bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative Gene Expression of Somatostatin Receptors and Noradrenaline Transporter Underlying Scintigraphic Results in Patients with Neuroendocrine Tumors
Authors: Binderup Tina , Knigge Ulrich , Mellon Mogensen Anne , Palnaes Hansen Carsten , Kjaer Andreas
Published: January 2008

Aim: To measure, by a quantitative approach, the gene expression underlying the results of somatostatin receptor (sst) scintigraphy (111In-DTPA-octreotide) and noradrenaline transporter (NAT) scintigraphy (123I-MIBG) in patients with neuroendocrine (NE) tumors. Methods: The gene expression of somatostatin receptors 1–5 (sst) and NAT was measured quantitatively by real-time PCR in a group of patients with NE tumors (n = 14) and compared to a group of patients with colorectal adenocarcinomas (n = 15). If available, scintigraphic results were compared with gene expression results (9 octreotide and 3 MIBG scintigraphies). Results: The sst2 was upregulated in 13 of 14 patients (93%) with NE tumors, and the absolute level of gene expression was highest for sst2. Gene expression alterations of NAT and the other sst subtypes were more variable. Gene expression of sst2 was in all cases in agreement with positive octreotide scintigraphies. In 2 of 3 cases where MIBG scintigraphy was positive, NAT was also upregulated. Sst2 was generally downregulated in the colorectal tumor group with the gene expression of the other receptors being more heterogeneous. Conclusions: In general, changes in gene expression of sst2 corresponded with scintigraphic results. Our data support that sst2 is the best target for visualization of NE tumors, whereas NAT is only a useful target in a subpopulation of NE tumors. Comparison of scintigraphic results with quantitative gene expression may be used to achieve a better understanding of the link between them, which in turn could aid in planning and development of noninvasive molecular imaging of key molecular processes.
Elevate Level of Glycosaminoglycans and Altered Sulfation Pattern of Chondroitin Sulfate Are Associated with Differentiation Status and Histological Type of Human Primary Hepatic Carcinoma
Authors: Lv Huizhong , Yu Guangli , Sun Linlin , Zhang Zheng , Zhao Xia , Chai Wengang
Published: January 2008

Objectives: The characteristics of glycosaminoglycans (GAGs) in many carcinomas have been reported to be different from those in normal tissues, which can be used as prognostic indices in some cancers. However, the difference in GAG characteristics among various differentiation status or histological types of the same cancer has not been described. The aim of this study was to investigate the relationship between GAG characteristics and human primary hepatic carcinomas of divers differentiation status or histological type. Methods: GAGs from intrahepatic cholangiocarcinomas and differently differentiated hepatocellular carcinomas were extracted, purified and enzymatically digested. Their content, relative molecular size distribution and disaccharide composition were analyzed and compared using electrophoresis and high-performance liquid chromatography. Results: A progressive increase in the content of chondroitin sulfate, low molecular size GAGs, and nonsulfated and disulfated chondroitin sulfate disaccharide units, together with a gradual decrease in heparan sulfate, have been found as the differentiation status of hepatocellular carcinoma became poorer. A significant increase in hyaluronic acid, which only slightly increased in hepatocellular carcinoma, was found in intrahepatic cholangiocarcinomas. Conclusion: The alterations in GAG characteristics in primary hepatic carcinoma were associated with both the differentiation status and the histological type of the tumor.
Serum Concentration of Reg IV in Patients with Colorectal Cancer: Overexpression and High Serum Levels of Reg IV Are Associated with Liver Metastasis
Authors: Oue Naohide , Kuniyasu Hiroki , Noguchi Tsuyoshi , Sentani Kazuhiro , Ito Masanori , Tanaka Shinji , Setoyama Tetsuro , Sakakura Chouhei , Natsugoe Shoji , Yasui Wataru
Published: January 2008

Objective: Regenerating islet-derived family, member 4 (regenerating gene type IV, Reg IV) is overexpressed in colorectal cancer (CRC). The aim of this study was to investigate the diagnostic utility of Reg IV determination in sera from patients with CRC. Methods: We examined the expression and distribution of Reg IV in CRC by immunohistochemistry and determined Reg IV levels in sera from patients with CRC by enzyme-linked immunosorbent assay. Results: Immunostaining revealed that 23 of 80 (29%) CRC cases were positive for Reg IV. CRC cases with metastatic recurrence in the liver showed more frequently Reg IV staining than those without (p = 0.0102). Patients with CRC showing Reg IV staining had a significantly worse survival than those without Reg IV staining (p = 0.0117). Preoperatively, serum Reg IV concentrations were not elevated in CRC patients at stage 0–III, being in contrast to the significantly increased preoperative levels in stage IV CRC patients with liver metastasis. Conclusion: These results suggest that Reg IV is a prognosticator for poor survival. Serum Reg IV concentration may predict CRC recurrence in the liver.
Evaluation of the Prognostic and Predictive Value of HER-1/EGFR in Breast Cancer Patients Participating in a Randomized Study with Dose-Dense Sequential Adjuvant Chemotherapy
Authors: Tzaida Olympia , Gogas Helen , Dafni Urania , Kyroudi Aspasia , Papaspyrou Irene , Kyriakou Vasiliki , Malamou-Mitsi Vasiliki , Alamani Maria , Skopa Chrisoula , Kostopoulos Ioannis , Kastritis Efstathios , Pectasides Dimitrios , Briasoulis Evangelos , Kalofonos Haralabos P. , Aravantinos Gerasimos , Fountzilas George , Arapantoni-Dadioti Petroula
Published: January 2008

