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Supplementary Material (supplementary + material)
Terms modified by Supplementary Material Selected AbstractsThe biogeography of seaweeds in Southeast AlaskaJOURNAL OF BIOGEOGRAPHY, Issue 3 2009Sandra C. Lindstrom Abstract Aim, This article reviews the history of seaweed collections in Southeast Alaska from the early Russian explorers to contemporary efforts. It summarizes other studies of Southeast Alaskan seaweeds from a biogeographical perspective, and compares the known seaweed flora near three population centres (Ketchikan, Sitka and Juneau) with those of other regions within Alaska, and with nearby regions. Location, For this article, Southeast Alaska includes all inside and outside waters of the Alexander Archipelago from Dixon Entrance (54°40, N, 133°00, W) to Icy Point (58°23,10, N, 137°04,20, W). Methods, The literature on seaweeds occurring in Southeast Alaska is reviewed from a biogeographical perspective, and herbarium records for Southeast Alaska from the Alaska Seaweed Database project are used to provide an overview of the biogeography of the area. Records for the population centres of Ketchikan, Sitka and Juneau are compared with records from other areas within Alaska and with nearby regions to determine floristic similarities. Results, Southeast Alaska has the most diverse seaweed flora of any region of Alaska. A list of species known to occur in Southeast Alaska is appended (in Supplementary Material) and includes their reported occurrences in three population centres (Juneau, Ketchikan and Sitka). Recognition of at least three distinct biogeographical areas associated with these three centres is supported by a comparison of their floras with those of other regions in the North Pacific. A close relationship of some species with conspecifics in the north-west Atlantic is also noted. In contrast, ecological, physiological and genetic differentiation of Southeast Alaskan seaweeds from conspecifics in Washington State or even from different areas of Southeast Alaska are documented. A ShoreZone coastal habitat system, which is being implemented to inventory and map the entire shoreline of Southeast Alaska, is defining new biogeographical units called ,bioareas' on the basis of the distribution of canopy kelps and lower intertidal algal assemblages. Main conclusions, Southeast Alaska has the most diverse seaweed flora of any region of Alaska. This is a reflection of its extensive coastline, with varied past and present environmental conditions. Different parts of Southeast Alaska show similarities to different areas outside Southeast Alaska. Despite this, much remains to be learned about the biogeography of seaweeds in Southeast Alaska, and many questions remain to be answered. [source] Assessment by M-FISH of karyotypic complexity and cytogenetic evolution in bladder cancer in vitroGENES, CHROMOSOMES AND CANCER, Issue 4 2005Sarah V. Williams We carried out multiplex fluorescence in situ hybridization (M-FISH) and follow-up FISH studies on a large series of transitional cell carcinoma (TCC) cell lines and 2 normal urothelium,derived cell lines, several of which have not had karyotypes reported previously. M-FISH analysis, with appropriate follow-up, complements conventional cytogenetic analysis and array CGH studies, allowing a more accurate definition of karyotype. The detailed karyotypic data obtained will assist in choosing suitable cell lines for functional studies and identifies common losses, gains, breakpoints and potential fusion gene sites in TCC. We have shown changes in cell lines RT112 and DSH1 following prolonged culture, and differences in karyotype, between RT112 cultures obtained from different sources. We propose a model for the evolutionary changes leading to these differences. A comparison with the literature found other examples of differences in cell-line karyotypes between different sources. Nevertheless, several karyotypic changes were preserved between different sources of the same cell line and were also seen in more than one cell line. These may be the most important changes and include ,8p, +20, 4q,, 10p,, 16p, and breaks in 8p21. We carried out a more detailed follow-up of some regions, which showed involvement of 8p breaks and losses in 15 of 16 TCC cell lines but in neither of the normal urothelium,derived cell lines. Some changes represented distal loss, whereas others were small deletions. Further study of this region is warranted. Supplementary material for this article can be found on the Genes, Chromosomes and Cancer website at http://www.interscience.wiley.com/jpages/1045-2257/suppmat/index.html. © 2005 Wiley-Liss, Inc. [source] Ischemic preconditioning of the murine liver protects through the Akt kinase pathway,HEPATOLOGY, Issue 3 2006Kunihiko Izuishi Hepatic ischemia-reperfusion (I/R) injury occurs in the settings of transplantation, trauma, and elective liver resection. Ischemic preconditioning has been used as a strategy to reduce inflammation and organ damage from I/R of the liver. However, the mechanisms involved in this process are poorly understood. We examined the role of the phosphatidylinositol 3 (PI3) kinase/Akt-signaling pathway during hepatic ischemic preconditioning (IPC). Prior to a prolonged warm ischemic insult, BALB/c mice were subjected to a 20-minute IPC period consisting of 10 minutes of ischemia and 10 minutes of reperfusion. Mice undergoing IPC demonstrated a significantly greater level and earlier activation of Akt in the liver compared with control animals. IPC also resulted in markedly less hepatocellular injury and improved survival compared with control animals. Akt activation associated with hepatic IPC suppressed the activity of several modulators of apoptosis, including Bad, glycogen synthase kinase ,, and caspase-3. In addition, IPC also inhibited the activities of c-Jun N -terminal kinase and nuclear factor ,B after I/R. Pretreatment of mice with PI3 kinase inhibitors completely abolished Akt phosphorylation and the protective effects seen with IPC. In conclusion, these results indicate that the PI3 kinase/Akt pathway plays an essential role in the protective effects of IPC in hepatic I/R injury. Modulation of this pathway may be a potential strategy in clinical settings of ischemic liver injury to decrease organ damage. