julilili42/papers huggingface dataset:
Kinetics of ptaquiloside hydrolysis in aqueous solution
2006-09-14

Abstract Ptaquiloside (PTA) is a well-known toxin produced by the bracken fern (Pteridium aquilinum (L.) Kuhn). It is proposed that PTA from bracken stands can leach through soil and sediments into drinking-water reservoirs, thus representing a concern for human health. To predict the persistence of the toxin, a full understanding of the PTA degradation in aqueous environments is important. The kinetics of PTA hydrolysis was examined at 22°C in aqueous buffered solutions (pH 2.88–8.93). The reaction was found to follow first-order kinetics with respect to PTA at all pH and temperature conditions. At pH lower than 4.43 (±0.32), the reaction is acid-mediated, whereas the reaction is base-mediated at pH higher than 6.39 (±0.28). The rate constants for the acidcatalyzed, base-catalyzed, and neutral hydrolysis are 25.70 (±0.96), 4.83 (±0.03) × 104, and 9.49 (±6.02) × 10−4 h−1, respectively. The PTA hydrolysis at pH 4.46 is strongly dependent on temperature, with an activation energy of 74.4 (±2.6) kJ mol−1. Stoichiometric calculations, reaction kinetics, and ultraviolet-visible spectrophotometry strongly indicates the formation of an intermediary compound at pH 5.07 and 6.07 via a mechanism comprising two first-order consecutive reactions. Ptaquiloside has the lowest rate of hydrolysis at slightly acidic pH and low temperatures. Therefore, because PTA is not sorbed in soil, slightly acidic sandy soils in cold climates are most prone to PTA leaching to deeper soil layers and aquifers.
Near‐field imaging and spectroscopy of electronic states in single‐walled carbon nanotubes
2006-09-14

Abstract Near‐field photoluminescence spectroscopy was used to study the electronic properties of semiconducting Single‐Walled Carbon Nanotubes in different environments. A sharp laser‐illuminated metal tip was raster scanned over the sample and served as a strongly confined excitation source. We observed localization of photoluminescence and variations of emission energies along nanotubes on a length scale of about 30 nm. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Electron Microscopy of Biomolecules
2006-09-14

Electron microscopy (EM) is a method appropriate for examining details of the sizes and shapes of biological macromolecules and is particularly useful in studying isolated or reconstituted macromolecular assemblies. Small amounts of material (often < 1 μg) can be used and prepared in a state suitable for viewing in as short a time as several minutes. The basic procedure involves adsorption of the biomolecules onto a support film, followed by staining or shadowing of the preparation and viewing of the dehydrated molecules in vacuo in an electron beam. A resolution of 1 to 2 nm is routine with conventional microscopes. The basic procedure can be adapted to give information about sites of specific epitopes, location of newly synthesized components, internal structures, and atomic composition. Structures most suitable for EM analysis are nucleoprotein complexes, including ribosomes, spliceosomes, nucleosomes, and virus particles. DNA and RNA molecules are also suitable, and their lengths can be directly related to the number of base pairs or nucleotide residues determined biochemically. In general, it is difficult to visualize small proteins (<50 000 Da), but good detail can be obtained if they are isolated as multimeric complexes or if they can be induced to form filaments or crystalline arrays. A wide range of applications are available using EM techniques, including virus identification, mapping of hybridized regions in heteroduplexes, detailing of macromolecular interaction, and analysis of the organization of molecular components in replication, transcription, splicing, and translation complexes.
Reproduction of Plants
2006-09-14

Plant reproduction involves both asexual propagation (with various types of vegetative reproduction) and sexual reproduction. Alternation of haploid and diploid phases is typical for sexual reproduction. Processes leading to the formation of haploid male and female gamete and their subsequent fusion restoring the diploid state are parts of one plant life cycle. Various types of apomixis represent modified forms of asexual reproduction by which seeds are produced without fertilization.
Oligonucleotides
2006-09-14

Oligonucleotides are important tools in biochemistry and in molecular and cellular biology. Moreover, oligonucleotides such as antisense oligonucleotides or small interfering RNAs hold promise as therapeutic agents to combat human disease. The main prerequisite for the wide use of oligonucleotides was the development of efficient and robust synthesis protocols, which allow for the production of oligonucleotides at a wide range of synthesis scales with very affordable costs. Furthermore, the chemical synthesis permits the site-specific introduction of chemical modifications such as phosphate, sugar or base derivatives, which affect the chemical and biological properties of oligonucleotides. Oligonucleotides are used in molecular biology for sequence detection and determination as well as in cell biology and molecular medicine for functional genomics, target validation, and drug development. This review describes recent advancements of oligonucleotide synthesis and discusses several common applications of oligonucleotides.
IL-12 Instructs Skin Homing of Human Th2 Cells
2006-09-15

