bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Selectivity and Specificity of the Proteasome Inhibitors BzLLLCOCHO, PS-341, and MG-132
Authors: Crawford Lisa J.A. , Walker Brian , Ovaa Huib , Chauhan Dharminder , Anderson Kenneth C. , Morris Treen C.M. , Irvine Alexandra E.
Published: June 2006

The 26S proteasome is a multicatalytic protease responsible for regulated intracellular protein degradation. Its function is mediated by three main catalytic activities: (a) chymotrypsin-like (CT-L), (b) trypsin-like, and (c) peptidylglutamyl peptide hydrolysing (PGPH). Proteasome inhibition is an emerging therapy for many cancers and is a novel treatment for multiple myeloma. Here, we profile the contributions of the three catalytic activities in multiple myeloma cell lines and compare the specificity and cytotoxicity of the novel proteasome inhibitor BzLLLCOCHO and inhibitors PS-341 (Velcade, bortezomib) and MG-132. Using fluorogenic substrates and an active site-directed probe specific for proteasome catalytic subunits, we show differential subunit specificity for each of the inhibitors. Addition of BzLLLCOCHO strongly inhibited all three catalytic activities, treatment with PS-341 completely inhibited CT-L and PGPH activities, and treatment with MG-132 resulted in weak inhibition of the CT-L and PGPH activities. Multiple myeloma cells were more sensitive to induction of apoptosis by PS-341 and MG-132 than BzLLLCOCHO. This study emphasizes the need for further investigation of the effects of these compounds on gene and protein expression in the cell to allow for the development of more specific and targeted inhibitors. (Cancer Res 2006; 66(12): 6379-86)
Mutagen Sensitivity Has High Heritability: Evidence from a Twin Study
Authors: Wu Xifeng , Spitz Margaret R. , Amos Christopher I. , Lin Jie , Shao Lina , Gu Jian , de Andrade Mariza , Benowitz Neal L. , Shields Peter G. , Swan Gary E.
Published: June 2006

Despite numerous studies showing that mutagen sensitivity is a cancer predisposition factor, the heritability of mutagen sensitivity has not been clearly established. In this report, we used a classic twin study design to examine the role of genetic and environmental factors on the mutagen sensitivity phenotype. Mutagen sensitivity was measured in peripheral blood lymphocytes from 460 individuals [148 pairs of monozygotic (MZ) twins, 57 pairs of dizygotic (DZ) twins, and 50 siblings]. The intraclass correlation coefficients were all significantly higher in MZ twins than in dizygotes (DZ pairs and MZ-sibling pairs combined) for sensitivity to four different mutagen challenges. Applying biometric genetic modeling, we calculated a genetic heritability of 40.7%, 48.0%, 62.5%, and 58.8% for bleomycin, benzo[a]pyrene diol epoxide, γ-radiation, and 4-nitroquinoline-1-oxide sensitivity, respectively. This study provides the strongest and most direct evidence that mutagen sensitivity is highly heritable, thereby validating the use of mutagen sensitivity as a cancer susceptibility factor. (Cancer Res 2006; 66(12): 5993-6)
Phase 1 and Pharmacokinetic Study of Intravenous Irinotecan in Refractory Solid Tumor Patients with Hepatic Dysfunction
Authors: Schaaf Larry J. , Hammond Lisa A. , Tipping Stuart J. , Goldberg Richard M. , Goel Rakesh , Kuhn John G. , Miller Langdon L. , Compton Linda D. , Cisar Laura A. , Elfring Gary L. , Gruia Gabriela , McGovren J. Patrick , Pirotta Nicoletta , Yin Donghua , Sharma Amarnath , Duncan Barbara A. , Rothenberg Mace L.
Published: June 2006

Purpose: To determine the recommended starting doses and pharmacokinetics of irinotecan in cancer patients with impaired liver function treated on a weekly schedule.

Experimental Design: Patients with solid tumors who had impaired liver function were enrolled into four groups based on baseline serum total bilirubin and aspartate aminotransferase (AST)/alanine aminotransferase (ALT): Group 1 (n = 19): total bilirubin 1.5 to 3.0 × institutional upper limit of normal (IULN) and ALT/AST ≤5.0 × IULN; Group 2 (n = 7): total bilirubin 3.1 to 5.0 × IULN and ALT/AST ≤5.0 × IULN; Group 3 (n = 6): total bilirubin ≤1.5 × IULN and ALT/AST 5.1 to 20.0 × IULN; Group 4 (n = 10): total bilirubin 1.5 to 3.0 × IULN and ALT/AST 5.1 to 20.0 × IULN. Irinotecan was given as a 90-minute i.v. infusion weekly for the first 4 weeks in each 6-week cycle at starting doses which escalated from 40 to as much as 75 mg/m2. After the first treatment, doses were adjusted based on individual patient toxicities. Starting doses for patients with hepatic dysfunction were derived from the maximum tolerated doses noted in the four hepatic dysfunction groups.

Results: Forty-two patients were treated. Among the most frequent adverse events were neutropenia (41%, grades 3/4), diarrhea (15%, grades 3/4), nausea (10%, grade 3), and vomiting (5%, grades 3/4). Two patients died from drug-induced neutropenic sepsis. Two patients had objective tumor responses (complete response, liver metastases from unknown primary; partial response, colon cancer). Hepatic dysfunction reduced irinotecan clearance while increasing relative exposure to the active metabolite, 7-ethyl-10-hydroxycamptothecin (SN-38). SN-38 exposures in patients receiving doses of 40 to 75 mg/m2 were comparable to exposures in patients with normal liver function treated with a starting dose of 125 mg/m2.

