Genetic dissection of gene regulation in multiple mouse tissues

The analysis of the influence of genetic variation on regulation of gene expression at a near-genome-wide level has become the focus of much recent interest. It is widely appreciated that many genes are expressed in a tissue-specific manner and that others are more ubiquitously expressed but relatively little is known about how genetic variation might influence these tissue patterns of gene expression. In this review we discuss what is known about the tissue specificity of the influence of genetic variation and review the challenges that we face in combining hugely parallel, microarray-based gene analysis with equally expensive genetic analysis. We conclude that the available data suggest that genetic variation is essentially tissue specific in its effects upon gene expression and this has important implications for experimental analysis.     

Epigallocatechin-3-gallate delivers hydrogen peroxide to induce death of ovarian cancer cells and enhances their cisplatin susceptibility

The green tea polyphenol epigallocatechin-3-gallate (EGCG) has cancer chemopreventive properties against various types of cancers. The compound is known to attack various targets in transformed cells. In this report, we examined the action of EGCG on ovarian cancer cells. Eight ovarian cancer cell lines were tested (SKOV3, CAOV3, OVCAR3, OVCAR10, A2780, CP70, C30, and C200) and showed IC50s for EGCG at the micromolar range, including ones that are resistant to the chemotherapeutic drug cisplatin. The ovarian cancer cells were sensitive to H2O2 at similar concentrations, and EGCG treatment led to enhanced intracellular H2O2. Neutralization with pyruvate, a scavenger of H2O2, suggests that the toxicity of EGCG may be mediated by oxidative stress from the free radical. Addition of Tempol, a superoxide dismutase mimetic, demonstrates that H2O2 might be generated endogenously from superoxide. The toxicity of cisplatin and the development of cisplatin resistance are major obstacles in treatment of ovarian cancer. We found that addition of EGCG amplified the toxicity of cisplatin. EGCG increased cisplatin potency by three to six-fold in SKOV3, CAOV3, and C200 cells, the latter being a cell line induced to have several hundred fold resistant to cisplatin above the parental line. Our findings suggest that EGCG may accentuate oxidative stress to inhibit growth of ovarian cancer cells and sensitize them to cisplatin.     

Nuclear magnetic resonance structure-based epitope mapping and modulation of dust mite group 13 allergen as a hypoallergen

IgE-mediated allergic response involves cross-linking of IgE bound on mast cells by specific surface epitopes of allergens. Structural studies on IgE epitopes of allergens are essential in understanding the characteristics of an allergen and for development of specific allergen immunotherapy. We have determined the structure of a group 13 dust mite allergen from Dermatophagoides farinae, Der f 13, using nuclear magnetic resonance. Sequence comparison of Der f 13 with homologous human fatty acid-binding proteins revealed unique surface charged residues on Der f 13 that may be involved in IgE binding and allergenicity. Site-directed mutagenesis and IgE binding assays have confirmed four surface charged residues on opposite sides of the protein that are involved in IgE binding. A triple mutant of Der f 13 (E41A_K63A_K91A) has been generated and found to have significantly reduced IgE binding and histamine release in skin prick tests on patients allergenic to group 13 dust mite allergens. The triple mutant is also able to induce PBMC proliferation in allergic patients with indices similar to those of wild-type Der f 13 and shift the secretion of cytokines from a Th2 to a Th1 pattern. Mouse IgG serum raised using the triple mutant is capable to block the binding of IgE from allergic patients to wild-type Der f 13, indicating potential for the triple mutant as a hypoallergen for specific immunotherapy. Findings in this study imply the importance of surface charged residues on IgE binding and allergenicity of an allergen, as was also demonstrated in other major allergens studied.     

