bluuebunny/crossref_metadata_2025_split huggingface dataset:
STABILIZED1, a Stress-Upregulated Nuclear Protein, Is Required for Pre-mRNA Splicing, mRNA Turnover, and Stress Tolerance in Arabidopsis
Authors: Lee Byeong-ha , Kapoor Avnish , Zhu Jianhua , Zhu Jian-Kang 
Published: June 2006

Abstract
In plants, many gene transcripts are very unstable, which is important for the tight control of their temporal and spatial expression patterns. To identify cellular factors controlling the stability of unstable mRNAs in plants, we used luciferase imaging in Arabidopsis thaliana to isolate a recessive mutant, stabilized1-1 (sta1-1), with enhanced stability of the normally unstable luciferase transcript. The sta1-1 mutation also causes the stabilization of some endogenous gene transcripts and has a range of developmental and stress response phenotypes. STA1 encodes a nuclear protein similar to the human U5 small ribonucleoprotein–associated 102-kD protein and to the yeast pre-mRNA splicing factors Prp1p and Prp6p. STA1 expression is upregulated by cold stress, and the sta1-1 mutant is defective in the splicing of the cold-induced COR15A gene. Our results show that STA1 is a pre-mRNA splicing factor required not only for splicing but also for the turnover of unstable transcripts and that it has an important role in plant responses to abiotic stresses.
X‐ray structure of potato epoxide hydrolase sheds light on substrate specificity in plant enzymes
Authors: Mowbray Sherry L. , Elfström Lisa T. , Ahlgren Kerstin M. , Andersson C. Evalena , Widersten Mikael 
Published: June 2006

AbstractEpoxide hydrolases catalyze the conversion of epoxides to diols. The known functions of such enzymes include detoxification of xenobiotics, drug metabolism, synthesis of signaling compounds, and intermediary metabolism. In plants, epoxide hydrolases are thought to participate in general defense systems. In the present study, we report the first structure of a plant epoxide hydrolase, one of the four homologous enzymes found in potato. The structure was solved by molecular replacement and refined to a resolution of 1.95 Å. Analysis of the structure allows a better understanding of the observed substrate specificities and activity. Further, comparisons with mammalian and fungal epoxide hydrolase structures reported earlier show the basis of differing substrate specificities in the various epoxide hydrolase subfamilies. Most plant enzymes, like the potato epoxide hydrolase, are expected to be monomers with a preference for substrates with long lipid‐like substituents of the epoxide ring. The significance of these results in the context of biological roles and industrial applications is discussed.
Enhancement of bound‐state residual dipolar couplings: Conformational analysis of lactose bound to Galectin‐3
Authors: Zhuang Tiandi , Leffler Hakon , Prestegard James H. 
Published: June 2006

AbstractResidual dipolar couplings (RDCs) have proven to be a valuable NMR tool that can provide long‐range constraints for molecular structure determination. The constraints are orientational in nature and are, thus, highly complementary to conventional distance constraints from NOE data. This complementarity would seem to extend to the study of the geometry of ligands bound to proteins. However, unlike transferred NOEs, where collection, even with a large excess of free ligand, results in measurements dominated by bound contributions, RDCs of exchanging ligands can be dominated by free‐state contributions. Here we present a strategy for enhancement of RDCs from bound states that is based on specifically enhancing the alignment of the protein to which a ligand will bind. The protein is modified by addition of a hydrophobic alkyl tail that anchors it to the bicelles that are a part of the ordering medium needed for RDC measurement. As an illustration, we have added a propyl chain to the C terminus of the carbohydrate recognition domain of the protein, Galectin‐3, and report enhanced RDCs that prove consistent with known bound‐ligand geometries for this protein.
The effects of sodium sulfate, glycosaminoglycans, and Congo red on the structure, stability, and amyloid formation of an immunoglobulin light‐chain protein
Authors: Mclaughlin Richard W. , De Stigter Janelle K. , Sikkink Laura A. , Baden Elizabeth M. , Ramirez‐Alvarado Marina 
Published: June 2006