Background: To assess the prognostic and predictive significance of HER-1/EGFR protein levels in high-risk patients with breast cancer treated with dose-dense sequential adjuvant chemotherapy. Methods: 595 high-risk breast cancer patients were treated with adjuvant anthracycline-based dose-dense sequential chemotherapy (E-CMF vs. E-T-CMF). Disease-free survival (DFS) was the primary end point. HER-1/EGFR was assessed by immunohistochemistry (IHC) in 312 patients. Results: HER-1/EGFR expression was detected in 54 of 312 patients (17%). Positive expression of HER-1/EGFR was significantly associated with negative receptor status (52 vs. 17%, p < 0.001), worse histological grade (70 vs. 45%, p = 0.001), HER-2 overexpression (46 vs. 27%, p = 0.01) and positive p53 expression (48 vs. 19%, p < 0.001). With a median follow-up of 7 years, the total number of relapses was 105 (34%), and the total number of deaths 69 (22%). The analysis for DFS provides significant evidence that the HER-1/EGFR effect on the risk of disease progression was different according to treatment (interaction p = 0.02). Regarding overall survival, a trend towards a significant difference for an interaction of HER-1/EGFR and treatment was found (p = 0.07). Conclusion: The present study demonstrated a differential effect of positive HER-1/EGFR expression in the two treatment groups, with HER-1/EGFR being a negative prognostic marker in the absence of paclitaxel.
CD47
Authors: Isenberg Jeff S. , Roberts David D. , Frazier William A.
Published: January 2008

CD47, originally named integrin-associated protein, is a receptor for thrombospondin-1. A number of important roles for CD47 have been defined in regulating the migration, proliferation, and survival of vascular cells, and in regulation of innate and adaptive immunity. The recent discovery that thrombospondin-1 acts via CD47 to inhibit nitric oxide signaling throughout the vascular system has given new importance and perhaps a unifying mechanism of action to these enigmatic proteins. Here we trace the development of this exciting new paradigm for CD47 function in vascular physiology.
Correction of Bleeding Symptoms in von Willebrand Factor–Deficient Mice by Liver-Expressed von Willebrand Factor Mutants
Authors: Marx Isabelle , Lenting Peter J. , Adler Thure , Pendu Ronan , Christophe Olivier D. , Denis Cécile V.
Published: January 2008

Objective—

von Willebrand Factor (vWF) structure-function relationship has been studied only in vitro. To investigate the physiological importance of particular vWF domains, we have introduced mutations into murine vWF (mvWF) cDNA inhibiting vWF binding to glycoprotein (Gp) Ib, GpIIbIIIa, and to fibrillar collagen.

Methods and Results—

We delivered wild-type (WT) or mutant mvWF cDNA into vWF-deficient (
Vwf
−/−
) mice using hydrodynamic injection and assessed whether hemorrhagic symptoms could be corrected. Hydrodynamic gene transfer resulted in high expression of plasma mvWF 24 hours after injection (438±63% for 50 μg of cDNA). Factor VIII activity was normalized in
Vwf
−/−
mice injected with mvWF cDNA and multimerization was achieved. Bleeding time was corrected after injection of WT mvWF cDNA in
Vwf
−/−
mice whereas noninjected mice did not stop bleeding. Injection of the GpIIbIIIa and the collagen binding mutants in
Vwf
−/−
mice also resulted in a correction of bleeding time whereas mice injected with the GpIb binding mutant were bleeding for as long they were observed, although blood loss was decreased compared with noninjected mice (61±21 μL versus 232±63 μL).

Conclusion—

Our model allows the rapid in vivo evaluation of specific mutations on plasma vWF function.
Cross Talk Among Smad, MAPK, and Integrin Signaling Pathways Enhances Adventitial Fibroblast Functions Activated by Transforming Growth Factor–β1 and Inhibited by Gax
Authors: Liu Ping , Zhang Cheng , Feng Jin Bo , Zhao Yu Xia , Wang Xu Ping , Yang Jian Min , Zhang Ming Xiang , Wang Xing Li , Zhang Yun
Published: January 2008

Objective—

We investigated whether Smad, mitogen-activated protein kinase (MAPK), and integrin signaling pathways cross-talk to enhance adventitial fibroblast (AF) bioactivity, which was activated by transforming growth factor (TGF)-β1 and inhibited by Gax.

Methods and Results—

Cultured AFs were stimulated with Ad-Gax, TGF-β1, and siRNA-Gax. Assays for AFs viabilities demonstrated that TGF-β1 and siRNA-Gax enhanced AFs proliferative, migratory, and adherent abilities, whereas Gax counteracted TGF-β1–activated actions. Flow cytometry revealed that TGF-β1 and siRNA-Gax increased S phase cells; however, Gax decreased AFs in the S phase and increased those in the G0-G1 and apoptotic phases. RT-PCR, Western blotting, and immunocytochemistry showed that TGF-β1 and siRNA-Gax upregulated the expression of cytokines in Smad, MAPK, and integrin signaling pathways, and downregulated that of p15, p16, and p21. Conversely, Gax induced downregulation of these cytokines and upregulation of p15, p16, and p21. Thus, these signaling pathways cross-talk to enhance AF bioactivity; Gax effectively counteracts TGF-β1 effects, blocks the cross-talk of these pathways, inhibits AF functions, and increases AF apoptosis.

