Search results for: genetic polymorphisms

Authors: Farman Ali, Asif Mahmood

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The utilization of genetic markers in prostate cancer management represents a significant advance in personalized medicine, offering the potential for more precise diagnosis and tailored treatment strategies. This paper explores the pivotal role of genetic markers in the diagnosis and treatment of prostate cancer, emphasizing their contribution to the identification of individual risk profiles, tumor aggressiveness, and response to therapy. By integrating current research findings, we discuss the application of genetic markers in developing targeted therapies and the implications for patient outcomes. Despite the promising advancements, challenges such as accessibility, cost, and the need for further validation in diverse populations remain. The paper concludes with an outlook on future directions, underscoring the importance of genetic markers in revolutionizing prostate cancer care.

Keywords: prostate cancer, genetic markers, personalized medicine, BRCA1 and BRCA2

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Authors: Amy Gooden, Meshandren Naidoo

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Genetic research and transfers of big data are not confined to a particular jurisdiction, but there is a lack of clarity regarding the legal requirements for importing and exporting such data. Using direct-to-consumer genetic testing (DTC-GT) as an example, this research assesses the status of data sharing into and out of South Africa (SA). While SA laws cover the sending of genetic data out of SA, prohibiting such transfer unless a legal ground exists, the position where genetic data comes into the country depends on the laws of the country from where it is sent – making the legal position less clear.

Keywords: cross-border, data, genetic testing, law, regulation, research, sharing, South Africa

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Authors: Abejide Dorcas Ropo, , Falusi Olamide Ahmed, Daudu Oladipupo Abdulazeez Yusuf, Salihu Bolaji Zuluquri Neen, Muhammad Liman Muhammad, Gado Aishatu Adamu

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Water stress is a major factor limiting the productivity of crops in the world today. This study evaluated the morpho-agronomic response of twenty-four (24) Nigerian Bambara groundnut landraces to water stress and genetic diversity of some selected accessions using SSR markers. The studies was carried out in the Botanical garden of the Department of Plant Biology, Federal University of Technology, Minna, Niger State, Nigeria in a randomized complete block design using three replicates. Molecular analysis using SSR primers was carried out at the Centre for Bio- Science, International Institute of Tropical Agriculture (IITA) Ibadan, Nigeria in order to characterize ten selected accessions comprising of the seven most drought tolerant and the three most susceptible accessions detected from the morpho-agronomic studies. Results revealed that water stress decreased morpho-agronomic traits such as plant height, leaf area, number of leaves per plant and seed yield etc. A total of 22 alleles were detected by the SSR markers used with a mean number of 4 allelles. Simple Sequence Repeat (SSR) markers MBamCO33, Primer 65 and G358B2-D15 each detected 4 allelles while Primer 3FR and 4FR detected 5 allelles each. The study revealed significantly high polymorphisms in 10 Loci. The mean value of Polymorpic information content was 0.6997 implying the usefulness of the primers used in identifying genetic similarities and differences among the Bambara groundnut genotypes. The SSR analysis revealed a comparable pattern between genetic diversity and drought tolerance of the genotypes. The Unweighted Paired Group Method with Arithmethic Mean (UPGMA) dendrogram showed that at a genetic distance of 0.1, the accessions were grouped into three groups according to their level of tolerance to drought. The two most drought tolerant accessions were grouped together and the 5th and 6th most drought tolerant accession were also grouped together. This suggests that the genotypes grouped together may be genetically close, may possess similar genes or have a common origin. The degree of genetic variants obtained could be useful in bambara groundnut breeding for drought tolerance. The identified drought tolerant bambara groundnut landraces are important genetic resources for drought stress tolerance breeding programme of bambara groundnut. The genotypes are also useful for germplasm conservation and global implications.

Keywords: bambara groundnut, genetic diversity, germplasm, SSR markers, water stress

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Authors: Ju-Chun Chien

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The Ottawa Charter for Health Promotion proposed that the role of health services should shift the focus from cure to prevention. Nowadays, besides having physical examinations, people could also conduct genetic tests to provide important information for diagnosing, treating, and/or preventing illnesses. However, because of the incompletion of the Chinese Genetic Database, people in Taiwan were still unfamiliar with genetic testing. The purposes of the present study were to: (1) Figure out people’s attitudes towards genetic testing. (2) Examine factors that influence people’s intention to pursue genetic testing by means of the Health Belief Model (HBM). A pilot study was conducted on 249 Taiwanese in 2017 to test the feasibility of the self-developed instrument. The reliability and construct validity of scores on the self-developed questionnaire revealed that this HBM-based questionnaire with 40 items was a well-developed instrument. A total of 542 participants were recruited and the valid participants were 535 (99%) between the ages of 20 and 86. Descriptive statistics, one-way ANOVA, two-way contingency table analysis, Pearson’s correlation, and stepwise multiple regression analysis were used in this study. The main results were that only 32 participants (6%) had already undergone genetic testing; moreover, their attitude towards genetic testing was more positive than those who did not have the experience. Compared with people who never underwent genetic tests, those who had gone for genetic testing had higher self-efficacy, greater intention to pursue genetic testing, had academic majors in health-related fields, had chronic and genetic diseases, possessed Catastrophic Illness Cards, and all of them had heard about genetic testing. The variables that best predicted people’s intention to pursue genetic testing were cues to action, self-efficacy, and perceived benefits (the three variables all correlated with one another positively at high magnitudes). To sum up, the HBM could be effective in designing and identifying the needs and priorities of the target population to pursue genetic testing.

