamnogalacturonan-I and homogalacturonans. The IA labelled for chitin and beta-1,3-glucans, and for a fungal polygalacturonase. Plant wall appositions reacted with antibodies against callose, xyloglucans and rhamnogalacturonan-I. Cymadothea trifolii partly degrades the host cell wall. Structural elements remain intact, but the pectin matrix is dissolved. A fungal polygalacturonase detected in the IA is probably a key factor in this process. Owing to the presence of chitin and beta-1,3-glucans, the IA itself is considered an apoplastic compartment.
Microscopic analysis of low-frequency flux noise in YBa2Cu3O7 direct current superconducting quantum interference devices
2004-12-09

We use low-temperature scanning electron microscopy combined with superconducting quantum interference device (SQUID) detection of magnetic flux to image vortices and to investigate low-frequency flux noise in YBa2Cu3O7 thin film SQUIDs. The low-frequency flux noise shows a nonlinear increase with magnetic cooling field up to 60μT. This effect is explained by the surface potential barrier at the SQUID hole. By correlating flux noise data with the spatial distribution of vortices, we obtain information on spatial fluctuations of vortices on a microscopic scale, e.g., an average vortex hopping length of ∼10nm.
Reliability and Validity of the Form 90 Interview
2004-12-10

&lt;i&gt;Objective:&lt;/i&gt; Alcohol consumption is a central variable in substance abuse research and treatment. The study reports the psychometric characteristics of the German version of the Form 90 interview for the assessment of recent alcohol consumption. &lt;i&gt;Method:&lt;/i&gt; Reliability was evaluated in a test-retest study (7 days) with 30 consecutively admitted psychiatric inpatients with alcohol dependence. Validity of Form 90 was assessed with a second sample of 60 alcohol-dependent inpatients. &lt;i&gt;Results:&lt;/i&gt; Form 90 demonstrated good to excellent retest reliability for the central variables of alcohol consumption. Retest reliability Pearson correlation coefficients (r) ranged from 0.76 to 0.99 and Intraclass Correlation Coefficients (ICC) ranged from 0.74 to 0.98. Reliability coefficients proved to be stable throughout the whole assessment window (90 days). Confidence intervals demonstrated sufficient precision of measures of alcohol consumption. Validity was supported by significant correlations of the amount of alcohol consumed with outcome parameters of the Lifetime Drinking History Interview (r = 0.47 and 0.58), γ-glutamyltransferase on admission to detoxification treatment (r = 0.37), physical withdrawal symptoms (r = 0.56) and the withdrawal symptom index (r = 0.48). &lt;i&gt;Conclusions:&lt;/i&gt; Form 90 presented evidence of good to excellent psychometric properties, and its applicability to clinical populations of alcohol-dependent patients in German-speaking countries could be confirmed.