Conclusions—

Our findings indicate that cross-talk among Smad, MAPK, and integrin signaling pathways may account mainly for the mechanism of AF functions. Gax is a promising therapeutic gene for dissecting the signaling pathways controlling AF bioactivities.
Niemann-Pick C1-Like 1 Is Required for an LXR Agonist to Raise Plasma HDL Cholesterol in Mice
Authors: Tang Weiqing , Ma Yinyan , Jia Lin , Ioannou Yiannis A. , Davies Joanna P. , Yu Liqing
Published: January 2008

Objectives—Activation of liver x receptor (LXR) raises plasma HDL-cholesterol (HDL-C) in mice. Interestingly, the LXR agonist GW3965 fails to raise plasma HDL-C in mice lacking intestinal ABCA1, indicating that intestinal ABCA1 plays a predominant role in GW3965-mediated HDL production. How this is coupled to intestinal function remains elusive. Because cholesterol is essential for HDL assembly and directly regulates intestinal ABCA1 expression via activating LXR, we hypothesized that cholesterol absorption, a major function of intestine, modulates LXR-dependent HDL formation.

Methods and Results—Mice lacking Niemann-Pick C1-Like 1 (NPC1L1) (L1-KO mice), a gene that is essential for cholesterol absorption, were treated with LXR agonist T0901317 for 7 days. Intriguingly, this treatment failed to significantly raise plasma HDL-C but caused a much greater fecal cholesterol excretion in L1-KO mice. The intestinal ABCA1 mRNA level was about 4-fold lower in L1-KO versus wild-type mice, and increased 3.9-fold and 8.8-fold after T0901317 treatment in wild-type and L1-KO mice, respectively. Hepatic ABCA1 failed to respond to T0901317 in mice of both genotypes, although hepatic mRNAs for many LXR target genes were higher in the T0901317-treated versus untreated wild-type animals.

Conclusions—NPC1L1 is required for an LXR agonist to increase plasma HDL-C in mice.
In Human Macrophages the Complement Component C5a Induces the Expression of Oncostatin M via AP-1 Activation
Authors: Kastl Stefan P. , Speidl Walter S. , Kaun Christoph , Katsaros Katharina M. , Rega Gersina , Afonyushkin Taras , Bochkov Valery N. , Valent Peter , Assadian Afshin , Hagmueller Georg W. , Hoeth Martina , de Martin Rainer , Ma Yongsheng , Maurer Gerald , Huber Kurt , Wojta Johann
Published: January 2008

Objective—

Macrophages produce the cytokine oncostatin M (OSM), which beside other functions is also involved in inflammation. The complement component C5a mobilizes and activates these cells at inflammatory sites. We examined the effect of C5a on OSM production in human monocytes and in human monocyte-derived macrophages.

Methods and Results—

For macrophage transformation peripheral blood monocytes were cultivated for 8 to 10 days in the presence of human serum. C5a significantly increased in these cells OSM antigen as determined by specific ELISA and mRNA as quantitated by real-time polymerase chain reaction in these cells as well as in plaque macrophages. This effect was blocked by antibodies against the receptor C5aR/CD88 and by pertussis toxin. The C5a-induced phosphorylation of p38 and JNK and the C5a-induced increase in OSM production in macrophages was abolished by 2 p38 inhibitors and by a JNK inhibitor. Furthermore C5a increased the nuclear translocation of c-fos and c-jun. Using different OSM promoter deletion mutant constructs we show that the putative AP-1 element is responsible for activation of OSM promoter activity by C5a.

Conclusion—

Our data establish a link between the complement system and the gp130 receptor cytokine family with possible implications for the pathology of inflammatory diseases.
c-Myb–Dependent Smooth Muscle Cell Differentiation
Authors: Kolodziejska Karolina M. , Noyan-Ashraf M.H. , Nagy Andras , Bacon Andrea , Frampton Jon , Xin Hong-Bo , Kotlikoff Michael I. , Husain Mansoor
Published: January 2008

Both in vitro and in vivo studies have implicated the c-Myb transcription factor in vascular smooth muscle cell (SMC) proliferation and hematopoiesis. However, its role in differentiation and maturation of contractile, as opposed to proliferating, SMCs has not been investigated. Here we demonstrate that
c-myb
−/−
embryonic stem cells (ESCs) are incapable of producing embryoid bodies (EBs) with spontaneously contracting SMCs but can differentiate into contracting cardiomyocytes unimpaired. Quantitative real-time RT-PCR revealed that whereas mesodermal differentiation was unaffected, myocardin, a critical determinant of SMC differentiation, became upregulated at day 7 in wild-type, but not in
c-myb
−/−
EBs. SMC-specific genes, smooth muscle α-actin, SM22α and smooth muscle myosin heavy chain reached peak expression levels by day 15 of differentiation and were 2- to 3-fold higher in wild-type as compared with
c-myb
−/−
derived EBs. Similarly, fluorescence-activated cell-sorting analysis confirmed significantly different proportions of smooth muscle α-actin–positive cells in wild-type (26.8±0.7%) versus
c-myb
−/−
(12.3±0.4%) EBs. Temporal induction of these SMC-specific markers preceded and paralleled contractile SMC appearance and predicted the relative (in)ability of
c-myb
−/−
and wild-type ESC lines to generate EBs with contracting SMCs. Importantly, data from EBs faithfully predicted a significant reduction in
c-myb
−/−
cell contribution to SMC lineage in vivo, in chimeric E11.5 embryo and adult aortas relative to brain and skin chimerism, respectively. Moreover, the visceral SMC population in chimeric embryos was nearly devoid of
c-myb
−/−
cells. Our data are the first to implicate c-Myb in SMC differentiation from precursor stem cell–derived populations, reinforcing its potential role in phenotypic modulation of SMCs and vascular disease.
Dongus Tapa – An Iron Age Settlement in the Udabno-Steppe, Eastern Kakheti
Authors: Nieling Jens
Published: January 2008