AbstractLight‐chain amyloidosis (AL) is characterized by immunoglobulin light‐chain fragments aggregating into amyloid fibrils that deposit extracellularly in vital organs such as the kidney, the heart, and the liver, resulting in tissue degeneration and organ failure, leading to death. Cardiac involvement is found in 50% of AL patients and presents the most severe cases with a life expectancy of less than a year after diagnosis. In this study, we have characterized the variable domain of a cardiac AL patient light chain called AL‐09. AL‐09 folds as a β‐sheet and is capable of forming amyloid fibrils both in the presence of sodium sulfate and in self‐seeded reactions under physiological conditions. Glycosaminoglycans such as dermatan sulfate and heparin promote amyloid formation of self‐seeded AL‐09 reactions, while the glycosaminoglycan chondroitin sulfate A stabilized oligomeric intermediates and did not elongate the preformed fibrils (nucleus) present in the reaction. Finally, the histological dye Congo red, known to bind to the cross β‐sheet structure of amyloid fibrils, inhibits AL‐09 amyloid fibril formation in the presence of sodium sulfate and in self‐seeded reactions. This paper provides insight into the impact of different reagents on light‐chain stability, structure, amyloid fibril formation, and inhibition.
A composite score for predicting errors in protein structure models
Authors: Eramian David , Shen Min‐yi , Devos Damien , Melo Francisco , Sali Andrej , Marti‐Renom Marc A. 
Published: June 2006

AbstractReliable prediction of model accuracy is an important unsolved problem in protein structure modeling. To address this problem, we studied 24 individual assessment scores, including physics‐based energy functions, statistical potentials, and machine learning–based scoring functions. Individual scores were also used to construct ∼85,000 composite scoring functions using support vector machine (SVM) regression. The scores were tested for their abilities to identify the most native‐like models from a set of 6000 comparative models of 20 representative protein structures. Each of the 20 targets was modeled using a template of <30% sequence identity, corresponding to challenging comparative modeling cases. The best SVM score outperformed all individual scores by decreasing the average RMSD difference between the model identified as the best of the set and the model with the lowest RMSD (ΔRMSD) from 0.63 Å to 0.45 Å, while having a higher Pearson correlation coefficient to RMSD (r = 0.87) than any other tested score. The most accurate score is based on a combination of the DOPE non‐hydrogen atom statistical potential; surface, contact, and combined statistical potentials from MODPIPE; and two PSIPRED/DSSP scores. It was implemented in the SVMod program, which can now be applied to select the final model in various modeling problems, including fold assignment, target–template alignment, and loop modeling.
Mutagenic exploration of the cross‐seeding and fibrillation propensity of Alzheimer's β‐amyloid peptide variants
Authors: Peim Alexander , Hortschansky Peter , Christopeit Tony , Schroeckh Volker , Richter Walter , Fändrich Marcus 
Published: June 2006

AbstractAmyloid formation is a nucleation‐dependent process that is accelerated dramatically in vivo and in vitro upon addition of appropriate fibril seeds. A potent species barrier can be effective in this reaction if donor and recipient come from different biological species. This species barrier is thought to reflect differences in the amino acid sequence between seed and target polypeptide. Here we present an in vitro mutagenic cross‐seeding analysis of Alzheimer's Aβ(1‐40) peptide in which we mapped out the effect of systematically varied amino acid replacements on the propensity of seed‐dependent amyloid fibril formation. We find that the susceptibility of different peptides toward cross‐seeding relates to the intrinsic aggregation propensity of the respective polypeptide chain and, therefore, to properties such as β‐sheet propensity and hydrophobicity. These data imply that the seed‐dependent formation of amyloid‐like fibrils is affected by the intrinsic properties of the polypeptide chain in a manner that is similar to what has been described previously for aggregation reactions in general. Hence, the nucleus acts in this case as a catalyst that promotes the fibrillation of different polypeptide chains according to their intrinsic structural predilection.
Native state energetics of the Src SH2 domain: Evidence for a partially structured state in the denatured ensemble
Authors: Wildes David , Anderson L. Meadow , Sabogal Alex , Marqusee Susan 
Published: June 2006

AbstractWe have defined the free‐energy profile of the Src SH2 domain using a variety of biophysical techniques. Equilibrium and kinetic experiments monitored by tryptophan fluorescence show that Src SH2 is quite stable and folds rapidly by a two‐state mechanism, without populating any intermediates. Native state hydrogen–deuterium exchange confirms this two‐state behavior; we detect no cooperative partially unfolded forms in equilibrium with the native conformation under any conditions. Interestingly, the apparent stability of the protein from hydrogen exchange is 2 kcal/mol greater than the stability determined by both equilibrium and kinetic studies followed by fluorescence. Native‐state proteolysis demonstrates that this “super protection” does not result from a deviation from the linear extrapolation model used to fit the fluorescence data. Instead, it likely arises from a notable compaction in the unfolded state under native conditions, resulting in an ensemble of conformations with substantial solvent exposure of side chains and flexible regions sensitive to proteolysis, but backbone amides that exchange with solvent ∼30‐fold slower than would be expected for a random coil. The apparently simple behavior of Src SH2 in traditional unfolding studies masks the significant complexity present in the denatured‐state ensemble.
Molecular architecture of E. coli purine nucleoside phosphorylase studied by analytical ultracentrifugation and CD spectroscopy
Authors: Modrak‐Wójcik Anna , Stępniak Katarzyna , Akoev Vladimir , Żółkiewski Michał , Bzowska Agnieszka 
Published: June 2006