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2006;44:573,580.) [source] Fibroblast activation protein increases apoptosis, cell adhesion, and migration by the LX-2 human stellate cell line,HEPATOLOGY, Issue 4 2005Xin Maggie Wang Injury and repair in chronic liver disease involve cell adhesion, migration, apoptosis, proliferation, and a wound healing response. In liver, fibroblast activation protein (FAP) has both collagenase and dipeptidyl peptidase IV (DPIV) activities and is expressed only by activated hepatic stellate cells (HSC) and myofibroblasts, which produce and degrade extracellular matrix (ECM). FAP was colocalized with collagen fibers, fibronectin, and collagen type I in human liver. FAP function was examined in vitro by expressing green fluorescent protein FAP fusion protein in cell lines cultured on collagen-I, fibronectin, and Matrigel. Glutamates at 203 and 204 as well as serine624 of FAP were essential for peptidase activity. Human embryonic kidney 293T cells overexpressing FAP showed reduced adhesion and migration. FAP overexpression in the human HSC line LX-2 caused increased cell adhesion and migration on ECM proteins as well as invasion across transwells in the absence or presence of transforming growth factor beta-1. FAP overexpression enhanced staurosporine streptomyces,stimulated apoptosis in both cell lines. Interestingly, the enzyme activity of FAP was not required for these functions. Overexpressing FAP increased the expression of matrix metalloproteinase-2 and CD44 and reduced integrin-,1 expression in 293T cells, suggesting potential pathways of FAP-mediated impairment of cell adhesion and migration in this epithelial cell line. In conclusion, these findings further support a pro-fibrogenic role for FAP by indicating that, in addition to its enzymatic functions, FAP has important nonenzymatic functions that in chronic liver injury may facilitate tissue remodeling through FAP-mediated enhancement of HSC cell adhesion, migration, and apoptosis. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2005;42:935,945.) [source] An inhibitor of cyclin-dependent kinase, stress-induced p21Waf-1/Cip-1, mediates hepatocyte mito-inhibition during the evolution of cirrhosis,HEPATOLOGY, Issue 6 2005John G. Lunz III During the evolution of cirrhosis, there is a relative decrease in volume percentage of hepatocytes and a relative increase in biliary epithelial cells and myofibroblasts. This is recognized histopathologically as a ductular reaction and leads to gradual distortion of the normal hepatic architecture. The final or decompensated stage of cirrhosis is characterized by a further decline in hepatocyte proliferation and loss of functional liver mass that manifests clinically as ascites, encephalopathy, and other signs of liver failure. In this report, we tested the hypothesis that p21-mediated hepatocyte mito-inhibition accelerates the evolution of cirrhosis using an established mouse model of decompensated biliary cirrhosis, p21-deficient mice, and liver tissue from humans awaiting liver replacement. Despite the same insult of long-term (12-week) bile duct ligation, mice prone to decompensation showed significantly more oxidative stress and hepatocyte nuclear p21 expression, which resulted in less hepatocyte proliferation, an exaggerated ductular reaction, and more advanced disease compared with compensation-prone controls. Mice deficient in p21 were better able than wild-type controls to compensate for long-term bile duct ligation because of significantly greater hepatocyte proliferation, which led to a larger liver mass and less architectural distortion. Mito-inhibitory hepatocyte nuclear p21 expression in humans awaiting liver replacement directly correlated with pathological disease stage and model of end-stage liver disease scoring. In conclusion, stress-induced upregulation of hepatocyte p21 inhibits hepatocyte proliferation during the evolution of cirrhosis. These findings have implications for understanding the evolution of cirrhosis and associated carcinogenesis. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2005.) [source] Genome-wide analysis of gene expression in human intrahepatic cholangiocarcinoma,HEPATOLOGY, Issue 6 2005Kazutaka Obama Intrahepatic cholangiocarcinoma is a neoplasm arising in the liver, and its incidence is increasing in Japan as well as in Western countries. Prognosis of patients with this type of tumor remains unsatisfactory because no effective chemotherapeutic drugs are available, we have no sensitive tumor markers to detect this tumor in its early stage, and it is difficult to identify a high-risk group for the disease. To clarify the molecular mechanism of tumorigenesis and identify molecular targets for diagnosis and treatment, we analyzed global gene-expression profiles of 25 intrahepatic cholangiocarcinomas using tumor cell populations purified by laser microbeam microdissection and a cDNA microarray containing 27,648 genes. We identified 52 genes that were commonly upregulated and 421 that were downregulated in intrahepatic cholangiocarcinomas compared with noncancerous biliary epithelial cells. From the 52 upregulated genes, we selected P-cadherin and survivin for further investigation and corroborated enhanced expression of their products in cancer tissues by immunohistochemical staining. Furthermore, comparison between tumors with lymph node metastasis and those without metastasis identified 30 genes that were associated with lymph node involvement. In conclusion, these data should be helpful for a better understanding of the tumorigenesis of intrahepatic cholangiocarcinoma and should contribute to the development of diagnostic and therapeutic strategies for this type of tumor. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2005.) [source] A mouse model for cystic biliary dysgenesis in autosomal recessive polycystic kidney disease (ARPKD),HEPATOLOGY, Issue 5 2005Markus Moser Autosomal recessive polycystic kidney disease (ARPKD) is an important cause of liver- and renal-related morbidity and mortality in childhood. Recently, PKHD1, the gene encoding the transmembrane protein polyductin, was shown to be mutated in ARPKD patients. We here describe the first mouse strain, generated by targeted mutation of Pkhd1. Due to exon skipping, Pkhd1ex40 mice express a modified Pkhd1 transcript and develop severe malformations of intrahepatic bile ducts. Cholangiocytes maintain a proliferative phenotype and continuously synthesize TGF-,1. Subsequently, mesenchymal cells within the hepatic portal tracts continue to synthesize collagen, resulting in progressive portal fibrosis and portal hypertension. Fibrosis did not involve the hepatic lobules, and we did not observe any pathological changes in morphology or function of hepatocytes. Surprisingly and in contrast to human ARPKD individuals, Pkhd1ex40 mice develop morphologically and functionally normal kidneys. In conclusion,our data indicate that subsequent to formation of the embryonic ductal plate, dysgenesis of terminally differentiated bile ducts occurs in response to the Pkhd1ex40 mutation. The role of polyductin in liver and kidney may be functionally divergent, because protein domains essential for bile duct development do not affect nephrogenesis in our mouse model. Supplementary material for this article can be found on the HEPATOLOGYwebsite (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2005.) [source] Induction or expansion of T-cell responses by a hepatitis B DNA vaccine administered to chronic HBV carriersHEPATOLOGY, Issue 4 2004Maryline Mancini-Bourgine Despite the availability of effective hepatitis B vaccines for many years, over 370 million people remain persistently infected with hepatitis B virus (HBV). Viral persistence is thought to be related to poor HBV-specific T-cell responses. A phase I clinical trial was performed in chronic HBV carriers to investigate whether HBV DNA vaccination could restore T-cell responsiveness. Ten patients with chronic active hepatitis B nonresponder to approved treatments for HBV infection were given 4 intramuscular injections of 1 mg of a DNA vaccine encoding HBV envelope proteins. HBV-specific T-cell responses were assessed by proliferation, ELISpot assays, and tetramer staining. Secondary end points included safety and the monitoring of HBV viraemia and serological markers. Proliferative responses to hepatitis B surface antigen were detected in two patients after DNA injections. Few HBV-specific interferon ,,secreting T cells were detectable before immunization, but the frequency of such responses was significantly increased by 3 DNA injections. Immunization was well tolerated. Serum HBV DNA levels decreased in 5 patients after 3 vaccine injections, and complete clearance was observed in 1 patient. In conclusion, this study provides evidence that HBV DNA vaccination is safe and immunologically effective. We demonstrate that DNA vaccination can specifically but transiently activate T-cell responses in some chronic HBV carriers who do not respond to current antiviral therapies. Supplementary material for this article can be found on the HEPATOLOGYwebsite (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2004;40:874,882.) [source] Interleukin 6 alleviates hepatic steatosis and ischemia/reperfusion injury in mice with fatty liver diseaseHEPATOLOGY, Issue 4 2004Feng Hong Fatty liver, formerly associated predominantly with excessive alcohol intake, is now also recognized as a complication of obesity and an important precursor state to more severe forms of liver pathology including ischemia/reperfusion injury. No standard protocol for treating fatty liver exists at this time. We therefore examined the effects of 10 days of interleukin 6 (IL-6) injection in 3 murine models of fatty liver: leptin deficient ob/ob mice, ethanol-fed mice, and mice fed a high-fat diet. In all 3 models, IL-6 injection decreased steatosis and normalized serum aminotransferase. The beneficial effects of IL-6 treatment in vivo resulted in part from an increase in mitochondrial , oxidation of fatty acid and an increase in hepatic export of triglyceride and cholesterol. However, administration of IL-6 to isolated cultured steatotic hepatocytes failed to decrease lipid contents, suggesting that the beneficial effects of IL-6 in vivo do not result from its effects on hepatocytes alone. IL-6 treatment increased hepatic peroxisome proliferator-activated receptor (PPAR) , and decreased liver and serum tumor necrosis factor (TNF) ,. Finally, 10 days of treatment with IL-6 prevented the susceptibility of fatty livers to warm ischemia/reperfusion injury. In conclusion, long-term IL-6 administration ameliorates fatty livers and protects against warm ischemia/reperfusion fatty liver injury, suggesting the therapeutic potential of IL-6 in treating human fatty liver disease. Supplementary material for this article can be found on the Hepatology website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2004;40:933,941.) [source] Peptide antibiotic human beta-defensin-1 and ,2 contribute to antimicrobial defense of the intrahepatic biliary treeHEPATOLOGY, Issue 4 2004Kenichi Harada Human beta-defensins (hBDs) are