Search results for: spatial gene

Authors: I. Boroňová, J.Bernasovská, J. Kľoc, Z. Tomková, E. Petrejčíková, D. Gabriková, S. Mačeková

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Osteoporosis is a complex health disease characterized by low bone mineral density, which is determined by an interaction of genetics with metabolic and environmental factors. Current research in genetics of osteoporosis is focused on identification of responsible genes and polymorphisms. TNFRSF11B gene plays a key role in bone remodeling. The aim of this study was to investigate the genotype and allele distribution of A163G (rs3102735) osteoprotegerin gene promoter and G1181C (rs2073618) osteoprotegerin first exon polymorphisms in the group of 180 unrelated postmenopausal women with diagnosed osteoporosis and 180 normal controls. Genomic DNA was isolated from peripheral blood leukocytes using standard methodology. Genotyping for presence of different polymorphisms was performed using the Custom Taqman®SNP Genotyping assays. Hardy-Weinberg equilibrium was tested for each SNP in the groups of participants using the chi-square (χ2) test. The distribution of investigated genotypes in the group of patients with osteoporosis were as follows: AA (66.7%), AG (32.2%), GG (1.1%) for A163G polymorphism; GG (19.4%), CG (44.4%), CC (36.1%) for G1181C polymorphism. The distribution of genotypes in normal controls were follows: AA (71.1%), AG (26.1%), GG (2.8%) for A163G polymorphism; GG (22.2%), CG (48.9%), CC (28.9%) for G1181C polymorphism. In A163G polymorphism the variant G allele was more common among patients with osteoporosis: 17.2% versus 15.8% in normal controls. Also, in G1181C polymorphism the phenomenon of more frequent occurrence of C allele in the group of patients with osteoporosis was observed (58.3% versus 53.3%). Genotype and allele distributions showed no significant differences (A163G: χ2=0.270, p=0.605; χ2=0.250, p=0.616; G1181C: χ2= 1.730, p=0.188; χ2=1.820, p=0.177). Our results represents an initial study, further studies of more numerous file and associations studies will be carried out. Knowing the distribution of genotypes is important for assessing the impact of these polymorphisms on various parameters associated with osteoporosis. Screening for identification of “at-risk” women likely to develop osteoporosis and initiating subsequent early intervention appears to be most effective strategy to substantially reduce the risks of osteoporosis.

Keywords: osteoporosis, real-time PCR method, SNP polymorphisms

Procedia PDF Downloads 318

Authors: Babawale Akin Adeyemi, Esan Temitayo, Adeyemi Olabisi Omowumi

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The paper analyzed waste disposal system in Akure, Ondo State using GIS techniques. Specifically, the study identified the spatial distribution of collection points and existing dumpsite; evaluated the accessibility of waste collection points and their proximity to each other with the view of enhancing better performance of the waste disposal system. Data for the study were obtained from both primary and secondary sources. Primary data were obtained through the administration of questionnaire. From field survey, 35 collection points were identified in the study area. 10 questionnaires were administered around each collection point making a total of 350 questionnaires for the study. Also, co-ordinates of each collection point were captured using a hand-held Global Positioning System (GPS) receiver which was used to analyze the spatial distribution of collection points. Secondary data used include administrative map collected from Akure South Local Government Secretariat. Data collected was analyzed using the GIS analytical tools which is neighborhood function. The result revealed that collection points were found in all parts of Akure with the highest concentration around the central business district. The study also showed that 80% of the collection points enjoyed efficient waste service while the remaining 20% does not. The study further revealed that most collection points in the core of the city were in close proximity to each other. In conclusion, the paper revealed the capability of Geographic Information System (GIS) as a technique in management of waste collection and disposal technique. The application of Geographic Information System (GIS) in the evaluation of the solid waste management in Akure is highly invaluable for the state waste management board which could also be beneficial to other states in developing a modern day solid waste management system. Further study on solid waste management is also recommended especially for updating of information on both spatial and non-spatial data.

Keywords: assessment, geospatial, system, waste disposal

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Authors: Endeshaw Assefa Derso, Maria Gabriella Campolo, Angela Alibrandi

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Objectives:Early childhood malnutrition can have long-term and irreversible effects on a child's health and development. This study uses the Bayesian method with spatial variation to investigate the flexible trends of metrical covariates and to identify communities at high risk of injury. Methods: Cross-sectional data on underweight are collected from the 2016 Ethiopian Demographic and Health Survey (EDHS). The Bayesian geo-additive model is performed. Appropriate prior distributions were provided for scall parameters in the models, and the inference is entirely Bayesian, using Monte Carlo Markov chain (MCMC) stimulation. Results: The results show that metrical covariates like child age, maternal body mass index (BMI), and maternal age affect a child's underweight non-linearly. Lower and higher maternal BMI seem to have a significant impact on the child’s high underweight. There was also a significant spatial heterogeneity, and based on IDW interpolation of predictive values, the western, central, and eastern parts of the country are hotspot areas. Conclusion: Socio-demographic and community- based programs development should be considered compressively in Ethiopian policy to combat childhood underweight malnutrition.

Keywords: bayesX, Ethiopia, malnutrition, MCMC, semi-parametric bayesian analysis, spatial distribution, P- splines

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Authors: András Farkas, István Molnár, Jan Vrána, Veronika Burešová, Petr Cápal, András Cseh, Márta Molnár-Láng, Jaroslav Doležel

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Species of Aegilops played a central role in the evolution of wheat and are sources of traits related to yield quality and tolerance against biotic and abiotic stresses. These wild genes and alleles are desirable to use in crop improvement programs via introgressive hybridization. However, the success of chromosome mediated gene transfer to wheat are hampered by the pour knowledge on the genome structure of Aegilops relative to wheat and by the low number of cost-effective molecular markers specific for Aegilops chromosomes. The COS markers specific for genes conserved throughout evolution in both sequence and copy number between Triticeae/Aegilops taxa and define orthologous regions, thus enabling the comparison of regions on the chromosomes of related species. The present study compared individual chromosomes of Aegilops umbellulata (UU), Ae. comosa (MM), Ae. speltoides (SS) and Ae. caudata (CC) purified by flourescent labelling with oligonucleotid SSR repeats and biparametric flow cytometry with wheat by identifying orthologous chromosomal regions by COS markers. The linear order of bin-mapped COS markers along the wheat D chromosomes was identified by the use of chromosome-specific sequence data and virtual gene order. Syntenic regions of wheat identifying genome rearrangements differentiating the U, M, S or C genomes from the D genome of wheat were detected. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species and wheat will facilitate the targeted development of new markers specific for U, M, S and C genomic regions and will contribute to the understanding of molecular processes related to the evolution of Aegilops.