Conclusions: Irinotecan starting doses that seem to be safe for hepatically impaired patients treated with the weekly schedule are 60, 50, 60, and 40 mg/m2 for groups 1 to 4, respectively. At these starting doses, exposure to SN-38 and the adverse event profile are similar to that observed in patients with normal liver function and antitumor activity can be observed.
Local Targeting of Malignant Gliomas by the Diffusible Peptidic Vector 1,4,7,10-Tetraazacyclododecane-1-Glutaric Acid-4,7,10-Triacetic Acid-Substance P
Authors: Kneifel Stefan , Cordier Dominik , Good Stephan , Ionescu Mihai C.S. , Ghaffari Anthony , Hofer Silvia , Kretzschmar Martin , Tolnay Markus , Apostolidis Christos , Waser Beatrice , Arnold Marlene , Mueller-Brand Jan , Maecke Helmut R. , Reubi Jean Claude , Merlo Adrian
Published: June 2006

Purpose: Malignant glial brain tumors consistently overexpress neurokinin type 1 receptors. In classic seed-based brachytherapy, one to several rigid 125I seeds are inserted, mainly for the treatment of small low-grade gliomas. The complex geometry of rapidly proliferating high-grade gliomas requires a diffusible system targeting tumor-associated surface structures to saturate the tumor, including its margins.

Experimental Design: We developed a new targeting vector by conjugating the chelator 1,4,7,10-tetraazacyclododecane-1-glutaric acid-4,7,10-triacetic acid to Arg1 of substance P, generating a radiopharmaceutical with a molecular weight of 1,806 Da and an IC50 of 0.88 ± 0.34 nmol/L. Cell biological studies were done with glioblastoma cell lines. neurokinin type-1 receptor (NK1R) autoradiography was done with 58 tumor biopsies. For labeling, 90Y was mostly used. To reduce the “cross-fire effect” in critically located tumors, 177Lut and 213Bi were used instead. In a pilot study, we assessed feasibility, biodistribution, and early and long-term toxicity following i.t. injection of radiolabeled 1,4,7,10-tetraazacyclododecane-1-glutaric acid-4,7,10-triacetic acid substance P in 14 glioblastoma and six glioma patients of WHO grades 2 to 3.

Results: Autoradiography disclosed overexpression of NK1R in 55 of 58 gliomas of WHO grades 2 to 4. Internalization of the peptidic vector was found to be specific. Clinically, the radiopharmeutical was distributed according to tumor geometry. Only transient toxicity was seen as symptomatic radiogenic edema in one patient (observation period, 7-66 months). Disease stabilization and/or improved neurologic status was observed in 13 of 20 patients. Secondary resection disclosed widespread radiation necrosis with improved demarcation.

Conclusions: Targeted radiotherapy using diffusible peptidic vectors represents an innovative strategy for local control of malignant gliomas, which will be further assessed as a neoadjuvant approach.
Molecular Targeting and Treatment of EGFRvIII-Positive Gliomas Using Boronated Monoclonal Antibody L8A4
Authors: Yang Weilian , Barth Rolf F. , Wu Gong , Kawabata Shinji , Sferra Thomas J. , Bandyopadhyaya Achintya K. , Tjarks Werner , Ferketich Amy K. , Moeschberger Melvin L. , Binns Peter J. , Riley Kent J. , Coderre Jeffrey A. , Ciesielski Michael J. , Fenstermaker Robert A. , Wikstrand Carol J.
Published: June 2006

Purpose: The purpose of the present study was to evaluate a boronated EGFRvIII-specific monoclonal antibody, L8A4, for boron neutron capture therapy (BNCT) of the receptor-positive rat glioma, F98npEGFRvIII.

Experimental Design: A heavily boronated polyamido amine (PAMAM) dendrimer (BD) was chemically linked to L8A4 by two heterobifunctional reagents, N-succinimidyl 3-(2-pyridyldithio)propionate and N-(k-maleimidoundecanoic acid)hydrazide. For in vivo studies, F98 wild-type receptor-negative or EGFRvIII human gene-transfected receptor-positive F98npEGFRvIII glioma cells were implanted i.c. into the brains of Fischer rats. Biodistribution studies were initiated 14 days later. Animals received [125I]BD-L8A4 by either convection enhanced delivery (CED) or direct i.t. injection and were euthanized 6, 12, 24, or 48 hours later.

Results: At 6 hours, equivalent amounts of the bioconjugate were detected in receptor-positive and receptor-negative tumors, but by 24 hours the amounts retained by receptor-positive gliomas were 60.1% following CED and 43.7% following i.t. injection compared with 14.6% ID/g by receptor-negative tumors. Boron concentrations in normal brain, blood, liver, kidneys, and spleen all were at nondetectable levels (<0.5 μg/g) at the corresponding times. Based on these favorable biodistribution data, BNCT studies were initiated at the Massachusetts Institute of Technology Research Reactor-II. Rats received BD-L8A4 (∼40 μg 10B/∼750 μg protein) by CED either alone or in combination with i.v. boronophenylalanine (BPA; 500 mg/kg). BNCT was carried out 24 hours after administration of the bioconjugate and 2.5 hours after i.v. injection of BPA for those animals that received both agents. Rats that received BD-L8A4 by CED in combination with i.v. BPA had a mean ± SE survival time of 85.5 ± 15.5 days with 20% long-term survivors (>6 months) and those that received BD-L8A4 alone had a mean ± SE survival time of 70.4 ± 11.1 days with 10% long-term survivors compared with 40.1 ± 2.2 days for i.v. BPA and 30.3 ± 1.6 and 26.3 ± 1.1 days for irradiated and untreated controls, respectively.