important antimicrobial peptides that contribute to innate immunity at mucosal surfaces. This study was undertaken to investigate the expression of hBD-1 and hBD-2 in intrahepatic biliary epithelial cells in specimens of human liver, and 4 cultured cell lines (2 consisting of biliary epithelial cells and 2 cholangiocarcinoma cells). In addition, hBD-1 and hBD-2 were assayed in specimens of bile. hBD-1 was nonspecifically expressed immunohistochemically in intrahepatic biliary epithelium and hepatocytes in all patients studied, but expression of hBD-2 was restricted to large intrahepatic bile ducts in 8 of 10 patients with extrahepatic biliary obstruction (EBO), 7 of 11 with hepatolithiasis, 1 of 6 with primary biliary cirrhosis (PBC), 1 of 5 with primary sclerosing cholangitis (PSC), 0 of 6 with chronic hepatitis C (CH-C), and 0 of 11 with normal hepatic histology. hBD-2 expression was evident in bile ducts exhibiting active inflammation. Serum C reactive protein levels correlated with biliary epithelial expression of hBD-2. Real-time PCR revealed that in all of 28 specimens of fresh liver, including specimens from patients with hepatolithiasis, PBC, PSC, CH-C and normal hepatic histology, hBD-1 messenger RNA was consistently expressed, whereas hBD-2 messenger RNA was selectively expressed in biliary epithelium of patients with hepatolithiasis. Immunobloting analysis revealed hBD-2 protein in bile in 1 of 3 patients with PSC, 1 of 3 with PBC, and each of 6 with hepatolithiasis; in contrast, hBD-1 was detectable in all bile samples examined. Four cultured biliary epithelial cell lines consistently expressed hBD-1; in contrast these cell lines did not express hBD-2 spontaneously but were induced to express hBD-2 by treatment with Eschericia coli, lipopolysaccharide, interleukin-1, or tumor necrosis factor-,. In conclusion, these findings suggest that in the intrahepatic biliary tree, hBD-2 is expressed in response to local infection and/or active inflammation, whereas hBD-1 may constitute a preexisting component of the biliary antimicrobial defense system. Supplementary material for this article can be found on the Hepatology website (http:/interscience.wley.com/jpages/0270,9139/suppmat/index.html). (Hepatology 2004;40:925-932). [source] S-adenosylhomocysteine sensitizes to TNF-, hepatotoxicity in mice and liver cells: A possible etiological factor in alcoholic liver diseaseHEPATOLOGY, Issue 4 2004Zhenyuan Song In alcoholic liver disease, tumor necrosis factor-, (TNF,) is a critical effector molecule, and abnormal methionine metabolism is a fundamental acquired metabolic abnormality. Although hepatocytes are resistant to TNF,-induced killing under normal circumstances, previous studies have shown that primary hepatocytes from rats chronically fed alcohol have increased TNF, cytotoxicity. Therefore, there must be mechanisms by which chronic alcohol exposure "sensitizes" to TNF, hepatotoxicity. S-adenosylhomocysteine (SAH) is product of methionine in transsulfuration pathway and a potent competitive inhibitor of most methyltransferases. In this study, we investigated the effects of increased SAH levels on TNF, hepatotoxicity. Our results demonstrated that chronic alcohol consumption in mice not only decreased hepatic S-adenosylmethionine levels but also increased hepatic SAH levels, which resulted in a significantly decreased S-adenosylmethionine-to-SAH ratio. This was associated with significant increases in hepatic TNF, levels, caspase-8 activity, and cell death. In vitro studies demonstrated that SAH-enhancing agents sensitized hepatocytes to TNF, killing, and the death was associated with increased caspase-8 activity, which was blocked by a caspase-8 inhibitor. In addition, increased intracellular SAH levels had no effect on nuclear factor ,B activity induced by TNF,. In conclusion, these results provide a new link between abnormal methionine metabolism and abnormal TNF, metabolism in alcoholic liver disease. Increased SAH is a potent and clinically relevant sensitizer to TNF, hepatotoxicity. These data further support improving the S-adenosylmethionine-to-SAH ratio and removal of intracellular SAH as potential therapeutic options in alcoholic liver disease. Supplementary material for this article can be found on the HEPATOLOGYwebsite (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2004;40:989,997.) [source] Characterization of mutations in ATP8B1 associated with hereditary cholestasisHEPATOLOGY, Issue 1 2004Leo W. J. Klomp Progressive familial intrahepatic cholestasis (PFIC) and benign recurrent intrahepatic cholestasis (BRIC) are clinically distinct hereditary disorders. PFIC patients suffer from chronic cholestasis and develop liver fibrosis. BRIC patients experience intermittent attacks of cholestasis that resolve spontaneously. Mutations in ATP8B1 (previously FIC1) may result in PFIC or BRIC. We report the genomic organization of ATP8B1 and mutation analyses of 180 families with PFIC or BRIC that identified 54 distinct disease mutations, including 10 mutations predicted to disrupt splicing, 6 nonsense mutations, 11 small insertion or deletion mutations predicted to induce frameshifts, 1 large genomic deletion, 2 small inframe deletions, and 24 missense mutations. Most mutations are rare, occurring in 1,3 families, or are limited to specific populations. Many patients are compound heterozygous for 2 mutations. Mutation type or location correlates overall with clinical severity: missense mutations are more common in BRIC (58% vs. 38% in PFIC), while nonsense, frameshifting, and large deletion mutations are more common in PFIC (41% vs. 16% in BRIC). Some mutations, however, lead to a wide range of phenotypes, from PFIC to BRIC or even no clinical disease. ATP8B1 mutations were detected in 30% and 41%, respectively, of the PFIC and BRIC patients screened. