bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeting PBR by Hexaminolevulinate-Mediated Photodynamic Therapy Induces Apoptosis through Translocation of Apoptosis-Inducing Factor in Human Leukemia Cells
Authors: Furre Ingegerd Eggen , Shahzidi Susan , Luksiene Zivile , Møller Michael T.N. , Borgen Elin , Morgan Janet , Tkacz-Stachowska Kinga , Nesland Jahn M. , Peng Qian
Published: December 2005

Photodynamic therapy (PDT) with endogenous protoporphyrin IX derived from 5-aminolevulinic acid or its derivatives has been established for treatments of several premalignancies and malignancies; however, the mechanism of the modality is not fully elucidated. The mitochondrial permeability transition pore consists mainly of the mitochondrial outer membrane voltage-dependent anion channel and the peripheral benzodiazepine receptor (PBR) and the mitochondrial inner membrane adenine nucleotide translocator (ANT). These mitochondrial proteins are responsible for the permeability transition that leads to apoptosis. In the present study, the human leukemia cell line, Reh, was treated with PDT using hexaminolevulinate (HAL). More than 80% of apoptotic Reh cells were found after HAL-mediated PDT (HAL-PDT) with high-molecular-weight (50 kbp) DNA fragmentation. Addition of PK11195 or Ro5-4864, two ligands of PBR, during HAL-PDT significantly inhibited the apoptotic effect. Bongkrekic acid, a ligand for ANT, also reduced the PDT effect. Although the mitochondrial transmembrane potential collapsed, neither cytosolic translocation of mitochondrial cytochrome c nor activation of caspase-9, caspase-8, caspase-3, and poly(ADP-ribose) polymerase were found. However, nuclear translocation of mitochondrial apoptosis-inducing factor (AIF) was shown by both immunoblotting and immunocytochemistry. Because AIF is the sole one among all proapoptotic factors involved in caspase-dependent and caspase-independent pathways that induces the high-molecular-weight DNA fragmentation, we conclude that HAL-PDT specifically targets PBR, leading to apoptosis of the Reh cells through nuclear translocation of mitochondrial AIF. This study suggests PBR as a possible novel therapeutic target for HAL-based PDT of cancer.
Evidence for the Direct Binding of Phosphorylated p53 to Sites of DNA Breaks In vivo
Authors: Al Rashid Shahnaz T. , Dellaire Graham , Cuddihy Andrew , Jalali Farid , Vaid Mita , Coackley Carla , Folkard Melvyn , Xu Yang , Chen Benjamin P.C. , Chen David J. , Lilge Lothar , Prise Kevin M. , Bazett Jones David P. , Bristow Robert G.
Published: December 2005

Despite a clear link between ataxia-telangiectasia mutated (ATM)–dependent phosphorylation of p53 and cell cycle checkpoint control, the intracellular biology and subcellular localization of p53 phosphoforms during the initial sensing of DNA damage is poorly understood. Using G0-G1 confluent primary human diploid fibroblast cultures, we show that endogenous p53, phosphorylated at Ser15 (p53Ser15), accumulates as discrete, dose-dependent and chromatin-bound foci within 30 minutes following induction of DNA breaks or DNA base damage. This biologically distinct subpool of p53Ser15 is ATM dependent and resistant to 26S-proteasomal degradation. p53Ser15 colocalizes and coimmunoprecipitates with γ-H2AX with kinetics similar to that of biochemical DNA double-strand break (DNA-dsb) rejoining. Subnuclear microbeam irradiation studies confirm p53Ser15 is recruited to sites of DNA damage containing γ-H2AX, ATMSer1981, and DNA-PKcsThr2609 in vivo. Furthermore, studies using isogenic human and murine cells, which express Ser15 or Ser18 phosphomutant proteins, respectively, show defective nuclear foci formation, decreased induction of p21WAF, decreased γ-H2AX association, and altered DNA-dsb kinetics following DNA damage. Our results suggest a unique biology for this p53 phosphoform in the initial steps of DNA damage signaling and implicates ATM-p53 chromatin-based interactions as mediators of cell cycle checkpoint control and DNA repair to prevent carcinogenesis.
Effects of VHL Deficiency on Endolymphatic Duct and Sac
Authors: Gläsker Sven , Lonser Russell R. , Tran Maxine G.B. , Ikejiri Barbara , Butman John A. , Zeng Weifen , Maxwell Patrick H. , Zhuang Zhengping , Oldfield Edward H. , Vortmeyer Alexander O.
Published: December 2005

The von Hippel-Lindau (VHL) disease is caused by VHL germ line mutation. Inactivation of the wild-type copy of the VHL gene leads to up-regulation of hypoxic response and tumor formation within central nervous system (CNS), kidneys, pancreas, adrenal glands, epididymis, broad ligament, and the endolymphatic sac/petrous bone. Endolymphatic sac tumors (ELST) have been proposed to be derived from endolymphatic sac epithelium, but other possible structures of origin have been implicated. To clarify the anatomic and cellular origin of ELSTs, we did a morphologic and molecular pathologic analysis of 16 tumors. In addition, we investigated effects of VHL deficiency on “tumor-free” endolymphatic duct and sac of VHL patients. Several tumors included in this study were <1 cm in size, and their origin could be placed in the intraosseous portion of the endolymphatic duct/sac. Furthermore, by analysis of clinically uninvolved “tumor-free” endolymphatic duct and sac tissues of VHL patients, we discovered a variety of VHL-deficient microscopic abnormalities with morphologic similarities to ELSTs. We conclude that most, if not all, ELSTs arise within the intraosseous portion of the endolymphatic duct/sac, the vestibular aqueduct. In analogy to renal parenchyma and selected topographical sites within the CNS, endolymphatic duct/sac epithelia are preferentially and multifocally targeted in VHL disease. The primary effect of VHL deficiency on human endolymphatic duct/sac epithelium seems to be the generation of multifocal sites of VHL-deficient cell proliferations from which tumorigenesis may or may not occur. Therefore, inactivation of the VHL wild-type allele seems necessary but not sufficient for the formation of tumor.
Hypoxia-Induced Phosphorylation of Chk2 in an Ataxia Telangiectasia Mutated–Dependent Manner
Authors: Gibson Shannon L. , Bindra Ranjit S. , Glazer Peter M.
Published: December 2005