Conclusions: These data convincingly show the therapeutic efficacy of molecular targeting of EGFRvIII using either boronated monoclonal antibody L8A4 alone or in combination with BPA and should provide a platform for the future development of combinations of high and low molecular weight delivery agents for BNCT of brain tumors.
Expression of Tumor Necrosis Factor–Related Apoptosis-Inducing Ligand Receptors 1 and 2 in Melanoma
Authors: McCarthy Mary M. , DiVito Kyle A. , Sznol Mario , Kovacs Daniela , Halaban Ruth , Berger Aaron J. , Flaherty Keith T. , Camp Robert L. , Lazova Rossitza , Rimm David L. , Kluger Harriet M.
Published: June 2006

Purpose: The proapoptotic receptors tumor necrosis factor–related apoptosis-inducing ligand receptor 1 (TRAIL-R1) and TRAIL-R2 are targets of drugs in clinical development, and receptor expression levels may be important determinants of sensitivity to receptor agonists. We assessed TRAIL-R1 and TRAIL-R2 expression patterns in a large cohort of melanomas and benign nevi.

Experimental Design: We analyzed tissue microarrays containing 546 melanomas and 540 nevi using our automated quantitative method to measure protein levels in situ (AQUA). The system uses S100 to define pixels as melanoma (tumor mask) within the array spot and measures intensity of TRAIL-receptor expression using Cy5-conjugated antibodies within the mask. AQUA scores were correlated with clinical and pathologic variables.

Results: TRAIL-R1 and TRAIL-R2 expression was higher in melanomas than in nevi (P < 0.0001), and higher in primary than in metastatic specimens (P = 0.0031 and P < 0.0001, respectively). TRAIL-R1 and TRAIL-R2 expression exceeding the 95th percentile for nevi was found in 19% and 74% of melanoma specimens, respectively. Although on univariate analysis, high TRAIL-R2 expression correlated with increased survival (P = 0.0439), it was not associated with survival within the primary or metastatic subcohorts. TRAIL-R1 expression was not associated with survival.

Conclusions: TRAIL-R1 and TRAIL-R2 expression is higher in malignant melanocytes than in their benign counterparts, suggesting that these receptors might be effective therapeutic targets in melanoma. Expression is higher in early-stage disease than in metastatic specimens, and expression exceeding that found in nevi is found in a substantially larger fraction of melanomas for TRAIL-R2 compared with TRAIL-R1. Assessment of baseline tumor TRAIL receptor expression may be important in analysis of clinical trials involving TRAIL receptor agonists.
Functional Screen for Genes Responsible for Tamoxifen Resistance in Human Breast Cancer Cells
Authors: Meijer Danielle , van Agthoven Ton , Bosma Peter T. , Nooter Kees , Dorssers Lambert C.J.
Published: June 2006

Antiestrogens, such as tamoxifen, are widely used for endocrine treatment of estrogen receptor–positive breast cancer. However, as breast cancer progresses, development of tamoxifen resistance is inevitable. The mechanisms underlying this resistance are not well understood. To identify genes involved in tamoxifen resistance, we have developed a rapid screening method. To alter the tamoxifen-sensitive phenotype of human ZR-75-1 breast cancer cells into a tamoxifen-resistant phenotype, the cells were infected with retroviral cDNA libraries derived from human placenta, human brain, and mouse embryo. Subsequently, the cells were selected for proliferation in the presence of 4-hydroxy-tamoxifen (OH-TAM) and integrated cDNAs were identified by sequence similarity searches. From 155 OH-TAM-resistant cell colonies, a total of 25 candidate genes were isolated. Seven of these genes were identified in multiple cell colonies and thus cause antiestrogen resistance. The epidermal growth factor receptor, platelet-derived growth factor receptor-α, platelet-derived growth factor receptor-β, colony-stimulating factor 1 receptor, neuregulin1, and fibroblast growth factor 17 that we have identified have been described as key regulators in the mitogen-activated protein kinase pathway. Therefore, this pathway could be a valuable target in the treatment of patients with breast cancer resistant to endocrine treatment. In addition, the putative gene LOC400500, predicted by in silico analysis, was identified. We showed that ectopic expression of this gene, designated as breast cancer antiestrogen resistance 4 (BCAR4), caused OH-TAM resistance and anchorage-independent cell growth in ZR-75-1 cells and that the intact open reading frame was required for its function. We conclude that retroviral transfer of cDNA libraries into human breast cancer cells is an efficient method for identifying genes involved in tamoxifen resistance. (Mol Cancer Res 2006;4(6):379–86)
Lateral Reynolds Stress and Eddy Viscosity in a Coastal Strait
Authors: Colbo Keir
Published: June 2006