Keywords: Aegilops, cos-markers, flow-sorting, wheat

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Authors: J. S. Bedi, J. P. S. Gill, R. S. Aulakh, Prabhjit Kaur

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The present study was undertaken to monitor organochlorine, organophosphate and synthetic pyrethroid pesticide residues in butter and ghee samples collected from six different districts of Punjab. The estimation of pesticide residues was done by multiple residue analytical technique using gas chromatography equipped with GC-ECD and GC-FTD. The confirmation of residues was done on gas chromatography mass spectrometry in both SIM and Scan mode. Results indicated the presence of HCH and pp DDE as predominant contaminant in both butter and ghee even after their ban/restriction on usage in India. Residues of HCH were detected in 25.5 and 23.2 % samples of butter and ghee, respectively, while residues of pp DDE were recorded in 29.3 and 25.0 % butter and ghee samples, respectively. More importantly, the presence of endosulfan, cypermethrin, fenvalerate, deltamethrin and chlorpyrifos was observed in few butter and ghee samples indicating the serious concerns. The spatial variation of pesticide residues occurrence indicated the cotton belt of Punjab as most affected.

Keywords: butter, ghee, pesticides residues, Punjab

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Authors: Lianxue Shi

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Riverside Street has the dual characteristics of street space and waterfront space, which is not only a vital place for residents to travel and communicate but also a high-frequency space for people's leisure and entertainment. However, under the development of cities and towns pursuing efficiency, riverfront streets appear to have a variety of problems, such as a lack of multifunctionality, insufficient facilities, and loss of characteristics, which fail to meet the needs of various groups of people, and their inclusiveness is facing a great challenge. It is, therefore, evident that the optimization of riverfront street space from an inclusivity perspective is important to the establishment of a human-centered, high-quality urban space. Therefore, this article starts by exploring the interactive relationship between inclusive design and street space. Based on the analysis of the characteristics of the riverfront street space and people's needs, it proposes the four inclusive design orientations of natural inclusion, group inclusion, spatial inclusion, and social inclusion. It then constructs a design framework for the inclusive optimization of riverfront street space, aiming to create streets that are “safe and accessible, diverse and shared, distinctive and friendly, green and sustainable.” Riverfront streets in Wansheng District, Chongqing, are selected as a practice case, and specific strategies are put forward in four aspects: the creation of an accessible slow-traffic system, the provision of diversified functional services, the reshaping of emotional bonds and the integration of ecological spaces.

Keywords: inclusiveness design, riverfront street, spatial optimization, street spaces

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Authors: Dalia G. Aseel

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The potato (Solanum tubersum, L.) has become one of the major vegetable crops in Egypt and all over the world. Potato leafroll virus(PLRV) was observed on potato plants collected from different governorates in Egypt. Three cultivars, Spunta, Diamont, and Cara, infected with PLRV were collected; RNA was extracted and subjected to Real-Time PCR using the coat protein gene primers. The results showed that the expression of the coat protein was 39.6-fold, 12.45-fold, and 47.43-fold, respectively, for Spunta, Diamont, and Cara cultivars. Differential Display Polymerase Chain Reaction (DD-PCR) using pathogenesis-related protein 1 (PR-1), β-1,3-glucanases (PR-2), chitinase (PR-3), peroxidase (POD), and polyphenol oxidase (PPO) forward primers for pathogenesis-related proteins (PR). The obtained data revealed different banding patterns depending on the viral type and the region of infection. Regarding PLRV, 58 up-regulated and 19 down-regulated genes were detected. Sequence analysis of the up-and down-regulated genes revealed that infected plants were observed in comparison with the healthy control. Sequence analysis of the up-regulated gene was performed, and the encoding sequence analysis showed that the obtained genes include: induced stolen tip protein. On the other hand, two down-regulated genes were identified: disease resistance RPP-like protein and non-specific lipid-transfer protein. In this study, the expressions of PR-1, PR-2, PR-3, POD, and PPO genes in the infected leaves of three potato cultivars were estimated by quantitative real-time PCR. We can conclude that the PLRV-infection of potato plants inhibited the expression of the five PR genes. On the contrary, infected leaves by PLRV elevated the expression of some defense genes. This interaction may also induce and/or suppress the expression of some genes responsible for the plant's defense mechanisms.

Keywords: PLRV, pathogenesis-related proteins (PRs), DD-PCR, sequence, real-time PCR

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Authors: Sahar Javadi-Novashnagh, Mohammad Moradi-Shahrbabak, Mostafa Sadeghi, Katarzyna Ropka-Molik, Hossein Moradi-Shahrbabak, Maria Consuelo Mura

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The objective of this study was to investigate two single nucleotide polymorphisms located in exon 2 (g.939A > G) and intron 3 (g.4349A > G) of fatty acid binding protein 3 (FABP3) gene in two Iranian sheep breeds, Lori-Bakhtiari and Zel, using polymerase chain reaction -restriction fragment length polymorphism (PCR-RFLP) approach. The association of the polymorphisms with growth traits and blood parameters was also examined. Results revealed a g.939A > G SNP (single nucleotide polymorphism) in the exon 2 exhibiting three genotypes: AA, AG, and GG. Statistical analysis indicated that this polymorphism significantly influenced blood triglyceride (P < 0.05) and cholesterol (P < 0.08) levels as well as weaning weight (P < 0.05). Animals with AG genotype had the highest blood triglyceride level and weaning weight while the highest amount of blood cholesterol was observed in animals with GG genotype. On the other hand, no significant effect was observed on birth and fat-tail weight traits. The intron 3 (g.4349A > G) was monomorphic across the studied samples. Lori-Bakhtiari breed showed significantly higher blood triglyceride and cholesterol levels, as also birth and weaning weight compared to Zel breed (P < 0.01). Considering that the literature is bereft of any report on the association study between FABP3 SNPs and sheep growth traits and blood parameters, our findings suggest that the investigated polymorphism might be one of the main genetic factors affecting growth and physiological traits in sheep.