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html) and at www.atp8b1-primers.nl (HEPATOLOGY 2004;40:27,38.) [source] Covalent modification as a mechanism for the breakdown of immune tolerance to pyruvate dehydrogenase complex in the mouseHEPATOLOGY, Issue 6 2004Jeremy M. Palmer The autoimmune liver disease primary biliary cirrhosis (PBC) is characterized by the breakdown of normal immune self tolerance to pyruvate dehydrogenase complex (PDC). How tolerance is broken to such a central and highly conserved self antigen in the initiation of autoimmunity remains unclear. One postulated mechanism is that reactivity arises to an altered form of self antigen with subsequent cross-reactivity to native self. In this murine study, we set out to examine whether sensitization with a covalently modified form of self PDC can give rise to the pattern of breakdown of B-cell and T-cell tolerance to self PDC seen in PBC patients. The notion that altered self can lead to tolerance breakdown was studied by sensitizing SJL/J mice with a covalently modified (biotinylated) preparation of self murine PDC (mP/O-B). Subsequently, antibody and T-cell reactivities to unmodified self mP/O were studied. Sensitization with mP/O-B elicited high-titre, high-affinity antibody responses reactive with both the mP/O-B immunogen and, importantly, native mP/O. In addition, significant MHC class II restricted splenic T-cell responses to native mP/O (i.e., true autoimmune responses) were seen in mP/O-B sensitized animals. The breakdown of T-cell self tolerance to mP/O was not seen in animals sensitized with irrelevant biotinylated antigens. In conclusion, this study provides evidence to support the concept that exposure to covalently modified self PDC can, in the correct proimmune environment, replicate the full breakdown of B-cell and T-cell immune tolerance to PDC seen in PBC. One potential etiological pathway in PBC therefore could be the breakdown of tolerance to self PDC occurring after exposure to self antigen covalently modified in the metabolically active environment of the liver. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2004;39:1583,1592.) [source] Altered gene expression in acute systemic inflammation detected by complete coverage of the human liver transcriptomeHEPATOLOGY, Issue 2 2004Cédric Coulouarn The goal of the current study was to provide complete coverage of the liver transcriptome with human probes corresponding to every gene expressed in embryonic, adult, and/or cancerous liver. We developed dedicated tools, namely, the Liverpool nylon array of complementary DNA (cDNA) probes for approximately 10,000 nonredundant genes and the LiverTools database. Inflammation-induced transcriptome changes were studied in liver tissue samples from patients with an acute systemic inflammation and from control subjects. One hundred and fifty-four messenger RNAs (mRNA) correlated statistically with the extent of inflammation. Of these, 134 mRNA samples were not associated previously with an acute-phase (AP) response. The hepatocyte origin and proinflammatory cytokine responsiveness of these mRNAs were confirmed by quantitative reverse-transcription polymerase chain reaction (Q-RT-PCR) in cytokine-challenged hepatoma cells. The corresponding gene promoters were enriched in potential binding sites for inflammation-driven transcription factors in the liver. Some of the corresponding proteins may provide novel blood markers of clinical relevance. The mRNAs whose level is most correlated with the AP extent (P < .05) were enriched in intracellular signaling molecules, transcription factors, glycosylation enzymes, and up-regulated plasma proteins. In conclusion, the hepatocyte responded to the AP extent by fine tuning some mRNA levels, controlling most, if not all, intracellular events from early signaling to the final secretion of proteins involved in innate immunity. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2004;39:353,364.) [source] Cancer-associated molecular signature in the tissue samples of patients with cirrhosis,HEPATOLOGY, Issue 2 2004Jin Woo Kim Several types of aggressive cancers, including hepatocellular carcinoma (HCC), often arise as a multifocal primary tumor. This suggests a high rate of premalignant changes in noncancerous tissue before the formation of a solitary tumor. Examination of the messenger RNA expression profiles of tissue samples derived from patients with cirrhosis of various etiologies by complementary DNA (cDNA) microarray indicated that they can be grossly separated into two main groups. One group included hepatitis B and C virus infections, hemochromatosis, and Wilson's disease. The other group contained mainly alcoholic liver disease, autoimmune hepatitis, and primary biliary cirrhosis. Analysis of these two groups by the cross-validated leave-one-out machine-learning algorithms revealed a molecular signature containing 556 discriminative genes (P < .001). It is noteworthy that 273 genes in this signature (49%) were also significantly altered in HCC (P < .001). Many genes were previously known to be related to HCC. The 273-gene signature was validated as cancer-associated genes by matching this set to additional independent tumor tissue samples from 163 patients with HCC, 56 patients with lung carcinoma, and 38 patients with breast carcinoma. From this signature, 30 genes were altered most significantly in tissue samples from high-risk individuals with cirrhosis and from patients with HCC. Among them, 12 genes encoded secretory proteins found in sera. In conclusion, we identified a unique gene signature in the tissue samples of patients with cirrhosis, which may be used as candidate markers for diagnosing the early onset of HCC in high-risk populations and may guide new strategies for chemoprevention. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2004;39:518,527.) [source] Gene expression profiling of 30 cancer cell lines predicts resistance towards 11 anticancer drugs at clinically achieved concentrationsINTERNATIONAL JOURNAL OF CANCER, Issue 7 2006Balazs Györffy Abstract Cancer patients with tumors of similar grading, staging and histogenesis can have markedly different treatment responses to different chemotherapy agents. So far, individual markers have failed to correctly predict resistance against anticancer agents. We tested 30 cancer cell lines for sensitivity to 5-fluorouracil, cisplatin, cyclophosphamide, doxorubicin, etoposide, methotrexate, mitomycin C, mitoxantrone, paclitaxel, topotecan and vinblastine at drug concentrations that can be systemically achieved in patients. The resistance index was determined to designate the cell lines as sensitive or resistant, and then, the subset of resistant vs. sensitive cell lines for each drug was compared. Gene expression signatures for all cell lines were obtained by interrogating Affymetrix U133A arrays. Prediction Analysis of Microarrays was applied for feature selection. An individual prediction profile for the resistance against each chemotherapy agent was constructed, containing 42,297 genes. The overall accuracy of the predictions in a leave-one-out cross validation was 86%. A list of the top 67 multidrug resistance candidate genes that were associated with the resistance against at least 4 anticancer agents was identified. Moreover, the differential expressions of 46 selected genes were also measured by quantitative RT-PCR using a TaqMan micro fluidic card system. As a single gene can be correlated with resistance against several agents, associations with resistance were detected all together for 76 genes and resistance phenotypes, respectively. This study focuses on the resistance at the in vivo concentrations, making future clinical cancer response prediction feasible. The TaqMan-validated gene expression patterns provide new gene candidates for multidrug resistance. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7136/suppmat. © 2005 Wiley-Liss, Inc. [source] ApcMin/+ mouse model of colon cancer: Gene expression profiling in tumorsJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2004Daniel Leclerc Abstract The ApcMin/+ mouse is a popular animal model for studies of human colon cancer, but the molecular changes associated with neoplasia in this system have only been partially characterized. Our aim was to identify novel genes involved in tumorigenesis in this model. RNA from intestinal adenomas and from pre-neoplastic small intestine were prepared from six ApcMin/+ mice. The tumor transcriptomes were analyzed with high-density oligonucleotide microarrays representing ,12,000 probe sets; we compared their profiles with those of matched pre-neoplastic intestine. Stringent analysis revealed reproducible changes for 98 probe sets representing 90 genes, including novel observations regarding 50 genes whose involvement in this mouse model has never been reported. In addition to the expected changes in growth regulatory genes, the altered gene products could be assigned to four functional groupings that should enhance tumorigenesis: metabolic changes that would result in a high rate of glycolysis, alterations in enzymes involved in reactive oxygen species or carcinogen metabolism, cytoskeletal elements, and proteins involved in tumor invasion or angiogenesis. A fifth group consisted of expression changes that might restrict tumor progression, suggesting that the adenomatous state reflects a balance of pro- and anti-tumorigenic factors. Since many of the altered genes had not previously been reported to be involved in any tumorigenic processes, our observations provide a host of new candidates for potential modulation to prevent or treat intestinal neoplasia. Supplementary material for this article can be found at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/v93.html. © 2004 Wiley-Liss, Inc. [source] Advancing the diagnosis and treatment of hepatocellular carcinomaLIVER TRANSPLANTATION, Issue 4 2005J. Wallis Marsh MD We analyzed global gene expression patterns of 91 human hepatocellular carcinomas (HCCs) to define the molecular characteristics of the tumors and to test the prognostic value of the expression profiles. Unsupervised classification methods revealed two distinctive subclasses of HCC that are highly associated with patient survival. This association was validated via 5 independent supervised learning methods. We also identified the genes most strongly associated with survival by using the Cox proportional hazards survival analysis. This approach identified a limited number of genes that accurately predicted the length of survival and provides new molecular insight into the pathogenesis of HCC. Tumors from the low survival subclass have strong cell proliferation and antiapoptosis gene expression signatures. In addition, the low survival subclass displayed higher expression of genes involved in ubiquitination and histone modification, suggesting an etiological involvement of these processes in accelerating the progression of HCC. In conclusion, the biological differences identified in the HCC subclasses should provide an attractive source for the development of therapeutic targets (e.g., HIF1a) for selective treatment of HCC patients. Supplementary material for this article can be found on the HEPATOLOGY Web site (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html) Copyright 2004 American Association for the Study of Liver Diseases. Hepatology. 