2011
22
3
3
100
Two Steps Methylation Specific PCR for Assessment of APC Promoter Methylation in Gastric Adenocarcinoma
Two Steps Methylation Specific PCR for Assessment of APC Promoter Methylation in Gastric Adenocarcinoma
2
2
Gastric Cancer (GC) is the second most common cancer in the world and a leading cause of cancer-related mortality. Methylation of promoter CpG islands (CGIs) belonging to tumor suppressor genes causes transcriptional silencing of their corresponding genes leading to carcinogenesis and other disorders. Adenomatous Polyposis Coli (APC) a tumor suppressor gene is inactivated by methylation of promoter region in CpG islands. In current study, methylation of CGIs in the promoter of APC was analyzed using two steps Methylation Specific PCR in 36 tumor tissue samples together with an equal number of normal tissues belonging to patients with confirmed diagnosis of gastric carcinoma. Methylation specific PCR (MSP) was positive for 28 out of 36 (77.77%) of the tumors. No correlation was found between APC hypermethylation and the age of patients regardless of the relevant cofactors in aberrant methylation. Our study showed that hypermethylation of the APC gene was frequent among our patients with gastric cancer. Although the APC hypermethylation has been proposed to be involved in the early stages of gastric carcinogenesis, but the APC gene alone, does not seem to be a reliable marker for the different stages of cancer prognosis. Thus, it is recommended to use a panel of genes for evaluating the CpG Island methylator phenotype (CIMP) phenomena as an early event in gastric cancer, both for tumor and serum samples.
1
Gastric Cancer (GC) is the second most common cancer in the world and a leading cause of cancer-related mortality. Methylation of promoter CpG islands (CGIs) belonging to tumor suppressor genes causes transcriptional silencing of their corresponding genes leading to carcinogenesis and other disorders. Adenomatous Polyposis Coli (APC) a tumor suppressor gene is inactivated by methylation of promoter region in CpG islands. In current study, methylation of CGIs in the promoter of APC was analyzed using two steps Methylation Specific PCR in 36 tumor tissue samples together with an equal number of normal tissues belonging to patients with confirmed diagnosis of gastric carcinoma. Methylation specific PCR (MSP) was positive for 28 out of 36 (77.77%) of the tumors. No correlation was found between APC hypermethylation and the age of patients regardless of the relevant cofactors in aberrant methylation. Our study showed that hypermethylation of the APC gene was frequent among our patients with gastric cancer. Although the APC hypermethylation has been proposed to be involved in the early stages of gastric carcinogenesis, but the APC gene alone, does not seem to be a reliable marker for the different stages of cancer prognosis. Thus, it is recommended to use a panel of genes for evaluating the CpG Island methylator phenotype (CIMP) phenomena as an early event in gastric cancer, both for tumor and serum samples.
205
212
Rastgar
Jazii
Rastgar
Jazii
National Institute of Genetic Engineering
National Institute of Genetic Engineering
Iran
Gastric cancer (GC)
Methylation specific PCR (MSP)
Hypermethylation
CpG islands (CGIs)
Adenomatous polyposis Coli (APC)
The Study of Biodesulfurization Activity in Recombinant E. coli Strain by Cloning
the dsz Genes Involve in 4S Pathway
The Study of Biodesulfurization Activity in Recombinant E. coli Strain by Cloning
the dsz Genes Involve in 4S Pathway
2
2
Several research groups have attempted to make recombinant bacteria capable of efficient desulfurization of oil fraction. The main aim of this study was to design a recombinant strain in order to desulfurize dibenzothiophen (DBT) and its components found in petroleum. In this study the pVLT31 vector harboring dszABC genes was transferred into recombinant E. coli BL21 which contained the dszD gene previously. We found that the recombinant E. coli BL21 containing the pVLT31 plasmid harboring dszABC genes and the pET21a plasmid harboring dszD gene had the highest capability for desulfurization of dibenzothiophen, when these four genes co-expressed. The data obtained in this study were confirmed by using Gibbs test, High-performance liquid chromatography (HPLC) and measuring of dry Cell weight. These analyses showed that dszABC and dszD genes co-express under the heterologous promoter in the strains which are stable in oil and petroleum compounds. In the next step the pUC18 plasmid harboring dszAB genes of Rhodococcous FMF was transferred into E. coli DH5? in order to evaluate the Effect of elimination of dszC gene in the rate of biodesulfurization process. This analysis demonstrated that 2-hydroxybiphenyl (2-HBP) production of recombinant E. coli DH5? using broken 4s pathway was less than that of Rhodococcous FMF in comparison. In this report we showed that the existence of the third gene (dszC) is necessary for enhancement of desulfurization activity.