The article is a preliminary report on an excavation carried out on the Iron Age settlement Dongus Tapa in Kakheti (Eastern Georgia). This fortified settlement existed from the Late Bronze Age till the 7th century BC and lasted longer than the settlements in the Shiraki plain, which end in the same century.
Achaemenian Seals Found in Georgia
Authors: Dzhavakhishvili Ketevan
Published: January 2008

In the article six Achaemenian seals are published, which were found in Georgia. Two of them belong to the seals of the "Oriental Royal Style" according to J. Boardman, the third is an "Occidental Royal Style" seal, one belongs to the "Greco-Oriental" group and two others to the "Bern group". Three of them were found in burials of the Roman period, two in burials of the 4th century BC, while the origin of the last one is unknown.
Lower Extremity Paralysis in a Male Preadolescent
Authors: Gallizzi Gina , Kaly Perry , Takagishi Jennifer
Published: January 2008

A 12-year-old boy presented to the emergency department with bilateral lower leg sensory loss and inability to walk. The initial work-up revealed no significant abnormalities on physical examination other than bilateral paralysis and no laboratory abnormalities. The inpatient work-up included neurologic, psychiatric, and psycho-logic evaluations. The patient was diagnosed with a conversion disorder, and treatment included relaxation exercises and guided imagery as well as antidepressants. Upon discharge, the patient was walking without assistance. Follow-up therapy was initiated for stress and behavior management. No further episodes have occurred. Diagnosis, therapy options, and outcomes of conversion disorder are further discussed as they relate to treatment by general pediatricians.
Being Young and Black
Authors: Leiber Michael J. , Johnson Joseph D.
Published: January 2008

This study examined the extent to which race and age individually and jointly determined juvenile justice case outcomes at intake and judicial disposition among males in one county juvenile court in the state of Iowa. Using an interpretation of the symbolic threat thesis and the emphasis on stereotyping as the theoretical framework, we discovered that being Black and older increased a youth's chances of receiving an intake court referral and decreased the odds of participation in intake diversion. Age did not condition intake decision making for African Americans but was discovered to temper case outcomes for Whites. Although individual relationships were found, there was no evidence of joint race-age effects in decision making at judicial disposition.
The Role the Collegiate American Marketing Association Plays in Professional and Entrepreneurial Skill Development
Authors: Peltier James W. , Scovotti Carol , Pointer Lucille
Published: January 2008

Professional student organizations offer members a wide range of learning opportunities for applied marketing experiences. Little research exists in the marketing education literature on the role student organizations play in preparing their members for life beyond school. Understanding what students seek as members of such organizations and how satisfied they are with their experiences is not only important for continued chapter development but also useful for faculty not directly involved with such organizations but impacted by their activities. A model, developed and tested through a large-scale study of American Marketing Association collegiate members, suggests four experiential dimensions affect member satisfaction and professional development—strategic and tactical activities, interpersonal and networking skills, entrepreneurial and venture experience, and applied learning through contacts with professionals. Recommendations for improving American Marketing Association chapters are presented.
Bringing the Spatial In
Authors: Peterson Anne F. , Kinsey Barbara Sgouraki , Bartling Hugh , Baybeck Brady
Published: January 2008

Contests over public goods remain at the forefront of urban political battles in nearly every major city in the United States. The spatial location of the good can play an instrumental role in understanding the contours and outcomes of such conflicts. The authors explore a particular case—voting for a growth-related development project, the monorail, by referendum in the city of Seattle—and examine how a grassroots campaign successfully mobilized voters by targeting both their particularistic and collective interests. The authors conduct analysis at the precinct level and use spatial tools of analysis and ecological inference, finding that voter support for the monorail stemmed from the location of the proposed route and the campaign's progressive appeals to environmental, social justice, and high tech concerns. Although cost overruns ultimately derailed construction of the monorail in 2005, when passed in 2002, the monorail was the most expensive infrastructure project in Seattle's history.
Dispersing the Crowd
Authors: Smithsimon Gregory
Published: January 2008

Research has found that most bonus plazas in front of Manhattan office buildings are barren, uninviting spaces. But there has been little study of why that is so. Existing explanations suggest unusable plazas are unintended consequences of other processes—architects' slavishly reproducing modernist architectural styles, or developers' minimizing costs by neglecting public spaces. Such explanations are found to be unsupported by the facts. This study of 291 Manhattan bonus plazas and the development process in New York—including site observations; analysis of newly available plaza data; and interviews of architects, planners, and building managers-reveals that spaces were intentionally made uninviting, and that developers acted to make the plazas inaccessible. Implications for the study and creation of public space are discussed.
Advantage or Disadvantage? The Changing Institutional Landscape of Underserved Mortgage Markets
Authors: Ashton Philip
Published: January 2008