The lateral Reynolds stress uυ, representing the transfer of along-strait momentum toward the sides of Juan de Fuca Strait, is measured with an array of ADCPs. The contributions to the stress from a number of frequency bands are analyzed to highlight the roles of different processes. Motion in a frequency band that includes internal waves and Doppler-shifted subinertial eddies gives a Reynolds stress that, when scaled by the observed shear, is consistent with an eddy viscosity of O(10 m2 s−1). This viscosity acts on the tides and the estuarine flow. The tides can also impart a viscous stress upon the low-frequency estuarine flow. These tidal currents, although strong, are largely nondivergent within the area of the array and thus appear to be less important for the cross-strait transfer of momentum. The long-term mean estuarine circulation can be acted upon by meanders of the estuarine flow, defined as features with periods of 3–5 days. These meanders are found to also have a horizontal eddy viscosity of O(10 m2 s−1). The measured Reynolds stress divergences are consistent with both the strongly curved profile of the estuarine mean flow and also the more slablike tidal current profile. This paper represents the first direct calculation of eddy viscosity on the medium-sized scale of the array, O(1 km).
Possible Sources Driving the Potential Vorticity Structure and Long-Wave Instability of Coastal Upwelling and Downwelling Currents
Authors: Morel Yves G. , Darr David S. , Talandier Claude
Published: June 2006

It is well known that upwelling and downwelling currents are unstable to perturbations. Less is, however, known about the physical mechanism responsible for the observed and modeled instabilities. It is shown that the origin of the long-wave barotropic/baroclinic instability observed on upwelling currents has to be sought among diabatic or thermobaric mechanisms. In particular, the role of mixing associated with Kelvin–Helmholtz instability and of wind forcing is investigated. Low Richardson numbers occur when the pycnocline outcrops at the sea surface. The criterion for instability (Ri ≤ 1/4) can be reached in a narrow region close to the upwelling front, permitting Kelvin–Helmholtz instability and mixing. This can precondition the current for long-wave instability by transforming the current's potential vorticity. A constant wind can likewise modify the potential vorticity. The resulting potential vorticity anomaly is always negative for both upwelling and downwelling currents, and this anomaly interacts with the outcropped front, destabilizing it. Examples are provided via numerical calculations using an idealized front. A wind stress is an effective means of inducing the negative PV necessary for instability; with wind, Kelvin–Helmholz instability, when present, merely modifies the instability characteristics. In addition, upwelling fronts are always less stable than comparable downwelling fronts.
A Coupled Coastal Polynya–Atmospheric Boundary Layer Model
Authors: Walkington I. A. , Willmott A. J.
Published: June 2006

This paper formulates and presents opening solutions of a one-dimensional coastal polynya flux model in which frazil ice is characterized by its depth and concentration. In comparison with polynya flux models in which variable frazil ice concentration is absent, this model is found to predict a smaller heat flux to the atmosphere. Consequently the model in this paper exhibits a wider steady-state polynya and longer opening times when compared with models in which ice concentration is neglected. The aforementioned polynya flux model is then coupled to a lower-atmosphere boundary layer model, and it is demonstrated that the polynya opening time and the steady-state width are significantly altered in the coupled, as compared with the decoupled, system. In essence, the heating of the lower atmosphere above the evolving polynya in the coupled system reduces the sensible heat flux between the ocean and atmosphere, thereby reducing the frazil ice production rate and hence leading to longer polynya opening time and wider steady-state width. This phenomenon is particularly noticeable when the potential temperature of the atmosphere at the coast is only slightly below the freezing point. In addition, a cutoff atmospheric wind speed is shown to exist, above which a steady-state polynya can never be obtained. Solutions calculated by the two models, using parameters representative of the St. Lawrence Island polynya, show that the new models contain substantial predictive capability.
Two-Way Feedback Interaction between the Thermohaline and Wind-Driven Circulations
Authors: MacMynowski Douglas G. , Tziperman Eli
Published: June 2006

The thermohaline circulation (THC) affects the meridional atmospheric temperature gradient and therefore the atmospheric wind and the wind-driven ocean circulation. The wind-driven circulation (WDC), in turn, affects the THC by the advection of salinity anomalies into deep-water formation sites. This paper considers this two-way coupling between the WDC and THC using a simple box-type model and analysis tools from engineering feedback control. The two-way feedback can have a significant effect on the dynamics of the coupled system. For a reasonable choice of parameters, the feedback destabilizes the THC equilibrium for low freshwater forcing. For higher freshwater forcing, the feedback results in a new stable equilibrium instead of the large amplitude oscillation that develops without feedback. It is expected that the analysis approach used here may be broadly applicable to the study of feedback interconnections of other climate systems as well.
Evolution of the Deep Water in the Canadian Basin in the Arctic Ocean
Authors: Timmermans M-L. , Garrett Chris
Published: June 2006

An overflow of magnitude 0.25 Sv (Sv ≡ 106 m−3 s−1) has been predicted to enter the Makarov Basin (part of the Canadian Basin in the Arctic Ocean) from the Eurasian Basin via a deep gap in the dividing Lomonosov ridge. The authors argue that this overflow does not ventilate the deep Makarov Basin (below 2400 m) where the water is too warm and salty to be compatible with such a large cold fresh inflow. However, complete isolation of the homogeneous bottom layer of the Makarov Basin must be ruled out because changes there are too small to arise from more than a small fraction of the measured geothermal heat flux into the basin. A small cold fresh inflow of about 0.01 Sv from the Amundsen Basin seems to be required. This could occur if the gap in the dividing Lomonosov Ridge is shallower than previously thought. It could also occur if there is active mixing and dilution of the predicted overflow in the gap, leaving only a small fraction to descend into the deep Makarov Basin. Hydraulic theory and hydrographic observations are used to rule out any significant flow of dense water from the Makarov Basin into the deep Canada Basin, confirming previous hypotheses of isolation of the deep water in the Canada Basin.
Brazilian Fiction and the Postmodern Horizon
Authors: Pellegrini Tânia
Published: June 2006