The glycosaminoglycan-binding domain of decoy receptor 3 is essential for induction of monocyte adhesion

Decoy receptor 3 (DcR3), a soluble receptor for Fas ligand, LIGHT (homologous to lymphotoxins shows inducible expression and competes with HSV glycoprotein D for herpes virus entry mediator, a receptor expressed by T lymphocytes), and TNF-like molecule 1A, is highly expressed in cancer cells and in tissues affected by autoimmune disease. DcR3.Fc has been shown to stimulate cell adhesion and to modulate cell activation and differentiation by triggering multiple signaling cascades that are independent of its three known ligands. In this study we found that DcR3.Fc-induced cell adhesion was inhibited by heparin and heparan sulfate, and that DcR3.Fc was unable to bind Chinese hamster ovary K1 mutants defective in glycosaminoglycan (GAG) synthesis. Furthermore, the negatively charged, sulfated GAGs of cell surface proteoglycans, but not their core proteins, were identified as the binding sites for DcR3.Fc. A potential GAG-binding site was found in the C-terminal region of DcR3, and the mutation of three basic residues, i.e., K256, R258, and R259, to alanines abolished its ability to trigger cell adhesion. Moreover, a fusion protein comprising the GAG-binding region of DcR3 with an Fc fragment (DcR3_HBD.Fc) has the same effect as DcR3.Fc in activating protein kinase C and inducing cell adhesion. Compared with wild-type THP-1 cells, cell adhesion induced by DcR3.Fc was significantly reduced in both CD44v3 and syndecan-2 knockdown THP-1 cells. Therefore, we propose a model in which DcR3.Fc may bind to and cross-link proteoglycans to induce monocyte adhesion.     

Functional significance of factor H binding to Neisseria meningitidis

Neisseria meningitidis is an important cause of septicemia and meningitis. To cause disease, the bacterium must successfully survive in the bloodstream where it has to avoid being killed by host innate immune mechanisms, particularly the complement system. A number of pathogenic microbes bind factor H (fH), the negative regulator of the alternative pathway of complement activation, to promote their survival in vivo. In this study, we show that N. meningitidis binds fH to its surface. Binding to serogroups A, B, and C N. meningitidis strains was detected by FACS and Far Western blot analysis, and occurred in the absence of other serum factors such as C3b. Unlike Neisseria gonorrhoeae, binding of fH to N. meningitidis was independent of sialic acid on the bacterium, either as a component of its LPS or its capsule. Characterization of the major fH binding partner demonstrated that it is a 33-kDa protein; examination of insertion mutants showed that porins A and B, outer membrane porins expressed by N. meningitidis, do not contribute significantly to fH binding. We examined the physiological consequences of fH bound to the bacterial surface. We found that fH retains its activity as a cofactor of factor I when bound to the bacterium and contributes to the ability of N. meningitidis to avoid complement-mediated killing in the presence of human serum. Therefore, the recruitment of fH provides another mechanism by which this important human pathogen evades host innate immunity.     

Imaging and therapy of malignant pleural mesothelioma using replication-competent herpes simplex viruses

BACKGROUND: Malignant pleural mesothelioma (MPM) is an aggressive cancer that is refractory to current treatment modalities. Oncolytic herpes simplex viruses (HSV) used for gene therapy are genetically engineered, replication-competent viruses that selectively target tumor cells while sparing normal host tissue. The localized nature, the potential accessibility and the relative lack of distant metastasis make MPM a particularly suitable disease for oncolytic viral therapy. METHODS: The infectivity, selective replication, vector spread and cytotoxic ability of three oncolytic HSV: G207, NV1020 and NV1066, were tested against eleven pathological types of MPM cell lines including those that are resistant to radiation therapy, gemcitabine or cisplatin. The therapeutic efficacy and the effect on survival of NV1066 were confirmed in a murine MPM model. RESULTS: All three oncolytic HSV were highly effective against all the MPM cell lines tested. Even at very low concentrations of MOI 0.01 (MOI: multiplicity of viral infection, ratio of viral particles per cancer cell), HSV were highly effective against MPM cells that are resistant to radiation, gemcitabine and cisplatin. NV1066, an oncolytic HSV that expresses green fluorescent protein (GFP), was able to delineate the extent of the disease in a murine model of MPM due to selective infection and expression of GFP in tumor cells. Furthermore, NV1066 was able to reduce the tumor burden and prolong survival even when treatment was at an advanced stage of the disease. CONCLUSION: These findings support the continued investigation of oncolytic HSV as potential therapy for patients with therapy-resistant MPM.     