Chk2 is a serine/threonine kinase that signals to cell cycle arrest, DNA repair, and apoptotic pathways following DNA damage. It is activated by phosphorylation in response to ionizing radiation, UV light, stalled replication forks, and other types of DNA damage. Hypoxia is a common feature of solid tumors and has been shown to affect the regulation of many genes, including several DNA repair factors. We show here that Chk2 is phosphorylated on Thr68 and thereby activated in cells in response to hypoxia, and that this phosphorylation is dependent on the damage response kinase ataxia telangiectasia mutated (ATM) but not on the related kinase ATM and Rad3-related. Moreover, phosphorylation of Chk2 under hypoxia was attenuated in cells deficient in the repair factors MLH1 or NBS1. Finally, Chk2 serves to protect cells from apoptosis under hypoxic growth conditions. These results identify hypoxia as a new stimulus for Chk2 activation in an ATM-, MLH1-, and NBS1-dependent manner, and they suggest a novel pathway by which tumor hypoxia may influence cell survival and DNA repair.
Cyclin E Both Regulates and Is Regulated by Calpain 2, a Protease Associated with Metastatic Breast Cancer Phenotype
Authors: Libertini Stephen J. , Robinson Brian S. , Dhillon Navdeep K. , Glick Danielle , George Michael , Dandekar Satya , Gregg Jeffrey P. , Sawai Earl , Mudryj Maria
Published: December 2005

Overexpression of cyclin E in breast tumors is associated with a poor response to tamoxifen therapy, greater genomic instability, more aggressive behavior, and a poor clinical prognosis. These tumors also express low molecular weight isoforms of cyclin E that are associated with higher kinase activity and increased metastatic potential. In the current study, we show that cyclin E overexpression in MCF7 cells transactivates the expression of calpain 2, leading to proteolysis of cyclin E as well as several known calpain substrates including focal adhesion kinase (FAK), calpastatin, pp60src, and p53. In vivo inhibition of calpain activity in MCF7-cyclin E cells impedes cyclin E proteolysis, whereas in vivo induction of calpain activity promotes cyclin E proteolysis. An analysis of human breast tumors shows that high levels of cyclin E are coincident with the expression of the low molecular weight isoforms, high levels of calpain 2 protein, and proteolysis of FAK. Lastly, studies using a mouse model of metastasis reveal that highly metastatic tumors express proteolyzed cyclin E and FAK when compared to tumors with a low metastatic potential. Our results suggest that cyclin E–dependent deregulation of calpain may be pivotal in modifying multiple cellular processes that are instrumental in the etiology and progression of breast cancer.
Persistent Organochlorine Chemicals in Plasma and Risk of Non-Hodgkin's Lymphoma
Authors: De Roos Anneclaire J. , Hartge Patricia , Lubin Jay H. , Colt Joanne S. , Davis Scott , Cerhan James R. , Severson Richard K. , Cozen Wendy , Patterson Donald G. , Needham Larry L. , Rothman Nathaniel
Published: December 2005

Polychlorinated biphenyls (PCB) have been suspected as possible contributors to increasing non-Hodgkin's lymphoma incidence during the latter half of the 20th century based on their toxicologic properties and provocative epidemiologic reports. We investigated PCBs and other organochlorines and risk of non-Hodgkin's lymphoma in a population-based case-control study in the United States. Congeners of PCBs (including coplanar congeners), dioxins, furans and pesticides or pesticide metabolites were measured in plasma of 100 untreated cases and 100 control subjects. We used a multiple imputation procedure to fill in missing values of levels determined to be below the detection limits. Risks of non-Hodgkin's lymphoma associated with each analyte were estimated using conditional logistic regression for the continuous measure, exposure quartiles, trend across quartile categories, and exposures above the 95th percentile. Certain PCB congeners were associated with increased risk of non-Hodgkin's lymphoma, including coplanar PCBs 156, 180, and 194, with odds ratios for the highest versus lowest quartile ranging from 2.7 to 3.5, and significant trends. Each of the furan congeners was associated with risk of non-Hodgkin's lymphoma, as were total furans, with 3.5-fold increased risk for the highest versus lowest quartile and a significant trend across quartiles (P = 0.006). The toxic equivalency quotient (TEQ), a summed metric that weights congeners by their dioxin-like potency, was associated with non-Hodgkin's lymphoma, with 35% increased risk per 10 TEQ pg/g lipid (95% confidence interval, 1.02-1.79). Our results add to existing literature, which suggests that exposure to organochlorines contributes to non-Hodgkin's lymphoma risk; these risks were most apparent for certain PCBs and furans.
Vascular Endothelial Growth Factor Contributes to Prostate Cancer–Mediated Osteoblastic Activity
Authors: Kitagawa Yasuhide , Dai Jinlu , Zhang Jian , Keller Jill M. , Nor Jacques , Yao Zhi , Keller Evan T.
Published: December 2005

