AIM: To establish the methylation profile of the promoter CpG islands of 31 genes that might play etiological roles in colon carcinogenesis.METHODS: The methylation specific PCR in conjunction of sequendng verificatio...AIM: To establish the methylation profile of the promoter CpG islands of 31 genes that might play etiological roles in colon carcinogenesis.METHODS: The methylation specific PCR in conjunction of sequendng verification was used to establish the methylationprofile of the promoter CpG islands of 31 genes in colorectal cancer (n = 65), the neighboring non-cancerous tissues (n = 5), colorectal adenoma (n = 8), and normal mucosa (n = 1). Immunohistochemically, expression of 10 genes was assessed on the home-made tissue microarrays of tissues from 58 patients. The correlation of tumor specific changes with each of clinical-pathologic features was scrutinized with relevant statistic tools.RESULTS: In comparison with the normal mucosa of the non-cancer patients, the following 14 genes displayed no tumor associated changes: breast cancer 1, early onset (BRCA1), cadherin 1, type 1, E-cadherin (epithelial) (CDH1),death-associated protein kinase 1 (DAPK1), DNA (cytosine-5-)-methyltransferase 1 (DNMT1), melanoma antigen, family A, 1 (directs expression of antigen MZ2-E) (MAGEA1), tumor suppressor candidate 3 (N33), cyclin-dependent kinase inhibitor 1A (p21, Cipl) (p21^WAF1), cyclin-dependent kinase inhibitor 1B (p27, 10pl) (p27^WAF1), phosphatase and tensin hornolog (mutated in multiple advanced cancers 1) (PTEN), retinoic acid receptor, beta (RAR-, Ras association (RaIGDS/AF-6) domain family 1 C (RASSFIC), secreted frizzled-related protein 1 (SFRP1), tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinfiammatory) (TIMP3),and von HippeI-Lindau syndrome (VHL). The rest 17 targets exhibited to various extents the tumor associated changes.As changes in methylation of the following genes occurred marginally, their impact on the formation of colorectal cancer were trivial: adenomatous polyposis coli (APC) (8%, 5165),Ras association (RaIGDS/AF-6) domain family 1A (RASSFIA) (3%, 2/65) and cyclin-dependent kinase inhibitor 2A,alternated reading frame Co14~) (6%, 4/65). The following genes exhibited moderate changes in rnethylation: O-6rnethylguanine-DNA rnethyltransferase (MGMT) (20%, 13/65),rnutL hornolog 1, colon cancer, nonpolyposis type 2 (E. coli) (hMLH1) (18%, 12/65), cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) P16^NK4a) (10%, 10/65),rnethylated in tumor 1 (MINT1) (15%, 10/65), methylated in tumor 31 (MINT31) (11%, 7/65). The rest changed greatly in the rnethylation pattern in colorectal cancer (CRC): cyclin A1 (cyclin al) (100%, 65/65), caudal type homeobox transcriptdon factor 1 (CDX1) (100%, 65/65), RAR(85%, 55/65), myogenic factor 3 (MYOD1) (69%, 45/65),cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)(p15^INK4b) (68%, 44/65), prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) (COX2) (72%, 47/65), cadherin 13, H-cadherin (heart) (CDH13) (65%, 42/65), CAAX box 1 (OO~/) (58%, 38/65),tumor protein p73 (p73) (63%, 41/65) and Wilrns tumor 1 (WT/) (58%, 38/65). However, no significant correlation of changes in rnethylation with any given clinical-pathological features was detected. Furthermore, the frequent changes in rnethylation appeared to be an early phase event of colon carcinogenesis. The in situ expression of 10 genes was assessed by the irnrnunohistochernical approach at the protein level: CDH1, CDH13, COX2, cyclin A1, hMLH1,MGMT, p14^ARF, p73, RAR-, and TIMP3 genes in the context of the rnethylation status in colorectal cancer. No clear correlation between the hyperrnethylation of the promoter CpG islands and the negative expression of the genes was established.CONCLUSION: The methylation profile of 31 genes was established in patients with colon cancer and colorectal adenornas, which provides new insights into the DNA rnethylation mediated mechanisms underlying the carcinogenesis of colorectal cancer and may be of prognostic values for colorectal cancer.展开更多