Human cytomegalovirus induced cyclooxygenase-2 in human retinal pigment epithelial cells augments viral replication through a prostaglandin pathway

Cytomegalovirus (CMV) retinitis is characterized by alterations in retinal cell function and host responses to virus replication. The goal of this study was to evaluate the induction of cyclooxygenase-2 (COX-2) and prostaglandin (PGE) in CMV infected human retinal pigment epithelial (RPE) cells and to determine their effect on virus replication. CMV immediate early (IE) protein and COX-2 proteins were identified in RPE cells in retinal tissue sections from patients with CMV retinitis. COX-2 mRNA and protein were induced after CMV infection of human RPE cell cultures. CMV infection of RPE cells induced translocation of NF-kappaB from the cytoplasm to the nucleus. PGE1 and PGE2 were significantly (p<0.001) increased in human RPE cell cultures infected with CMV. Inhibition of CMV IE gene by antisense oligonucleotides abrogated induction of mRNA for COX-2 and protein synthesis of COX-2 and PGE2. PGE enhanced CMV plaque formation and real time PCR analysis revealed that PGE treatment significantly increased CMV DNA copy numbers. These studies demonstrate that when CMV replicates within human RPE cells, COX-2 induction augments virus replication via the PGE pathway. The induction of COX-2 and PGE during retinal CMV infection may augment virus replication and alter a variety of retinal physiological responses.     

A taxonomy of application scheduling tools for high performance cluster computing

Application scheduling plays an important role in high-performance cluster computing. Application scheduling can be classified as job scheduling and task scheduling. This paper presents a survey on the software tools for the graph-based scheduling on cluster systems with the focus on task scheduling. The tasks of a parallel or distributed application can be properly scheduled onto multi-processors in order to optimize the performance of the program (e.g., execution time or resource utilization). In general, scheduling algorithms are designed based on the notion of task graph that represents the relationship of parallel tasks. The scheduling algorithms map the nodes of a graph to the processors in order to minimize overall execution time. Although many scheduling algorithms have been proposed in the literature, surprisingly not many practical tools can be found in practical use. After discussing the fundamental scheduling techniques, we propose a framework and taxonomy for the scheduling tools on clusters. Using this framework, the features of existing scheduling tools are analyzed and compared. We also discuss the important issues in improving the usability of the scheduling tools. This work is supported by the Hong Kong Polytechnic University under grant H-ZJ80 and by NASA Ames Research Center by a cooperative grant agreement with the University of Texas at Arlington. Jiannong Cao received the BSc degree in computer science from Nanjing University, Nanjing, China in 1982, and the MSc and the Ph.D degrees in computer science from Washington State University, Pullman, WA, USA, in 1986 and 1990 respectively. He is currently an associate professor in Department of Computing at the Hong Kong Polytechnic University, Hong Kong. He is also the director of the Internet and Mobile Computing Lab in the department. He was on the faculty of computer science at James Cook University and University of Adelaide in Australia, and City University of Hong Kong. His research interests include parallel and distributed computing, networking, mobile computing, fault tolerance, and distributed software architecture and tools. He has published over 120 technical papers in the above areas. He has served as a member of editorial boards of several international journals, a reviewer for international journals/conference proceedings, and also as an organizing/programme committee member for many international conferences. Dr. Cao is a member of the IEEE Computer Society, the IEEE Communication Society, IEEE, and ACM. He is also a member of the IEEE Technical Committee on Distributed Processing, IEEE Technical Committee on Parallel Processing, IEEE Technical Committee on Fault Tolerant Computing, and Computer Architecture Professional Committee of the China Computer Federation. Alvin Chan is currently an assistant professor at the Hong Kong Polytechnic University. He graduated from the University of New South Wales with a Ph.D. degree in 1995 and was subsequently employed as a Research Scientist by the CSIRO, Australia. From 1997 to 1998, he was employed by the Centre for Wireless Communications, National University of Singapore as a Program Manager. Dr. Chan is one of the founding members and director of a university spin-off company, Information Access Technology Limited. He is an active consultant and has been providing consultancy services to both local and overseas companies. His research interests include mobile computing, context-aware computing and smart card applications. Yudong Sun received the B.S. and M.S. degrees from Shanghai Jiao Tong University, China. He received Ph.D. degree from the University of Hong Kong in 2002, all in computer science. From 1988 to 1996, he was among the teaching staff in Department of Computer Science and Engineering at Shanghai Jiao Tong University. From 2002 to 2003, he held a research position at the Hong Kong Polytechnic University. At present, he is a Research Associate in School of Computing Science at University of Newcastle upon Tyne, UK. His research interests include parallel and distributed computing, Web services, Grid computing, and bioinformatics. Sajal K. Das is currently a Professor of Computer Science and Engineering and the Founding Director of the Center for Research in Wireless Mobility and Networking (CReWMaN) at the University of Texas at Arlington. His current research interests include resource and mobility management in wireless networks, mobile and pervasive computing, sensor networks, mobile internet, parallel processing, and grid computing. He has published over 250 research papers, and holds four US patents in wireless mobile networks. He received the Best Paper Awards in ACM MobiCom’99, ICOIN-16, ACM, MSWiM’00 and ACM/IEEE PADS’97. Dr. Das serves on the Editorial Boards of IEEE Transactions on Mobile Computing, ACM/Kluwer Wireless Networks, Parallel Processing Letters, Journal of Parallel Algorithms and Applications. He served as General Chair of IEEE PerCom’04, IWDC’04, MASCOTS’02 ACM WoWMoM’00-02; General Vice Chair of IEEE PerCom’03, ACM MobiCom’00 and IEEE HiPC’00-01; Program Chair of IWDC’02, WoWMoM’98-99; TPC Vice Chair of ICPADS’02; and as TPC member of numerous IEEE and ACM conferences. Minyi Guo received his Ph.D. degree in information science from University of Tsukuba, Japan in 1998. From 1998 to 2000, Dr. Guo had been a research scientist of NEC Soft, Ltd. Japan. He is currently a professor at the Department of Computer Software, The University of Aizu, Japan. From 2001 to 2003, he was a visiting professor of Georgia State University, USA, Hong Kong Polytechnic University, Hong Kong. Dr. Guo has served as general chair, program committee or organizing committee chair for many international conferences, and delivered more than 20 invited talks in USA, Australia, China, and Japan. He is the editor-in-chief of the Journal of Embedded Systems. He is also in editorial board of International Journal of High Performance Computing and Networking, Journal of Embedded Computing, Journal of Parallel and Distributed Scientific and Engineering Computing, and International Journal of Computer and Applications. Dr. Guo’s research interests include parallel and distributed processing, parallelizing compilers, data parallel languages, data mining, molecular computing and software engineering. He is a member of the ACM, IEEE, IEEE Computer Society, and IEICE. He is listed in Marquis Who’s Who in Science and Engineering.     