Abstract Distinct pattern of homing receptors determines the tissue preference for T cells to exert their effector functions. This homing competence is mostly determined early during T cell activation of naive T cells. In contrast, mechanisms governing the acquisition of particular homing receptors by T cells of the memory phenotype remain enigmatic. Th2 cell-mediated allergic diseases tend to flare during infections despite that these infections prime APCs to produce the prototypic Th1 cell-differentiating cytokine IL-12. In this study, we investigate the effect of IL-12 on the regulation of cutaneous lymphocyte Ag (CLA) on differentiated Th2 cells and consequences of this expression for allergic inflammation. Upon activation with IL-12, CLA− Th2 cells rapidly up-regulated IL-12Rβ2 chain, α(1-3)-fucosyltransferase VII, and CLA molecules. IL-12-mediated CLA expression on Th2 cells was functional because it mediated rolling of these Th2 cells on E-selectin in vitro and migration into human skin grafts in SCID mice. CLA induction occurred immediately after exposure to IL-12 and was independent of IFN-γ expression. In accordance, the transcription factor mediating IFN-γ expression, T-bet, does not directly affect CLA expression. However, CLA expression was further enhanced after IL-12 treatment of T-bet+-transfected Th2 cells in agreement with an increased IL-12 responsiveness of these cells caused by T-bet. The finding that IL-12 conferred skin-homing potential to already differentiated Th2 cells before inducing a switch in their cytokine production profile may explain the observed exacerbation of allergic skin diseases following bacterial infections.
Trifluoromethanesulfonic Acid
2006-09-15

[1493-13-6] CHF3O3S (MW 150.09) InChI = 1S/CHF3O3S/c2-1(3,4)8(5,6)7/h(H,5,6,7) InChIKey = ITMCEJHCFYSIIV-UHFFFAOYSA-N (one of the strongest organic acids; catalyst for oligomerization/polymerization of alkenes and ethers; precursor for triflic anhydride and several metal triflates; acid catalyst in various reactions) Alternate Name: triflic acid. Physical Data: bp 162 °C/760 mmHg, 84 °C/43 mmHg, 54 °C/8 mmHg; d 1.696 g cm−3. Solubility: sol water and in many polar organic solvents such as DMF, sulfolane, DMSO, dimethyl sulfone, acetonitrile; sol alcohols, ketones, ethers, and esters, but these generally are not suitable inert solvents (see below). Analysis of Reagent Purity: IR;2 19F NMR.4 Preparative Methods: best prepared by basic hydrolysis of CF3SO2F followed by acidification.2 Purification: distilled with a small amount of Tf2O.6 Handling, Storage, and Precautions: is a stable, hygroscopic liquid which fumes copiously on exposure to moist air. Transfer under dry nitrogen is recommended. Contact with cork, rubber, and plasticized materials will cause rapid discoloration of the acid and deterioration of the materials. Samples are best stored in sealed glass ampules or glass bottles with Kel-FTM or PTFE plastic screw cap linings. Use in a fume hood.
Phase II Trial of Lomustine Plus Temozolomide Chemotherapy in Addition to Radiotherapy in Newly Diagnosed Glioblastoma: UKT-03
2006-09-18