AbstractPurine nucleoside phosphorylase (PNP) is a key enzyme of the nucleoside salvage pathway and is characterized by complex kinetics. It was suggested that this is due to coexistence of various oligomeric forms that differ in specific activity. In this work, the molecular architecture of Escherichia coli PNP in solution was studied by analytical ultracentrifugation and CD spectroscopy. Sedimentation equilibrium analysis revealed a homohexameric molecule with molecular mass 150 ± 10 kDa, regardless of the conditions investigated—protein concentration, 0.18–1.7 mg/mL; presence of up to 10 mM phosphate and up to 100 mM KCl; temperature, 4–20°C. The parameters obtained from the self‐associating model also describe the hexameric form. Sedimentation velocity experiments conducted for broad protein concentration range (1 μg/mL–1.3 mg/mL) with boundary (classical) and band (active enzyme) approaches gave s020,w = 7.7 ± 0.3 and 8.3 ± 0.4 S, respectively. The molecular mass of the sedimenting particle (146 ± 30 kDa), calculated using the Svedberg equation, corresponds to the mass of the hexamer. Relative values of the CD signal at 220 nm and the catalytic activity of PNP as a function of GdnHCl concentration were found to be correlated. The transition from the native state to the random coil is a single‐step process. The sedimentation coefficient determined at 1 M GdnHCl (at which the enzyme is still fully active) is 7.7 S, showing that also under these conditions the hexamer is the only catalytically active form. Hence, in solution similar to the crystal, E. coli PNP is a hexameric molecule and previous suggestions for coexistence of two oligomeric forms are incorrect.
Altered expression of β‐catenin/E‐cadherin in meningiomas
Authors: Brunner E C , Romeike B F M , Jung M , Comtesse N , Meese E 
Published: June 2006

Aims : Meningiomas are generally slow‐growing benign tumours representing approximately 20% of all primary intracranial tumours. The hallmark of tumorigenesis of meningiomas is the loss of chromosome 22, including loss of heterozygosity of the neurofibromatosis type 2 (NF2) gene. The NF2 encoded protein merlin appears to function as a tumour suppressor gene by controlling cadherin‐mediated cell–cell adhesion. The E‐cadherin cell adhesion system includes β‐catenin that indirectly connects cadherin to actin filaments. The aim of this study was to analyse the expression and the subcellular location of E‐cadherin and β‐catenin in human meningiomas, including meningiomas of different histomorphological subtypes and different World Health Organization (WHO) grades.Methods and results : Immunohistochemical analysis revealed lack of E‐cadherin expression at the cell membrane in 34% of meningiomas independent of their WHO grade. Loss of membranous β‐catenin occurred in 79% of meningiomas. An intense perinuclear granular immunoreactivity of β‐catenin without nuclear location was detected in the majority of meningiomas. Both immunofluorescence and Western blot analysis of fractionated meningioma cells located β‐catenin mostly on the Golgi apparatus and ER/Golgi intermediate compartment (ERGIC). Cytogenetic analysis of meningiomas showed no correlation between NF2 loss and the loss of the proper location of β‐catenin.Conclusions : The lack of membranous β‐catenin and/or membranous E‐cadherin in meningiomas may indicate an altered interaction between meningioma cells independent of loss of NF2 and independent of the tumour grade.
Vascular endothelial growth factor C—a potent risk factor in childhood acute lymphoblastic leukaemia: an immunocytochemical approach
Authors: Nowicki M , Ostalska‐Nowicka D , Kaczmarek E , Miskowiak B , Witt M 
Published: June 2006