AIM: To evaluate the effects of survivin on cell proliferation and apoptosis in liver cancer. METHODS: MTT assay was used to generate and optimize phosphorothioate antisense oligonucleotides (ODNs)-LipofectamineTM2000...AIM: To evaluate the effects of survivin on cell proliferation and apoptosis in liver cancer. METHODS: MTT assay was used to generate and optimize phosphorothioate antisense oligonucleotides (ODNs)-LipofectamineTM2000 (LiP) compound by varying ODNs (μg): LiP (μL) ratios from 1:0.5 to 1:5. Then, liver cancer cells (HepG2) were transfected with the compound. By using RT-PCR and Western blot, the expression levels of survivin mRNA and proteins were detected in HepG2 cells treated with antisense compounds (ODNs:LiP=1:4), and compared with those treated with sense compounds (1:4) as control. MTT assay was applied to the determination of cell proliferation in HepG2 cells. Active caspase-3 was evaluated by flow cytometric analysis. The morphological changes were assessed by electron microscopy. Laser scanning confocal microscopy was performed to detect the subcellular localization of survivin proteins in treated and untreated cells. RESULTS: Antisense compounds (1:4) down-regulated survivin expression (mRNA and protein) in a dose-dependent manner with an IC50 of 250 nmol/L. Its maximum effect was achieved at a concentration of 500 nmol/L, at which mRNA and protein levels were down-regulated by 80%. The similar results were found in MTT assay. Antisense compound (l:4)-treated cells revealed increased caspase-3-like protease activity compared with untreated cells. Untreated cells as control were primarily negative for the presence of active-caspase-3. As shown by transmission electron microscopy, treated cells with antisense compounds (1:4) resulted in morphological changes such as blebbing and loss of microvilli, vacuolization in the cytoplasm, condensation of the cytoplasm and nuclei, and fragmented chromatin. Immunofluorescence analysis confirmed the presence of survivin protein pool inside the cytoplasm in untreated cells. Labeled-FITC immunofluorescence staining of survivin clearly showed that survivin was distributed mainly in a spotted form inside the cytoplasm. Whereas cells treated with antisense compounds were rare and weak inside the cytoplasm. CONCLUSION: Down-regulation of survivin expression induced by the antisense compounds reduces tumor growth potential, promotes apoptosis and affects the localization of survivin proteins in HepG2 cells. Furthermore, survivin protein is a key molecule associated with proliferation and apoptosis, and antisense oligonucleotides targeting survivin have a bright prospect in the therapy of liver cancer.展开更多
Combinatorial optimization problems are found in many application fields such as computer science, engineering and economy. In this paper, a new efficient meta-heuristic, Intersection-Based Scaling (IBS for abbreviati...Combinatorial optimization problems are found in many application fields such as computer science, engineering and economy. In this paper, a new efficient meta-heuristic, Intersection-Based Scaling (IBS for abbreviation), is proposed and it can be applied to the combinatorial optimization problems. The main idea of IBS is to scale the size of the instance based on the intersection of some local optima, and to simplify the search space by extracting the intersection from the instance, which makes the search more efficient. The combination of IBS with some local search heuristics of different combinatorial optimization problems such as Traveling Salesman Problem (TSP) and Graph Partitioning Problem (GPP) is studied, and comparisons are made with some of the best heuristic algorithms and meta-heuristic algorithms. It is found that it has significantly improved the performance of existing local search heuristics and significantly outperforms the known best algorithms. Keywords combinatorial optimization - TSP (Traveling Salesman Problem) - GPP (Graph Partitioning Problem) - IBS (Intersection-Based Scaling) - meta heuristic Regular PaperThis work is supported by the National Basic Research 973 Program of China (Grant No.TG1998030401).Peng Zou was born in 1979. He received the B.S. degree in computer software from University of Science and Technology of China (USTC) in 2000. Now he is a Ph.D. candidate in computer science of USTC. His current research interests include algorithms for NP-hard problems and parallel computing.Zhi Zhou was born in 1976. He received the B.S. degree in computer software from USTC in 1995. Now he is a Ph.D. candidate in computer science of USTC. His current research interests include combinatorial problem and parallel computing.Ying-Yu Wan was born in 1976. He received the B.S. degree in computer software from USTC in 1997, and the Ph.D. degree from USTC in 2002. His current research interests include parallel computing and combinatorial problem.Guo-Liang Chen was born in 1938. Now he is an Academician of CAS and Ph.D. supervisor in Department of Computer Science at USTC, director of the National High Performance Computing Center at Hefei. His current research interests include parallel computing, computer architecture and combinatorial optimization.Jun Gu was born in 1956. He received the B.S. degree in electronic engineering from USTC in 1982, and the Ph.D. degree in computer science from University of Utah. Now he is a professor and Ph.D. supervisor in computer science at USTC and Hong Kong University of Science and Technology. His main research interrests include algorithms for NP-hard problems.展开更多