Purpose To evaluate toxicity and efficacy of the combination of lomustine, temozolomide (TMZ) and involved-field radiotherapy in patients with newly diagnosed glioblastoma (GBM). Patients and Methods Thirty-one adult patients (median Karnofsky performance score 90; median age, 51 years) accrued in two centers received involved-field radiotherapy (60 Gy in 2-Gy fractions) and chemotherapy with lomustine 100 mg/m 2 (day 1) and TMZ 100 mg/m 2 /d (days 2 to 6) with individual dose adjustments according to hematologic toxicity. Results A median of five courses (range, one to six courses) were delivered. WHO grade 4 hematotoxicity was observed in five patients (16%) and one of these patients died as a result of septicemia. Nonhematologic toxicity included one patient with WHO grade 4 drug-induced hepatitis (leading to discontinuation of lomustine and TMZ) and one patient with WHO grade 2 lung fibrosis (leading to discontinuation of lomustine). The progression-free survival (PFS) rate at 6 months was 61.3%. The median PFS was 9 months (95% CI, 5.3 to 11.7 months), the median overall survival time (MST) was 22.6 months (95% CI, 12.5 to not assessable), the 2-year survival rate was 44.7%. O 6 -Methylguanine–DNA methyltransferase (MGMT) gene-promoter methylation in the tumor tissue was associated with longer PFS (P = .014, log-rank test) and MST (P = .037). Conclusion The combination of lomustine, TMZ, and radiotherapy had acceptable toxicity and yielded promising survival data in patients with newly diagnosed GBM. MGMT gene-promoter methylation was a strong predictor of survival.
High quality ferromagnetic 0 and π Josephson tunnel junctions
2006-09-18

The authors fabricated high quality Nb∕Al2O3∕Ni0.6Cu0.4∕Nb superconductor-insulatorferromagnet-superconductor Josephson tunnel junctions. Depending on the thickness of the ferromagnetic Ni0.6Cu0.4 layer and on the ambient temperature, the junctions were in the 0 or π ground state. All junctions have homogeneous interfaces showing almost perfect Fraunhofer patterns. The Al2O3 tunnel barrier allows one to achieve rather low damping, which is desired for many experiments especially in the quantum domain. The McCumber parameter βc increases exponentially with decreasing temperature and reaches βc≈700 at T=2.11K. The critical current density in the π state was up to 5A∕cm2 at T=2.11K, resulting in a Josephson penetration depth λJ as low as 160μm. Experimentally determined junction parameters are well described by theory taking into account spin-flip scattering in the Ni0.6Cu0.4 layer and different transparencies of the interfaces.
C/EBPbeta is over‐expressed in gastric carcinogenesis and is associated with COX‐2 expression
2006-09-18

Abstract The CCAAT/enhancer‐binding protein beta (C/EBPbeta) transcription factor has been associated with several cancer models. In this study, the expression of C/EBPbeta was analysed in a series of 90 gastric carcinomas (GCs). We also assessed the effect of C/EBPbeta on COX‐2 expression. In normal gastric mucosa, C/EBPbeta expression was restricted to cells in the proliferative zone. In intestinal metaplasia, dysplasia, and GC of the intestinal and atypical subtypes, C/EBPbeta was over‐expressed ( p &lt; 0.0001, for the association with histological type). C/EBPbeta and Ki67, a marker of cell proliferation, were also co‐expressed in primary GC. We also observed an overlap between C/EBPbeta and COX‐2 expression in GC. Using GC cell lines we show that C/EBPbeta can regulate the expression of endogenous COX‐2 and transactivate the promoter of the COX‐2 gene, depending on its methylation status. These results suggest that C/EBPbeta may be a marker of neoplastic transformation and also play an active role in gastric tumourigenesis by regulating COX‐2 expression. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.
The PPARγ Agonist Troglitazone Induces Musclin mRNA Expression in Human Myotubes
2006-09-18

Very recently, a novel skeletal muscle-derived secreted protein, or myokine, was identified in mice and named musclin [1]. Murine musclin was shown to be almost exclusively expressed in skeletal muscle [1]. More than 10-fold lower expression levels were detected in brown adipose tissue, testis, spleen, and bone, where it is known as osteocrin, a factor secreted by osteoblasts and young osteocytes [2]. Musclin consists of 100 amino acids, contains a C-terminal domain highly homologous to natriuretic peptides, and similar to those, is cleaved at an internal serine protease cleavage site [1] [2]. Its expression is repressed by fasting and catecholamines and induced by insulin [1]. Finally, treatment of murine C2C12 myocytes with recombinant musclin revealed inhibitory effects of this protein on insulin-stimulated glucose uptake as well as on basal and insulin-stimulated glycogen synthesis [1].
Behavioral abnormalities precede neuropathological markers in rats transgenic for Huntington's disease
2006-09-19