This article argues that the resolution to the banking crisis after 1989 created a set of market rules promoting financial consolidation and giving large financial conglomerates competitive advantages that could allow them to more effectively tap historically underserved mortgage markets. Focusing on Chicago during the period 1993—2000, the author assesses the role played by consolidating lenders and their counterparts in altering the allocation of home purchase mortgages so as to benefit historically underserved markets. The results indicate that even as consolidating lenders are often leaders in more permissive mortgage market outcomes, substantial variations across time and between different areas of the city are suggestive of how underserved markets fare in the new financial marketplace.
Using Artificial Neural Networks to Model Nonlinearity
Authors: Somers Mark John , Casal Jose C.
Published: January 2008

Neural networks are advanced pattern recognition algorithms capable of extracting complex, nonlinear relationships among variables. This study examines those capabilities by modeling nonlinearities in the job satisfaction—job performance relationship with multilayer perceptron and radial basis function neural networks. A framework for studying nonlinear relationships with neural networks is offered. It is implemented using the job satisfaction—job performance relationship with results indicative of pervasive patterns of nonlinearity.
Applying Critical Discourse Analysis in Strategic Management Research
Authors: Phillips Nelson , Sewell Graham , Jaynes Steve
Published: January 2008

Critical discourse analysis has become an increasingly popular methodology in organization and management studies. In this article, the authors explore the potential for this methodology to be more widely used in strategic management research. They begin by identifying three research approaches that, to a greater or lesser extent, share a concern with the relationship between language and the formulation and implementation of strategy—strategy as a system of shared meaning, strategy as text and talk, and strategy as truth. They then discuss how critical discourse analysis can be used to extend and develop these approaches by exploiting their underlying complementarities. Finally, using the example of a recently completed case study of strategic change in a large banking and financial services institution, they explore the practical implications of applying critical discourse analysis in strategic management research.
A dynamic prognostic model to predict survival in post–polycythemia vera myelofibrosis
Authors: Passamonti Francesco , Rumi Elisa , Caramella Marianna , Elena Chiara , Arcaini Luca , Boveri Emanuela , Del Curto Cecilia , Pietra Daniela , Vanelli Laura , Bernasconi Paolo , Pascutto Cristiana , Cazzola Mario , Morra Enrica , Lazzarino Mario
Published: January 2008

Post–polycythemia vera myelofibrosis (post-PV MF) is a late evolution of PV. In 647 patients with PV, we found that leukocytosis leukocyte count > (15 × 109/L) at diagnosis is a risk factor for the evolution of post-PV MF. In a series of 68 patients who developed post-PV MF, median survival was 5.7 years. Hemoglobin level less than 100 g/L (10 g/dL) at diagnosis of post-PV MF was an independent risk factor for survival. The course of post-PV MF, however, is a dynamic process that implies a progressive worsening of clinical parameters. Using a multivariate Cox proportional hazard regression with time-dependent covariates, we found that a dynamic score based on hemoglobin level less than 100 g/L (10 g/dL), platelet count less than 100 × 109/L, and leukocyte count more than 30 × 109/L is useful to predict survival at any time from diagnosis of post-PV MF. The resulting hazard ratio of the score was 4.2 (95% CI: 2.4-7.7; P < .001), meaning a 4.2-fold worsening of survival for each risk factor acquired during follow up. In conclusion, leukocytosis at diagnosis of PV is a risk factor for evolution in post-PV MF. A dynamic score based on hemoglobin level, and platelet and leukocyte count predicts survival at any time from diagnosis of post-PV MF.
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
Authors: Kristensen David M , Ward R Matthew , Lisewski Andreas Martin , Erdin Serkan , Chen Brian Y , Fofanov Viacheslav Y , Kimmel Marek , Kavraki Lydia E , Lichtarge Olivier
Published: January 2008

Background

Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions. One approach to recover this information is to use3D templates– structure-function motifs that consist of a few functionally critical amino acids and may suggest functional similarity when geometrically matched to other structures. Since experimentally determined functional sites are not common enough to define 3D templates on a large scale, this work tests a computational strategy to select relevant residues for 3D templates.

Results

Based on evolutionary information and heuristics, an Evolutionary Trace Annotation (ETA) pipeline built templates for 98 enzymes, half taken from the PSI, and sought matches in a non-redundant structure database. On average each template matched 2.7 distinct proteins, of which 2.0 share the first three Enzyme Commission digits as the template's enzyme of origin. In many cases (61%) a single most likely function could be predicted as the annotation with the most matches, and in these cases such a plurality vote identified the correct function with 87% accuracy. ETA was also found to be complementary to sequence homology-based annotations. When matches are required to both geometrically match the 3D template and to be sequence homologs found by BLAST or PSI-BLAST, the annotation accuracy is greater than either method alone, especially in the region of lower sequence identity where homology-based annotations are least reliable.

Conclusion

These data suggest that knowledge of evolutionarily important residues improves functional annotation among distant enzyme homologs. Since, unlike other 3D template approaches, the ETA method bypasses the need for experimental knowledge of the catalytic mechanism, it should prove a useful, large scale, and general adjunct to combine with other methods to decipher protein function in the structural proteome.
The CMV early enhancer/chicken β actin (CAG) promoter can be used to drive transgene expression during the differentiation of murine embryonic stem cells into vascular progenitors
Authors: Alexopoulou Annika N , Couchman John R , Whiteford James R
Published: January 2008

Background

Mouse embryonic stem cells cultured in vitro have the ability to differentiate into cells of the three germ layers as well as germ cells. The differentiation mimics early developmental events, including vasculogenesis and early angiogenesis and several differentiation systems are being used to identify factors that are important during the formation of the vascular system. Embryonic stem cells are difficult to transfect, while downregulation of promoter activity upon selection of stable transfectants has been reported, rendering the study of proteins by overexpression difficult.

