Search results for: genetic engineering

Authors: Hong Nguyen Thi Hai, Ryota Konda, Dat Kieu Tuan, Cao Tran Thanh, Khang Phung Van, Hau Tran Tin, Harry Wu

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Melaleuca cajuputi is a moderately fast-growing species and considered as a multi-purpose tree as it provides fuelwood, piles and frame poles in construction, leaf essential oil and honey. It occurs in Australia, Papua New Guinea, and South-East Asia. M. cajuputi plantation can be harvested on 6-7 year rotations for wood products. Its timber can also be used for pulp and paper, fiber and particle board, producing quality charcoal and potentially sawn timber. However, most reported M. cajuputi breeding programs have been focused on oil production rather than wood production. In this study, breeding program of M. cajuputi aimed to improve wood production was examined by estimating genetic parameters for growth (tree height, diameter at breast height (DBH), and volume), stem form, stiffness (modulus of elasticity (MOE)), bark thickness and bark ratio in a half-sib family progeny trial including 80 families in the Mekong Delta of Vietnam. MOE is one of the key wood properties of interest to the wood industry. Non-destructive wood stiffness was measured indirectly by acoustic velocity using FAKOPP Microsecond Timer and especially unaffected by bark mass. Narrow-sense heritability for the seven traits ranged from 0.13 to 0.27 at age 7 years. MOE and stem form had positive genetic correlations with growth while the negative correlation between bark ratio and growth was also favorable. Breeding for simultaneous improvement of multiple traits, faster growth with higher MOE and reduction of bark ratio should be possible in M. cajuputi. Index selection based on volume and MOE showed genetic gains of 31 % in volume, 6 % in MOE and 13 % in stem form. In addition, heritability and age-age genetic correlations for growth traits increased with time and optimal early selection age for growth of M. cajuputi based on DBH alone was 4 years. Selected thinning resulted in an increase of heritability due to considerable reduction of phenotypic variation but little effect on genetic variation.

Keywords: acoustic velocity, age-age correlation, bark thickness, heritability, Melaleuca cajuputi, stiffness, thinning effect

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Authors: Fumiko Kojima, Shuji Fujimoto

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Anisakiasis is a disease caused by infection with an anisakid larvae, mostly Anisakis simplex. The larvae commonly infect in marine fish and the disease is frequently reported in areas of the world where fish is consumed raw, lightly pickled or salted. In Japan, people have the habit of eating raw fish such as ‘sushi’ or ‘sashimi’, so they have more chance of infection with larvae of anisakid nematodes. There are three sibling species in A. simplex larvae, namely, A. simplex sensu stricto (Asss), A. pegreffii (Ap) and A. simplex C. It was revealed that Ap is dominant among the larvae from fish (Scomber japonics) in the Japan Sea side and Asss is dominant among those of the Pacific Ocean side conversely. Although anisakiasis has happened in Japan among both the Japan Sea side area and the Pacific Ocean side area. The aim of this study was to investigate genetic variations between the siblings (Asss and Ap) and within the same sibling species by random amplified polymorphic DNA (RAPD) technique. In order to investigate the genetic difference among the each A. simplex larvae, we used RAPD technique to differentiate individuals of A. simplex obtained from Scomber japonics fish those were caught in the Japan sea (Goto Islands in Nagasaki Prefecture) and the cost of Pacific Ocean (Kanagawa Prefecture). The RAPD patterns of the control DNA (Genus Raphidascaris) were markedly different from those of the A. simplex. There were differences in amplification patterns between Asss and Ap. The RAPD patterns for larvae obtained from fish of the same sea were somewhat different and variations were detected even among larvae from the same fish. These results suggest the considerable high genetic variability between Asss and Ap and the possible existence of genetic variation within the sibling species.

Keywords: Anisakiasis in Japan, Anisakis simplex, genomic identification, PCR-RAPD

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Authors: Yun-Hsiang Wang, Huai-Yi Chen, Kin Fong Lei

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Deoxyribonucleic acid (DNA) hybridization is a common technique used in genetic assay widely. However, the hybridization ratio and rate are usually limited by the diffusion effect. Here, microfluidic electrode platform producing electroosmosis generated by alternating current signal has been proposed to enhance the hybridization ratio and rate. The electrode was made of aurum fabricated by microfabrication technique. Thiol-modified oligo probe was immobilized on the electrode for specific capture of target, which is modified by fluorescent tag. Alternative electroosmosis can induce local microfluidic vortexes to accelerate DNA hybridization. This study provides a strategy to enhance the rate of DNA hybridization in the genetic assay.