Prostate cancer frequently metastasizes to bone resulting in the formation of osteoblastic metastases through unknown mechanisms. Vascular endothelial growth factor (VEGF) has been shown recently to promote osteoblast activity. Accordingly, we tested if VEGF contributes to the ability of prostate cancer to induce osteoblast activity. PC-3, LNCaP, and C4-2B prostate cancer cell lines expressed both VEGF-165 and VEGF-189 mRNA isoforms and VEGF protein. Prostate cancer cells expressed the mRNA for VEGF receptor (VEGFR) neuropilin-1 but not the VEGFRs Flt-1 or KDR. In contrast, mouse pre-osteoblastic cells (MC3T3-E1) expressed Flt-1 and neuropilin-1 mRNA but not KDR. PTK787, a VEGFR tyrosine kinase inhibitor, inhibited the proliferation of human microvascular endothelial cells but not prostate cancer proliferation in vitro. C4-2B conditioned medium induced osteoblast differentiation as measured by production of alkaline phosphatase and osteocalcin and mineralization of MC3T3-E1. PTK787 blocked the C4-2B conditioned medium–induced osteoblastic activity. VEGF directly induced alkaline phosphatase and osteocalcin but not mineralization of MC3T3-E1. These results suggest that VEGF induces initial differentiation of osteoblasts but requires other factors, present in C4-2B, to induce mineralization. To determine if VEGF influences the ability of prostate cancer to develop osteoblastic lesions, we injected C4-2B cells into the tibia of mice and, after the tumors grew for 6 weeks, administered PTK787 for 4 weeks. PTK787 decreased both intratibial tumor burden and C4-2B–induced osteoblastic activity as measured by bone mineral density and serum osteocalcin. These results show that VEGF contributes to prostate cancer–induced osteoblastic activity in vivo.
CD155/PVR Enhances Glioma Cell Dispersal by Regulating Adhesion Signaling and Focal Adhesion Dynamics
Authors: Sloan Kevin E. , Stewart Jean K. , Treloar Allison F. , Matthews Russell T. , Jay Daniel G.
Published: December 2005

We recently identified the immunoglobulin-CAM CD155/PVR (the poliovirus receptor) as a regulator of cancer invasiveness and glioma migration, but the mechanism through which CD155/PVR controls these processes is unknown. Here, we show that expression of CD155/PVR in rat glioma cells that normally lack this protein enhances their dispersal both in vitro and on primary brain tissue. CD155/PVR expression also reduced substrate adhesion, cell spreading, focal adhesion density, and the number of actin stress fibers in a substrate-dependent manner. Furthermore, we found that expression of CD155/PVR increased Src/focal adhesion kinase signaling in a substrate-dependent manner, enhancing the adhesion-induced activation of paxillin and p130Cas in cells adhering to vitronectin. Conversely, depletion of endogenous CD155/PVR from human glioma cells inhibited their migration, increased cell spreading, and down-regulated the same signaling pathway. These findings implicate CD155/PVR as a regulator of adhesion signaling and suggest a pathway through which glioma and other cancer cells may acquire a dispersive phenotype.
The Expression of Migration Stimulating Factor, a Potent Oncofetal Cytokine, Is Uniquely Controlled by 3′-Untranslated Region–Dependent Nuclear Sequestration of Its Precursor Messenger RNA
Authors: Kay Richard A. , Ellis Ian R. , Jones Sarah J. , Perrier Stéphane , Florence Margaret M. , Schor Ana M. , Schor Seth L.
Published: December 2005

Migration stimulating factor (MSF) is a truncated oncofetal fibronectin isoform expressed by fetal and tumor-associated cells. MSF mRNA is distinguished from other fibronectin isoforms by its size (2.1 kb) and the inclusion of a specific intronic sequence at its 3′ end. Initial Northern blot analysis with a MSF-specific probe indicated the presence of this 2.1-kb transcript and an additional unexpected 5.9-kb RNA present in both MSF-secreting (fetal) and nonsecreting (adult) fibroblasts. Our investigations into the nature of these transcripts and their relationship to MSF protein secretion revealed that the 5.9-kb mRNA is a second MSF-encoding transcript. Both these mRNAs have identical coding sequence and differ only in the length of their intron-derived 3′-untranslated region (UTR). The 5.9-kb MSF mRNA is retained in the nucleus whereas the 2.1-kb mRNA is not. MSF-secreting fetal fibroblasts have significantly lower nuclear levels of the 5.9-kb mRNA and correspondingly higher cytoplasmic levels of the 2.1-kb transcript than their nonsecreting adult counterparts. Adult fibroblasts induced to secrete MSF by treatment with transforming growth factor-β1 displayed similar changes in their respective levels of MSF mRNA, but not those of a control gene. When cloned downstream of a reporter gene, only the longer 3′-UTR retained coding sequence within the nucleus. We conclude that expression of MSF protein is regulated by 3′-UTR truncation of the 5.9-kb nuclear-sequestered “precursor” MSF mRNA and nuclear export of mature 2.1-kb message. Inducible 3′-UTR processing represents a novel regulatory mechanism involved in cancer pathogenesis that may open new avenues for therapeutic gene delivery.
Unexpected Effect of Matrix Metalloproteinase Down-Regulation on Vascular Intravasation and Metastasis of Human Fibrosarcoma Cells Selected In vivo for High Rates of Dissemination
Authors: Deryugina Elena I. , Zijlstra Andries , Partridge Juneth J. , Kupriyanova Tatyana A. , Madsen Mark A. , Papagiannakopoulos Thales , Quigley James P.
Published: December 2005