Keywords: FABP3 gene, fatness, weaning weight, blood triglyceride, cholesterol, Zel, Lori-Bakhtiari

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Authors: Amr A. El Hanafy, Muhammad I. Qureshi, Jamal Sabir, Mohamed Mutawakil, Mohamed M. Ahmed, Hassan El Ashmaoui, Hassan Ramadan, Mohamed Abou-Alsoud, Mahmoud Abdel Sadek

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β-Lactoglobulin (β-LG) is the dominant non-casein whey protein found in bovine milk and of most ruminants. The amino acid sequence of β-LG along with its 3-dimensional structure illustrates linkage with the lipocalin superfamily. Preliminary studies in goats indicated that milk yield can be influenced by polymorphism in genes coding for whey proteins. The aim of this study is to identify and evaluate the incidence of functional polymorphisms in the exonic and intronic portions of β-LG gene in native Saudi goat breeds (Ardi, Habsi, and Harri). Blood samples were collected from 300 animals (100 for each breed) and genomic DNA was extracted using QIAamp DNA extraction Kit. A fragment of the β-LG gene from exon 7 to 3’ flanking region was amplified with pairs of specific primers. Subsequent digestion with Sac II restriction endonuclease revealed two alleles (A and B) and three different banding patterns or genotypes i.e. AA, AB and BB. The statistical analysis showed that β-LG AA genotype had higher milk yield than β-LG AB and β-LG BB genotypes. Nucleotide sequencing of the selected β-LG fragments was done and submitted to GenBank NCBI (Accession No. KJ544248, KJ588275, KJ588276, KJ783455, KJ783456 and KJ874959). Two already established SNPs in exon 7 (+4601 and +4603) and one fresh SNP in the 3’ UTR region were detected in the β-LG fragments with designated AA genotype. The polymorphisms in exon 7 did not produce any amino acid change. Phylogenetic analysis on the basis of nucleotide sequences of native Saudi goats indicated evolutional similarity with the GenBank reference sequences of goat, Bubalus bubalis and Bos taurus.

Keywords: β-Lactoglobulin, Saudi goats, PCR-RFLP, functional polymorphism, nucleotide sequencing, phylogenetic analysis

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Authors: Jung-En Kuan, Whei-Fen Wu

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In this study, a symbiotic bacteria from yellow mealworm's (Tenebrio molitor) mid-gut was isolated with characteristics of growth on minimal-tributyrin medium. After a PCR-amplification of its 16s rDNA, the resultant nucleotide sequences were then analyzed by schemes of the phylogeny trees. Accordingly, it was designated as Pseudomonas nitroreducens D-01. Next, by searching the lipolytic enzymes in its protein data bank, one of those potential lipolytic α/β hydrolases was identified, again using PCR-amplification and nucleotide-sequencing methods. To construct an expression of this lipolytic gene in plasmids, the target-gene primers were then designed, carrying the C-terminal his-tag sequences. Using the vector pET21a, a recombinant lipolytic hydrolase D gene with his-tag nucleotides was successfully cloned into it, of which the lipolytic D gene is under a control of the T7 promoter. After transformation of the resultant plasmids into Eescherichia coli BL21 (DE3), an IPTG inducer was used for the induction of the recombinant proteins. The protein products were then purified by metal-ion affinity column, and the purified proteins were found capable of forming a clear zone on tributyrin agar plate. Shortly, its enzyme activities were determined by degradation of p-nitrophenyl ester(s), and the substantial yellow end-product, p-nitrophenol, was measured at O.D.405 nm. Specifically, this lipolytic enzyme efficiently targets p-nitrophenyl butyrate. As well, it shows the most reactive activities at 40°C, pH 8 in potassium phosphate buffer. In thermal stability assays, the activities of this enzyme dramatically drop when the temperature is above 50°C. In metal ion assays, MgCl₂ and NH₄Cl induce the enzyme activities while MnSO₄, NiSO₄, CaCl₂, ZnSO₄, CoCl₂, CuSO₄, FeSO₄, and FeCl₃ reduce its activities. Besides, NaCl has no effects on its enzyme activities. Most organic solvents decrease the activities of this enzyme, such as hexane, methanol, ethanol, acetone, isopropanol, chloroform, and ethyl acetate. However, its enzyme activities increase when DMSO exists. All the surfactants like Triton X-100, Tween 80, Tween 20, and Brij35 decrease its lipolytic activities. Using Lineweaver-Burk double reciprocal methods, the function of the enzyme kinetics were determined such as Km = 0.488 (mM), Vmax = 0.0644 (mM/min), and kcat = 3.01x10³ (s⁻¹), as well the total efficiency of kcat/Km is 6.17 x10³ (mM⁻¹/s⁻¹). Afterwards, based on the phylogenetic analyses, this lipolytic protein is classified to type IV lipase by its homologous conserved region in this lipase family.

