bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutation analysis of the MLH1, MSH2 and MSH6 genes in patients with double primary cancers of the colorectum and the endometrium: A population‐based study in northern Sweden
Authors: Cederquist Kristina , Emanuelsson Monica , Göransson Ingela , Holinski‐Feder Elke , Müller‐Koch Yvonne , Golovleva Irina , Grönberg Henrik 
Published: February 2004

AbstractHereditary nonpolyposis colorectal cancer (HNPCC) is an autosomal dominant disorder that predisposes to predominantly colorectal and endometrial cancers due to germline mutations in DNA mismatch repair genes, mainly MLH1, MSH2 and in families with excess endometrial cancer also MSH6. In this population‐based study, we analysed the mutation spectrum of the MLH1, MSH2 and MSH6 genes in a cohort of patients with microsatellite unstable double primary tumours of the colorectum and the endometrium by PCR, DHPLC and sequencing. Fourteen of the 23 patients (61%) had sequence variants in MLH1, MSH2 or MSH6 that likely affect the protein function. A majority (10/14) of the mutations was found among probands diagnosed before age 50. Five of the mutations (36%) were located in MLH1, 3 (21%) in MSH2 and 6 (43%) in MSH6. MSH6 seem to have larger impact in our population than in other populations, due to a founder effect since all of the MSH6 families originate from the same geographical area. MSH6 mutation carriers have later age of onset of both colorectal cancer (62 vs. 51 years) and endometrial cancer (58 vs. 48 years) and a larger proportion of endometrial cancer than MLH1 or MSH2 mutation carriers. We can conclude that patients with microsatellite unstable double primary cancers of the colorectum and the endometrium have a very high risk of carrying a mutation not only in MLH1 or MSH2 but also in MSH6, especially if they get their first cancer diagnosis before the age of 50. © 2004 Wiley‐Liss, Inc.
WT1 is a tumor‐associated antigen in colon cancer that can be recognized by in vitro stimulated cytotoxic T cells
Authors: Koesters Robert , Linnebacher Michael , Coy Johannes F. , Germann Anja , Schwitalle Yvette , Findeisen Peter , von Knebel Doeberitz Magnus 
Published: February 2004

AbstractThe Wilms' tumor suppressor gene (WT1) has been shown to be overexpressed in acute and chronic leukemias and in a variety of solid human malignancies, including cancers of the breast and lung. In our present study, we investigated the potential role of WT1 gene in human colon cancer. WT1 mRNA and protein expression was analyzed in a panel of human colon cancer cell lines and primary colon carcinomas by RT‐PCR and Western blot analysis, respectively. A mutational screen of WT1′ zinc‐finger region was carried out by sequence analysis. Finally, using peptide‐stimulated cytotoxic T cells it was investigated whether WT1‐expressing colon tumor cells are a potential target for antigen‐specific immunotherapy. Medium to high abundant levels of WT1 mRNA were detected by RT‐PCR in 10 of 12 (83%) colon cell lines and by quantitative, real‐time RT‐PCR in 13 of 15 (87%) primary tumors, whereas only very low levels of expression were found in 2 primary tumors. Interestingly, however, low levels of WT1 mRNA were also detected in all samples derived from normal colon mucosa. When RT‐PCR products were examined by sequence analysis, both +KTS and −KTS splice isoforms but no zinc‐finger mutations were found, suggesting that the wild‐type form of the WT1 gene is expressed. To determine whether the WT1 protein can serve as a target antigen for immunotherapy, 2 HLA‐A2.1‐restricted WT1 peptides (Db126 and WH187) were used for the in vitro induction of WT1‐specific cytotoxic T lymphocytes (CTLs). The WH187‐specific CTLs not only lysed target cells pulsed exogenously with cognate peptide but also WT1‐expressing colon tumor cells in a HLA‐restricted manner. These findings identify the WT1 protein as an attractive target for the development of antigen‐specific immunotherapy in human colon cancer. © 2004 Wiley‐Liss, Inc.
Frequent alterations of Ras signaling pathway genes in sporadic malignant melanomas
Authors: Reifenberger Julia , Knobbe Christiane B. , Sterzinger Astrid A. , Blaschke Britta , Schulte Klaus W. , Ruzicka Thomas , Reifenberger Guido 
Published: February 2004