Huntington's disease (HD) is caused by an expanded CAG repeat leading to the synthesis of an aberrant protein and to the formation of polyglutamine (polyQ)-containing inclusions and aggregates. Limited information is available concerning the association of neuropathological markers with the development of behavioral markers in HD. Using a previously generated transgenic rat model of HD (tgHD rat), we performed association studies on the time-course of behavioral symptoms (motor function, learning, anxiety) and the appearance of striatal atrophy, 1C2 immunopositive aggregates and polyQ recruitment sites, a precursor to these aggregates. At the age of 1 month, tgHD rats exhibited reduced anxiety and improved motor performance, while at 6 months motor impairments and at 9 months cognitive decline occurred. In contrast, polyQ recruitment sites appeared at around 6-9 months of age, indicating that HD-like behavioral markers preceded the appearance of currently detectable neuropathological markers. Interestingly, numerous punctate sites containing polyQ aggregates were also seen in areas receiving afferents from the densely recruiting regions suggesting either transport of recruitment-competent aggregates to terminal projections where initially 1C2 positive aggregates were formed or different internal properties of neurons in different regions. Furthermore, striatal atrophy was observed at the age of 12 months. Taken together, our findings support the hypothesis of a dynamic process leading to region- and age-specific polyQ recruitment and aggregation. The dissociation of onset between behavioral and neuropathological markers is suggestive of as yet undetected processes, which contribute to the early phenotype of these HD transgenic rats.
Progression-specific Genes Identified by Expression Profiling of Matched Ductal Carcinomas in situ and Invasive Breast Tumors, Combining Laser Capture Microdissection and Oligonucleotide Microarray Analysis
2006-09-19

In breast cancer the progression of DCIS (ductal carcinoma in situ) to IDC (invasive ductal carcinoma) is a crucial step in developing metastasis–the major cause of mortality from malignant tumours. Understanding the molecular events accompanying this transition will be the basis (1) to improve the classification in high- and low-risk groups for DCIS patients according to risk of relapse or progression and (2) to advance in individualizing therapy for DCIS and IDC patients. In order to identify new prognostic markers and drug targets correlated with breast cancer progression, we combined Affymetrix microarray analysis with laser capture microdissection (LCM) to analyze matched DCIS and IDC tissue from nine patients. After extensive statistical analysis 548 Affymetrix probe sets were identified to be expressed differentially in either case of the nine tumors (446 up-regulated, 102 down-regulated, p-value <0.01), characterizing the transition from DCIS to IDC. Examples for known genes already associated with breast cancer invasion are e.g. PLAU/uPa and MMP11. Differential gene expression of 18 candidate genes was validated, analyzing triplicate real-time PCR experiments. Further 4 PCR-validated candidates were selected for in situ hybridization (ISH) experiments. Proteins of 5 PCR-validated candidates were detected using immunohistochemistry (IHC). Results of ISH and IHC confirm the localization for all transcripts to epithelial tumour cells. In conclusion, we identified progression-specific candidate genes using an accurate approach, combining LCM and microarray analysis. New candidates, not yet correlated with breast cancer progression, were evaluated using real-time PCR and transcript and protein could be localized to the epithelial tumour cells, respectively. Among these candidates are transmembrane receptors, transcription factors and tumour antigens, thus gene products with potential clinical importance.
Purification, crystallization and preliminary X-ray study of the fungal laccase fromCerrena maxima
2006-09-19

Laccases are members of the blue multi-copper oxidase family that oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. Crystals of the laccase from Cerrena maxima have been obtained and X-ray data were collected to 1.9 A resolution using synchrotron radiation. A preliminary analysis shows that the enzyme has the typical laccase structure and several carbohydrate sites have been identified. The carbohydrate chains appear to be involved in stabilization of the intermolecular contacts in the crystal structure, thus promoting the formation of well ordered crystals of the enzyme. Here, the results of an X-ray crystallographic study on the laccase from the fungus Cerrena maxima are reported. Crystals that diffract well to a resolution of at least 1.9 A (R factor = 18.953%; R(free) = 23.835; r.m.s.d. bond lengths, 0.06 A; r.m.s.d. bond angles, 1.07 degrees) have been obtained despite the presence of glycan moieties. The overall spatial organization of C. maxima laccase and the structure of its copper-containing active centre have been determined by the molecular-replacement method using the laccase from Trametes versicolor (Piontek et al., 2002) as a structural template. In addition, four glycan-binding sites were identified and the 1.9 A X-ray data were used to determine the previously unknown primary structure of this protein. The identity (calculated from sequence alignment) between the C. maxima laccase and the T. versicolor laccase is about 87%. Tyr196 and Tyr372 show significant extra density at the ortho positions and this has been interpreted in terms of NO(2) substituents.
Breast cancer proteomics by laser capture microdissection, sample pooling, 54 cm immobilised pH gradient isoelectric focussing, and differential iodine radioisotope detection
2006-09-19