The human tumor/chick embryo model involving grafting of human HT-1080 fibrosarcoma cells on the chorioallantoic membrane was used in conjunction with quantitative real-time Alu PCR to select in vivo a pair of isogenic cell lines (HT-hi/diss and HT-lo/diss), dramatically differing in their ability to disseminate from the primary tumor (i.e., intravasate into the chorioallantoic membrane vasculature and metastasize to the lungs). During an immunohistochemical time course study, HT-hi/diss cells were sequentially visualized having escaped from the primary tumors, engaged with the blood vessels, and eventually observed inside the chorioallantoic membrane capillaries, thus reflecting early intravasating events. In contrast, HT-lo/diss cells seemed restricted to their primary tumor. Importantly, after i.v. inoculation, both variants arrested, extravasated, and proliferated in host tissues with similar efficiencies, highlighting that the observed earlier events at the periphery of the primary tumor could account for their differential dissemination. In a mechanistic probing of these events, we determined that HT-hi/diss intravasation was sensitive to a broad-range matrix metalloproteinase (MMP) inhibitor. To analyze the possible role of individual MMPs, membrane-bound MMP-14 and secreted MMP-9 were individually down-regulated in HT-hi/diss cells with their corresponding small interfering RNAs. Despite efficient down-regulation of MMP-14, neither intravasation nor metastasis of HT-hi/diss cells was affected significantly. However, a substantial down-regulation of MMP-9 was accompanied by a surprising 3-fold increase in intravasation and metastasis. The results emphasize a rising awareness that targeting certain MMPs might result in an enhanced malignancy, exemplified herein at the intravasation level as this step of the metastatic cascade is dissected and quantified.
Automated Quantitative Analysis of Activator Protein-2α Subcellular Expression in Melanoma Tissue Microarrays Correlates with Survival Prediction
Authors: Berger Aaron J. , Davis Darren W. , Tellez Carmen , Prieto Victor G. , Gershenwald Jeffrey E. , Johnson Marcella M. , Rimm David L. , Bar-Eli Menashe
Published: December 2005

The activator protein-2α (AP-2) transcription factor plays a key role in regulating expression of genes involved in tumor growth and metastasis of human melanoma. We sought to assess the prognostic significance of AP-2 expression and its role in the transition of nevi to metastatic melanoma. Two cohorts were analyzed. One was a “progression” microarray containing melanoma specimens from M.D. Anderson Cancer Center representing 84 cases and the other was a retrospective cohort from Yale University representing 214 primary melanomas and 293 metastases. Analysis of total AP-2 expression using two quantitative systems [automated quantitative analysis (AQUA) and laser scanning cytometry (LSC)] revealed no correlation with diagnosis group. LSC analysis of the M.D. Anderson Cancer Center array showed that the number of cells expressing nuclear AP-2 was highest in the benign nevi group (11.85%) and significantly decreased in each phase of melanoma progression to 0.39% in the metastatic group. Both LSC and AQUA showed decreased nuclear AP-2 levels and increased cytoplasmic AP-2 that is directly proportional to progression. Neither nuclear nor cytoplasmic expression levels correlated with outcome. Intriguingly, the ratio of cytoplasmic to nuclear AP-2 predicted outcome in the entire population and in the primary tumors alone, demonstrating the power of the ratio to normalize for variations. Furthermore, the AP-2 ratio directly correlated with other clinicopathologic factors, including Breslow depth (R = 0.334, P < 0.001). We show that a high level of AP-2 expression in the cytoplasm relative to the nucleus correlates with poor prognosis and the loss of nuclear AP-2 expression is associated with malignant transformation and progression of melanoma.
Short Hairpin RNA–Mediated Inhibition of Matrix Metalloproteinase-1 in MDA-231 Cells: Effects on Matrix Destruction and Tumor Growth
Authors: Wyatt Colby A. , Geoghegan James C. , Brinckerhoff Constance E.
Published: December 2005

Increased matrix metalloproteinase-1 (MMP-1) expression is associated with advanced stages of breast cancer and may be a predictive marker for the development of invasive disease. In this report, we used short hairpin RNA (shRNA) molecules to investigate whether MMP-1 production in MDA-231 breast cancer cells contributed to the degradation of a collagen matrix or tumor formation in nude mice. We created two groups of MDA-231 cell lines. MDA-231 cells containing a vector producing shRNA specific for MMP-1 had a >90% decrease in MMP-1 mRNA and protein compared with cells containing an empty vector, and blocking MMP-1 expression inhibited the in vitro collagenolytic activity of MDA-231 cells. When the cells were injected into the mammary fat pad, there was no difference in the frequency of tumor formation in mice. However, the average tumor size was larger in mice injected with cells containing the empty vector (1,216 ± 334 mm3) than in mice injected with cells expressing the MMP-1 shRNA (272 ± 117 mm3; P = 0.027). We conclude that MMP-1 expression is essential for the ability of MDA-231 cells to invade and destroy a collagen matrix and in vivo experiments suggest an important role for MMP-1 in breast tumor growth.
Tumor Immunotherapy Targeting Fibroblast Activation Protein, a Product Expressed in Tumor-Associated Fibroblasts
Authors: Lee Jaewoo , Fassnacht Martin , Nair Smita , Boczkowski David , Gilboa Eli
Published: December 2005