Keywords: genetic testing, knowledge of GT, people in Taiwan, the health belief model

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Authors: Afsaneh Mohammadnejad, Marianne Nygaard, Jan Baumbach, Shuxia Li, Weilong Li, Jesper Lund, Jacob v. B. Hjelmborg, Lene Christensen, Qihua Tan

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Cognitive impairment in the elderly is a key issue affecting the quality of life. Despite a strong genetic background in cognition, only a limited number of single nucleotide polymorphisms (SNPs) have been found. These explain a small proportion of the genetic component of cognitive function, thus leaving a large proportion unaccounted for. We hypothesize that one reason for this missing heritability is the misspecified modeling in data analysis concerning phenotype distribution as well as the relationship between SNP dosage and the phenotype of interest. In an attempt to overcome these issues, we introduced a model-free method based on the generalized correlation coefficient (GCC) in a genome-wide association study (GWAS) of cognitive function in twin samples and compared its performance with two popular linear regression models. The GCC-based GWAS identified two genome-wide significant (P-value < 5e-8) SNPs; rs2904650 near ZDHHC2 on chromosome 8 and rs111256489 near CD6 on chromosome 11. The kinship model also detected two genome-wide significant SNPs, rs112169253 on chromosome 4 and rs17417920 on chromosome 7, whereas no genome-wide significant SNPs were found by the linear mixed model (LME). Compared to the linear models, more meaningful biological pathways like GABA receptor activation, ion channel transport, neuroactive ligand-receptor interaction, and the renin-angiotensin system were found to be enriched by SNPs from GCC. The GCC model outperformed the linear regression models by identifying more genome-wide significant genetic variants and more meaningful biological pathways related to cognitive function. Moreover, GCC-based GWAS was robust in handling genetically related twin samples, which is an important feature in handling genetic confounding in association studies.

Keywords: cognition, generalized correlation coefficient, GWAS, twins

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Authors: Aizati N. A. Daud, Jorieke E. H. Bergman, Wilhelmina S. Kerstjens-Frederikse, Pieter Van Der Vlies, Eelko Hak, Rolf M. F. Berger, Henk Groen, Bob Wilffert

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Prenatal use of SRIs was previously associated with Congenital Heart Anomalies (CHA). The aim of the study is to explore whether pharmacogenetics plays a role in this teratogenicity using a gene-environment interaction study. A total of 33 case-mother dyads and 2 mother-only (children deceased) registered in EUROCAT Northern Netherlands were included in a case-only study. Five case-mother dyads and two mothers-only were exposed to SRIs (paroxetine=3, fluoxetine=2, venlafaxine=1, paroxetine and venlafaxine=1) in the first trimester of pregnancy. The remaining 28 case-mother dyads were not exposed to SRIs. Ten genes that encode the enzymes or proteins important in determining fetal exposure to SRIs or its mechanism of action were selected: CYPs (CYP1A2, CYP2C9, CYP2C19, CYP2D6), ABCB1 (placental P-glycoprotein), SLC6A4 (serotonin transporter) and serotonin receptor genes (HTR1A, HTR1B, HTR2A, and HTR3B). All included subjects were genotyped for 58 genetic variations in these ten genes. Logistic regression analyses were performed to determine the interaction odds ratio (OR) between genetic variations and SRIs exposure on the risk of CHA. Due to low phenotype frequencies of CYP450 poor metabolizers among exposed cases, the OR cannot be calculated. For ABCB1, there was no indication of changes in the risk of CHA with any of the ABCB1 SNPs in the children and their mothers. Several genetic variations of the serotonin transporter and receptors (SLC6A4 5-HTTLPR and 5-HTTVNTR, HTR1A rs1364043, HTR1B rs6296 & rs6298, HTR3B rs1176744) were associated with an increased risk of CHA, but with too limited sample size to reach statistical significance. For SLC6A4 genetic variations, the mean genetic scores of the exposed case-mothers tended to be higher than the unexposed mothers (2.5 ± 0.8 and 1.88 ± 0.7, respectively; p=0.061). For SNPs of the serotonin receptors, the mean genetic score for exposed cases (children) tended to be higher than the unexposed cases (3.4 ± 2.2, and 1.9 ± 1.6, respectively; p=0.065). This study might be among the first to explore the potential gene-environment interaction between pharmacogenetic determinants and SRIs use on the risk of CHA. With small sample sizes, it was not possible to find a significant interaction. However, there were indications for a role of serotonin receptor polymorphisms in fetuses exposed to SRIs on fetal risk of CHA which warrants further investigation.