AbstractRas signaling is important for the intracellular transduction of mitogenic stimuli from activated growth factor receptors. We have investigated 37 sporadic malignant melanomas (15 primary cutaneous melanomas and 22 melanoma metastases) and 6 melanoma cell lines for mutations in the 3 Ras genes NRAS, KRAS and HRAS. All tumors and cell lines were additionally analyzed for mutation and expression of BRAF, which encodes a Ras‐regulated serine/threonine kinase with oncogenic properties, as well as for expression of RASSF1A, which encodes a Ras‐binding protein with tumor suppressor properties. Mutational analyses identified somatic NRAS mutations in 2 primary melanomas, 4 melanoma metastases and 2 cell lines. One melanoma metastasis showed a somatic KRAS mutation whereas HRAS mutations were not detected. Eight primary melanomas, 6 melanoma metastases and 4 melanoma cell lines carried BRAF mutations affecting the known hot‐spot codon 599. None of the tumors or cell lines with BRAF mutation demonstrated NRAS or KRAS mutations. Real‐time reverse transcription‐PCR showed that 8 melanomas (3 primary tumors, 5 melanoma metastases) had reduced RASSF1A transcript levels of ≤50% relative to benign melanocytic nevi and normal skin. Three melanoma cell lines lacked detectable RASSF1A transcripts. The RASSF1A gene promoter was hypermethylated in these 3 cell lines as well as in 6 of 8 melanomas with reduced RASSF1A mRNA levels. Treatment of the cell lines with 5‐aza‐2′‐deoxycytidine and trichostatin A resulted in demethylation of the RASSF1A promoter and re‐expression of RASSF1A transcripts. Most tumors and all cell lines with RASSF1A promoter methylation additionally carried BRAF or NRAS mutations, suggesting a synergistic effect of these aberrations on melanoma growth. Taken together, 57% of the investigated melanomas and 100% of the melanoma cell lines carried mutations in either NRAS, KRAS or BRAF. In addition, 22% of the melanomas and 50% of the cell lines showed reduced RASSF1A transcript levels. Thus, alterations of Ras pathway genes are of paramount importance in the pathogenesis of sporadic melanomas. © 2004 Wiley‐Liss, Inc.
Enhanced radiosensitivity of rat autochthonous mammary tumors by dietary docosahexaenoic acid
Authors: Colas Séverine , Paon Lénaic , Denis Fabrice , Prat Marie , Louisot Pascal , Hoinard Claude , Le Floch Olivier , Ogilvie Gregory , Bougnoux Philippe 
Published: February 2004

AbstractDietary docosahexaenoic acid (DHA), which integrates into tumor cell membranes, has been reported to enhance the efficacy against tumors of cytotoxic drugs that induce reactive oxygen species (ROS). Because ionizing radiation also generate ROS, we initiated a study to determine whether dietary DHA might sensitize mammary tumors to irradiation. Mammary tumors were induced by N‐methylnitrosourea (NMU) in Sprague‐Dawley rats. The optimal dose of radiation to examine the effect of DHA on tumor response to irradiation was determined to be 18 grays (Gy) using a 4–6 MeV electron beam (according to the depth of the target volume) delivered in a single fraction from a linear accelerator. Two groups of rats were fed a basal diet containing 7% of a mixture of peanut and rapeseed oils enriched with 8% of an oil containing either a low (palm oil) or high (DHASCO oil containing 40% DHA) DHA content. DHA group was equally subdivided into 2 groups without or with addition of vitamin E (100 IU/kg diet). Irradiation was carried out when the first tumor in each rat reached 1.5 cm2 and subsequent change in tumor size was documented over time. DHA level in adipose tissue, taken as a biomarker, was higher in the DHA supplemented group compared to the control group. Vitamin E level in liver, the best storage for this compound, was higher in the vitamin E supplemented DHA group compared to the DHA group. Tumor size decreased by 60% at 12 days after irradiation in the DHA group vs. 31% in the control group (p = 0.03) and 36% in the DHA plus vitamin E group. Therefore, dietary DHA sensitized mammary tumors to radiation. The addition of vitamin E inhibited the beneficial effect of DHA, suggesting that this effect might be mediated by oxidative damage to the peroxidizable lipids. © 2004 Wiley‐Liss, Inc.
IMGT standardized criteria for statistical analysis of immunoglobulin V‐REGION amino acid properties
Authors: Pommié Christelle , Levadoux Séverine , Sabatier Robert , Lefranc Gérard , Lefranc Marie‐Paule 
Published: February 2004