Bounded Slice-line Grid (BSG) is an elegant representation of block placement, because it is very intuitionistic and has the advantage of handling various placement constraints. However, BSG has attracted little atten...Bounded Slice-line Grid (BSG) is an elegant representation of block placement, because it is very intuitionistic and has the advantage of handling various placement constraints. However, BSG has attracted little attention because its evaluation is very time-consuming. This paper proposes a simple algorithm independent of the BSG size to evaluate the BSG representation in O(n log log n) time, where n is the number of blocks. In the algorithm, the BSG-rooms are assigned with integral coordinates firstly, and then a linear sorting algorithm is applied on the BSG-rooms where blocks are assigned to compute two block sequences, from which the block placement can be obtained in O(n log log n) time. As a consequence, the evaluation of the BSG is completed in O(n log log n) time, where n is the number of blocks. The proposed algorithm is much faster than the previous graph-based O(n(2)) algorithm. The experimental results demonstrate the efficiency of the algorithm.展开更多
This paper studies the buffer planning problem for interconnect-centric floorplanning for nanometer technologies. The dead-spaces are the spaces left unused within a placement that are not held by any circuit block. I...This paper studies the buffer planning problem for interconnect-centric floorplanning for nanometer technologies. The dead-spaces are the spaces left unused within a placement that are not held by any circuit block. In this paper, we proposed a buffer planning algorithm based on dead space redistribution to make good use of dead-spaces for buffer insertion. Associated with circuit blocks under topological representations, the dead space can be redistributed by moving freely some circuit blocks within their rooms in the placement. The total area and the topology of the placement keep unchanged while doing the dead space redistribution. The number of nets satisfying the delay constraint can be increased by redistributing the dead space all over the placement, which has been demonstrated by the experimental results. The increment of the number of nets that meet delay constraint is 9% on an average.展开更多
基金Supported by the National High Technology Research and DevelopmentProgram of China (863 Program),No.2002AA2Z3352,the ScienceFoundation of Shanghai Municipal Government,No.02DJ14056,and the Special Fund set up by the State-Key Laboratory for Oncogenes
文摘AIM: To establish the methylation profile of the promoter CpG islands of 31 genes that might play etiological roles in colon carcinogenesis.METHODS: The methylation specific PCR in conjunction of sequendng verification was used to establish the methylationprofile of the promoter CpG islands of 31 genes in colorectal cancer (n = 65), the neighboring non-cancerous tissues (n = 5), colorectal adenoma (n = 8), and normal mucosa (n = 1). Immunohistochemically, expression of 10 genes was assessed on the home-made tissue microarrays of tissues from 58 patients. The correlation of tumor specific changes with each of clinical-pathologic features was scrutinized with relevant statistic tools.RESULTS: In comparison with the normal mucosa of the non-cancer patients, the following 14 genes displayed no tumor associated changes: breast cancer 1, early onset (BRCA1), cadherin 1, type 1, E-cadherin (epithelial) (CDH1),death-associated protein kinase 1 (DAPK1), DNA (cytosine-5-)-methyltransferase 1 (DNMT1), melanoma antigen, family A, 1 (directs expression of antigen MZ2-E) (MAGEA1), tumor suppressor candidate 3 (N33), cyclin-dependent kinase inhibitor 1A (p21, Cipl) (p21^WAF1), cyclin-dependent kinase inhibitor 1B (p27, 10pl) (p27^WAF1), phosphatase and tensin hornolog (mutated in multiple advanced cancers 1) (PTEN), retinoic acid receptor, beta (RAR-, Ras association (RaIGDS/AF-6) domain family 1 C (RASSFIC), secreted frizzled-related protein 1 (SFRP1), tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinfiammatory) (TIMP3),and von HippeI-Lindau syndrome (VHL). The rest 17 targets exhibited to various extents the tumor associated changes.As changes in methylation of the following genes occurred marginally, their impact on the