Aims : To investigate the immunocytochemical expression of vascular endothelial growth factor C (VEGF‐C) and its receptors (VEGFR‐2 and VEGFR‐3) in childhood acute lymphoblastic leukaemia (ALL) blasts and to determine the possible role of this complex in the pathogenesis and prognosis of ALL.Methods and results : Bone marrow samples were taken from 120 children diagnosed with ALL. An indirect immunocytochemical procedure was performed with the use of monoclonal mouse anti‐human antibodies against VEGF‐C, VEGFR‐2 and VEGFR‐3 (diluted 1 : 100). The immunocytochemical expression of VEGF‐C was confirmed exclusively in the cytoplasm of ALL lymphoblasts (the mean percentage was 36.4 ± 7.2). It was absent from the cytoplasm of normal haematopoietic cells in the control group. No VEGFR‐2 or VEGFR‐3 expression was detected in the children of either the study or control groups. The risk of induction failure or leukaemic relapse was found to be significant in all VEGF‐C+ patients (P < 0.0001 and P < 0.02, respectively; Fisher's exact test).Conclusions : The absence of VEGF‐C in blast cells predicts long‐lasting remission in all leukaemic children. Our findings also suggest that leukaemic cell invasion, following VEGF‐C‐driven lymphangiogenesis, could be related to a mediating role of this peptide produced by blast cells themselves.
Heparanase expression in nasopharyngeal carcinoma inversely correlates with patient survival
Authors: Bar‐Sela G , Kaplan‐Cohen V , Ilan N , Vlodavsky I , Ben‐Izhak O 
Published: June 2006

Aim : To determine the expression and prognostic significance of heparanase in nasopharyngeal carcinoma (NPC).Methods : Immunohistochemistry was performed on formalin‐fixed paraffin‐embedded sections of 46 patients with NPC. Clinical and immunohistochemical data were correlated with gender, age, histological type, Epstein–Barr virus (EBV) status, stage and survival.Results : Heparanase immunoreactivity was found in 35% (16/46) of specimens. The cumulative survival of patients diagnosed as heparanase negative (n = 30) at 10 years was 70%. In contrast, the cumulative survival of patients diagnosed as heparanase positive (n = 16) at 10 years was 25%, differences that are highly statistically significant (P = 0.03). No significant correlations were found between heparanase immunoreactivity and gender, age, EBV status, tumour histology or tumour stage.Conclusion : Heparanase expression is inversely correlated with survival of NPC patients, clearly indicating that heparanase is a reliable prognostic factor for this malignancy, and further supports the notion that heparanase is a valid target for the development of anti‐cancer drugs.
Correlation of c‐erbB‐2 oncogene and p53 tumor suppressor gene with malignant transformation of hydatidiform mole
Authors: Yazaki‐Sun Sue , Daher Silvia , De Souza Ishigai Márcia Marcelino , Alves Maria Teresa Seixas , Mantovani Teresa Meire , Mattar Rosiane 
Published: June 2006

AbstractAim:  Considering the roles of c‐erB‐2 and p53 oncoproteins in tumor progression, we aimed to evaluate their expression in hydatidiform moles, and the possible predictive value of this immunoexpression in postmolar follow‐up.Methods:  Group I comprised 35 patients with progression to gestational trophoblastic tumor, and group II included 32 patients with progression to spontaneous remission. Immunohistochemical tests were performed by streptavidin‐peroxidase method. c‐erbB‐2 immunoexpression was evaluated according to quantitative and semiquantitative criteria; p53 according to percentage of cells with stained nuclei. Data were analyzed by Student t‐test, Mann–Whitney test, ROC curve and logistic regression analysis.Results:  c‐erbB‐2 and p‐53 expressions were significantly increased in group I. Quantitative and semiquantitative analysis of c‐erb‐2 showed that its expression may be associated with mole hydatidiform progression to gestational trophoblastic tumor. Taking into account cells with complete membranous delineation we proposed a cut‐off value of 10.8%. Similarly, considering the percentage of cells presenting nuclei marked by p53 we suggested a cut‐off value of 40.1% for the prediction of malignant transformation of mole hydatidiform.Conclusions:  c‐erbB‐2 and p53 immunoexpression in hydatidiform mole are usually increased with malignant transformation. In addition to β‐fraction of human chorionic gonadotropin, they could possibly help the establishment of a therapeutic protocol.
Comparison of two freezing protocols in an open freezing system for cryopreservation of rat ovarian tissue
Authors: Maltaris Theodoros , Dimmler Arno , Müller Andreas , Hoffmann Inge , Beckmann Matthias W. , Dittrich Ralf 
Published: June 2006