Keywords: gene-environment interaction, heart defects, pharmacogenetics, serotonin reuptake inhibitors, teratogenicity

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Authors: Li Dan, Zhao Junsuo, Zhang Wenjun

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Aiming at the shortcomings of the Quantum Genetic Algorithm such as the multimodal function optimization problems easily falling into the local optimum, and vulnerable to premature convergence due to no closely relationship between individuals, the paper presents an Improved Many Worlds Quantum Genetic Algorithm (IMWQGA). The paper using the concept of Many Worlds; using the derivative way of parallel worlds’ parallel evolution; putting forward the thought which updating the population according to the main body; adopting the transition methods such as parallel transition, backtracking, travel forth. In addition, the algorithm in the paper also proposes the quantum training operator and the combinatorial optimization operator as new operators of quantum genetic algorithm.

Keywords: quantum genetic algorithm, many worlds, quantum training operator, combinatorial optimization operator

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Authors: Abhishikta Ghosh Roy

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Breast cancer is the most common malignancy among women globally, including India. Human breast cancer results from the genetic and environmental interaction. The present study attempts to understand the molecular heterogeneity of BRCA1 and BRCA2 genes, as well as to understand the association of various lifestyle and reproductive variables for the Breast Cancer risk. The study was conducted amongst 110 patients and 128 controls with total DNA sequencing of flanking and coding regions of BRCA1 BRCA2 genes that revealed ten Single Nucleotide Polymorphisms (SNPs) (6 novels). The controls selected for the study were age, sex and ethnic group matched. After written and informed consent biological samples were collected from the subjects. After detailed molecular analysis, significant (p < 0.005) molecular heterogeneity is revealed in terms of SNPs in BRCA1 (4 Exonic & 1 Intronic) and BRCA2 (2exonic and 3 Intronic) genes. The augmentation study investigated significant (p < 0.05) association with positive family history, early age at menarche, irregular menstrual periods, menopause, prolong contraceptive use, nulliparity, history of abortions, consumption of alcohol and smoking for breast cancer risk. To the best of authors knowledge, this study is the first of its kind, envisaged that the identification of the SNPs and modification of the lifestyle factors might aid to minimize the risk among the Bengalee Hindu females.

Keywords: breast cancer, BRCA, lifestyle, India

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Authors: Athicha Cherdpunt, Patompong Satapornpong

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The medical cannabis is made up of components also known as cannabinoids, which consists of two ingredients which are Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD). Interestingly, the Cannabinoid can be used for many treatments such as chemotherapy, including nausea and vomiting, cachexia, anorexia nervosa, spinal cord injury and disease, epilepsy, pain, and many others. However, the adverse drug reactions (ADRs) of THC can cause sedation, anxiety, dizziness, appetite stimulation and impairments in driving and cognitive function. Furthermore, genetic polymorphisms of CYP2C9, CYP2C19 and CYP3A4 influenced the THC metabolism and might be a cause of ADRs. Particularly, CYP2C19*17 allele increases gene transcription and therefore results in ultra-rapid metabolizer phenotype (UM). The aim of this study, is to investigate the frequency of CYP2C19*17 alleles in Thai patients who have been treated with medical cannabis. We prospectively enrolled 60 Thai patients who were treated with medical cannabis and clinical data from College of Pharmacy, Rangsit University. DNA of each patient was isolated from EDTA blood, using the Genomic DNA Mini Kit. CYP2C19*17 genotyping was conducted using the real time-PCR ViiA7 (ABI, Foster City, CA, USA). 30 patients with medical cannabis-induced ADRs group, 20 (67%) were female, and 10 (33%) were male, with an age range of 30-69 years. On the other hand, 30 patients without medical cannabis-induced ADRs (control group) consist of 17 (57%) female and 13 (43%) male. The most ADRs for medical cannabis treatment in the case group were dry mouth and dry throat (77%), tachycardia (70%), nausea (30%) and arrhythmia(10%). Accordingly, the case group carried CYP2C19*1/*1 (normal metabolizer) approximately 93%, while 7% patients carrying CYP2C19*1/*17 (ultra rapid metabolizers) exhibited in this group. Meanwhile, we found 90% of CYP2C19*1/*1 and 10% of CYP2C19*1/*17 in control group. In this study, we identified the frequency of CYP2C19*17 allele in Thai population which will support the pharmacogenetics biomarkers for screening and avoid ADRs of medical cannabis treatment.