Murine studies have shown that immunologic targeting of the tumor vasculature, a key element of the tumor stroma, can lead to protective immunity in the absence of significant pathology. In the current study, we expand the scope of stroma-targeted immunotherapy to antigens expressed in tumor-associated fibroblasts, the predominant component of the stroma in most types of cancer. Mice were immunized against fibroblast activation protein (FAP), a product up-regulated in tumor-associated fibroblasts, using dendritic cells transfected with FAP mRNA. Using melanoma, carcinoma, and lymphoma models, we show that tumor growth was inhibited in tumor-bearing mice vaccinated against FAP and that the magnitude of the antitumor response was comparable to that of vaccination against tumor cell–expressed antigens. Both s.c. implanted tumors and lung metastases were susceptible to anti-FAP immunotherapy. The antitumor response could be further enhanced by augmenting the CD4+ T-cell arm of the anti-FAP immune response, achieved by using a lysosomal targeting sequence to redirect the translated FAP product into the class II presentation pathway, or by covaccination against FAP and a tumor cell–expressed antigen, tyrosinase-related protein 2. No morbidity or mortality was associated with anti-FAP vaccination except for a small delay in wound healing. The study suggests that FAP, a product which is preferentially expressed in tumor-associated fibroblasts, could function as a tumor rejection antigen in a broad range of cancers.
Koran und Konziliarismus. Anmerkungen zum Verhältnis von Heymericus de Campo und Nikolaus von Kues
Authors: Hamann Florian
Published: November 2005

This paper deals with the relation between Nicholas of Cusa and the Dutch philosopher Heymericus de Campo. Nicholas is celebrated for his rather positive attitude towards Islam. In De pace fidei (1453) he presents the vision of una religio in rituum varietate and in his Cribratio Alkorani (1460/61) Nicholas tries to prove Christian dogmas on the basis of the Koran. This idea he had discussed with his Dutch friend several decades earlier. In his Disputatio de potestate ecclesiastica (1433/34) Heymeric scrutinizes the question, whether the highest authority in the church belongs to the pope or the council, on the basis of the Koran. He presents ten arguments in favour of the council and one in favour of the pope. This shows that Nicholas developed parts of his exceptional thought in conversation with Heymeric and suggests that a closer examination of Heymeric's texts will reveal a new side of the young Cusanus.
Linking enzyme sequence to function using conserved property difference locator to identify and annotate positions likely to control specific functionality
Authors: Mayer Kimberly M , McCorkle Sean R , Shanklin John
Published: December 2005

Background

Families of homologous enzymes evolved from common progenitors. The availability of multiple sequences representing each activity presents an opportunity for extracting information specifying the functionality of individual homologs. We present a straightforward method for the identification of residues likely to determine class specific functionality in which multiple sequence alignments are converted to an annotated graphical form by the Conserved Property Difference Locator (CPDL) program.

Results

Three test cases, each comprised of two groups of funtionally-distinct homologs, are presented. Of the test cases, one is a membrane and two are soluble enzyme families. The desaturase/hydroxylase data was used to design and test the CPDL algorithm because a comparative sequence approach had been successfully applied to manipulate the specificity of these enzymes. The other two cases, ATP/GTP cyclases, and MurD/MurE synthases were chosen because they are well characterized structurally and biochemically. For the desaturase/hydroxylase enzymes, the ATP/GTP cyclases and the MurD/MurE synthases, groups of 8 (of ~400), 4 (of ~150) and 10 (of >400) residues, respectively, of interest were identified that contain empirically defined specificity determining positions.

Conclusion

CPDL consistently identifies positions near enzyme active sites that include those predicted from structural and/or biochemical studies to be important for specificity and/or function. This suggests that CPDL will have broad utility for the identification of potential class determining residues based on multiple sequence analysis of groups of homologous proteins. Because the method is sequence, rather than structure, based it is equally well suited for designing structure-function experiments to investigate membrane and soluble proteins.
Computational modeling reveals molecular details of epidermal growth factor binding
Authors: Mayawala Kapil , Vlachos Dionisios G , Edwards Jeremy S
Published: December 2005

Background

The ErbB family of receptors are dysregulated in a number of cancers, and the signaling pathway of this receptor family is a critical target for several anti-cancer drugs. Therefore a detailed understanding of the mechanisms of receptor activation is critical. However, despite a plethora of biochemical studies and recent single particle tracking experiments, the early molecular mechanisms involving epidermal growth factor (EGF) binding and EGF receptor (EGFR) dimerization are not as well understood. Herein, we describe a spatially distributed Monte Carlo based simulation framework to enable the simulation ofin vivoreceptor diffusion and dimerization.

Results

Our simulation results are in agreement with the data from single particle tracking and biochemical experiments on EGFR. Furthermore, the simulations reveal that the sequence of receptor-receptor and ligand-receptor reaction events depends on the ligand concentration, receptor density and receptor mobility.

Conclusion

Our computer simulations reveal the mechanism of EGF binding on EGFR. Overall, we show that spatial simulation of receptor dynamics can be used to gain a mechanistic understanding of receptor activation which may in turn enable improved cancer treatments in the future.
Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates
Authors: Smits Bart MG , Guryev Victor , Zeegers Dimphy , Wedekind Dirk , Hedrich Hans J , Cuppen Edwin
Published: November 2005

Background

The laboratory rat (Rattus norvegicus) is an important model for studying many aspects of human health and disease. Detailed knowledge on genetic variation between strains is important from a biomedical, particularly pharmacogenetic point of view and useful for marker selection for genetic cloning and association studies.