AbstractAim:  To compare two freezing protocols in an automatic open‐vessel freezing system for cryopreservation of rat ovarian tissue.Methods:  Ovarian tissue was transplanted heterotopically into the neck muscle, either without cryopreservation (group 1, n = 6) or with cryopreservation after equilibration with 1.5 mol/L dimethyl sulfoxide and propanediol (protocol A, group 2, n = 6) or 1.5 mol/L ethyl glycol (protocol B, group 3, n = 6). The ovarian tissue was examined with LIVE/DEAD fluorescent viability staining and histologically after isotransplantation.Results:  The healthy follicular loss (intact oocyte and >50% granulosa cells alive) due to cryopreservation was 15.5% with protocol A and 12.2% with protocol B. Histological examination showed follicles in all developmental phases in all groups: group 1, 35.5 ± 5.7/mm2 (mean ± SD); group 2, 16.0 ± 5.0/mm2; group 3, 17.3 ± 5.7/mm2. The differences between groups 1 and 2 and between groups 1 and 3 were significant (P < 0.001). The difference between groups 2 and 3 was not significant (P = 0.33).Conclusions:  These results demonstrate that the use of an open freezing system with both freezing protocols allows cryopreservation of rat ovarian tissue with equally good survival rates.
Effects of metformin on insulin resistance, androgen concentration, ovulation and pregnancy rates in women with polycystic ovary syndrome following laparoscopic ovarian drilling  THIS ARTICLE HAS BEEN RETRACTED
Authors: Kocak Idris , Üstün Cazip 
Published: June 2006

AbstractAim:  To evaluate the effects of metformin on insulin resistance, androgen concentration, ovulation rates and pregnancy rates in infertile women with polycystic ovary syndrome (PCOS).Methods:  Forty‐two infertile women with PCOS were selected in this randomized clinical study. Basal steroid and gonadotropin levels were measured, and oral glucose tolerance test (OGTT) was performed. The patients were randomly divided into group 1 (n = 21) and group 2 (n = 21). Group 1 patients were treated with laparoscopic ovarian drilling (LOD). Group 2 patients underwent laparoscopic ovarian drilling (LOD) and received 1700 mg per day of metformin for 6 months. LOD was performed in women with PCOS using a unipolar electrode. Serum progesterone (P) level > 5 ng/mL was considered as a confirmation of ovulation. Ovulation and pregnancy rates were determined after six cycles.Results:  Serum androgens and insulin response to OGTT decreased significantly after metformin therapy. Mean serum P levels and endometrial thickness were significantly higher in cycles treated with metformin plus LOD (34.6 ± 25.4 ng/mL, 8.4 ± 1.1 mm) than in those treated with LOD alone (26.2 ± 24.7 ng/mL, 7.9 ± 2.8 mm) (P < 0.05). The ovulation (56 of 65 cycles, 86.1% vs 29 of 65 cycles, 44.6%) and pregnancy rates (nine of 21 women, 47.6% vs four of 21 women, 19.1%) were significantly higher in group 2 than in group I.Conclusions:  Metformin improves insulin resistance, reduces androgen levels and significantly increases the ovulation and pregnancy rates in infertile women, following LOD.
Randomized study of preoperative chemotherapy versus primary surgery for stage IB cervical cancer
Authors: Cai Hong‐Bing , Chen Hui‐Zhen , Yin Hou‐Han 
Published: June 2006

AbstractAim:  To determine the most effective treatment and long‐term outcome of patients with stage IB carcinoma of the cervix.Methods:  From January 1999 to December 2001, 106 women with cervical cancer stage IB received neoadjuvant chemotherapy (n = 52) or primary surgery (n = 54). These were randomly assigned. Clinical effects and pathological changes were simultaneously recorded.Results:  The overall clinical response rate was 84.6% and included a complete response (CR) in four patients (7.7%), partial response (PR) in 40 patients (76.9%), and stable disease (SD) in the remaining eight patients (15.4%). Surgery revealed positive nodes in 9.6% neoadjuvant chemotherapy group patients and in 29.6% primary surgery group patients (P = 0.014). Similar results occurred with vascular space involvement: 27.8% in the primary surgery group compared to 9.6% in the neoadjuvant chemotherapy group (P = 0.024). However, parametrial infiltration was found in 7.4% of the patients in the primary surgery group, while only 3.8% showed it in the neoadjuvant chemotherapy group (P = 0.679). The overall 5‐year survival rate was significantly higher for all patients who received neoadjuvant chemotherapy (84.6%) than for the control group (75.9%) (P = 0.0112). The median survival time in patients with complete response and partial response to chemotherapy (83.3 months) was significantly higher than that of patients with stable disease to chemotherapy (55.2 months) (P = 0.0049). 27.3% of patients developed recurrent disease within 5 years of the primary treatment. The women with recurrence included partial response in six patients (60.0%), and stable disease in four patients (40.0%). For the other patients there was partial response and complete response in 38 patients (90.5%), and stable disease in the remaining four patients (9.5%) (P = 0.035).Conclusion:  Neoadjuvant chemotherapy can effectively eliminate the pathological risk factors and improve long‐term survival in patients with locally advanced cervical cancer.