formation of colorectal cancer were trivial: adenomatous polyposis coli (APC) (8%, 5165),Ras association (RaIGDS/AF-6) domain family 1A (RASSFIA) (3%, 2/65) and cyclin-dependent kinase inhibitor 2A,alternated reading frame Co14~) (6%, 4/65). The following genes exhibited moderate changes in rnethylation: O-6rnethylguanine-DNA rnethyltransferase (MGMT) (20%, 13/65),rnutL hornolog 1, colon cancer, nonpolyposis type 2 (E. coli) (hMLH1) (18%, 12/65), cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) P16^NK4a) (10%, 10/65),rnethylated in tumor 1 (MINT1) (15%, 10/65), methylated in tumor 31 (MINT31) (11%, 7/65). The rest changed greatly in the rnethylation pattern in colorectal cancer (CRC): cyclin A1 (cyclin al) (100%, 65/65), caudal type homeobox transcriptdon factor 1 (CDX1) (100%, 65/65), RAR(85%, 55/65), myogenic factor 3 (MYOD1) (69%, 45/65),cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)(p15^INK4b) (68%, 44/65), prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) (COX2) (72%, 47/65), cadherin 13, H-cadherin (heart) (CDH13) (65%, 42/65), CAAX box 1 (OO~/) (58%, 38/65),tumor protein p73 (p73) (63%, 41/65) and Wilrns tumor 1 (WT/) (58%, 38/65). However, no significant correlation of changes in rnethylation with any given clinical-pathological features was detected. Furthermore, the frequent changes in rnethylation appeared to be an early phase event of colon carcinogenesis. The in situ expression of 10 genes was assessed by the irnrnunohistochernical approach at the protein level: CDH1, CDH13, COX2, cyclin A1, hMLH1,MGMT, p14^ARF, p73, RAR-, and TIMP3 genes in the context of the rnethylation status in colorectal cancer. No clear correlation between the hyperrnethylation of the promoter CpG islands and the negative expression of the genes was established.CONCLUSION: The methylation profile of 31 genes was established in patients with colon cancer and colorectal adenornas, which provides new insights into the DNA rnethylation mediated mechanisms underlying the carcinogenesis of colorectal cancer and may be of prognostic values for colorectal cancer.
基金Supported by the National Natural Science Foundation of China, No.30171059
文摘AIM: To evaluate the effects of survivin on cell proliferation and apoptosis in liver cancer. METHODS: MTT assay was used to generate and optimize phosphorothioate antisense oligonucleotides (ODNs)-LipofectamineTM2000 (LiP) compound by varying ODNs (μg): LiP (μL) ratios from 1:0.5 to 1:5. Then, liver cancer cells (HepG2) were transfected with the compound. By using RT-PCR and Western blot, the expression levels of survivin mRNA and proteins were detected in HepG2 cells treated with antisense compounds (ODNs:LiP=1:4), and compared with those treated with sense compounds (1:4) as control. MTT assay was applied to the determination of cell proliferation in HepG2 cells. Active caspase-3 was evaluated by flow cytometric analysis. The morphological changes were assessed by electron microscopy. Laser scanning confocal microscopy was performed to detect the subcellular localization of survivin proteins in treated and untreated cells. RESULTS: Antisense compounds (1:4) down-regulated survivin expression (mRNA and protein) in a dose-dependent manner with an IC50 of 250 nmol/L. Its maximum effect was achieved at a concentration of 500 nmol/L, at which mRNA and protein levels were down-regulated by 80%. The similar results were found in MTT assay. Antisense compound (l:4)-treated cells revealed increased caspase-3-like protease activity compared with untreated cells. Untreated cells as control were primarily negative for the presence of active-caspase-3. As shown by transmission electron microscopy, treated cells with antisense compounds (1:4) resulted in morphological changes such as blebbing and loss of microvilli, vacuolization in the cytoplasm, condensation of the cytoplasm and nuclei, and fragmented chromatin. Immunofluorescence analysis confirmed the presence of survivin protein pool inside the cytoplasm in untreated cells. Labeled-FITC immunofluorescence staining of survivin clearly showed that survivin was distributed mainly in a spotted form inside the cytoplasm. Whereas cells treated with antisense compounds were rare and weak inside the cytoplasm. CONCLUSION: Down-regulation of survivin expression induced by the antisense compounds reduces tumor growth potential, promotes apoptosis and affects the localization of survivin proteins in HepG2 cells. Furthermore, survivin protein is a key molecule associated with proliferation and apoptosis, and antisense oligonucleotides targeting survivin have a bright prospect in the therapy of liver cancer.