Keywords: CYP2C19, allele frequency, ultra rapid metabolizer, medical cannabis

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Authors: M. F. Miah, K. M. A. Zinnah, M. J. Raihan, H. Ali, M. N. Naser

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As genetic diversity is most important for existing, breeding and production of any fish; this study was undertaken for investigating genetic diversity of freshwater mud eel, Monopterus cuchia at population level where three ecological populations such as flooded area of Sylhet (P1), open water of Moulvibazar (P2) and open water of Sunamganj (P3) districts of Bangladesh were considered. Four arbitrary RAPD primers (OPB-12, C0-4, B-03 and OPB-08) were screened and RAPD banding patterns were analyzed among the populations considering 15 individuals of each population. In total 174, 138 and 149 bands were detected in the populations of P1, P2 and P3 respectively; however, each primer revealed less number of bands in each population. 100% polymorphic loci were recorded in P2 and P3 whereas only one monomorphic locus was observed in P1, recorded 97.5% polymorphism. Different genetic parameters such as inter-individual pairwise similarity, genetic distance, Nei genetic similarity, linkage distances, cluster analysis and allelic information, etc. were considered for measuring genetic diversity. The average inter-individual pairwise similarity was recorded 2.98, 1.47 and 1.35 in P1, P2 and P3 respectively. Considering genetic distance analysis, the highest distance 1 was recorded in P2 and P3 and the lowest genetic distance 0.444 was found in P2. The average Nei genetic similarity was observed 0.19, 0.16 and 0.13 in P1, P2 and P3, respectively; however, the average linkage distance was recorded 24.92, 17.14 and 15.28 in P1, P3 and P2 respectively. Based on linkage distance, genetic clusters were generated in three populations where 6 clades and 7 clusters were found in P1, 3 clades and 5 clusters were observed in P2 and 4 clades and 7 clusters were detected in P3. In addition, allelic information was observed where the frequency of p and q alleles were observed 0.093 and 0.907 in P1, 0.076 and 0.924 in P2, 0.074 and 0.926 in P3 respectively. The average gene diversity was observed highest in P2 (0.132) followed by P3 (0.131) and P1 (0.121) respectively.

Keywords: genetic diversity, Monopterus cuchia, population, RAPD, Bangladesh

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Authors: Masoud Sheidaei, Fahimeh Koohdar

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Date palms are economically important tree plants with high nutrition and medicinal values. More than 400 date palm cultivars are cultivated in many regions of Iran, but no report is available on landscape genetics and species distribution modeling of these trees from the country. Therefore, the present study provides a detailed insight into the genetic diversity and structure of date palm populations in Iran and investigates the effects of geographical and climatic variables on the structuring of genetic diversity in them. We used different computational methods in the study like, spatial principal components analysis (sPCA), redundancy analysis (RDA), latent factor mixed model (LFMM), and Maxent and Dismo models of species distribution modeling. We used a combination of different molecular markers for this study. The results showed that both global and local spatial features play an important role in the genetic structuring of date palms, and the genetic regions associated with local adaptation and climatic variables were identified. The effects of climatic change on the distribution of these taxa and the genetic regions adaptive to these changes will be discussed.

Keywords: adaptive genetic regions, genetic diversity, isolation by distance, populations divergence

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Authors: Abbas Mirakhorli

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A hub covering problem is a type of hub location problem that tries to maximize the coverage area with the least amount of installed hubs. There have not been many studies in the literature about multi-objective hubs covering location problems. Thus, in this paper, a bi-objective model for the hub covering problem is presented. The two objectives that are considered in this paper are the minimization of total transportation costs and the maximization of coverage of origin-destination nodes. A genetic algorithm is presented to solve the model when the number of nodes is increased. The genetic algorithm is capable of solving the model when the number of nodes increases by more than 20. Moreover, the genetic algorithm solves the model in less amount of time.

Keywords: facility location, hub covering, multi-objective optimization, genetic algorithm

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Authors: Nadir Ali Rind, Özlem Aksoy, Muhammad Umar Dahot, Salih Dikilitaş, Muhammad Rafiq, Burçak Tütünoğlu

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Melia azedarach L. is freshly fruited small to medium sized tree native to China and North western India. It is growing in Pakistan and Turkey in various areas facing great environmental changes to maintain its survival. The species is valued for its high quality wood, medicinal, ornamental and shade purposes. The present work was aimed to estimate the genetic variation among the populations of Melia azedarach L. leaf samples that were collected from five different locations of Turkey and three different areas of Pakistan. These populations were chosen on the random bases by applying RAPD primers in order to construct a dendogram using UPGMA method to show genetic diversity. After that appropriate conservation strategies were suggested. 14 primers producing polymorphic and monomorphic bands were analyzed. Genetic distances were calculated for all the species studied by RAPD-PCR methods. According to the results the lowest genetic identity values and the highest genetic polymorphic values were determined. It is observed that there was a clear split among populations from different areas in Turkey and Pakistan. These differences may be due to eco-geographical association with genetic variation and should be conserved to retain the genetic variation of the species.