AbstractIMGT, the international ImMunoGeneTics information system® (http://imgt.cines.fr) is a high‐quality integrated information system specializing in immunoglobulins (IG), T cell receptors (TR) and major histocompatibility complex (MHC) of human and other vertebrates. IMGT comprises IMGT/LIGM‐DB, the comprehensive database of IG and TR sequences from human and other vertebrates (76 846 sequences in September 2003). In order to define the IMGT criteria necessary for standardized statistical analyses, the sequences of the IG variable regions (V‐REGIONs) from productively rearranged human IG heavy (IGH) and IG light kappa (IGK) and lambda (IGL) chains were extracted from IMGT/LIGM‐DB. The framework amino acid positions of 2474 V‐REGIONs (1360 IGHV, 585 IGKV, 529 IGLV) were numbered according to the IMGT unique numbering. Two statistical methods (correspondence analysis and hierarchic classification) were used to analyze the 237 framework positions (80 for IGHV, 79 for IGKV, 78 for IGLV), for three properties (hydropathy, volume and chemical characteristics) of the 20 common amino acids. Results of the analyses are shown as standardized two‐dimensional representations, designated as IMGT Colliers de Perles statistical profiles. They provide a characterization of the amino acid properties at each framework position of the expressed IG V‐REGIONs, and a visualization of the resemblances and differences between heavy and light, and between kappa and lambda sequences. The standardized criteria defined in this paper, amino acid positions and property classes, will be useful to study the mutations and allele polymorphisms, to establish correlations between amino acids in the IG and TR protein three‐dimensional structures and to extract new knowledge from V‐like domains of chains, other than IG and TR, belonging to the immunoglobulin superfamily. Copyright © 2004 John Wiley & Sons, Ltd.
Protein stabilization by salt bridges: concepts, experimental approaches and clarification of some misunderstandings
Authors: Bosshard Hans Rudolf , Marti Daniel N. , Jelesarov Ilian 
Published: February 2004

AbstractSalt bridges in proteins are bonds between oppositely charged residues that are sufficiently close to each other to experience electrostatic attraction. They contribute to protein structure and to the specificity of interaction of proteins with other biomolecules, but in doing so they need not necessarily increase a protein's free energy of unfolding. The net electrostatic free energy of a salt bridge can be partitioned into three components: charge–charge interactions, interactions of charges with permanent dipoles, and desolvation of charges. Energetically favorable Coulombic charge–charge interaction is opposed by often unfavorable desolvation of interacting charges. As a consequence, salt bridges may destabilize the structure of the folded protein. There are two ways to estimate the free energy contribution of salt bridges by experiment: the pKa approach and the mutation approach. In the pKa approach, the contribution of charges to the free energy of unfolding of a protein is obtained from the change of pKa of ionizable groups caused by altered electrostatic interactions upon folding of the protein. The pKa approach provides the relative free energy gained or lost when ionizable groups are being charged. In the mutation approach, the coupling free energy between interacting charges is obtained from a double mutant cycle. The coupling free energy is an indirect and approximate measure of the free energy of charge–charge interaction. Neither the pKa approach nor the mutation approach can provide the net free energy of a salt bridge. Currently, this is obtained only by computational methods which, however, are often prone to large uncertainties due to simplifying assumptions and insufficient structural information on which calculations are based. This state of affairs makes the precise thermodynamic quantification of salt bridge energies very difficult. This review is focused on concepts and on the assessment of experimental methods and does not cover the vast literature. Copyright © 2004 John Wiley & Sons, Ltd.
Factors contributing to the development of aluminum resistance in the Madeiran maize germplasm
Authors: Pinheiro de Carvalho Miguel Â. A. , Slaski Jan J. , Abreu Ivo , Ganança Filipe T. , dos Santos Teresa M. M. , Freitas Lurdes , Clemente Vieira Maria R. , Nunes Antonieta , Domingues Ana , Taylor Gregory J. 
Published: February 2004

AbstractForty genotypes representing maize genetic diversity from the Island of Madeira were screened for resistance to aluminum (Al) in nutrient solution. Seeds of maize were obtained from local farmers from field plots spread around the island in a range of altitudes from 99 to 1000 m above sea level. The content of ionic aluminum and the pH of soils cultivated with maize were determined. The mean pH value of all examined soils was 4.9, while the mean ionic Al content was 0.76 cmol kg–1. Seventy‐two hours (h) exposure to 100 and 200 μM Al followed by a 48 h recovery period of 4‐day old seedlings revealed significant differences in Al resistance in the Madeiran maize germplasm. Root survival and regrowth exceeding 80 % of the seedlings were observed in 22 and 8 of the tested genotypes screened at 100 and 200 μM Al in nutrient solution. High Al resistance among Madeiran maize genotypes appeared not to be associated with the lower pH of soil, and did not correlate with the amount of soil Al3+ or the altitude at the site of collection. The high level of Al resistance of the maize cultivars indicates an initial genetic trait enhanced by open pollination of maize.
Immobilization of heavy metals in soils by the application of bauxite residues: pot experiments under field conditions
Authors: Friesl Wolfgang , Horak Othmar , Wenzel Walter W. 
Published: February 2004