Keywords: DNA hybridization, electroosmosis, electrical enhancement, hybridization ratio

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Authors: Wathig Hashim Mohamed Ibrahim

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Twenty Five polymorphic microsatellite out of 50 Loci were used to genotype some camel (Camelus dromedarius) types and subtypes in Sudan (Naylawi, Shanapla, Lahawi, Kinani, Rashaydi, Bani-Aamir, Annafi, Bishari Shallagyai and Bishari Arririt) and that from Qatar (OmmaniHJ, OmmaniKH, Majaheem, Pakistani Sindi, Pakistani Punjabi and Pakistani) and for comparative; one type from Somalia (Aarhou) and another from Chad (Spotted) were investigated. The highest number of alleles were 23 in Locus CVRL 01, and lowest were 2 in YWLL 59. The observed heterozygosity (Hobs) were 0.950 and 0.049 for VOLP08 and YWLL09, respectively, while the expected heterozygosity (HExp) were 0.915 and 0.362 for Locus VOLP67 and YWLL58, respectively, and the HExp mean was 0.7378. Polymorphic Information Content (PIC) ranged between 0.907 - 0.345 in Locus VOLP67 and YWLL58, and the PIC mean was 0.7002. The genetic distance ranged between 0.545 – 0.098 for Shallagyai (Bishari subtype) – Pakistani Sindi subtype and between Annafi - Rashaydi, respectively. The genetic distance between spotted and all types ranged between 0.223 with Arririt (Bishari subtype) and 0.463 with Punjabi (Pakistani subtype) that found in Qatar, while all types with Aarhou ranged between 0.215 for Arririt and 0.469 with Punjabi (Pakistani subtype). The dondrogram shows that there is a relationship between the genetic makeup and geographical distributions and also between the genetic makeup and phenotypic characteristic. Individual assignment was calculated, 46.62% correctly assigned and 46.87% quality index. Hardy Weinberg Equivalent (HWE) was also calculated. Key words: Camel, genotype, polymorphic microsatellite

Keywords: camel, genotype, polymorphic microsatellite, types and subtypes

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Authors: Riffat Iqbal, Sidra Ihsan, Andleeb Batool, Maryam Mukhtar

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Glaucoma is a gathering of optic neuropathies described by dynamic degeneration of retinal ganglionic cells. It is clinically and innately heterogenous illness containing a couple of particular forms each with various causes and severities. Primary open-angle glaucoma (POAG) is the most generally perceived kind of glaucoma. This study investigated the genetic association of single nucleotide polymorphisms (SNPs; rs10483727 and rs33912345) at the SIX1/SIX6 locus with primary open-angle glaucoma (POAG) in the Pakistani population. The SIX6 gene plays an important role in ocular development and has been associated with morphology of the optic nerve. A total of 100 patients clinically diagnosed with glaucoma and 100 control individuals of age over 40 were enrolled in the study. Genomic DNA was extracted by organic extraction method. The SNP genotyping was done by (i) PCR based restriction fragment length polymorphism (RFLP) and sequencing method. Significant genetic associations were observed for rs10483727 (risk allele T) and rs33912345 (risk allele C) with POAG. Hence, it was concluded that Six6 gene is genetically associated with pathogenesis of Glaucoma in Pakistan.

Keywords: genotyping, Pakistani population, primary open-angle glaucoma, SIX6 gene

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Authors: Othman Elmahdy Othman, Agnés Germot, Daniel Petit, Muhammad Khodary, Abderrahman Maftah