Keywords: enzyme, esterase, lipotic hydrolase, type IV

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Authors: Hanno Schmidt, Assaf Malik, Anne Bicker, Gesa Poetzsch, Aaron Avivi, Imad Shams, Thomas Hankeln

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The blind subterranean mole rat Spalax shows a remarkable tolerance to hypoxia, cancer-resistance and longevity. Unravelling the genomic basis of these adaptations will be important for biomedical applications. RNA-Seq gene expression data were obtained from normoxic and hypoxic Spalax and rat liver tissue. Hypoxic Spalax broadly downregulates genes from major liver function pathways. This energy-saving response is likely a crucial adaptation to low oxygen levels. In contrast, the hypoxiasensitive rat shows massive upregulation of energy metabolism genes. Candidate genes with plausible connections to the mole rat’s phenotype, such as important key genes related to hypoxia-tolerance, DNA damage repair, tumourigenesis and ageing, are substantially higher expressed in Spalax than in rat. Comparative liver transcriptomics highlights the importance of molecular adaptations at the gene regulatory level in Spalax and pinpoints a variety of starting points for subsequent functional studies.

Keywords: cancer, hypoxia, longevity, transcriptomics

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Authors: Arfan Ali, Muhammad Shahzad Iqbal, Idrees Ahmad Nasir

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Potato (Solanum tuberosum L.) is ranked among the top leading staple foods in the world. Salinity adversely affects potato crop yield and quality. Therefore, increased level of salt tolerance is a key factor to ensure high yield. The present study focused on the Agrobacterium-mediated transformation of Atriplex canescens betaine aldehyde dehydrogenase (BADH) gene, using single, double and triple CAMV35s promoter to improve salt tolerance in potato. Detection of seven potato lines harboring BADH gene, followed by identification of T-DNA insertions, determination of transgenes copies no through Southern Hybridization and quantification of BADH protein through Enzyme Linked Immunosorbent Assay were considered in this study. The results clearly depict that the salt tolerance of potato was found to be promoter-dependent, as the potato transgenic lines with triple promoter showed 4.4 times more glycine betaine production which consequently leads towards high resistance to salt stress as compared to transgenic potato lines with single and double promoters having least production of glycine betaine. Moreover, triple promoter transgenic potato lines have also shown lower levels of H2O2, malondialdehyde (MDA), relative electrical conductivity, high proline and chlorophyll content as compared other two lines having a single and double promoter. Insilco analysis also confirmed that Atriplex canescens BADH has the tendency to interact with sodium ions and water molecules. Taken together these facts it can be concluded that over-expression of BADH under triple CAMV35s promoter with more glycine betaine, chlorophyll & MDA contents, high relative quantities of other metabolites results in an enhanced level of salt tolerance in potato.

Keywords: Atriplex canescens, BADH, CAMV35s promotor, potato, Solanum tubersum

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Authors: Andra Costache, Rădiţa Alexe

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The analysis of the spatial disparities of social marginalization is a requirement in the present-day socio-economic and political context of Romania, an East-European state, member of the European Union since 2007, at present faced with the imperatives of the growth of its territorial cohesion. The main objective of this article is to develop a methodology for the assessment of social marginalization, in order to understand the intensity of the marginalization phenomenon at different spatial scales. The article proposes a social marginalization index (SMI), calculated through the integration of ten indicators relevant for the two components of social marginalization: the material component and the symbolical component. The results highlighted a strong connection between the total degree of social marginalization and the dependence on social benefits, unemployment rate, non-inclusion in the compulsory education, criminality rate, and the type of pension insurance.

Keywords: Romania, social marginalization index, territorial disparities, EU

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Authors: Muhammad G. Almatar, Mohammad A. Alnasrallah

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This research focuses on the study of three main issues: 1) The temporal analysis of leukemia for a period of six years (2006-2012), 2) spatial analysis by investigating this phenomenon in the Kuwaiti society spatially in the residential areas within the six governorates, 3) the use of Geographic Information System technology in investigating the hypothesis of the research and its variables using the linear regression, to show the pattern of linear relationship. The study depends on utilizing the map to understand the distribution of blood cancer in Kuwait. Several geodatabases were created for the number of patients and air pollution. Spatial interpolation models were used to generate layers of air pollution in the study area. These geodatabases were tested over the past six years to reach the conclusion: Is there a relationship with significant significance between the two main variables of the study: blood cancer and air pollution? This study is the first to our best knowledge. As far as the researchers know, the distribution of this disease has not been studied geographically at the level of regions in Kuwait within six years and in specific areas as described above. This study investigates the concentration of this type of disease. The study found that there is no relationship of significant value between the two variables studied, and this may be due to the nature of the disease, which are often hereditary. On the other hand, this study has reached a number of suggestions and recommendations that may be useful to decision-makers and interested in the study of leukemia in Kuwait by focusing on the study of genetic diseases, which may be a cause of leukemia rather than air pollution.

Keywords: Kuwait, GIS, cancer, geography

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Authors: Savitha Janakiraman, Shivakumar M. C

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Anidulafungin, an advanced class of antifungal agent used for the treatment of chronic fungal infections, is derived from Echinocandin B nucleus, an intermediate metabolite of Echinocandin B produced by Aspergillus nidulans. The enzyme acylase derived from the fermentation broth of Actinoplanes utahensis (NRRL 12052) plays a key role in the bioconversion of echinocandin B to echinocandin B nucleus. The membrane-bound nature of acylase and low levels of expression contributes to the rate-limiting process of enzymatic deacylation, hence low yields of ECB nucleus and anidulafungin. In the present study, this is addressed through novel genetic engineering approaches of overexpression and heterologous expression studies, immobilization of whole cells of Actinoplanes utahensis (NRRL 12052) and Co-cultivation studies. Overexpression of the acylase gene in Actinoplanes utahensis (NRRL 12052) was done by increasing the gene copy number to increase the echinocandin B nucleus production. Echinocandin B acylase gene, under the control of a PermE* promoter, was cloned in pSET152 vector and introduced into Actinoplanes utahensis (NRRL12052) by a ɸC31-directed site-specific recombination method. The resultant recombinant strain (C2-18) showed a 3-fold increase in acylase expression, which was confirmed by HPLC analysis. Pichia pastoris is one of the most effective and versatile host systems for the production of heterologous proteins. The ECB acylase gene was cloned into pPIC9K vector with AOX1 promoter and was transformed into Pichia pastoris (GS115). The acylase expression was confirmed by protein expression and bioconversion studies. The heterologous expression of acylase in Pichia pastoris, is a milestone in the development of antifungals. Actively growing cells of Actinoplanes utahensis (NRRL 12052) were immobilized and tested for bioconversion ability which showed >90% conversion in each cycle. The stability of immobilized cell beads retained the deacylation ability up to 60 days and reusability was confirmed up to 4 cycles. The significant findings from the study have revealed that immobilization of whole cells of Actinoplanes utahensis (NRRL 12052) could be an alternative option for bioconversion of echinocandin B to echinocandin B nucleus, which has not been reported to date. The concept of co-cultivation of Aspergillus nidulans and Actinoplanes utahensis strains for the production of the echinocandin B nucleus was also carried out in order to produce echinocandin B nucleus. The process completely reduced the ECB purification step and, therefore, could be recommended as an ingenious method to improve the yield of the ECB nucleus.