Examination of trends in postmodernist theory with regard to cultural production from a Brazilian perspective and an analysis of the production of Brazilian writers reveals that postmodernism creates a “market culture” and that the pressures and limits of this culture influence the form and content of texts.
Brazilian Indifference to Racial Inequality in the Labor Market
Authors: Santos Sales Augusto dos , Silva Nelson Olokafá Inocêncio da
Published: June 2006

Statistical data show that the perverse inequality between blacks and whites in the Brazilian labor market has not caused the society to develop and implement concrete proposals to eliminate racism in Brazil. There are various explanations for this moral indifference. One element that is essential to any analysis of it is that Brazilians have been socialized by images disseminated by the mass media that prevent blacks from being considered ordinary citizens or even human beings.
Forodesine, an inhibitor of purine nucleoside phosphorylase, induces apoptosis in chronic lymphocytic leukemia cells
Authors: Balakrishnan Kumudha , Nimmanapalli Ramadevi , Ravandi Farhad , Keating Michael J. , Gandhi Varsha
Published: June 2006

Purine nucleoside phosphorylase (PNP) deficiency in humans results in T lymphocytopenia. Forodesine, a potent inhibitor of PNP, was designed based on the transition-state structure stabilized by the enzyme. Previous studies established that forodesine in the presence of deoxyguanosine (dGuo) inhibits the proliferation of T lymphocytes. A phase 1 clinical trial of forodesine in T-cell malignancies demonstrated significant antileukemic activity with an increase in intracellular dGuo triphosphate (dGTP). High accumulation of dGTP in T cells may be dependent on the levels of deoxynucleoside kinases. Because B-cell chronic lymphocytic leukemia (B-CLL) cells have high activity of deoxycytidine kinase (dCK), we hypothesized that these lymphocytes would respond to forodesine. This postulate was tested in primary lymphocytes during in vitro investigations. Lymphocytes from 12 patients with CLL were incubated with forodesine and dGuo. These CLL cells showed a wide variation in the accumulation of intracellular dGTP without any effect on other deoxynucleotides. This was associated with DNA damage-induced p53 stabilization, phosphorylation of p53 at Ser15, and activation of p21. The dGTP accumulation was related to induction of apoptosis measured by caspase activation, changes in mitochondrial membrane potential, and PARP cleavage. Based on these data, a phase 2 clinical trial of forodesine has been initiated for CLL patients.
ESTimating plant phylogeny: lessons from partitioning
Authors: de la Torre Jose EB , Egan Mary G , Katari Manpreet S , Brenner Eric D , Stevenson Dennis W , Coruzzi Gloria M , DeSalle Rob
Published: June 2006

Background

While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies.

Results

A maximum parsimony (MP) analysis resulted in a single tree with relatively high support at all nodes in the tree despite rampant conflict among trees generated from the separate analysis of individual partitions. In a comparison of broader-scale groupings based on cellular compartment (ie: chloroplast, mitochondrial or nuclear) or function, only the nuclear partition tree (based largely on EST data) was found to be topologically identical to the tree based on the simultaneous analysis of all data. Despite topological conflict among the broader-scale groupings examined, only the tree based on morphological data showed statistically significant differences.

Conclusion

Based on the amount of character support contributed by EST data which make up a majority of the nuclear data set, and the lack of conflict of the nuclear data set with the simultaneous analysis tree, we conclude that the inclusion of EST data does provide a viable and efficient approach to address phylogenetic questions within a parsimony framework on a genomic scale, if problems of orthology determination and potential sequencing errors can be overcome. In addition, approaches that examine conflict and support in a simultaneous analysis framework allow for a more precise understanding of the evolutionary history of individual process partitions and may be a novel way to understand functional aspects of different kinds of cellular classes of gene products.
Glutamate-induced apoptosis in neuronal cells is mediated via caspase-dependent and independent mechanisms involving calpain and caspase-3 proteases as well as apoptosis inducing factor (AIF) and this process is inhibited by equine estrogens
Authors: Zhang YueMei , Bhavnani Bhagu R
Published: June 2006

Background

Glutamate, a major excitatory amino acid neurotransmitter, causes apoptotic neuronal cell death at high concentrations. Our previous studies have shown that depending on the neuronal cell type, glutamate-induced apoptotic cell death was associated with regulation of genes such as Bcl-2, Bax, and/or caspase-3 and mitochondrial cytochrome c. To further delineate the intracellular mechanisms, we have investigated the role of calpain, an important calcium-dependent protease thought to be involved in apoptosis along with mitochondrial apoptosis inducing factor (AIF) and caspase-3 in primary cortical cells and a mouse hippocampal cell line HT22.

Results

Glutamate-induced apoptotic cell death in neuronal cells was associated with characteristic DNA fragmentation, morphological changes, activation of calpain and caspase-3 as well as the upregulation and/or translocation of AIF from mitochondria into cytosol and nuclei. Our results reveal that primary cortical cells and HT22 cells display different patterns of regulation of these genes/proteins. In primary cortical cells, glutamate induces activation of calpain, caspase-3 and translocation of AIF from mitochondria to cytosol and nuclei. In contrast, in HT22 cells, only the activation of calpain and upregulation and translocation of AIF occurred. In both cell types, these processes were inhibited/reversed by 17β-estradiol and Δ8,17β-estradiol with the latter being more potent.