1
Several research groups have attempted to make recombinant bacteria capable of efficient desulfurization of oil fraction. The main aim of this study was to design a recombinant strain in order to desulfurize dibenzothiophen (DBT) and its components found in petroleum. In this study the pVLT31 vector harboring dszABC genes was transferred into recombinant E. coli BL21 which contained the dszD gene previously. We found that the recombinant E. coli BL21 containing the pVLT31 plasmid harboring dszABC genes and the pET21a plasmid harboring dszD gene had the highest capability for desulfurization of dibenzothiophen, when these four genes co-expressed. The data obtained in this study were confirmed by using Gibbs test, High-performance liquid chromatography (HPLC) and measuring of dry Cell weight. These analyses showed that dszABC and dszD genes co-express under the heterologous promoter in the strains which are stable in oil and petroleum compounds. In the next step the pUC18 plasmid harboring dszAB genes of Rhodococcous FMF was transferred into E. coli DH5? in order to evaluate the Effect of elimination of dszC gene in the rate of biodesulfurization process. This analysis demonstrated that 2-hydroxybiphenyl (2-HBP) production of recombinant E. coli DH5? using broken 4s pathway was less than that of Rhodococcous FMF in comparison. In this report we showed that the existence of the third gene (dszC) is necessary for enhancement of desulfurization activity.
213
219
Jamshid
Raheb
Jamshid
Raheb
National Institute of Genetic Engineering
and Biotechnology (NIGEB)
National Institute of Genetic Engineering
Iran
2-Hydroxybiphenyl
Desulfurization
Dibenzothiophen
Application of Spectral Analysis in Mapping Hydrothermal Alteration of the Northwestern Part of the Kerman Cenozoic Magmatic Arc, Iran
Application of Spectral Analysis in Mapping Hydrothermal Alteration of the Northwestern Part of the Kerman Cenozoic Magmatic Arc, Iran
2
2
The northwestern part of the Kerman Cenozoic magmatic arc (KCMA) contains many areas with porphyry copper mineralization. In this research, we used the advanced space-borne thermal emission and reflection radiometer (ASTER) and Enhanced Thematic Mapper plus (ETM+) images of this region to map the distribution of hydrothermally altered rocks, based on their mineral assemblages. The spectral measurements based on the spectra of field samples and on ASTER and ETM+ data, show dominantly Al-OH (sericite and clays) and FeO absorption features in the VNIR/SWIR spectral regions. Directed principal components analysis (DPCA), spectral angle mapper (SAM) and linear spectral unmixing (LSU) were performed on ASTER/ETM+ images to map zones of hydrothermal alteration and iron oxide/hydroxide minerals. The individual principal components (PC) images generated by DPCA reveal the distribution of individual alteration minerals such as sericite, illite, kaolinite, chlorite, and epidote. The best results, in terms of mapping the distribution of alteration, were obtained using the SAM and LSU methods; but the LSU method produced a more accurate map. The altered zones were sampled and then subjected to X-ray diffraction (XRD), laboratory spectral and chemical analyses. Microscopic studies of the thin sections were also conducted. Field observations reveal that more than 90% of the known copper mineralized localities occur within the interpreted alteration areas.