2004 Sep;40(3):667,76. [source] Experimental phasing: best practice and pitfallsACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Airlie J. McCoy Developments in protein crystal structure determination by experimental phasing are reviewed, emphasizing the theoretical continuum between experimental phasing, density modification, model building and refinement. Traditional notions of the composition of the substructure and the best coefficients for map generation are discussed. Pitfalls such as determining the enantiomorph, identifying centrosymmetry (or pseudo-symmetry) in the substructure and crystal twinning are discussed in detail. An appendix introduces combined real,imaginary log-likelihood gradient map coefficients for SAD phasing and their use for substructure completion as implemented in the software Phaser. Supplementary material includes animated probabilistic Harker diagrams showing how maximum-likelihood-based phasing methods can be used to refine parameters in the case of SIR and MIR; it is hoped that these will be useful for those teaching best practice in experimental phasing methods. [source] New roads lead to Rubisco in archaebacteriaBIOESSAYS, Issue 8 2007Oliver Mueller-Cajar The discovery of the CO2 -fixing enzyme Rubisco in the Archaebacteria has presented a conundrum in that they apparently lack the gene for phosphoribulokinase, which is required to generate Rubisco's substrate ribulose 1,5-bisphosphate (RuBP). However, two groups1, 2 have now demonstrated novel RuBP synthesis pathways, demystifying Rubisco's non-autotrophic and perhaps ancient role. A new CO2 fixing role for Rubisco, which is distinct from the globally dominant Calvin cycle, is providing important clues furthering our understanding of the evolution of autotrophy. This perspective is strengthened by the additional recognition in this commentary that some Rubisco-containing Archaea do also contain PRK and may represent an interesting autotrophic evolutionary transition. Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html). BioEssays 29:722,724, 2007. © 2007 Wiley Periodicals, Inc. [source] Insights into the evolution of the nucleolus by an analysis of its protein domain repertoireBIOESSAYS, Issue 5 2004Eike Staub Recently, the first investigation of nucleoli using mass spectrometry led to the identification of 271 proteins. This represents a rich resource for a comprehensive investigation of nucleolus evolution. We applied a protocol for the identification of known and novel conserved protein domains of the nucleolus, resulting in the identification of 115 known and 91 novel domain profiles. The phyletic distribution of nucleolar protein domains in a collection of complete proteomes of selected organisms from all domains of life confirms the archaebacterial origin of the core machinery for ribosome maturation and assembly, but also reveals substantial eubacterial and eukaryotic contributions to nucleolus evolution. We predict that, in different phases of nucleolus evolution, protein domains with different biochemical functions were recruited to the nucleolus. We suggest a model for the late and continous evolution of the nucleolus in early eukaryotes and argue against an endosymbiotic origin of the nucleolus and the nucleus. Supplementary material for this article can be found on the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html. BioEssays 26:567,581, 2004. © 2004 Wiley Periodicals, Inc. [source] Developmental gene expression profiling of mammalian, fetal orofacial tissueBIRTH DEFECTS RESEARCH, Issue 12 2004Partha Mukhopadhyay Abstract BACKGROUND The embryonic orofacial region is an excellent developmental paradigm that has revealed the centrality of numerous genes encoding proteins with diverse and important biological functions in embryonic growth and morphogenesis. DNA microarray technology presents an efficient means of acquiring novel and valuable information regarding the expression, regulation, and function of a panoply of genes involved in mammalian orofacial development. METHODS To identify differentially expressed genes during mammalian orofacial ontogenesis, the transcript profiles of GD-12, GD-13, and GD-14 murine orofacial tissue were compared utilizing GeneChip arrays from Affymetrix. Changes in gene expression were verified by TaqMan quantitative real-time PCR. Cluster analysis of the microarray data was done with the GeneCluster 2.0 Data Mining Tool and the GeneSpring software. RESULTS Expression of >50% of the ,12,000 genes and expressed sequence tags examined in this study was detected in GD-12, GD-13, and GD-14 murine orofacial tissues and the expression of several hundred genes was up- and downregulated in the developing orofacial tissue from GD-12 to GD-13, as well as from GD-13 to GD-14. Such differential gene expression represents changes in the expression of genes encoding growth factors and signaling molecules; transcription factors; and proteins involved in epithelial-mesenchymal interactions, extracellular matrix synthesis, cell adhesion, proliferation, differentiation, and apoptosis. Following cluster analysis of the microarray data, eight distinct patterns of gene expression during murine orofacial ontogenesis were selected for graphic presentation of gene expression patterns. CONCLUSIONS This gene expression profiling study identifies a number of potentially unique developmental participants and serves as a valuable aid in deciphering the complex molecular mechanisms crucial for mammalian orofacial development. Supplementary material for this article can be found at http://www.mrw.interscience.wiley.com/suppmat/1542-0752/suppmat/2004/70/v70.mukhopadhyay.html Birth Defects Research (Part A), 2004. © 2004 Wiley-Liss, Inc. [source] Microanatomical diversity of the humerus and lifestyle in lissamphibiansACTA ZOOLOGICA, Issue 2 2009Aurore Canoville Abstract A study of body size and the compactness profile parameters of the humerus of 37 species of lissamphibians demonstrates a relationship between lifestyle (aquatic, amphibious or terrestrial) and bone microstructure. Multiple linear regressions and variance partitioning