Keywords: acylase, anidulafungin, antifungals, Aspergillus nidulans

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Authors: Yen-Jong Chen, Jei-An Su

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Public use facilities provide the basic infrastructure supporting the needs of urban sustainable development. These facilities include roads (streets), parking areas, green spaces, public schools, and city parks. However, how to acquire land with the proper location and size still remains uncertain in a capitalist economy where land is largely privately owned, such as in cities in Taiwan. The issue concerning the proper acquisition of reserved land for local public facilities (RLPF) policies has been continuously debated by the Taiwanese government for more than 30 years. Lately, the government has been re-evaluating projects connected with existing RLPF policies from the viewpoints of the needs of local residents, including the living environments of older adults. This challenging task includes addressing the requests of official bureau administrators, citizens whose property rights and current use status are affected, and other stakeholders, along with the means of development. To simplify the decision to acquire or release public land, we selected only public facilities that are needed for living in the local community, including parks, green spaces, plaza squares, and land for kindergartens, schools, and local stadiums. This study categorized these spaces as the community’s “leisure public facilities” (LPF). By constructing an accessibility index of the services of such multi-function facilities, we computed and produced a GIS map of spatial buffer zones for each LPF. Through these procedures, the service needs provided by each LPF were clearly identified. We then used spatial buffer zone envelope mapping to evaluate these service areas. The results obtained can help decide which RLPF should be acquired or released so that community services can be maximized under a limited budget.

Keywords: urban public facilities, community demand, accessibility, spatial buffer zone, Taiwan

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Authors: Jiao F. Huang, Shi Chen, Shu C. Duan, Gang H. Wang

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Due to its complex spatial structure as well as dynamic temporal evolution, an analytic solution of an X-pinch process is out of question, and numerical simulation becomes an important tool in X-pinch studies. Intrinsically, simulations of X-pinch are three-dimensional (3D) because of the specific structure of its load. Furthermore, in order to resolve both its μm-scales and ns-durations, fine spatial mesh grid and short time steps are usually adopted. The resulting large computational scales make the parallelization of codes a vital problem to be solved if any practical simulations are to be carried out. In this work, we report OpenMP parallelization of our 3D magnetohydrodynamic (MHD) code FOI-PERFECT. Results of test runs confirm that computational efficiency has been improved after parallelization, and both the sequential and parallel versions give the same physical results under the same initial conditions.

Keywords: MHD simulation, OpenMP, parallelization, X-pinch

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Authors: Sinchul Back, Sun Ho Kim, Jennifer LaPrade, Ilju Seong

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Due to the advantage of using the Internet, cybercriminals can reach target(s) without border controls. Prior research on criminology and crime science has largely been void of empirical studies on journey-to-cybercrime and crime opportunity. Thus, the purpose of this study is to understand more about cyber offender spatial decision making associated with crime opportunity factors (i.e., co-offending, offender-stranger). Data utilized in this study were derived from 306 U.S. Federal court cases of cybercrime. The findings of this study indicated that there was a positive relationship between co-offending and journey-to-cybercrime, whereas there was no link between offender-stranger and journey-to-cybercrime. Also, the results showed that there was no relationship between cybercriminal sex, age, and journey-to-cybercrime. The policy implications and limitations of this study are discussed.

Keywords: co-offending, crime opportunity, journey-to-cybercrime, offender-stranger

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Authors: Amrutha Jayan

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The cities are attractors of the human population, offering opportunities for economic activities for different linguistic, cultural, and ethnic groups. The urban form and design of the city impact the life of these people. Social and cultural exclusions result in spatial segregation and gentrification. The spaces provided in cities must be inclusive for all these communities for them to feel part of the city and contribute to society. Intercultural urbanism is a theory and practice of city building, planning, and design of urban spaces and architectures that are cognizant of the social impact of the built environment. The postulate acknowledges cultural differences and opportunities for cultural exchange. Literature on intercultural urbanism, culture and space, spatial justice, and cultural inclusion are analyzed to identify parameters contributing to intercultural placemaking. A qualitative study on Mattancherry shows how the precinct has sustained throughout the years with different communities living together within a radius of 5 km, creating a diverse and vibrant environment. The research identifies the urban elements that contribute to intercultural interactions and maintain the synergy between these communities. The public spaces, porous edges, built-form, streets, and accessibility contribute to chance encounters and intercultural interactivity. The research seeks to find the factors that contribute to intercultural placemaking.

Keywords: intercultural urbanism, cultural inclusion, spatial justice, public space

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Authors: Sofia M. Karadimitriou, Kostas Triantafyllopoulos, Timothy Heaton

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Reduced dimension Dynamic Spatio-Temporal Models (DSTMs) jointly describe the spatial and temporal evolution of a function observed subject to noise. A basic state space model is adopted for the discrete temporal variation, while a continuous autoregressive structure describes the continuous spatial evolution. Application of such a DSTM relies upon the pre-selection of a suitable reduced set of basic functions and this can present a challenge in practice. In this talk, we propose an online estimation method for high dimensional spatio-temporal data based upon DSTM and we attempt to resolve this issue by allowing the basis to adapt to the observed data. Specifically, we present a wavelet decomposition in order to obtain a parsimonious approximation of the spatial continuous process. This parsimony can be achieved by placing a Laplace prior distribution on the wavelet coefficients. The aim of using the Laplace prior, is to filter wavelet coefficients with low contribution, and thus achieve the dimension reduction with significant computation savings. We then propose a Hierarchical Bayesian State Space model, for the estimation of which we offer an appropriate particle filter algorithm. The proposed methodology is illustrated using real environmental data.