1
The northwestern part of the Kerman Cenozoic magmatic arc (KCMA) contains many areas with porphyry copper mineralization. In this research, we used the advanced space-borne thermal emission and reflection radiometer (ASTER) and Enhanced Thematic Mapper plus (ETM+) images of this region to map the distribution of hydrothermally altered rocks, based on their mineral assemblages. The spectral measurements based on the spectra of field samples and on ASTER and ETM+ data, show dominantly Al-OH (sericite and clays) and FeO absorption features in the VNIR/SWIR spectral regions. Directed principal components analysis (DPCA), spectral angle mapper (SAM) and linear spectral unmixing (LSU) were performed on ASTER/ETM+ images to map zones of hydrothermal alteration and iron oxide/hydroxide minerals. The individual principal components (PC) images generated by DPCA reveal the distribution of individual alteration minerals such as sericite, illite, kaolinite, chlorite, and epidote. The best results, in terms of mapping the distribution of alteration, were obtained using the SAM and LSU methods; but the LSU method produced a more accurate map. The altered zones were sampled and then subjected to X-ray diffraction (XRD), laboratory spectral and chemical analyses. Microscopic studies of the thin sections were also conducted. Field observations reveal that more than 90% of the known copper mineralized localities occur within the interpreted alteration areas.
221
238
H
Ranjbar
H
Ranjbar
Shahid Bahonar University
Shahid Bahonar University
Iran
LSU
Porphyry copper
Hydrothermal alteration
DPCA
SAM
Sedimentary Facies, Architectural Elements and Trace Fossils of Kashkan Formation, Folded
Zagros Zone in SW Iran
Sedimentary Facies, Architectural Elements and Trace Fossils of Kashkan Formation, Folded
Zagros Zone in SW Iran
2
2
The Kashkan Formation (Paleocene to Middle Eocene), consists of conglomerate, sandstone, and siltstone in the Zagros Folded zone, southwest Iran. Type of the sedimentary facies, architectural elements and trace fossils show that Kashkan deposits were formed in a low sinuosity braided stream system, with north to south flow direction. The formation displays coarsening-upward succession reflects an overall regressive sequence. The clast–supported conglomerate is the major components of the formation. A thinning of the coarser–grained sediments toward the south, and southwest indicates that the source for the Kashkan formation was to the north and northwest from the study area. Trace fossils of Kashkan Formation are related to Scoyenia ichnofacies, include Arenicolites isp., Diplocraterion isp., Ophiomorpha isp., Skolithos isp., Steinichnus isp., Thalassinoides isp., Escape structure and vertebrate footprints. Sedimentological analysis and type of the trace fossils indicate the south the stream was restricted by a shoreface environment. Kashkan Formation becomes thinner and fine–grained in the southern part of the study area.
1
The Kashkan Formation (Paleocene to Middle Eocene), consists of conglomerate, sandstone, and siltstone in the Zagros Folded zone, southwest Iran. Type of the sedimentary facies, architectural elements and trace fossils show that Kashkan deposits were formed in a low sinuosity braided stream system, with north to south flow direction. The formation displays coarsening-upward succession reflects an overall regressive sequence. The clast–supported conglomerate is the major components of the formation. A thinning of the coarser–grained sediments toward the south, and southwest indicates that the source for the Kashkan formation was to the north and northwest from the study area. Trace fossils of Kashkan Formation are related to Scoyenia ichnofacies, include Arenicolites isp., Diplocraterion isp., Ophiomorpha isp., Skolithos isp., Steinichnus isp., Thalassinoides isp., Escape structure and vertebrate footprints. Sedimentological analysis and type of the trace fossils indicate the south the stream was restricted by a shoreface environment. Kashkan Formation becomes thinner and fine–grained in the southern part of the study area.
239
255
N
Abbassi
N
Abbassi
University of Lorestan
University of Lorestan
Iran
Kashkan Formation
Sedimentology
Zagros
Trace fossil
Lithofacies
A Strong Regular Relation on ?-Semihyperrings
A Strong Regular Relation on ?-Semihyperrings
2
2
The concept of algebraic hyperstructures introduced by Marty as a generalization of ordinary algebraic structures. In an ordinary algebraic structure, the composition of two elements is an element, while in an algebraic hyperstructure, the composition of two elements is a set. The concept of ?-semihyperrings is a generalization of semirings, a generalization of semihyperrings and a generalization of ?-semirings. In this paper, we introduce an equivalence relation ?* on a ?-semihyperrings R and we show that it is strongly regular. Furthermore, R/?*, the set of all equivalence classes of this relation is a ?/?*-semiring. The relation ?* is called the fundamental relation and the ?-semiring R/?* is called the fundamental semiring. Fundamental relations are the main tools in the study of ?-semihyperrings. We present some results about fundamental relations and fundamental semirings. Finally, we show that there is a covariant functor between the category of ?-semihyperrings and the category of semirings.