AbstractIn previous greenhouse experiments red mud, a residue of the alumina industry, was identified as effective amendment for in situ fixation of heavy metals. In the present study, we further evaluated the efficiency and potential drawbacks of red mud in an outdoor pot experiment. Application of 5 % (w/w) red mud (RM) should reveal possible drawbacks of red mud due to indigenous pollutants such as As, Cr, and V. Three soils from arable land in Lower Austria named Untertiefenbach (U) (Eutric Cambisol), Weyersdorf (W) (Dystric Cambisol), and Reisenberg (R) (Calcic Chernozem) were spiked with Cd, Zn, Cu, Ni, and V at two concentration levels in 1987, two soils originate from long‐term industrially polluted sites, located in Carinthia (Arnoldstein – Rendzic Leptosol; Zn, Cd, and Pb) and Tyrol (Brixlegg – Dystric Fluvisol; Cu, Zn). Zea mays was cultivated in pots for three months in outdoor conditions. Extraction with 1 M NH4NO3 was used to assess the influence of RM on the labile metals. Lability of Cd, Zn, Ni, and Pb was reduced upon RM treatment on a sandy soil up to 91 %, 94 %, 71 %, and 83 % of the control, respectively. Metal accumulation in shoots was reduced for Cd and Zn up to 54 % and for Ni up to 75 % (soil W), but not for Pb (soil A). Addition of RM (5 % w/w) increased the total As, Cr, and V concentrations in soils by 5, 20, and 50 mg kg–1, respectively. Whereas the lability of Cr was not affected, 1 M NH4NO3‐extractable As and V exceeded the trigger value for water quality according to Prüeß (1994). Lability of Cu increased upon RM application, especially on the Cu polluted industrial soil (B), while Cu toxicity appeared to be reduced as indicated by the higher corn biomass production. Red mud holds promise as soil amendment in terms of reduction Cd, Zn, and Ni bioavailability. However, at additions as high as 5 % (w/w) large As, Cr, and V concentrations of this material may limit its application.
Degradation of organotin compounds in organic and mineral forest soils
Authors: Huang Jen‐How , Matzner Egbert 
Published: February 2004

AbstractBroad industrial application of organotin compounds (OTC) leads to their release into the environment. OTC are deposited from the atmosphere into forest ecosystems and may accumulate in soils. Here, we studied the degradation of methyltin and butyltin compounds in a forest floor, a mineral, and a wetland soil with incubation experiments at 20 °C in the dark. OTC degraded slowly in soils with half‐lives estimated from 0.5 to 15 years. The first order degradation rate constants of OTC in soils ranged from 0.05 to 1.54 yr–1. The degradation rates in soils were generally in the order mono‐ ≥ di‐ > tri‐substituted OTC. Stepwise dealkylation was observed in all cases of di‐substituted OTC, but only in some cases of tri‐substituted OTC. Decomposition rates of OTC in the forest floor were higher than in wetland and mineral soils. Tetramethyltin in the gas phase was not detected, suggesting little tin methylation in the wetland soils. Slow degradation of OTC in soils might lead to long‐term storage of atmospherically deposited OTC in soils.
Soil biochemical and microbial indices in wet tropical forests: Effects of deforestation and cultivation
Authors: Dinesh R. , Ghoshal Chaudhuri S. , Sheeja T. E. 
Published: February 2004

AbstractLittle information is available about the long‐term effects of deforestation and cultivation on biochemical and microbial properties in wet tropical forest soils. In this study, we evaluated the general and specific biochemical properties of soils under evergreen, semi‐evergreen, and moist deciduous forests and adjacent plantations of coconut, arecanut, and rubber, established by clear felling portions of these forests. We also examined the effects of change in land use on microbial indices and their interrelationships in soils.Significant differences between the sites occurred for the biochemical properties reflecting soil microbial activity. Microbial biomass C, biomass N, soil respiration, N mineralization capacity, ergosterol, levels of adenylates (ATP, AMP, ADP), and activities of dehydrogenase and catalase were, in general, significantly higher under the forests than under the plantations. Likewise, the activities of various hydrolytic enzymes such as acid phosphomonoesterase, phosphodiesterase, casein‐protease, BAA‐protease, β‐glucosidase, CM‐cellulase, invertase, urease, and arylsulfatase were significantly higher in the forest soils which suggested that deforestation and cultivation markedly reduced microbial activity, enzyme synthesis and accumulation due to decreased C turnover and nutrient availability. While the ratios of microbial biomass C : N and microbial biomass C : organic C did not vary significantly between the sites, the ratios of ergosterol : biomass C and ATP : biomass C,qCO2 and AEC (Adenylate Energy Charge) levels were significantly higher in the forest sites indicating high energy requirements of soil microbes at these sites.
Zuordnung des Munsell‐Codes zu einem Farbnamen nach bodenkundlichen Kriterien
Authors: Albrecht Christoph , Huwe Bernd , Jahn Reinhold 
Published: February 2004