Up-regulation in expression of vesicular glutamate transporter 3 in substantia nigra but not in striatum of 6-hydroxydopamine-lesioned rats

Overactivity of the glutamatergic system is suggested to be closely related to the onset and pathogenesis of Parkinson's disease. Vesicular glutamate transporters (VGLUT1, T2 and T3) are a group of glutamate transporters in neurons that are responsible for transporting glutamate into synaptic vesicles and they are key elements for homeostasis of glutamate neurotransmission. The present study was aimed to investigate the expression of VGLUT1, T2 and T3 proteins after the onset of Parkinson's disease. A rat model of Parkinson's disease, the 6-hydroxydopamine-lesioned rat, was employed. Immunocytochemistry revealed that VGLUT1, T2 and T3 immunoreactivity was not modulated in the striatum of the lesioned rat. Western blotting analyses also showed that there was no change in the expression of T1, T2 and T3 proteins in the striatum. In contrast, no VGLUT1 protein was detected in the substantia nigra. After the lesion, levels of VGLUT2 immunoreactivity and protein were not modulated. Significant increase of VGLUT3 immunoreactivity was observed in the perikarya of GABAergic substantia nigra pars reticulata neurons (+14.7%) although VGLUT3 protein was not modulated in the nigral tissues. VGLUT3 in GABAergic neurons is suggested to play a role in GABA synthesis. The present results may therefore implicate that VGLUT1 and T2 are not modulated in the striatum and the substantia nigra of the 6-hydroxydopamine-lesioned rat and only VGLUT3 plays a role in pathogenesis of Parkinson's disease.