1
The concept of algebraic hyperstructures introduced by Marty as a generalization of ordinary algebraic structures. In an ordinary algebraic structure, the composition of two elements is an element, while in an algebraic hyperstructure, the composition of two elements is a set. The concept of ?-semihyperrings is a generalization of semirings, a generalization of semihyperrings and a generalization of ?-semirings. In this paper, we introduce an equivalence relation ?* on a ?-semihyperrings R and we show that it is strongly regular. Furthermore, R/?*, the set of all equivalence classes of this relation is a ?/?*-semiring. The relation ?* is called the fundamental relation and the ?-semiring R/?* is called the fundamental semiring. Fundamental relations are the main tools in the study of ?-semihyperrings. We present some results about fundamental relations and fundamental semirings. Finally, we show that there is a covariant functor between the category of ?-semihyperrings and the category of semirings.
257
266
B
Davaz
B
Davaz
Yazd University
Yazd University
Iran
davvaz@yazduni.ac.ir
Fundamental semiring
?-semihyperring
?-hyperring
Strongly regular relation
Estimating a Bounded Normal Mean Relative
to Squared Error Loss Function
Estimating a Bounded Normal Mean Relative
to Squared Error Loss Function
2
2
Let be a random sample from a normal distribution with unknown mean and known variance The usual estimator of the mean, i.e., sample mean is the maximum likelihood estimator which under squared error loss function is minimax and admissible estimator. In many practical situations, is known in advance to lie in an interval, say for some In this case, the maximum likelihood estimator changes and dominates but it is no longer admissible. Minimax and some other estimators for this problem have been studied by some researchers. In this paper, a new estimator is proposed and the risk function of it is compared with some other competitors. According to our findings, the use of and the maximum likelihood estimator is not recommended when some information are accessible about the finite bounds on in advance. Based on the values taken by in , the appropriate estimator is suggested.
1
Let be a random sample from a normal distribution with unknown mean and known variance The usual estimator of the mean, i.e., sample mean is the maximum likelihood estimator which under squared error loss function is minimax and admissible estimator. In many practical situations, is known in advance to lie in an interval, say for some In this case, the maximum likelihood estimator changes and dominates but it is no longer admissible. Minimax and some other estimators for this problem have been studied by some researchers. In this paper, a new estimator is proposed and the risk function of it is compared with some other competitors. According to our findings, the use of and the maximum likelihood estimator is not recommended when some information are accessible about the finite bounds on in advance. Based on the values taken by in , the appropriate estimator is suggested.
267
276
A.
Karimnezhad
A.
Karimnezhad
Allameh Tabataba’i
University
Allameh Tabataba’i
University
Iran
Admissibility
Squared error loss
Bounded normal mean
Maximum Likelihood Estimator
Rao-Blackwellization
A Boundary Meshless Method for Neumann Problem
A Boundary Meshless Method for Neumann Problem
2
2
Boundary integral equations (BIE) are reformulations of boundary value problems for partial differential equations. There is a plethora of research on numerical methods for all types of these equations such as solving by discretization which includes numerical integration. In this paper, the Neumann problem is reformulated to a BIE, and then moving least squares as a meshless method is described for solving this integral equation. Error analysis of this method is discussed and then its application and accuracy are illustrated by some case studies.
1
Boundary integral equations (BIE) are reformulations of boundary value problems for partial differential equations. There is a plethora of research on numerical methods for all types of these equations such as solving by discretization which includes numerical integration. In this paper, the Neumann problem is reformulated to a BIE, and then moving least squares as a meshless method is described for solving this integral equation. Error analysis of this method is discussed and then its application and accuracy are illustrated by some case studies.
277
286
k
Maleknejad
k
Maleknejad
Iran University
of Science and Technology
Iran University
of Science and Technology
Iran
Laplace’s equation
Moving least squares method
Neumann problem
Boundary integral equation
Meshless method