Keywords: multidimensional Laplace prior, particle filtering, spatio-temporal modelling, wavelets

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Authors: Kuo-Cheng Liu

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In the latest research efforts, the structures of the image in the spatial domain have been successfully analyzed and proved to deduce the visual masking for accurately estimating the visibility thresholds of the image. If the structural properties of the video sequence in the temporal domain are taken into account to estimate the temporal masking, the improvement and enhancement of the as-sessing spatio-temporal visibility thresholds are reasonably expected. In this paper, the temporal characteristics of human perception to the change in block structures on the time axis are analyzed. The temporal characteristics of human perception are represented in terms of the significant variation in block structures for the analysis of human visual system (HVS). Herein, the block structure in each frame is computed by combined the pattern masking and the contrast masking simultaneously. The contrast masking always overestimates the visibility thresholds of edge regions and underestimates that of texture regions, while the pattern masking is weak on a uniform background and is strong on the complex background with spatial patterns. Under considering the significant variation of block structures between successive frames, we extend the block structures of images in the spatial domain to that of video sequences in the temporal domain to analyze the relation between the inter-frame variation of structures and the temporal masking. Meanwhile, the subjective viewing test and the fair rating process are designed to evaluate the consistency of the temporal characteristics with the HVS under a specified viewing condition.

Keywords: temporal characteristic, block structure, pattern masking, contrast masking

Procedia PDF Downloads 398

Authors: Yunxiang Fang

Abstract:

With the aging trend continuing to accelerate, open space is important for the daily life of the elderly, and its old-age friendliness is worthy of attention. Based on behavioral observation and literature research, this paper studies the behavior of the elderly in urban open space. Through the investigation, classification and quantitative analysis of the activity types, time characteristics and spatial behavior order of the elderly in Xicheng Square in Hangzhou, it summarizes the square space suitable for the psychological needs, physiology and activity needs of the elderly, combined with the basis of literature research. Finally, the suggestions for the improvement of the old-age friendship of Xicheng Square are put forward, from the aspects of microclimate, safety and accessibility, space richness and service facility quality.

Keywords: behavior characteristics, old-age friendliness, open space, square

Procedia PDF Downloads 164

Authors: M. L. Mangena, N. Mokoena, K. Rashamuse, M. G. Tlou

Abstract:

Tertiary alcohol ester (TAE) hydrolases are a group of esterases (EC 3.1.1.-) that catalyze the kinetic resolution of TAEs and as a result, they are sought-after for the production of optically pure tertiary alcohols (TAs) which are useful as building blocks for number biologically active compounds. What sets these enzymes apart is, the presence of a GGG(A)X-motif in the active site which appears to be the main reason behind their activity towards the sterically demanding TAEs. The genome of Pseudomonas syringae pv. maculicola (Psm) comprises a multitude of genes that encode esterases. We therefore, hypothesize that some of these genes encode TAE hydrolases. In this study, Psm was screened for TAE hydrolase activity using the linalyl acetate (LA) plate assay and a positive reaction was observed. As a result, the genome of Psm was screened for esterases with a GGG(A)X-motif using the motif search tool and two potential TAE hydrolase genes (PsmEST1 and 2, 1100 and 1000bp, respectively) were identified, PsmEST1 was amplified by PCR and the gene sequenced for confirmation. Analysis of the sequence data with the SingnalP 4.1 server revealed that the protein comprises a signal peptide (22 amino acid residues) on the N-terminus. Primers specific for the gene encoding the mature protein (without the signal peptide) were designed such that they contain NdeI and XhoI restriction sites for directional cloning of the PCR products into pET28a. The gene was expressed in E. coli JM109 (DE3) and the clones screened for TAE hydrolase activity using the LA plate assay. A positive clone was selected, overexpressed and the protein purified using nickel affinity chromatography. The activity of the esterase towards LA was confirmed using thin layer chromatography.

Keywords: hydrolases, tertiary alcohol esters, tertiary alcohols, screening, Pseudomonas syringae pv., maculicola genome, esterase activity, linalyl acetate

Procedia PDF Downloads 347

Authors: R. L. P. De Lima, F. C. B. Boogaard, R. E. De Graaf-Van Dinther

Abstract:

Blue-green algae blooms (cyanobacteria) is currently a relevant ecological problem that is being addressed by most water authorities in the Netherlands. These can affect recreation areas by originating unpleasant smells and toxins that can poison humans and animals (e.g. fish, ducks, dogs). Contamination events usually take place during summer months, and their frequency is increasing with climate change. Traditional monitoring of this bacteria is expensive, labor-intensive and provides only limited (point sampling) information about the spatial distribution of algae concentrations. Recently, a novel handheld sensor allowed water authorities to quicken their algae surveying and alarm systems. This study converted the mentioned algae sensor into a mobile platform, by combining it with an underwater remotely operated vehicle (also equipped with other sensors and cameras). This provides a spatial visualization (mapping) of algae concentrations variations within the area covered with the drone, and also in depth. Measurements took place in different locations in the Netherlands: i) lake with thick silt layers at the bottom, very eutrophic former bottom of the sea and frequent / intense mowing regime; ii) outlet of waste water into large reservoir; iii) urban canal system. Results allowed to identify probable dominant causes of blooms (i), provide recommendations for the placement of an outlet, day-night differences in algae behavior (ii), or the highlight / pinpoint higher algae concentration areas (iii). Although further research is still needed to fully characterize these processes and to optimize the measuring tool (underwater drone developments / improvements), the method here presented can already provide valuable information about algae behavior and spatial / temporal variability and shows potential as an efficient monitoring system.