Conclusion

Depending upon the neuronal cell type, at least two mechanisms are involved in glutamate-induced apoptosis: a caspase-3-dependent pathway and a caspase-independent pathway involving calpain and AIF. Since HT22 cells lack caspase-3, glutamate-induced apoptosis is mediated via the caspase-independent pathway in this cell line. Kinetics of this apoptotic pathway further indicate that calpain rather than caspase-3, plays a critical role in the glutamate-induced apoptosis. Our studies further indicate that glutamate- induced changes of these proteins can be inhibited by estrogens, with Δ8,17β-estradiol, a novel equine estrogen being more potent than 17β-estradiol. To our knowledge, this is the first demonstration that glutamate-induced apoptosis involves regulation of multiple apoptotic effectors that can be inhibited by estrogens. Whether these observations can help in the development of novel therapeutic approaches for the prevention of neurodegenerative diseases with estrogens and calpain inhibitors remains to be investigated.
Identification of specific calcitonin-like receptor residues important for calcitonin gene-related peptide high affinity binding
Authors: Banerjee Sugato , Evanson Janel , Harris Erik , Lowe Stephen L , Thomasson Kathryn A , Porter James E
Published: June 2006

Background

Calcitonin gene-related peptide (CGRP) is a vasoactive neuropeptide whose biological activity has potential therapeutic value for many vascular related diseases. CGRP is a 37 amino acid neuropeptide that signals through a G protein-coupled receptor belonging to the secretin receptor family. Previous studies on the calcitonin-like receptor (CLR), which requires co-expression of the receptor-activity-modifying protein-1 (RAMP1) to function as a CGRP receptor, have shown an 18 amino acid N-terminus sequence important for binding CGRP. Moreover, several investigations have recognized the C-terminal amidated phenylalanine (F37) of CGRP as essential for docking to the mature receptor. Therefore, we hypothesize that hydrophobic amino acids within the previously characterized 18 amino acid CLR N-terminus domain are important binding contacts for the C-terminal phenylalaninamide of CGRP.

Results

Two leucine residues within this previously characterized CLR N-terminus domain, when mutated to alanine and expressed on HEK293T cells stably transfected with RAMP1, demonstrated a significantly decreased binding affinity for CGRP compared to wild type receptor. Additional decreases in binding affinity for CGRP were not found when both leucine mutations were expressed in the same CLR construct. Decreased binding characteristic of these leucine mutant receptors was observed for all CGRP ligands tested that contained the necessary amidated phenylalanine at their C-terminus. However, there was no difference in the potency of CGRP to increase cAMP production by these leucine mutant receptors when compared to wild type CLR, consistent with the notion that the neuropeptide C-terminal F37 is important for docking but not activation of the receptor. This observation was conserved when modified CGRP ligands lacking the amidated F37 demonstrated similar potencies to generate cAMP at both wild type and mutant CLRs. Furthermore, these modified CGRP ligands displayed a significant but similar loss of binding for all leucine mutant and wild type CLR because the important receptor contact on the neuropeptide was missing in all experimental situations.

Conclusion

These results are consistent with previous structure-function investigations of the neuropeptide and are the first to propose specific CLR binding contacts for the amidated F37 of CGRP that are important for docking but not activation of the mature CGRP receptor.
Identifying priorities in methodological research using ICD-9-CM and ICD-10 administrative data: report from an international consortium
Authors: De Coster Carolyn , Quan Hude , Finlayson Alan , Gao Min , Halfon Patricia , Humphries Karin H , Johansen Helen , Lix Lisa M , Luthi Jean-Christophe , Ma Jin , Romano Patrick S , Roos Leslie , Sundararajan Vijaya , Tu Jack V , Webster Greg , Ghali William A
Published: June 2006

Background

Health administrative data are frequently used for health services and population health research. Comparative research using these data has been facilitated by the use of a standard system for coding diagnoses, the International Classification of Diseases (ICD). Research using the data must deal with data quality and validity limitations which arise because the data are not created for research purposes. This paper presents a list of high-priority methodological areas for researchers using health administrative data.

Methods

A group of researchers and users of health administrative data from Canada, the United States, Switzerland, Australia, China and the United Kingdom came together in June 2005 in Banff, Canada to discuss and identify high-priority methodological research areas. The generation of ideas for research focussed not only on matters relating to the use of administrative data in health services and population health research, but also on the challenges created in transitioning from ICD-9 to ICD-10. After the brain-storming session, voting took place to rank-order the suggested projects. Participants were asked to rate the importance of each project from 1 (low priority) to 10 (high priority). Average ranks were computed to prioritise the projects.

Results

Thirteen potential areas of research were identified, some of which represented preparatory work rather than research per se. The three most highly ranked priorities were the documentation of data fields in each country's hospital administrative data (average score 8.4), the translation of patient safety indicators from ICD-9 to ICD-10 (average score 8.0), and the development and validation of algorithms to verify the logic and internal consistency of coding in hospital abstract data (average score 7.0).