Keywords: melia azedarach L., genetic diversity, conservation, RAPD-PCR, medicinal plant

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Authors: Jasbir Singh Gill, Baljit Singh

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Scheduling and mapping the application task graph on multiprocessor parallel systems is considered as the most crucial and critical NP-complete problem. Many genetic algorithms have been proposed to solve such problems. In this paper, two genetic approach based algorithms have been designed and developed with or without task duplication. The proposed algorithms work on two fitness functions. The first fitness i.e. task fitness is used to minimize the total finish time of the schedule (schedule length) while the second fitness function i.e. process fitness is concerned with allocating the tasks to the available highly efficient processor from the list of available processors (load balance). Proposed genetic-based algorithms have been experimentally implemented and evaluated with other state-of-art popular and widely used algorithms.

Keywords: parallel computing, task scheduling, task duplication, genetic algorithm

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Authors: Arbnor Pajaziti, Hasan Cana

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In this paper, the structural genetic algorithm is used to optimize the neural network to control the joint movements of robotic arm. The robotic arm has also been modeled in 3D and simulated in real-time in MATLAB. It is found that Neural Networks provide a simple and effective way to control the robot tasks. Computer simulation examples are given to illustrate the significance of this method. By combining Genetic Algorithm optimization method and Neural Networks for the given robotic arm with 5 D.O.F. the obtained the results shown that the base joint movements overshooting time without controller was about 0.5 seconds, while with Neural Network controller (optimized with Genetic Algorithm) was about 0.2 seconds, and the population size of 150 gave best results.

Keywords: robotic arm, neural network, genetic algorithm, optimization

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Authors: Kumar Ashwini, Nayak C. Vinod

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Sudden unexpected death in epilepsy (SUDEP) is a rarity. Each year, about one in 150 epileptics, whose seizures are not controlled, may die of SUDEP. It is a leading cause of death in young adults with uncontrolled seizures. Understanding the genetic basis for SUDEP, is crucial given that the rate of sudden death in epilepsy patients is 20 fold that of the general population. We encountered one such case of a young male, a known epileptic, who was brought dead after a sudden collapse. We hereby present a poster discussing the autopsy findings of this case and also highlighting the importance of understanding the genetic basis of SUDEP.

Keywords: sudden death, epilepsy, genetic, autopsy

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Authors: Azar Sharafianpor, Hossein Rassi, Fahimeh Nemati Mansur

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Cardiovascular diseases (CVD) are the most important cause of death in industrialized and developing countries such as Iran. The most important risk factors for the CVD, genetic factors and chronic infectious agents, such as Helicobacter pylori, can be mentioned. The TNFα gene is one of the most important anti-inflammatory cytokines that can affect the sensitivity, efficacy, and ability of the immune response to chronic infections. Some TNF-α gene polymorphisms, including the replacement of the G nucleotide G with A at position 308 in the promoter region of TNF-α, increase the transcription of cytokines in the target cells and thus predispose a person to chronic infections. This study examines the TNF-α 308 polymorphism and its association with Helicobacter pylori infection in this disease. This study was a case-control study in which 154 patients were examined as cases or patients with symptoms of myocardial infarction or angina and 160 as controls or healthy subjects. All of the subjects at different ages were given venous blood and age, BMI, cholesterol, LDL, and HDL were determined. DNA was extracted from the specimens, and the cagA gene from H. pylori and the TNF-α-308 polymorphism were determined by PCR in patients and healthy subjects. Statistical analysis was performed with Epi Info software. The results showed that the frequency of H. pylori infection in the patients and healthy group were 53.23% (82 out of 154) and 47.5% (76 out of 160). There was no significant difference in H. pylori outbreak between the two groups. The frequencies of TNF-α-308 genotype for GG, GA, and AA in patients were 0.17, 0.49, and 0.34, respectively, whereas for controls 0.47, 0.35, and 0.18 for GG, GA, and AA, respectively. The frequency of genotype analysis of TNF-α-308 polymorphisms in both patients and healthy groups showed that there was a significant difference in the frequency of genotypes and the AA genotype was higher in the affected individuals. Also, there was a significant relationship between the genotype and the contamination with H. pylori and changes in cholesterol, LDL, and HDL levels were observed. The results of the study indicate that H. pylori detection in individuals with AA genotype in people under 50 years of age can play an important role in early diagnosis and treatment of cardiovascular disease.

Keywords: Helicobacter pylori, TNFα gene, cardiovascular diseases, TNFα-308 polymorphism

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Authors: Maletsema Alina Mofokeng, Hussein Shimelis, Mark Laing, Pangirayi Tongoona

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Sorghum is one of the most important cereal crops grown for food, feed and bioenergy. Knowledge of genetic diversity is important for conservation of genetic resources and improvement of crop plants through breeding. The objective of this study was to assess the level of genetic diversity among sorghum genotypes using microsatellite markers. A total of 103 accessions of sorghum genotypes obtained from the Department of Agriculture, Forestry and Fisheries, the African Centre for Crop Improvement and Agricultural Research Council-Grain Crops Institute collections in South Africa were estimated using 30 microsatellite markers. For all the loci analysed, 306 polymorphic alleles were detected with a mean value of 6.4 per locus. The polymorphic information content had an average value of 0.50 with heterozygosity mean value of 0.55 suggesting an important genetic diversity within the sorghum genotypes used. The unweighted pair group method with arithmetic mean clustering based on Euclidian coefficients revealed two major distinct groups without allocating genotypes based on the source of collection or origin. The genotypes 4154.1.1.1, 2055.1.1.1, 4441.1.1.1, 4442.1.1.1, 4722.1.1.1, and 4606.1.1.1 were the most diverse. The sorghum genotypes with high genetic diversity could serve as important sources of novel alleles for breeding and strategic genetic conservation.