AbstractEine der zentralen Informationen für die Bodenklassifikation ist die Farbe. Bei Profilaufnahmen wird sie entweder verbal oder durch den Munsell‐Code beschrieben. Während der Name schnell und ohne Hilfsmittel zu bestimmen ist, hat der Munsell‐Code den Vorteil, dass er auf einem standardisierten Farbraum basiert und deshalb numerische Vergleiche zwischen einzelnen Farben gezogen werden können. Da in vielen bodenkundlichen Datensätzen nur der Farbname angegeben ist, ist die rechnergestützte Auswertung dieser Information oft nicht möglich. Um dieses Problem zu umgehen, wurde ein System entwickelt, mit dem zu jedem bodenkundlichen Farbnamen der mittlere Munsell‐Code bestimmt werden kann. Es ist in der plattformübergreifenden Programmiersprache Tcl/Tk als freie Software programmiert.
Characterisation and identification of proteinaceous binding media (animal glues) from their amino acid profile by capillary zone electrophoresis
Authors: Kaml Isabella , Vcelakova Katerina , Kenndler Ernst 
Published: February 2004

AbstractA capillary electrophoretic method for identifying different species of proteinaceous binders – collagen, egg white, and milk casein – is described. It allows characterisation of the proteins on the basis of the amino acid profiles obtained after their acidic hydrolysis. The profiles of the underivatised amino acids are recorded directly by capillary zone electrophoresis at pH 2.26 with the aid of a conductivity detector, thus eliminating the need for a derivatisation step. Identification is carried out by means of different relative peak areas of the amino acids. A scheme is given for identification, which is based on the main markers, hydroxyproline, proline, glycine, glutamic acid, and serine and valine.
Investigating the history of prehistoric glues by gas chromatography–mass spectrometry
Authors: Regert Martine 
Published: February 2004

AbstractAlthough organic materials are very sensitive to biochemical alteration processes, they may be preserved for millennia in various archaeological contexts. Remains of adhesives made during prehistory were discovered at different sites, in the form of residues adhering to flint tools and ceramic vessels or as free lumps in sediment. To characterise the natural substances exploited for adhesive production during late prehistory, we undertook GC and GC/MS analysis of 90 samples from 8 sites dating from the Neolithic to Iron Age periods. This paper discusses our approach to the study of organic adhesives preserved in archaeological contexts, with a particular focus on the presentation of the various categories of organic adhesives that we analysed and the choice of chromatographic conditions adapted to the specificity of such samples. The results obtained show that birch bark tar, a triterpenoid adhesive made by destructive distillation of white birch bark, was predominantly used during the neolithic period even though other materials such as various barks or organic fossil substance were also used. During the Bronze and Iron ages, which follow the Neolithic period, adhesive production is evolving through the expansion of the range of the natural substances used (identification of diterpenoid pine resin) and the addition of beeswax as a plasticiser to birch bark tar. By combining chromatographic analysis and archaeological data, it was thus possible to follow the evolution of adhesive making at the end of prehistory, testifying to the inventiveness of the craftsmen whatever the period considered.
Microbial diversity in biodeteriorated monuments as studied by denaturing gradient gel electrophoresis
Authors: Gonzalez Juan M. , Saiz‐Jimenez Cesareo 
Published: February 2004

AbstractStudies of the microorganisms living on cultural assets and their potential damaging effects begin with an understanding of the microbial diversity present in such samples. Recently, molecular techniques have started to attract considerable interest since they do not require the culture of microorganisms in order to detect their presence. The basic protocol followed during microbial diversity analysis on cultural heritage assets utilizes electrophoretic techniques for separating highly homologous sequences. At present, Denaturing Gradient Gel Electrophoresis (DGGE) is the most frequently reported technique for separating DNA fragments during microbial diversity studies of art objects. In this report, we describe DGGE profiling techniques, show the most common applications, and present some examples of their use in microbial diversity studies on cultural heritage.