Keywords: blue-green algae, cyanobacteria, underwater drones / ROV / AUV, water quality monitoring

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Authors: Moschos Vogiatzis, K. Perakis

Abstract:

Spatial-explicit and up-to-date land use/land cover information is fundamental for spatial planning, land management, sustainable development, and sound decision-making. In the last decade, many satellite-derived land cover products at different spatial, spectral, and temporal resolutions have been developed, such as the European Copernicus Land Cover product. However, more efficient and detailed information for land use/land cover is required at the regional or local scale. A typical Mediterranean basin with a complex landscape comprised of various forest types, crops, artificial surfaces, and wetlands was selected to test and develop our approach. In this study, we investigate the improvement of Copernicus Land Cover product (CLC2018) using Landsat 8 and Sentinel-2 pixel-based classification based on all available existing geospatial data (Forest Maps, LPIS, Natura2000 habitats, cadastral parcels, etc.). We examined and compared the performance of the Random Forest classifier for land use/land cover mapping. In total, 10 land use/land cover categories were recognized in Landsat 8 and 11 in Sentinel-2A. A comparison of the overall classification accuracies for 2018 shows that Landsat 8 classification accuracy was slightly higher than Sentinel-2A (82,99% vs. 80,30%). We concluded that the main land use/land cover types of CLC2018, even within a heterogeneous area, can be successfully mapped and updated according to CLC nomenclature. Future research should be oriented toward integrating spatiotemporal information from seasonal bands and spectral indexes in the classification process.

Keywords: classification, land use/land cover, mapping, random forest

Procedia PDF Downloads 115

Authors: Lin-Han Chiang Hsieh, Hsiao-Yi Lin

Abstract:

This study aims to determine the impact of the disclosure of flood potential map on housing prices. The disclosure is supposed to mitigate the market failure by reducing information asymmetry. On the other hand, opponents argue that the official disclosure of simulated results will only create unnecessary disturbances on the housing market. This study identifies the impact of the disclosure of the flood potential map by comparing the hedonic price of flood potential before and after the disclosure. The flood potential map used in this study is published by Taipei municipal government in 2015, which is a result of a comprehensive simulation based on geographical, hydrological, and meteorological factors. The residential property sales data of 2013 to 2016 is used in this study, which is collected from the actual sales price registration system by the Department of Land Administration (DLA). The result shows that the impact of flood potential on residential real estate market is statistically significant both before and after the disclosure. But the trend is clearer after the disclosure, suggesting that the disclosure does have an impact on the market. Also, the result shows that the impact of flood potential differs by the severity and frequency of precipitation. The negative impact for a relatively mild, high frequency flood potential is stronger than that for a heavy, low possibility flood potential. The result indicates that home buyers are of more concern to the frequency, than the intensity of flood. Another contribution of this study is in the methodological perspective. The classic hedonic price analysis with OLS regression suffers from two spatial problems: the endogeneity problem caused by omitted spatial-related variables, and the heterogeneity concern to the presumption that regression coefficients are spatially constant. These two problems are seldom considered in a single model. This study tries to deal with the endogeneity and heterogeneity problem together by combining the spatial fixed-effect model and geographically weighted regression (GWR). A series of literature indicates that the hedonic price of certain environmental assets varies spatially by applying GWR. Since the endogeneity problem is usually not considered in typical GWR models, it is arguable that the omitted spatial-related variables might bias the result of GWR models. By combing the spatial fixed-effect model and GWR, this study concludes that the effect of flood potential map is highly sensitive by location, even after controlling for the spatial autocorrelation at the same time. The main policy application of this result is that it is improper to determine the potential benefit of flood prevention policy by simply multiplying the hedonic price of flood risk by the number of houses. The effect of flood prevention might vary dramatically by location.

Keywords: flood potential, hedonic price analysis, endogeneity, heterogeneity, geographically-weighted regression

Procedia PDF Downloads 285

Authors: Rahma Fitriani, Eni Sumarminingsih, Suci Astutik

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In a fast growing region, conversion of agricultural lands which are surrounded by some new development sites will occur sooner than expected. This phenomenon has been experienced by many regions in Indonesia, especially the fringe of Jakarta (BoDeTaBek). Being Indonesia’s capital city, rapid conversion of land in this area is an unavoidable process. The land conversion expands spatially into the fringe regions, which were initially dominated by agricultural land or conservation sites. Without proper control or growth management, this activity will invite greater costs than benefits. The current land use is the use which maximizes its value. In order to maintain land for agricultural activity or conservation, some efforts are needed to keep the land value of this activity as high as possible. In this case, the knowledge regarding the functional relationship between land value and its driving forces is necessary. In a fast growing region, development externalities are the assumed dominant driving force. Land value is the product of the past decision of its use leading to its value. It is also affected by the local characteristics and the observed surrounded land use (externalities) from the previous period. The effect of each factor on land value has dynamic and spatial virtues; an empirical spatial dynamic land value model will be more useful to capture them. The model will be useful to test and to estimate the extent of land use externalities on land value in the short run as well as in the long run. It serves as a basis to formulate an effective urban growth management’s policy. This study will apply the model to the case of land value in the fringe of Jakarta Metropolitan. The model will be used further to predict the effect of externalities on land value, in the form of prediction map. For the case of Jakarta’s fringe, there is some evidence about the significance of neighborhood urban activity – negative externalities, the previous land value and local accessibility on land value. The effects are accumulated dynamically over years, but they will fully affect the land value after six years.