Results

CCE mouse embryonic stem cells were differentiated on collagen type IV for 4–5 days, Flk1+ mesodermal cells were sorted and replated either on collagen type IV in the presence of VEGFA to give rise to endothelial cells and smooth muscle cells or in collagen type I gels for the formation of vascular tubes. The activity of the CMV and β-actin promoters was downregulated during selection of stable transfectants and during differentiation to the Flk1 stage, while the CMV immediate enhancer/β-actin promoter in the pCAGIPuro-GFP vector led to 100% of stably transfected undifferentiated and differentiated cells expressing GFP. To further test this system we expressed syndecan-2 and -4 in these cells and demonstrated high levels of transgene expression in both undifferentiated cells and cells differentiated to the Flk1 stage.

Conclusion

Vectors containing the CAG promoter offer a valuable tool for the long term expression of transgenes during stem cell differentiation towards mesoderm, while the CMV and β-actin promoters lead to very poor transgene expression during this process.
A highly sensitive and specific system for large-scale gene expression profiling
Authors: Hu Guohong , Yang Qifeng , Cui Xiangfeng , Yue Gang , Azaro Marco A , Wang Hui-Yun , Li Honghua
Published: January 2008

Background

Rapid progress in the field of gene expression-based molecular network integration has generated strong demand on enhancing the sensitivity and data accuracy of experimental systems. To meet the need, a high-throughput gene profiling system of high specificity and sensitivity has been developed.

Results

By using specially designed primers, the new system amplifies sequences in neighboring exons separated by big introns so that mRNA sequences may be effectively discriminated from other highly related sequences including their genes, unprocessed transcripts, pseudogenes and pseudogene transcripts. Probes used for microarray detection consist of sequences in the two neighboring exons amplified by the primers. In conjunction with a newly developed high-throughput multiplex amplification system and highly simplified experimental procedures, the system can be used to analyze >1,000 mRNA species in a single assay. It may also be used for gene expression profiling of very few (n = 100) or single cells. Highly reproducible results were obtained from duplicate samples with the same number of cells, and from those with a small number (100) and a large number (10,000) of cells. The specificity of the system was demonstrated by comparing results from a breast cancer cell line, MCF-7, and an ovarian cancer cell line, NCI/ADR-RES, and by using genomic DNA as starting material.

Conclusion

Our approach may greatly facilitate the analysis of combinatorial expression of known genes in many important applications, especially when the amount of RNA is limited.
Characterization of a filamentous biofilm community established in a cellulose-fed microbial fuel cell
Authors: Ishii Shun'ichi , Shimoyama Takefumi , Hotta Yasuaki , Watanabe Kazuya
Published: January 2008

Background

Microbial fuel cells (MFCs) are devices that exploit microorganisms to generate electric power from organic matter. Despite the development of efficient MFC reactors, the microbiology of electricity generation remains to be sufficiently understood.

Results

A laboratory-scale two-chamber microbial fuel cell (MFC) was inoculated with rice paddy field soil and fed cellulose as the carbon and energy source. Electricity-generating microorganisms were enriched by subculturing biofilms that attached onto anode electrodes. An electric current of 0.2 mA was generated from the first enrichment culture, and ratios of the major metabolites (e.g., electric current, methane and acetate) became stable after the forth enrichment. In order to investigate the electrogenic microbial community in the anode biofilm, it was morphologically analyzed by electron microscopy, and community members were phylogenetically identified by 16S rRNA gene clone-library analyses. Electron microscopy revealed that filamentous cells and rod-shaped cells with prosthecae-like filamentous appendages were abundantly present in the biofilm. Filamentous cells and appendages were interconnected via thin filaments. The clone library analyses frequently detected phylotypes affiliated with Clostridiales, Chloroflexi, Rhizobiales and Methanobacterium. Fluorescence in-situ hybridization revealed that the Rhizobiales population represented rod-shaped cells with filamentous appendages and constituted over 30% of the total population.

Conclusion

Bacteria affiliated with the Rhizobiales constituted the major population in the cellulose-fed MFC and exhibited unique morphology with filamentous appendages. They are considered to play important roles in the cellulose-degrading electrogenic community.
Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling
Authors: Adam Benoit , Charloteaux Benoit , Beaufays Jerome , Vanhamme Luc , Godfroid Edmond , Brasseur Robert , Lins Laurence
Published: January 2008

Background

Lipocalins are widely distributed in nature and are found in bacteria, plants, arthropoda and vertebra. In hematophagous arthropods, they are implicated in the successful accomplishment of the blood meal, interfering with platelet aggregation, blood coagulation and inflammation and in the transmission of disease parasites such as Trypanosoma cruzi and Borrelia burgdorferi.

The pairwise sequence identity is low among this family, often below 30%, despite a well conserved tertiary structure. Under the 30% identity threshold, alignment methods do not correctly assign and align proteins. The only safe way to assign a sequence to that family is by experimental determination. However, these procedures are long and costly and cannot always be applied. A way to circumvent the experimental approach is sequence and structure analyze. To further help in that task, the residues implicated in the stabilisation of the lipocalin fold were determined. This was done by analyzing the conserved interactions for ten lipocalins having a maximum pairwise identity of 28% and various functions.