Keywords: Genetic Diversity, Genotypes, Microsatellites, Sorghum

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Authors: Younis R. Elhaddad, Mohamed A. Alshaari

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Since 2700 B.C the problem of constructing magic squares attracts many researchers. Magic squares one of most difficult challenges for mathematicians. In this work, we describe how to construct and enumerate Pan- magic squares using genetic algorithm, using new chromosome encoding technique. The results were promising within reasonable time.

Keywords: genetic algorithm, magic square, pan-magic square, computational intelligence

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Authors: Ashraf M. Ward, Ruban S. Yu

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Data consisting of 2757 records from tow Holstein herds made between 2000 and 2010 were used to examine environmental factors affecting age at first calving (AFC) and calving intervals (CI) and consequently estimate genetic and phenotypic parameters and trends. The overall means and standard errors for AFC and CI were 39.4 ± 7.2 months and 487.5 ± 151.6 days respectively. The respective heritability estimates were 0.091 ± 0.05 and 0.044 ± 0.032, while the repeatability estimate for CI was 0.096 ± 0.001. The genetic trends for CI and AFC were -0.6 d/yr and -0.01 mo/yr respectively and were both significant (P < 0.001), indicating a decrease in mean breeding value over the study period. Phenotypic trends were -0.31 mo/yr and -0.35 d/yr for AFC and CI respectively though non-significant (P > 0.05). The low heritability for CI and AFC indicated that temporary environmental influences were much greater than genetic influences or permanent environmental influences on these traits.

Keywords: Holstein, reproductive, genetic parameters, heritability

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

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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

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Authors: Rishabh Srivastav, Divyam Sharma

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We propose an algorithm to cluster categorical data named as ‘Genetic algorithm initialized rough set based fuzzy K-Modes for categorical data’. We propose an amalgamation of the simple K-modes algorithm, the Rough and Fuzzy set based K-modes and the Genetic Algorithm to form a new algorithm,which we hypothesise, will provide better Centroid Model clustering results, than existing standard algorithms. In the proposed algorithm, the initialization and updation of modes is done by the use of genetic algorithms while the membership values are calculated using the rough set and fuzzy logic.

Keywords: categorical data, fuzzy logic, genetic algorithm, K modes clustering, rough sets

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Authors: Zate Zewdneh Zana

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Coffea arabica (Arabica coffee), a cornerstone of the global beverage industry, necessitates rigorous genetic conservation due to its economic significance and genetic complexity. In this study, we performed whole-genome resequencing of wild species collected from its birthplace, Ethiopia. Advanced Illumina sequencing technology facilitated the mapping of a high percentage of clean reads to the C. arabica reference genome, revealing a substantial number of genetic variants, predominantly SNPs. Our comprehensive analysis not only uncovered a notable distribution of genomic variants across the coffee genome but also identified distinct genetic groups through phylogenetic and population structure analyses. This genomic study provides invaluable insights into the genetic diversity of C. arabica, highlighting the potential of identified SNPs and InDels in enhancing our understanding of key agronomic traits. The findings contribute significantly to genetic studies and support strategic breeding and conservation efforts essential for sustaining the global coffee industry.

Keywords: population genetics, wild species, evolutionary study, coffee plant

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Authors: Leandro Moura da Silva

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The international community has strived to create legal mechanisms to protect their biodiversity, but this can represent, sometimes, particularly in the case of regulatory regime on access to genetic resources, an excessive nationalism which transforms itself into a significant obstacle to scientific progress causing damages to the country and to local farmers. Although it has been poorly publicized in the media, the international legal system was marked, in 2014, by the entry into force of the Nagoya Protocol, which regulates the access and benefit sharing of genetic resources of the States Party to that legal instrument. However, it’s not reasonable to think of regulating access to genetic resources without reflecting on the links of this important subject with other related issues, such as family farming and agribusiness, food safety, food security, intellectual property rights (on seeds, genetic material, new plant varieties, etc.), environmental sustainability, biodiversity, and biosafety.