Conclusion

The group discussions resulted in a list of expert views on critical international priorities for future methodological research relating to health administrative data. The consortium's members welcome contacts from investigators involved in research using health administrative data, especially in cross-jurisdictional collaborative studies or in studies that illustrate the application of ICD-10.
Scrapie infectivity is quickly cleared in tissues of orally-infected farmed fish
Authors: Ingrosso Loredana , Novoa Beatriz , Valle Andrea Z Dalla , Cardone Franco , Aranguren Raquel , Sbriccoli Marco , Bevivino Simona , Iriti Marcello , Liu Quanguo , Vetrugno Vito , Lu Mei , Faoro Franco , Ciappellano Salvatore , Figueras Antonio , Pocchiari Maurizio
Published: June 2006

Background

Scrapie and bovine spongiform encephalopathy (BSE) belongs to the group of animal transmissible spongiform encephalopathy (TSE). BSE epidemic in the UK and elsewhere in Europe has been linked to the use of bovine meat and bone meals (MBM) in the feeding of cattle. There is concern that pigs, poultry and fish bred for human consumption and fed with infected MBM would eventually develop BSE or carry residual infectivity without disease. Although there has been no evidence of infection in these species, experimental data on the susceptibility to the BSE agent of farm animals other than sheep and cow are limited only to pigs and domestic chicken. In the framework of a EU-granted project we have challenged two species of fish largely used in human food consumption, rainbow trout (Oncorhynchus mykiss) and turbot (Scophthalmus maximus), with a mouse-adapted TSE strain (scrapie 139A), to assess the risk related to oral consumption of TSE contaminated food. In trout, we also checked the "in vitro" ability of the pathological isoform of the mouse prion protein (PrPSc) to cross the intestinal epithelium when added to the mucosal side of everted intestine.

Results

Fish challenged with a large amount of scrapie mouse brain homogenate by either oral or parenteral routes, showed the ability to clear the majority of infectivity load. None of the fish tissues taken at different time points after oral or parenteral inoculation was able to provoke scrapie disease after intracerebral inoculation in recipient mice. However, a few recipient mice were positive for PrPSc and spongiform lesions in the brain. We also showed a specific binding of PrPSc to the mucosal side of fish intestine in the absence of an active uptake of the prion protein through the intestinal wall.

Conclusion

These results indicate that scrapie 139A, and possibly BSE, is quickly removed from fish tissues despite evidence of a prion like protein in fish and of a specific binding of PrPSc to the mucosal side of fish intestine.
Neural tube derived signals and Fgf8 act antagonistically to specify eye versus mandibular arch muscles
Authors: von Scheven Gudrun , Alvares Lúcia E. , Mootoosamy Roy C. , Dietrich Susanne
Published: June 2006

Recent knockout experiments in the mouse generated amazing craniofacial skeletal muscle phenotypes. Yet none of the genes could be placed into a molecular network, because the programme to control the development of muscles in the head is not known. Here we show that antagonistic signals from the neural tube and the branchial arches specify extraocular versus branchiomeric muscles. Moreover, we identified Fgf8 as the branchial arch derived signal. However, this molecule has an additional function in supporting the proliferative state of myoblasts, suppressing their differentiation, while a further branchial arch derived signal, namely Bmp7, is an overall negative regulator of head myogenesis.
Thebrain tumorgene negatively regulates neural progenitor cell proliferation in the larval central brain ofDrosophila
Authors: Bello Bruno , Reichert Heinrich , Hirth Frank
Published: June 2006

Brain development in Drosophila is characterized by two neurogenic periods, one during embryogenesis and a second during larval life. Although much is known about embryonic neurogenesis, little is known about the genetic control of postembryonic brain development. Here we use mosaic analysis with a repressible cell marker (MARCM) to study the role of the brain tumor(brat) gene in neural proliferation control and tumour suppression in postembryonic brain development of Drosophila. Our findings indicate that overproliferation in brat mutants is due to loss of proliferation control in the larval central brain and not in the optic lobe. Clonal analysis indicates that the brat mutation affects cell proliferation in a cell-autonomous manner and cell cycle marker expression shows that cells of brat mutant clones show uncontrolled proliferation, which persists into adulthood. Analysis of the expression of molecular markers, which characterize cell types in wild-type neural lineages,indicates that brat mutant clones comprise an excessive number of cells, which have molecular features of undifferentiated progenitor cells that lack nuclear Prospero (Pros). pros mutant clones phenocopy brat mutant clones in the larval central brain, and targeted expression of wild-type pros in brat mutant clones promotes cell cycle exit and differentiation of brat mutant cells, thereby abrogating brain tumour formation. Taken together, our results provide evidence that the tumour suppressor brat negatively regulates cell proliferation during larval central brain development of Drosophila,and suggest that Prospero acts as a key downstream effector of bratin cell fate specification and proliferation control.
Induction and prepatterning of the zebrafish pectoral fin bud requires axial retinoic acid signaling
Authors: Gibert Yann , Gajewski Alexandra , Meyer Axel , Begemann Gerrit
Published: June 2006

Vertebrate forelimbs arise as bilateral appendages from the lateral plate mesoderm (LPM). Mutants in aldh1a2 (raldh2), an embryonically expressed gene encoding a retinoic acid (RA)-synthesizing enzyme, have been used to show that limb development and patterning of the limb bud are crucially dependent on RA signaling. However, the timing and cellular origin of RA signaling in these processes have remained poorly resolved. We have used genetics and chemical modulators of RA signaling to resolve these issues in the zebrafish. By rescuing pectoral fin induction in the aldh1a2/neckless mutant with exogenous RA and by blocking RA signaling in wild-type embryos, we find that RA acts as a permissive signal that is required during the six- to eight-somite stages for pectoral fin induction. Cell-transplantation experiments show that RA production is not only crucially required from flanking somites, but is sufficient to permit fin bud initiation when the trunk mesoderm is genetically ablated. Under the latter condition, intermediate mesoderm alone cannot induce the pectoral fin field in the LPM. We further show that induction of the fin field is directly followed by a continued requirement for somite-derived RA signaling to establish a prepattern of anteroposterior fates in the condensing fin mesenchyme. This process is mediated by the maintained expression of the transcription factor hand2, through which the fin field is continuously posteriorized, and lasts up to several hours prior to limb-budding. Thus, RA signaling from flanking somites plays a dual early role in the condensing limb bud mesenchyme.
Electroanalytical Determination of the Fungicides Folfet, Phosmet, and Dialifos in Grains and Soils
Authors: Sreedhar Neelam Yugandhar , Kumar Reddy Polu Rajendra , Subba Reddy Gopi Reddy Venkata , Jayarama Reddy Srinivasula Reddy
Published: June 2006