Results

It was determined that two hydrophobic clusters of residues are conserved by analysing the ten lipocalin structures and sequences. One cluster is internal to the barrel, involving all strands and the 310 helix. The other is external, involving four strands and the helix lying parallel to the barrel surface. These clusters are also present in RaHBP2, a unusual "outlier" lipocalin from tick Rhipicephalus appendiculatus. This information was used to assess assignment of LIR2 a protein from Ixodes ricinus and to build a 3D model that helps to predict function. FTIR data support the lipocalin fold for this protein.

Conclusion

By sequence and structural analyzes, two conserved clusters of hydrophobic residues in interactions have been identified in lipocalins. Since the residues implicated are not conserved for function, they should provide the minimal subset necessary to confer the lipocalin fold. This information has been used to assign LIR2 to lipocalins and to investigate its structure/function relationship. This study could be applied to other protein families with low pairwise similarity, such as the structurally related fatty acid binding proteins or avidins.
Distribution of Anopheles in Vietnam, with particular attention to malaria vectors of the Anopheles minimus complex
Authors: Garros Claire , Van Nguyen Cam , Trung Ho Dinh , Van Bortel Wim , Coosemans Marc , Manguin Sylvie
Published: January 2008

Background

The distribution of anopheline mosquitoes in Vietnam was examined, with a particular interest for the two sibling species of the Anopheles minimus complex (Cellia: Myzomyia), An. minimus and Anopheles harrisoni, respectively former species A and C. Because the morphological identification of both sibling species is difficult and may lead to misidentifications, accurate data on their respective distribution are missing. This is of fundamental importance since the two species seem to exhibit differential vectorial capacities for malaria transmission.

Methods

Large entomological surveys based on cattle collections and molecular identifications of An. minimus s.l. were carried out in 23 sites throughout northern, central and south-eastern regions of Vietnam.

Results

Based on previous molecular works and our data, the distribution of anopheline species and the relative densities of An. minimus and An. harrisoni were mapped. It is noteworthy that there was a high specific biodiversity at each study site. Anopheles minimus s.l. and Anopheles sinensis were the main anopheline species in the northern region, whereas Anopheles aconitus and Anopheles vagus were the most frequent ones in the central region. The southern limit of An. harrisoni was increased to the latitude of 11°N. Sympatry between both sibling species has been extended to new provinces.

Conclusion

Malaria transmission is still high in central Vietnam and along bordering countries. Therefore, it is important to know and map the precise distribution of the main and secondary malaria vectors in Vietnam for applying efficient vector control programmes. Moreover, these maps should be regularly updated and linked to environmental characteristics relative to disease epidemiology, and environmental and climatic changes occurring in southeast Asia.
p53 represses human papillomavirus type 16 DNA replication via the viral E2 protein
Authors: Brown Craig , Kowalczyk Anna M , Taylor Ewan R , Morgan Iain M , Gaston Kevin
Published: January 2008

Background

Human papillomavirus (HPV) DNA replication can be inhibited by the cellular tumour suppressor protein p53. However, the mechanism through which p53 inhibits viral replication and the role that this might play in the HPV life cycle are not known. The papillomavirus E2 protein is required for efficient HPV DNA replication and also regulates viral gene expression. E2 represses transcription of the HPV E6 and E7 oncogenes and can thereby modulate indirectly host cell proliferation and survival. In addition, the E2 protein from HPV 16 has been shown to bind p53 and to be capable of inducing apoptosis independently of E6 and E7.

Results

Here we use a panel of E2 mutants to confirm that mutations which block the induction of apoptosis via this E6/E7-independent pathway, have little or no effect on the induction of apoptosis by the E6/E7-dependent pathway. Although these mutations in E2 do not affect the ability of the protein to mediate HPV DNA replication, they do abrogate the repressive effects of p53 on the transcriptional activity of E2 and prevent the inhibition of E2-dependent HPV DNA replication by p53.

Conclusion

These data suggest that p53 down-regulates HPV 16 DNA replication via the E2 protein.
Melanotic medullary carcinoma of thyroid – report of a rare case with brief review of literature
Authors: Singh Kamaljeet , Sharma Mehar C , Jain Deepali , Kumar Rajinder
Published: January 2008

Background

Melanin production in medullary carcinoma is extremely uncommon.

Case presentation

We report a rare variant of medullary carcinoma of thyroid with melanin production in a 52-year-old woman who presented with swelling in the thyroid of 3 months duration. This tumor recurred thrice in two years after surgery and patient died with metastasis. Microscopic examination showed typical morphology of medullary carcinoma with numerous cells loaded with melanin pigment as confirmed by bleached Fontana-Masson, negative iron and immunohistochemical stains. Tumor cells were diffusely immunopositive for calcitonin, HMB-45, chromogranin, synaptophysin, CEA but showed focal paranuclear dot positivity for cytokeratin. No C-cell hyperplasia was seen in the adjacent thyroid gland. Nature of the pigment was further confirmed on ultra structural examination.

Conclusion

Melanotic medullary carcinoma is an extremely uncommon entity. There is a need to report more number of cases in the literature for exact categorization and prognostication of this subtype of medullary carcinoma.
Chylous ascites following radical nephrectomy: a case report
Authors: Shah Shahzad S , Ahmed Kamran , Smith Richard , Mallina Ravi , Akhbari Pouya , Khan Mohammad S
Published: January 2008

Introduction

Chylous ascites may result from diverse pathologies. Ascites results either due to blockage of the lymphatics or leak secondary to inadvertent trauma during surgery.

Case presentation

We report the first case of chylous ascites following radical nephrectomy for a renal cell carcinoma involving the right half of a crossed fused renal ectopia. The patient was managed conservatively.