Keywords: international law, regulation on agriculture, agronomy techniques, sustainability, genetic resources and new crop varieties, CBD, Nagoya Protocol, ITPGRFA

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Authors: V. Pourmostaghimi, M. Zadshakoyan

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Efficiency and productivity of the finish hard turning can be enhanced impressively by utilizing accurate predictive models for cutting tool wear. However, the ability of genetic programming in presenting an accurate analytical model is a notable characteristic which makes it more applicable than other predictive modeling methods. In this paper, the genetic equation for modeling of tool flank wear is developed with the use of the experimentally measured flank wear values and genetic programming during finish turning of hardened AISI D2. Series of tests were conducted over a range of cutting parameters and the values of tool flank wear were measured. On the basis of obtained results, genetic model presenting connection between cutting parameters and tool flank wear were extracted. The accuracy of the genetically obtained model was assessed by using two statistical measures, which were root mean square error (RMSE) and coefficient of determination (R²). Evaluation results revealed that presented genetic model predicted flank wear over the study area accurately (R² = 0.9902 and RMSE = 0.0102). These results allow concluding that the proposed genetic equation corresponds well with experimental data and can be implemented in real industrial applications.

Keywords: cutting parameters, flank wear, genetic programming, hard turning

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Authors: H. Imad, Q. Cheah, J. Mohammad, O. Aamera

Abstract:

The aim of this study is twofold. One is to determine the genetic structure of Iraq population and the second objective of the study was to evaluate the importance of these loci for forensic genetic purposes. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. Twenty STR loci and Amelogenin including D3S1358, D13S317, PentaE, D16S539, D18S51, D2S1338, CSF1PO, Penta D, THO1, vWA, D21S11, D7S820, TPOX, D8S1179, FGA, D2S1338, D5S818, D6S1043, D12S391, D19S433, and Amelogenin amplified by using power plex21® kit. PCR products detected by genetic analyzer 3730xL then data analyzed by PowerStatsV1.2. Based on the allelic frequencies, several statistical parameters of genetic and forensic efficiency have been estimated. This includes the homozygosity and heterozygosity, effective number of alleles (n), the polymorphism information content (PIC), the power of discrimination (DP), and the power of exclusion (PE). The power of discrimination values for all tested loci was from 75% to 96% therefore, those loci can be safely used to establish a DNA-based database for Iraq population.

Keywords: autosomal STR, genetic variation, Middle and South of Iraq, statistical parameters

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Authors: Mariam Khaled, Noha Farag, Ghada Mohamed Abdel Salam, Khaled Abu-Aisha, Mohamed El-Azizi

Abstract:

Gastric and colorectal cancers are among the most frequent causes of cancer-associated mortalities in Africa. They have been considered as a global public health concern, as nearly one million new cases are reported per year. IL-1β is a pro-inflammatory cytokine-produced by activated macrophages and monocytes- and a member of the IL-1 family. The inactive IL-1β precursor is cleaved and activated by caspase-1 enzyme, which itself is activated by the assembly of intracellular structures defined as NLRP3 (Nod Like receptor P3) inflammasomes. Activated IL-1β stimulates the Interleukin-1 receptor type-1 (IL-1R1), which is responsible for the initiation of a signal transduction pathway leading to cell proliferation. It has been proven that the IL-1β gene is a highly polymorphic gene in which single nucleotide polymorphisms (SNPs) may affect its expression. It has been previously reported that SNPs including base transitions between C and T at positions, -511 (C-T; dbSNP: rs16944) and -31 (C-T; dbSNP: rs1143627), from the transcriptional start site, contribute to the pathogenesis of gastric and colorectal cancers by affecting IL-1β levels. Altered production of IL-1β due to such polymorphisms is suspected to stimulate an amplified inflammatory response and promote Epithelial Mesenchymal Transition leading to malignancy. Allele frequency distribution of the IL-1β-31 and -511 SNPs, in different populations, and their correlation to the incidence of gastric and colorectal cancers, has been intriguing to researchers worldwide. The current study aims to investigate allele distributions of the IL-1β SNPs among gastric and colorectal cancers Egyptian patients. In order to achieve to that, 89 Biopsy and surgical specimens from the antrum and corpus mucosa of chronic gastritis subjects and gastric and colorectal carcinoma patients was collected for DNA extraction followed by restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR). The amplified PCR products of IL-1β-31C > T and IL-1β-511T > C were digested by incubation with the restriction endonuclease enzymes ALu1 and Ava1. Statistical analysis was carried out to determine the allele frequency distribution in the three studied groups. Also, the effect of the IL-1β -31 and -511 SNPs on nuclear factor binding was analyzed using Fluorescence Electrophoretic Mobility Shift Assay (EMSA), preceded by nuclear factor extraction from gastric and colorectal tissue samples and LPS stimulated monocytes. The results of this study showed that a significantly higher percentage of Egyptian gastric cancer patients have a homozygous CC genotype at the IL-1β-31 position and a heterozygous TC genotype at the IL-1β-511 position. Moreover, a significantly higher percentage of the colorectal cancer patients have a homozygous CC genotype at the IL-1β-31 and -511 positions as compared to the control group. In addition, the EMSA results showed that IL-1β-31C/T and IL-1β-511T/C SNPs do not affect nuclear factor binding. Results of this study suggest that the IL-1β-31 C/T and IL-1β-511 T/C may be correlated to the incidence of gastric cancer in Egyptian patients; however, similar findings couldn’t be proven in the colorectal cancer patients group for the IL-1β-511 T/C SNP. This is the first study to investigate IL-1β -31 and -511 SNPs in the Egyptian population.