Results

We show that Single Nucleotide Polymorphisms (SNPs) in commonly used rat strains are surprisingly well represented in wild rat isolates. Shotgun sequencing of 814 Kbp in one wild rat resulted in the identification of 485 SNPs as compared with the Brown Norway genome sequence. Genotyping 36 commonly used inbred rat strains showed that 84% of these alleles are also polymorphic in a representative set of laboratory rat strains.

Conclusion

We postulate that shotgun sequencing in a wild rat sample and subsequent genotyping in multiple laboratory or domesticated strains rather than direct shotgun sequencing of multiple strains, could be the most efficient SNP discovery approach. For the rat, laboratory strains still harbor a large portion of the haplotypes present in wild isolates, suggesting a relatively recent common origin and supporting the idea that rat inbred strains, in contrast to mouse inbred strains, originate from a single species,R. norvegicus.
Genomic responses in rat cerebral cortex after traumatic brain injury
Authors: von Gertten Christina , Morales Amilcar Flores , Holmin Staffan , Mathiesen Tiit , Nordqvist Ann-Christin Sandberg
Published: December 2005

Background

Traumatic brain injury (TBI) initiates a complex sequence of destructive and neuroprotective cellular responses. The initial mechanical injury is followed by an extended time period of secondary brain damage. Due to the complicated pathological picture a better understanding of the molecular events occurring during this secondary phase of injury is needed. This study was aimed at analysing gene expression patterns following cerebral cortical contusion in rat using high throughput microarray technology with the goal of identifying genes involved in an early and in a more delayed phase of trauma, as genomic responses behind secondary mechanisms likely are time-dependent.

Results

Among the upregulated genes 1 day post injury, were transcription factors and genes involved in metabolism, e.g. STAT-3, C/EBP-δ and cytochrome p450. At 4 days post injury we observed increased gene expression of inflammatory factors, proteases and their inhibitors, like cathepsins, α-2-macroglobulin and C1q. Notably, genes with biological function clustered to immune response were significantly upregulated 4 days after injury, which was not found following 1 day. Osteopontin and one of its receptors, CD-44, were both upregulated showing a local mRNA- and immunoreactivity pattern in and around the injury site. Fewer genes had decreased expression both 1 and 4 days post injury and included genes implicated in transport, metabolism, signalling, and extra cellular matrix formation, e.g. vitronectin, neuroserpin and angiotensinogen.

Conclusion

The different patterns of gene expression, with little overlap in genes, 1 and 4 days post injury showed time dependence in genomic responses to trauma. An early induction of factors involved in transcription could lead to the later inflammatory response with strongly upregulated CD-44 and osteopontin expression. An increased knowledge of genes regulating the pathological mechanisms in trauma will help to find future treatment targets. Since trauma is a risk factor for development of neurodegenerative disease, this knowledge may also reduce late negative effects.
Gait disorders are associated with non-cardiovascular falls in elderly people: a preliminary study
Authors: Montero-Odasso Manuel , Schapira Marcelo , Duque Gustavo , Soriano Enrique R , Kaplan Roberto , Camera Luis A
Published: December 2005

Background

The association between unexplained falls and cardiovascular causes is increasingly recognized. Neurally mediated cardiovascular disorders and hypotensive syndromes are found in almost 20 percent of the patients with unexplained falls. However, the approach to these patients remains unclear. Gait assessment might be an interesting approach to these patients as clinical observations suggests that those with cardiovascular or hypotensive causes may not manifest obvious gait alterations. Our primary objective is to analyze the association between gait disorders and a non-cardiovascular cause of falls in patients with unexplained falls. A second objective is to test the sensitivity and specificity of a gait assessment approach for detecting non-cardiovascular causes when compared with intrinsic-extrinsic classification.

Methods

Cross-sectional study performed in a falls clinic at a university hospital in 41 ambulatory elderly participants with unexplained falls. Neurally mediated cardiovascular conditions, neurological diseases, gait and balance problems were assessed. Gait disorder was defined as a gait velocity < 0.8 m/s or Tinetti Gait Score <9. An attributable etiology of the fall was determined in each participant. Comparisons between the gait assessment approach and the attributable etiology regarding a neurally mediated cardiovascular cause were performed. Fisher exact test was used to test the association hypothesis. Sensitivity and specificity of gait assessment approach and intrinsic-extrinsic classification to detect a non-cardiovascular mediated fall was calculated with 95% confidence intervals (CI95%).

Results

A cardiovascular etiology (orthostatic and postprandial hypotension, vasovagal syndrome and carotid sinus hypersensitivity) was identified in 14% of participants (6/41). Of 35 patients with a gait disorder, 34 had a non-cardiovascular etiology of fall; whereas in 5 out of 6 patients without a gait disorder, a cardiovascular diagnosis was identified (p < 0.001). Sensitivity and specificity of the presence of gait disorder for identifying a non-cardiovascular mediated cause was 97.1% (CI95% = 85–99) and 83% (CI95% = 36–99), respectively.

Conclusion

In community dwelling older persons with unexplained falls, gait disorders were associated with non-cardiovascular diagnosis of falls. Gait assessment was a useful approach for the detection of a non-cardiovascular mediated cause of falls, providing additional value to this assessment.
A novel surgical technique to localize small enteropouch fistula
Authors: Basiri Abbas , Mo'oudi Emadoddin , Akhavizadegan Hamed , ShakhsSalim Naser
Published: December 2005

Background

One of the rare complications of ileal neobladder after radical cystectomy is pouch-to-intestine fistula. There isn't a classic method to intraoperative diagnosis of small fistula.