文摘Combinatorial optimization problems are found in many application fields such as computer science, engineering and economy. In this paper, a new efficient meta-heuristic, Intersection-Based Scaling (IBS for abbreviation), is proposed and it can be applied to the combinatorial optimization problems. The main idea of IBS is to scale the size of the instance based on the intersection of some local optima, and to simplify the search space by extracting the intersection from the instance, which makes the search more efficient. The combination of IBS with some local search heuristics of different combinatorial optimization problems such as Traveling Salesman Problem (TSP) and Graph Partitioning Problem (GPP) is studied, and comparisons are made with some of the best heuristic algorithms and meta-heuristic algorithms. It is found that it has significantly improved the performance of existing local search heuristics and significantly outperforms the known best algorithms. Keywords combinatorial optimization - TSP (Traveling Salesman Problem) - GPP (Graph Partitioning Problem) - IBS (Intersection-Based Scaling) - meta heuristic Regular PaperThis work is supported by the National Basic Research 973 Program of China (Grant No.TG1998030401).Peng Zou was born in 1979. He received the B.S. degree in computer software from University of Science and Technology of China (USTC) in 2000. Now he is a Ph.D. candidate in computer science of USTC. His current research interests include algorithms for NP-hard problems and parallel computing.Zhi Zhou was born in 1976. He received the B.S. degree in computer software from USTC in 1995. Now he is a Ph.D. candidate in computer science of USTC. His current research interests include combinatorial problem and parallel computing.Ying-Yu Wan was born in 1976. He received the B.S. degree in computer software from USTC in 1997, and the Ph.D. degree from USTC in 2002. His current research interests include parallel computing and combinatorial problem.Guo-Liang Chen was born in 1938. Now he is an Academician of CAS and Ph.D. supervisor in Department of Computer Science at USTC, director of the National High Performance Computing Center at Hefei. His current research interests include parallel computing, computer architecture and combinatorial optimization.Jun Gu was born in 1956. He received the B.S. degree in electronic engineering from USTC in 1982, and the Ph.D. degree in computer science from University of Utah. Now he is a professor and Ph.D. supervisor in computer science at USTC and Hong Kong University of Science and Technology. His main research interrests include algorithms for NP-hard problems.
文摘Bounded Slice-line Grid (BSG) is an elegant representation of block placement, because it is very intuitionistic and has the advantage of handling various placement constraints. However, BSG has attracted little attention because its evaluation is very time-consuming. This paper proposes a simple algorithm independent of the BSG size to evaluate the BSG representation in O(n log log n) time, where n is the number of blocks. In the algorithm, the BSG-rooms are assigned with integral coordinates firstly, and then a linear sorting algorithm is applied on the BSG-rooms where blocks are assigned to compute two block sequences, from which the block placement can be obtained in O(n log log n) time. As a consequence, the evaluation of the BSG is completed in O(n log log n) time, where n is the number of blocks. The proposed algorithm is much faster than the previous graph-based O(n(2)) algorithm. The experimental results demonstrate the efficiency of the algorithm.
文摘This paper studies the buffer planning problem for interconnect-centric floorplanning for nanometer technologies. The dead-spaces are the spaces left unused within a placement that are not held by any circuit block. In this paper, we proposed a buffer planning algorithm based on dead space redistribution to make good use of dead-spaces for buffer insertion. Associated with circuit blocks under topological representations, the dead space can be redistributed by moving freely some circuit blocks within their rooms in the placement. The total area and the topology of the placement keep unchanged while doing the dead space redistribution. The number of nets satisfying the delay constraint can be increased by redistributing the dead space all over the placement, which has been demonstrated by the experimental results. The increment of the number of nets that meet delay constraint is 9% on an average.