Keywords: colorectal cancer, Egyptian patients, gastric cancer, interleukin-1β, single nucleotide polymorphisms

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Authors: Mehdi Mohebodini, Iman Khalili-Baseri, Mehdi Behnamian, Sara Dezhsetan

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Diversity analysis at the molecular level using PCR-based markers is the efficient and rapid method of identifying the relationships and differences among the genotypes. In the present study, genetic diversity and relationships among 20 collected purslane accessions were evaluated using ISSR markers. The genotyping data were used to understand the relationships among the collected accessions and identify genetically diverse purslane accessions. The 25 primers gave a total of 92 bands, of which 62 were polymorphic (67.4%). The genetic diversity as estimated by Shannon’s information index was 0.55, revealing a quite high level of genetic diversity in the germplasm. The average number of an observed allele, effective allele, polymorphic information content (PIC) and Nei’s index were 2, 1.65, 0.37 and 0.37, respectively.

Keywords: Portulaca oleracea L., genetic diversity, ISSR, germplasm

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Authors: Snezana Mugosa, Zoran Todorovic, Zoran Bukumiric, Ivan Radosavljevic, Natasa Djordjevic

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Introduction: Various studies have shown that the frequency of clopidogrel resistance ranges from 4-40%. The aim of this study was to provide in depth analysis of genetic and non-genetic factors that influence clopidogrel resistance in cardiology patients. Methods: We have conducted a prospective study in 200 hospitalized patients hospitalized at Cardiology Centre of the Clinical Centre of Montenegro. CYP2C19 genetic testing was conducted, and the PREDICT score was calculated in 102 out of 200 patients treated with clopidogrel in order to determine the influence of genetic and non-genetic factors on outcomes of interest. Adverse cardiovascular events and adverse reactions to clopidogrel were assessed during 12 months follow up period. Results: PREDICT score and CYP2C19 enzymatic activity were found to be statistically significant predictors of expressing lack of therapeutic efficacy of clopidogrel by multivariate logistic regression, without multicollinearity or interaction between the predictors (p = 0.002 and 0.009, respectively). Conclusions: Pharmacogenetics analyses that were done in the Montenegrin population of patients for the first time suggest that these analyses can predict patient response to the certain therapy. Stepwise approach could be used in assessing the clopidogrel resistance in cardiology patients, combining the PREDICT score, platelet aggregation test, and genetic testing for CYP2C19 polymorphism.

Keywords: clopidogrel, pharmacogenetics, pharmacotherapy, PREDICT score

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Authors: Saad Mahmud Khan, Sarah El Hajj Chehadeh, Mehera Abdulrahman, Wael Osman, Habiba Al Safar

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Obesity is a non-communicable disease that is widely prevalent with approximately 600 million people classified as obese worldwide. Its etiology is multifactorial and involves a complex interplay between genes and the environment. Over the past few decades, obesity rates among the Emirati population have been increasing. The aim of this study was to investigate the association of candidate gene single nucleotide polymorphisms (SNPs), namely the fat mass and obesity associated (FTO) gene SNP rs9939609 and Vitamin D Receptor (VDR) gene SNP rs1544410, with obesity in the UAE population. Methods: This is a case-control study in which 414 individuals were enrolled during their routine visit to endocrinology clinics in Abu Dhabi, United Arab Emirates between the period of June 2012 and December 2013. Several biochemical tests and clinical assessments along with a lifestyle questionnaire for each participant were completed at the clinic. Genomic DNA was extracted from saliva samples of 201 obese, 114 overweight and 99 normal subjects. Genotyping for the variants was performed using TaqMan assay. Results: The mean Body Mass Index (BMI) ± SD for the obese, overweight, and normal subjects was 35.76 ± 4.54, 27.53 ± 1.45 and 22.69 ± 1.84 kg/m2, respectively. Increasing BMI values were associated with an increase in values for systolic blood pressure, diastolic blood pressure, HbA1c, and triglycerides. The SNP rs9939609 in the FTO gene was found to be significantly associated with the BMI (p=0.028), with the minor allele A having a clear additive effect on BMI values. No significant association was detected between BMI and rs1544410 of the VDR gene. Conclusions: Our study findings indicate that the minor allele A of the rs9939609 has a significant association with increasing BMI values. In addition, our findings support the fact that increasing BMI is associated with increasing risks of other comorbidities such as higher blood pressure, poorer glycemic control and higher triglycerides.

Keywords: body mass index, FTO gene, obesity, rs9939609, United Arab Emirates

Procedia PDF Downloads 217