Case presentation

An entero-pouch fistula was occurred in a patient after radical cystectomy with illeal orthotopic pouch. Because of failed conservative management, the patient was candidate for surgery. The hidden small fistula in the small intestine was diagnosed by high intraluminal hydrostatic pressure (by intraluminal saline injection).

Conclusion

Intraoperative diagnosis the intestinal opening of a small fistula is very important. At the time of surgery if the fistula tract becomes open (during releasing the adhesions), it may leak in the peritoneum in postoperative period. Intraluminal high pressure is a useful method for intraoperative small hidden intestine opening.
Pharmacological reversal of endothelin-1 mediated constriction of the spiral modiolar artery: a potential new treatment for sudden sensorineural hearing loss
Authors: Scherer Elias Q , Arnold Wolfgang , Wangemann Philine
Published: November 2005

Background

Vasospasm of the spiral modiolar artery (SMA) may cause ischemic stroke of the inner ear. Endothelin-1 (ET-1) induces a strong, long-lasting constriction of the SMA by increasing contractile apparatus Ca2+sensitivity via Rho-kinase. We therefore tested several Rho-kinase inhibitors and a cell-permeable analogue of cAMP (dbcAMP) for their ability to reverse ET-1-induced constriction and Ca2+-sensitization.

Methods

The present study employed SMA isolated from gerbil temporal bones. Ca2+sensitivity was evaluated by correlating vascular diameter and smooth muscle cell [Ca2+]i, measured by fluo-4-microfluorometry and videomicroscopy.

Results

The Rho-kinase inhibitors Y-27632, fasudil, and hydroxy-fasudil reversed ET-1-induced vasoconstriction with anIC50of 3, 15, and 111 μmol/L, respectively. DbcAMP stimulated a dose-dependent vasodilation (Ec50= 1 mmol/L) and a reduction of [Ca2+]i(EC50= 0.3 μmol/L) of ET-1-preconstricted vessels (1 nmol/L). Fasudil and dbcAMP both reversed the ET-1-induced increase in Ca2+sensitivity.

Conclusion

Rho-kinase inhibition and dbcAMP reversed ET-1-induced vasoconstriction and Ca2+-sensitization. Therefore, Rho-kinase inhibitors or cAMP modulators could possess promise as pharmacological tools for the treatment of ET-1-induced constriction, ischemic stroke and sudden hearing loss.
Consumer involvement in Quality Use of Medicines (QUM) projects – lessons from Australia
Authors: Kirkpatrick Carl MJ , Roughead Elizabeth E , Monteith Gregory R , Tett Susan E
Published: December 2005

Background

It is essential that knowledge gained through health services research is collated and made available for evaluation, for policy purposes and to enable collaboration between people working in similar areas (capacity building). The Australian Quality Use of Medicine (QUM) on-line, web-based project database, known as the QUMmap, was designed to meet these needs for a specific sub-section of health services research related to improving the use of medicines. Australia's National Strategy for Quality Use of Medicines identifies the primacy of consumers as a major principle for quality use of medicines, and aims to support consumer led research. The aim of this study was to determine how consumers as a group have been represented in QUM projects in Australia. A secondary aim was to investigate how the projects with consumer involvement fit into Australia's QUM policy framework.

Method

Using the web-based QUMmap, all projects which claimed consumer involvement were identified and stratified into four categories, projects undertaken by; (a) consumers for consumers, (b) health professionals for consumers, (c) health professionals for health professionals, and (d) other. Projects in the first two categories were then classified according to the policy 'building blocks' considered necessary to achieve QUM.

Results

Of the 143 'consumer' projects identified, the majority stated to be 'for consumers' were either actually by health professionals for health professionals (c) or by health professionals for consumers (b) (47% and 40% respectively). Only 12 projects (9%) were directly undertaken by consumers or consumer groups for consumers (a). The majority of the health professionals for consumers (b) projects were directed at the provision of services and interventions, but were not focusing on the education, training or skill development of consumers.

Conclusion

Health services research relating to QUM is active in Australia and the projects are collated and searchable on the web-based interactive QUMmap. Healthcare professionals appear to be dominating nominally 'consumer focussed' research, with less than half of these projects actively involving the consumers or directly benefiting consumers. The QUMmap provides a valuable tool for policy analysis and for provision of future directions through identification of QUM initiatives.
Health-related quality of life in urban surgical emergency department patients: Comparison with a representative German population sample
Authors: Neuner Bruno , Miller Peter M , Felsmann Bodo , Weiss-Gerlach Edith , Neumann Tim , Wernecke Klaus Dieter , Spies Claudia
Published: December 2005

Background

Patients in emergency departments show a high prevalence of substance use. Quality of life is associated with substance use as well as socioeconomic status. Little is known about quality of life in substance-abusing young patients with minor trauma.

Methods

An investigation in an Emergency Department in an inner city university hospital was conducted during 8 months. Overall, 1,596 patients completed the SF-36 and an established SES-questionnaire and were screened for substance use (harmful alcohol consumption (≥ 8 points in men and ≥ 5 points in women on the Alcohol Use Disorders Identification Test (AUDIT), smoking and illicit drug use). Results were compared with a representative German population sample (German Federal Health Survey 1998).

Results

Median age of participants was 32 years and 61.8% were male. Mean physical component summary score (PCS) of the Short Form-36 Health Survey (SF-36) was 53.4 ± 8.3 points and significantly higher than the age and gender-stratified German Federal Health Survey-data. Mean mental component summary score (MCS) was 47.9 ± 10.0 points and significantly lower than the age and gender-stratified German Federal Health Survey-data. In Emergency Department patients, prevalence of substance use was high and harmful alcohol consumption and illicit drug use were strongly associated with impaired mental health. Education and occupational status were strongly positively associated with physical health.