Keywords: growth management, land use externalities, land value, spatial panel dynamic

Procedia PDF Downloads 247

Authors: Atul C. Mahajan, A. K. Chakravarty, V. Jamuna, C. S. Patil, Neeraj Kashyap, Bharti Deshmukh, Vijay Kumar

Abstract:

The selection of Sahiwal bulls on the basis of dams best lactation milk yield under breeding programme in herd of the country neglecting fertility traits leads to deterioration in their performances and economy. The goal of this study was to explore polymorphism of CRISP2 gene and their association with semen traits (Post Thaw Motility, Hypo-osmotic Swelling Test, Acrosome Integrity, DNA Fragmentation and capacitation status), scrotal circumference, expected predicted difference (EPD) for milk yield and fertility. Sahiwal bulls included in present study were 60 bulls used in breeding programme as well as 50 young bulls yet to be included in breeding programme. All the Sahiwal bulls were found to be polymorphic for CRISP2 gene (AA, AG and GG) present within exon 7 to the position 589 of CRISP2 mRNA by using PCR-SSCP and Sequencing. Semen analysis were done on 60 breeding bulls frozen semen doses pertaining to four season (winter, summer, rainy and autumn). The scrotal circumference was measured from existing Sahiwal breeding bulls in the herd (n=47). The effect of non-genetic factors on reproduction traits were studied by least-squares technique and the significant difference of means between subclasses of season, period, parity and age group were tested. The data were adjusted for the significant non-genetic factors to remove the differential environmental effects. The adjusted data were used to generate traits like Waiting Period (WP), Pregnancy Rate (PR), Expected Predicted Difference (EPD) of fertility, respectively. Genetic and phenotypic parameters of reproduction traits were estimated. The overall least-squares means of Age at First Calving (AFC), Service Period (SP) and WP were estimated as 36.69 ± 0.18 months, 120.47 ± 8.98 days and 79.78 ± 3.09 days respectively. Season and period of birth had significant effect (p < 0.01) on AFC. AFC was highest during autumn season of birth followed by summer, winter and rainy. Season and period of calving had significant effect (p < 0.01) on SP and WP of sahiwal cows. The WP for Sahiwal cows was standardized based on four developed predicted model for pregnancy rate 42, 63, 84 and 105 days using all lactation records. The WP for Sahiwal cows were standardized as 42 days. A selection criterion was developed for Sahiwal breeding bulls and young Sahiwal bulls on the basis of EPD of fertility. The genotype has significant effect on expected predicted difference of fertility and some semen parameters like post thaw motility and HOST. AA Genotype of CRISP2 gene revealed better EPD for fertility than EPD of milk yield. AA genotype of CRISP2 gene has higher scrotal circumference than other genotype. For young Sahiwal bulls only AA genotypes were present with similar patterns. So on the basis of association of genotype with seminal traits, EPD of milk yield and EPD for fertility status, AA and AG genotype of CRISP2 gene was better for higher fertility in Sahiwal bulls.

Keywords: expected predicted difference, fertility, sahiwal, waiting period

Procedia PDF Downloads 581

Authors: Weaam Aldeeban, Majd Aljamali, Lama A. Youssef

Abstract:

Background & Objective: Warfarin is considered a problematic drug due to its narrow therapeutic window and wide inter-individual response variations, which are attributed to demographic, environmental, and genetic factors, particularly single nucleotide polymorphism (SNPs) in the genes encoding VKORC1 and CYP2C9 involved in warfarin's mechanism of action and metabolism, respectively. CYP2C9*2rs1799853 and CYP2C9*3rs1057910 alleles are linked to reduced enzyme activity, as carriers of either or both alleles are classified as moderate or slow metabolizers, and therefore exhibit higher sensitivity of warfarin compared with wild type (CYP2C9*1*1). Our study aimed to assess the frequency of *1, *2, and *3 alleles in the CYP2C9 gene in a cohort of Syrian patients receiving a maintenance dose of warfarin for different indications, the impact of genotypes on warfarin dosing, and the frequency of adverse effects (i.e., bleedings). Subjects & Methods: This retrospective cohort study encompassed 94 patients treated with warfarin. Patients’ genotypes were identified by sequencing the polymerase chain reaction (PCR) specific products of the gene encoding CYP2C9, and the effects on warfarin therapeutic outcomes were investigated. Results: Sequencing revealed that 43.6% of the study population has the *2 and/or *3 SNPs. The mean weekly maintenance dose of warfarin was 37.42 ± 15.5 mg for patients with the wild-type allele (CYP2C9*1*1), whereas patients with one or both variants (*2 and/or *3) demanded a significantly lower dose (28.59 ±11.58 mg) of warfarin, (P= 0.015). A higher percentage (40.7%) of patients with allele *2 and/or *3 experienced hemorrhagic accidents compared with only 17.9% of patients with the wild type *1*1, (P = 0.04). Conclusions: Our study proves an association between *2 and *3 genotypes and higher sensitivity to warfarin and a tendency to bleed, which necessitates lowering the dose. These findings emphasize the significance of CYP2C9 genotyping prior to commencing warfarin therapy in order to achieve optimal and faster dose control and to ensure effectiveness and safety.

Keywords: warfarin, CYP2C9, polymorphisms, Syrian, hemorrhage

Procedia PDF Downloads 138

Authors: Jae Woong Sull

Abstract:

Lipid levels are related to the risk of cardiovascular diseases. Cholesterol ester transfer protein (CETP) gene is one of the candidate genes of cardiovascular diseases. A total of 2,304 persons were chosen from a Hospital (N=4,294) in South Korea. Female subjects with the CG/GG genotype had a 2.03 -fold (p=0.0001) higher risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. Male subjects with the CG/GG genotype had a 1.34 -fold (p=0.0019) higher risk than subjects with the CC genotype. When analyzed by body mass index, the association with CETP was much stronger in male subjects with BMI>=25.69 (OR=1.55, 95% CI: 1.15-2.07, P=0.0037) than in male lean subjects. When analyzed by family history of diabetes, the association with CETP was much stronger in male subjects with positive family history of low physical activity (OR=4.82, 95% CI: 1.86-12.5, P=0.0012) than in male subjects with negative family history of diabetes. This study clearly demonstrates that genetic variants in CETP influence HDL cholesterol levels in Korean adults.

Keywords: CETP, diabetes, obesity, polymorphisms

Procedia PDF Downloads 134