The presence of progesterone receptor (PR) in estrogen receptor (ER)-positive breast cancer is associated with good prognosis and indicates that tumors are likely to respond to tamoxifen. However, ER+/PR- respond less well. In order to reveal the potential molecular mechanism of this phenomenon we sought to identify differential protein abundances between invasive ductal carcinoma cells from cryopreserved ER+/PR+ and ER+/PR- mammary tumor specimens. Because current proteomics methods are hampered in the examination of most primary human tumor samples by extreme tissue heterogeneity, laser capture microdissection (LCM) was used to isolate tumor cells and a sample pooling strategy was developed to analyse small sample protein lysates. Proteins from LCM-harvested tumors were pooled into 4 sub-pools from each condition of 3 tumors/sub-pool, and proteins from respective paired sub-pools were co-electrophoresed by 2-DE using 54 cm IEF over pH 4–9. Abundance ratios were accurately quantified by differential multiplex radioactive ProteoTope method at low attomole level (3.6μg protein per labeling reaction, <180 ng per multiplex protein sample per 54 cm gel). Applying this approach, differentially displayed proteins were identified by mass spectrometry using co-migrating nonradioactively labelled tumor proteins. They include decreased cytochrome b5 and transgelin, and more abundant CRABP-II, cyclophilin A, Neudesin, and hemoglobin in ER+/PR+ tumors versus ER+/PR- providing a possible explanation for differential susceptibility against tamoxifen as a result of deregulated cytochrome b5-dependent metabolism. This study demonstrates the potential of ProteoTope and LCM to enable extremely sensitive and precise differential analyses from well defined primary clinical specimen.
Expression of estrogen receptor ß-isoforms in breast cancer cell lines with different potentials for mobility and invasiveness
2006-09-19

Estrogen receptor (ER) β is involved in physiological and pathological processes in the mammary gland. Different ERβ-isoforms are described in the literature, without providing their exact function. In order to determine the biological function of distinct ERß-isoforms for breast cancer patients it is important to get detailed information about their expressional regulation. For this purpose we have established four classic multiplex- and six real-time RT-PCRs to quantify wild-type ERβ (ERßwt), ERβcx-, ERβδ5-, ERβ5-splice variants. Expression of ERβ-splice variants was examined in seven standard-cultured breast cancer cell lines: Tamoxifen-resistant MCF-7 (MCF-7TR) cell line, its parental MCF-7 cell line, MCF-10A, MDA-MB 231, AR, KS, and BM cells. Invasion- and mobilityassays were performed using cambers coated with matrigel or uncoated, respectively. RT-PCR data indicate that ERßwt is expressed in MCF-7TR cells compared to MCF-7 cells missing expression of ERβwt. On the other hand MCF-7 cells express ERβ5 which could not be detected in MCF-7TR cells. Comparing the ERß isoform expression patterns of all cell lines investigated it can be observed that the expression pattern of ERβ-isoforms is very similar in MCF-7TR, MDA-MB 231 and AR cells with strong signals for ERβcx. In mobility assays MCF-7TR and AR cells like MDA-MB 231 cells are highly mobile. However, in contrast to MCF-7TR and MDA-MB 231 cells, AR cells are not able to pass through matrigel. PCR analysis of two separate fractions of MCF-7TR cells which passed through matrigel and MCF-7TR cells which remained in or on top of it show a different expression pattern of ERβ-isoforms with a signal for ERβcx only in the invasive cells. MCF-7, MCF10A, KS, and BM cells having a different expression pattern of ERβ-isoforms are neither mobile nor invasive. These data suggest that the expression pattern of ERß-isoforms might be correlated with the mobility of cells in breast cancer.
Significance of HBsAg and HDVRNA levels in patients with delta hepatitis recruited in the Hep-Net/International HDV intervention trial
2006-09-19

Aims: Hepatitis delta virus (HDV) infection is associated with severe liver disease with limited treatment options. We investigated the significance of HDV-RNA, HBsAg and HBV-DNA levels and analysed histological, biochemical and demographic parameters in patients recruited in an International-multicenter intervention trial.