Conclusion

We conclude that there is a high prevalence of substance use in young patients with minor trauma and mental quality of life is impaired. Screening and brief intervention strategies to reduce substance-use associated disorders should consider these findings.
Magnetic resonance imaging changes of sacroiliac joints in patients with recent-onset inflammatory back pain: inter-reader reliability and prevalence of abnormalities
Authors: Heuft-Dorenbosch Liesbeth , Weijers René , Landewé Robert , van der Linden Sjef , van der Heijde Désirée
Published: December 2005

To study the inter-reader reliability of detecting abnormalities of sacroiliac (SI) joints in patients with recent-onset inflammatory back pain by magnetic resonance imaging (MRI), and to study the prevalence of inflammation and structural changes at various sites of the SI joints.

Sixty-eight patients with inflammatory back pain (at least four of the five following criteria: symptom onset before age 40, insidious onset, morning stiffness, duration >3 months, improvement with exercise — or three out of five of these plus night pain) were included (38% male; mean age, 34.9 years [standard deviation 10.3]; 46% HLA-B27-positive; mean symptom duration, 18 months), with symptom duration <2 years. A MRI scan of the SI joints was made in the coronal plane with the following sequences: T1-weighted spin echo, short-tau inversion recovery, T2-weighted fast-spin echo with fat saturation, and T1-spin echo with fat saturation after the administration of gadolinium. Both SI joints were scored for inflammation (separately for subchondral bone and bone marrow, joint space, joint capsule, ligaments) as well as for structural changes (erosions, sclerosis, ankylosis), by two observers independently. Agreement between the two readers was analysed by concordance and discordance rates and by kappa statistics.

Inflammation was present in 32 SI joints of 22 patients, most frequently located in bone marrow and/or subchondral bone (29 joints in 21 patients). Readers agreed on the presence of inflammation in 85% of the cases in the right SI joint and in 78% of the cases in the left SI joint. Structural changes on MRI were present in 11 patients. Ten of these 11 patients also showed signs of inflammation.

Agreement on the presence or absence of inflammation and structural changes of SI joints by MRI was acceptable, and was sufficiently high to be useful in ascertaining inflammatory and structural changes due to sacroiliitis. About one-third of patients with recent-onset inflammatory back pain show inflammation, and about one-sixth show structural changes in at least one SI joint.
Evaluating mortality in intensive care units: contribution of competing risks analyses
Authors: Resche-Rigon Matthieu , Azoulay Elie , Chevret Sylvie
Published: December 2005

Introduction

Kaplan–Meier curves and logistic models are widely used to describe and explain the variability of survival in intensive care unit (ICU) patients. The Kaplan–Meier approach considers that patients discharged alive from hospital are 'non-informatively' censored (for instance, representative of all other individuals who have survived to that time but are still in hospital); this is probably wrong. Logistic models are adapted to this so-called 'competing risks' setting but fail to take into account censoring and differences in exposure time. To address these issues, we exemplified the usefulness of standard competing risks methods; namely, cumulative incidence function (CIF) curves and the Fine and Gray model.

Methods

We studied 203 mechanically ventilated cancer patients with acute respiratory failure consecutively admitted over a five-year period to a teaching hospital medical ICU. Among these patients, 97 died before hospital discharge. After estimating the CIF of hospital death, we used Fine and Gray models and logistic models to explain variability hospital mortality.

Results

The CIF of hospital death was 35.5% on day 14 and was 47.8% on day 60 (97/203); there were no further deaths. Univariate models, either the Fine and Gray model or the logistic model, selected the same eight variables as carrying independent information on hospital mortality at the 5% level. Results of multivariate were close, with four variables selected by both models: autologous stem cell transplantation, absence of congestive heart failure, neurological impairment, and acute respiratory distress syndrome. Two additional variables, clinically documented pneumonia and the logistic organ dysfunction, were selected by the Fine and Gray model.

Conclusion

The Fine and Gray model appears of interest when predicting mortality in ICU patients. It is closely related to the logistic model, through direct modeling of times to death, and can be easily extended to model non-fatal outcomes.
Identification of multipotent progenitors in the embryonic mouse kidney by a novel colony-forming assay
Authors: Osafune Kenji , Takasato Minoru , Kispert Andreas , Asashima Makoto , Nishinakamura Ryuichi
Published: December 2005

Renal stem or progenitor cells with a multilineage differentiation potential remain to be isolated, and the differentiation mechanism of these cell types in kidney development or regeneration processes is unknown. In an attempt to resolve this issue, we set up an in vitro culture system using NIH3T3 cells stably expressing Wnt4 (3T3Wnt4) as a feeder layer, in which a single renal progenitor in the metanephric mesenchyme forms colonies consisting of several types of epithelial cells that exist in glomeruli and renal tubules. We found that only cells strongly expressing Sall1(Sall1-GFPhigh cells), a zinc-finger nuclear factor essential for kidney development, form colonies, and that they reconstitute a three-dimensional kidney structure in an organ culture setting. We also found that Rac- and JNK-dependent planar cell polarity (PCP) pathways downstream of Wnt4 positively regulate the colony size, and that the JNK pathway is also involved in mesenchymal-to-epithelial transformation of colony-forming progenitors. Thus our colony-forming assay, which identifies multipotent progenitors in the embryonic mouse kidney, can be used for examining mechanisms of renal progenitor differentiation.