Conclusion

Post-operative chylous ascites is a rare complication of retroperitoneal and mediastinal surgery. Most cases resolve with conservative treatment which aims at decreasing lymph production and optimizing nutritional requirements along with palliative measures. Refractory cases need either open or laparoscopic ligation of the leaking lymphatic channels. A review of the current literature on the management of post-operative chylous ascites is presented.
Na+/H+exchanger regulatory factor 1 inhibits platelet-derived growth factor signaling in breast cancer cells
Authors: Pan Yong , Weinman Edward J , Le Dai Jia
Published: January 2008

Introduction

The gene encoding Na+/H+ exchanger regulatory factor 1 (NHERF1) is a putative tumor suppressor gene that harbors frequent loss of heterozygosity (LOH) and intragenic mutations in breast carcinoma. The exact biologic activity of NHERF1 in mammary glands, however, remains unclear. It was recently proposed that NHERF1 forms a ternary complex with platelet-derived growth factor receptor (PDGFR) and phosphatase and tensin homolog (PTEN), linking NHERF1 suppressor activity to PDGF-initiated phosphoinositide-3 kinase (PI3K)/PTEN signaling.

Methods

The effect of NHERF1 on the kinetics of PDGF-induced Akt activation was determined in cells with varied NHERF1 background. Levels of active Akt in mammary gland of NHERF1 knockout and wild-type mice were compared. We also examined how NHERF1 expression status affects cell sensitivity to PDGFR inhibitor. A plausible connection between NHERF1 and PTEN pathway was explored at the genetic level.

Results

We showed that NHERF1, through its PDZ-I domain, interacts directly with the carboxyl-terminal tail of PTEN. Knocking down NHERF1 expression in Zr75.1 cells markedly delayed the turnover of PDGF-induced phospho-Akt. Conversely, NHERF1 over-expression in MCF10A cells led to accelerated phospho-Akt degradation. The slowed decay of phospho-Akt that resulted from NHERF1 loss was evident in mouse embryonic fibroblasts isolated from NHERF1 knockout mice. In agreement with this, mammary gland tissues from these mice exhibited markedly elevated phospho-Akt. The responses of breast cancer cells to PDGFR inhibition were also altered by changes in NHERF1 expression level. Zr75.1 cells with NHERF1 knockdown were more resistant to STI-571-induced apoptosis than parental cells. Similarly, over-expression of NHERF1 rendered MCF10A cells more sensitive to STI-571. NHERF1-induced apoptotic response relies on an intact PTEN pathway; over-expression of NHERF1 in MCF10A cells with PTEN knockdown did not affect STI-571 sensitivity. It was found that NHERF1 LOH-positive breast cancer cells had reduced NHERF1 expression. Interestingly, these cells more frequently had wild-type PTEN or PI3KCA gene than the LOH-negative lines.

Conclusion

Our data indicate that the interaction of NHERF1 with PTEN counterbalances PI3K/Akt oncogenic signaling and may affect how cells respond to PDGFR inhibition in breast cancer. The dependence of NHERF1 responses on PTEN and genetic segregation of NHERF1 and PTEN (or PI3KCA) alterations suggest that NHERF1 is an active component of the PTEN pathway. Collectively, our study indicates that the biologic activity of NHERF1 in mammary gland is related to PTEN signaling.
Anisotropic correction of sonic logs in wells with large relative dip
Authors: Vernik Lev
Published: January 2008

Seismic reservoir characterization and pore-pressure prediction projects rely heavily on the accuracy and consistency of sonic logs. Sonic data acquisition in wells with large relative dip is known to suffer from anisotropic effects related to microanisotropy of shales and thin-bed laminations of sand, silt, and shale. Nonetheless, if anisotropy parameters can be related to shale content [Formula: see text] in siliciclastic rocks, then I show that it is straightforward to compute the anisotropy correction to both compressional and shear logs using [Formula: see text] and the formation relative dip angle. The resulting rotated P-wave sonic logs can be used to enhance time-depth ties, velocity to effective stress transforms, and low-frequency models necessary for prestack seismic amplitude variation with offset (AVO) inversion.
Stochastic sparse-spike deconvolution
Authors: Velis Danilo R.
Published: January 2008

Sparse-spike deconvolution can be viewed as an inverse problem where the locations and amplitudes of a number of spikes (reflectivity) are estimated from noisy data (seismic traces). The main objective is to find the least number of spikes that, when convolved with the available band-limited seismic wavelet estimate, fit the data within a given tolerance error (misfit). The detection of the spikes’ time lags is a highly nonlinear optimization problem that can be solved using very fast simulated annealing (SA). Amplitudes are easily estimated using linear least squares at each SA iteration. At this stage, quadratic regularization is used to stabilize the solution, to reduce its nonuniqueness, and to provide meaningful reflectivity sequences, thus avoiding the need to constrain the spikes’ time lags and/or amplitudes to force valid solutions. Impedance constraints also can be included at this stage, providing the low frequencies required to recover the acoustic impedance. One advantage of the proposed method over other sparse-spike deconvolution techniques is that the uncertainty of the obtained solutions can be estimated stochastically. Further, errors in the phase of the wavelet estimate are tolerated, for an optimum constant-phase shift is obtained to calibrate the effective wavelet that is present in the data. Results using synthetic data (including simulated data for the Marmousi2 model) and field 3D data show that physically meaningful high-resolution sparse-spike sections can be derived from band-limited noisy data, even when the available wavelet estimate is inaccurate.