The electrochemical behavior of the fungicides folfet, phosmet, and dialifos was studied using differential pulse polarography in unversal buffers of pH 2.0 to 6.0. The cathodic peak observed for folfet, phosmet, and dialifos is attributed to the reduction of the carbonyl group, and was shown to be pH-dependent. Differential pulse polarography was used to estimate folfet, phosmet, and dialifos in agricultural formulations, grains and soil samples. Both standard addition and calibration methods were used for the analytical measurements. The lower detection limits were found to be 1.9 × 10−9, 1.72 × 10−9, and 2.12 × 10−1 M, respectively.
Synthetic Studies of Archaeal Macrocyclic Tetraether Lipids: Practical Synthesis of 72-Membered Tetraether Model Compounds
Authors: Eguchi Tadashi , Kano Hiroki , Arakawa Kenji , Kakinuma Katsumi
Published: June 2006

Archaeal 72-membered macrocyclic tetraether model compounds (5 and 6) were synthesized by intramolecular dicarbonyl coupling with the aid of low-valent titanium, which is known as McMurry coupling. This synthetic methodology is the first practical way to obtain the two regioisomeric structures in quantity and appears to be applicable to the natural 72-membered tetraether lipids (3 and 4). Also described is the synthesis of the corresponding acyclic tetraether model counterparts (7 and 8) in reference to the cyclic lipids.
Preparation of 3,3-Bis(alkylthio)-1,1-dipiperidino-2-propenylium Iodides by S-Alkylation of Alkyl 3,3-Dipiperidinodithioacrylates
Authors: Akimoto Keiichi , Sugihara Yoshiaki , Nakayama Juzo
Published: June 2006

Methylation of propyl 3,3-dipiperidinodithioacrylate with iodomethane afforded a 93 : 7 mixture of (E)- and (Z)-3-methylthio-3-propylthio-1,1-dipiperidino-2-propenylium iodides nearly quantitatively, while propylation of methyl 3,3-dipiperidinodithioacrylate with 1-iodopropane produced a 6 : 94 mixture of the above isomers. Study of these iodides led to the conclusions that (a) free rotation about the C2–C3 bond is frozen for these carbenium ions, thus allowing the clearly distinguishable E- and Z-isomers to exist and (b) the alkylation takes place in such a manner that the newly formed S-alkyl group and the carbenium carbon atom become cis to each other. Such stereoselectivity was general for methylation of a series of alkyl 3,3-dipiperidinodithioacrylates and was explained by examining the preferred conformation of the starting dithioacrylates with NMR and X-ray diffraction analyses.
Synthesis via 2-Acylmethyl-2-oxazoline. I. A Novel Synthesis of 3-Acyl-2-pyridones by Michael Addition of 2-Acylmethyl-2-oxazoline to α,β-Acetylenic Ketones
Authors: Tohda Yasuo , Yanagidani Takeshi , Hiramatsu Shin-ichi , Nishiwaki Nagatoshi , Tani Keita , Imagawa Kazuko , Ariga Masahiro
Published: June 2006

The reaction of the sodium salt of 2-acylmethyl-4,4-dimethyl-2-oxazolines with α,β-acetylenic ketones in ethanol gave Michael adducts, which were easily transformed to 4,6-disubstituted 3-acyl-1-(2-hydroxy-1,1-dimethylethyl)-2-pyridones by silica gel. N-Dealkylation of the pyridones was performed using hydrochloric acid in good yields. Deacylation of the pyridones was performed using potassium hydroxide. A mild treatment of the pyridones with bases or silica gel gave 7-oxa-1-azabicyclo[4.3.0]non-3-en-2-one derivatives via intramolecular Michael addition. A similar reaction of 2-phenacyl-2-oxazoline with diphenylpropynone gave the corresponding 1-(2-hydroxyethyl)-2-pyridone derivative, which was inert against these 1-dealkylation, 3-deacylation, and intramolecular addition reactions.
Specific Inclusion of 1,2-Dimethoxybenzene Derivatives by Crystalline (R)-Arylglycyl-(R)-phenylglycines and Its Structure
Authors: Akazome Motohiro , Yanagita Yukiko , Sonobe Ryo-ichi , Ogura Katsuyuki
Published: June 2006

The crystallization of (R)-arylglycyl-(R)-phenylglycine (1, aryl = phenyl; 2, aryl = 1-naphthyl) in the presence of 1,2-dimethoxybenzene or its derivatives affords an inclusion compound. A single-crystal X-ray analysis has shown that, in a 1,2-dimethyoxybenzene inclusion compound, dipeptide molecules arrange in a sheet and the 1,2-dimethoxybenzene lies at the end in a void between the sheets by being anchored to an ammonio hydrogen on the sheet via three-center hydrogen bonding. The distance between the sheets was found to be variable according to the length of the guest 1,2-dimethoxybenzene derivatives, as if they were pillars that support the sheets.