with Phylogenetic eigenVector Regressions reveal an ecological and a phylogenetic signal in some body size and compactness profile parameters. Linear discriminant analyses segregate the various lifestyles (aquatic vs. amphibious or terrestrial) with a success rate of up to 89.2%. The models built from data on the humerus discriminate aquatic taxa relatively well from the other taxa. However, like previous models built from data on the radius of amniotes or on the femur of lissamphibians, the new models do not discriminate amphibious taxa from terrestrial taxa on the basis of body size or compactness profile data. To make our inference method accessible, spreadsheets (see supplementary material on the website), which allow anyone to infer a lissamphibian lifestyle solely from body size and bone compactness parameters, were produced. No such easy implementation of habitat inference models is found in earlier papers on this topic. [source] Multiple forms of genetic instability within a 2-Mb chromosomal segment of 3q26.3,q27 are associated with development of esophageal adenocarcinomaGENES, CHROMOSOMES AND CANCER, Issue 4 2006Lin Lin Gene amplification is one of the mechanisms to activate oncogenes in many cancers, including esophageal adenocarcinoma (EA). In the present study, we used two-dimensional restriction landmark genome scanning to clone a NotI/DpnII fragment that showed increased genomic dosage in 1 of 44 EAs analyzed. This fragment maps to 3q26.3,q27, and subsequent experiments identified two intrachromosomal amplicons within a 10-Mb DNA segment in 7 of 75 (9%) EAs. The distal amplified-core region maps centromeric to the PIK3CA locus, and a microsatellite (D3S1754) within this region exhibited significant instability (MSI), in stark contrast to the genomewide microsatellite stability found in EA. D3S1754-MSI arises in premalignant Barrett's dysplastic cells and preceded amplification of the nascent MSI allele in the corresponding EA. Seven ESTs within the amplified-core were overexpressed in amplicon-containing EAs. One of these, EST AW513672, represents a chimeric transcript that initiated from an antisense promoter sequence in the 5,UTR of a full-length LINE-1 element (L1-5,ASP). Similar chimeric transcripts encoding portions of the MET oncogene and the BCAS3 gene also were overexpressed in EAs, suggesting that L1-5,ASP activation may occur at a broad level in primary EAs. Thus, the fine dissection of a 2-Mb amplified DNA segment in 3q26.3,q27 in EA revealed multiple genetic alterations that had occurred sequentially and/or concurrently during EA development. This article has supplementary material, available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. © 2005 Wiley-Liss, Inc. [source] Comments on tables of magnetic space groupsACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2009Hans Grimmer Litvin [Acta Cryst. (2008), A64, 419,424 and supplementary material] extends much of the information contained in Volume A of International Tables for Crystallography for the 230 space-group types to the 1651 types of Shubnikov space groups, using Opechowski,Guccione (OG) notation for the space groups with a black,white lattice. It is pointed out that OG notation has crucial disadvantages compared to Belov,Neronova,Smirnova (BNS) notation. It is shown how Litvin's diagrams of symmetry elements for the orthorhombic Shubnikov space groups can be interpreted in terms of BNS symbols and how those containing e -glides can be simplified. A number of mistakes in the diagrams of Litvin are corrected. [source] Automatic Facsimile of Chinese Calligraphic WritingsCOMPUTER GRAPHICS FORUM, Issue 7 2008Songhua Xu Abstract To imitate personal handwritings is non-trivial. In this paper, we attempt to address the challenging problem of automatic handwriting facsimile. We focus on Chinese calligraphic writings due to their rich variation in style, high artistic values and also the fact that they are among the most difficult candidates for the problem. We first analyze the structures and shapes of the constituent components, i.e., strokes and radicals, of characters in sample calligraphic writings by the same writer. To generate calligraphic writing in the style of the writer, we facsimile the individual character elements as well as the layout relationships used to compose the character, both in the writer's personal writing style. To test our algorithm, we compare our facsimileing results of Chinese calligraphic writings with the original writings. Our results are found to be acceptable for most cases, some of which are difficult to differentiate from the real ones. More results and supplementary materials are provided in our project website at http://www.cs.hku.hk/~songhua/facsimile/. [source] Thermal decomposition, combustion and flame-retardancy of epoxy resins,a review of the recent literaturePOLYMER INTERNATIONAL, Issue 12 2004Sergei V Levchik Abstract An overview of the recent literature on combustion and flame-retardancy of epoxy resins is presented. A brief overview of the structures of cured epoxy resins is also presented as a background for better understanding of the thermal decomposition and combustion phenomena. The literature sources were mostly taken from the publications of 1995 and later; however, for basic descriptions of the structural and thermal decomposition principles, older publications are also cited. New developments in flame-retardant additives, epoxy monomers and curing agents are described. It is shown that the main attention in recent years has been focused on phosphorus-containing epoxy monomers and epoxy resins. Silicon-containing or nitrogen-containing products and inorganic additives remain of great interest as supplementary materials to phosphorus flame-retardants. Copyright © 2004 Society of Chemical Industry [source] | |||||||||||||||||||