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Recently, the control (D-loop) and cytochrome b (Cyt b) regions of mtDNA have received more attention due to their role in the genetic diversity and phylogenetic studies in different livestock which give important knowledge towards the genetic resource conservation. Studies based on sequencing of sheep mitochondrial DNA showed that there are five maternal lineages in the world for domestic sheep breeds; A, B, C, D and E. By using cytochrome B sequencing, we aimed to clarify the genetic affinities and phylogeny of six Egyptian sheep breeds. Blood samples were collected from 111 animals belonging to six Egyptian sheep breeds; Barki, Rahmani, Ossimi, Saidi, Sohagi and Fallahi. The total DNA was extracted and the specific primers were used for conventional PCR amplification of the cytochrome B region of mtDNA. PCR amplified products were purified and sequenced. The alignment of sequences was done using BioEdit software and DnaSP 5.00 software was used to identify the sequence variation and polymorphic sites in the aligned sequences. The result showed that the presence of 39 polymorphic sites leading to the formation of 29 haplotypes. The haplotype diversity in six tested breeds ranged from 0.643 in Rahmani breed to 0.871 in Barki breed. The lowest genetic distance was observed between Rahmani and Saidi (D: 1.436 and Dxy: 0.00127) while the highest distance was observed between Ossimi and Sohagi (D: 6.050 and Dxy: 0.00534). Neighbour-joining (Phylogeny) tree was constructed using Mega 5.0 software. The sequences of 111 analyzed samples were aligned with references sequences of different haplogroups; A, B, C, D and E. The phylogeny result showed the presence of four haplogroups; HapA, HapB, HapC and HapE in the examined samples whereas the haplogroup D was not found. The result showed that 88 out of 111 tested animals cluster with haplogroup B (79.28%), whereas 12 tested animals cluster with haplogroup A (10.81%), 10 animals cluster with haplogroup C (9.01%) and one animal belongs to haplogroup E (0.90%).

Keywords: phylogeny, genetic biodiversity, MtDNA, cytochrome B, Egyptian sheep

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Authors: Hanieh Tarbiat Khosrowshahi, Mojtaba Shakeri

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Wireless Sensor Networks (WSNs) consist of a set of sensor nodes with limited capability. WSNs may suffer from multiple node failures when they are exposed to harsh environments such as military zones or disaster locations and lose connectivity by getting partitioned into disjoint segments. Relay nodes (RNs) are alternatively introduced to restore connectivity. They cost more than sensors as they benefit from mobility, more power and more transmission range, enforcing a minimum number of them to be used. This paper addresses the problem of RN placement in a multiple disjoint network by developing a genetic algorithm (GA). The problem is reintroduced as the Steiner tree problem (which is known to be an NP-hard problem) by the aim of finding the minimum number of Steiner points where RNs are to be placed for restoring connectivity. An upper bound to the number of RNs is first computed to set up the length of initial chromosomes. The GA algorithm then iteratively reduces the number of RNs and determines their location at the same time. Experimental results indicate that the proposed GA is capable of establishing network connectivity using a reasonable number of RNs compared to the best existing work.

Keywords: connectivity restoration, genetic algorithms, multiple-node failure, relay nodes, wireless sensor networks

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Authors: Aminu Bashir Mohammad, Agwu Ezera, Abdulrazaq G. Habib, Garba Iliyasu

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Background: Drug resistance tuberculosis (DR-TB) continues to be a challenge in developing countries with poor resources. Routine screening for primary DR-TB before commencing treatment is not done in public hospitals in Nigeria, even with the large body of evidence that shows a high prevalence of primary DR-TB. Data on drug resistance and its genetic determinant among follow up TB patients is lacking in Nigeria. Hence the aim of this study was to determine the prevalence and genetic determinant of drug resistance among follow up TB patients in a tertiary hospital in Nigeria. Methods: This was a cross-sectional laboratory-based study conducted on 384 sputum samples collected from consented follow-up tuberculosis patients. Standard microbiology methods (Zeil-Nielsen staining and microscopy) and PCR (Line Probe Assay)] were used to analyze the samples collected. Person’s Chi-square was used to analyze the data generated. Results: Out of three hundred and eighty-four (384) sputum samples analyzed for mycobacterium tuberculosis (MTB) and DR-TB twenty-five 25 (6.5%) were found to be AFB positive. These samples were subjected to PCR (Line Probe Assay) out of which 18(72%) tested positive for DR-TB. Mutations conferring resistance to rifampicin (rpo B) and isoniazid (katG, and or inhA) were detected in 12/18(66.7%) and 6/18(33.3%), respectively. Transmission dynamic of DR-TB was not significantly (p>0.05) dependent on demographic characteristics. Conclusion: There is a need to strengthened the laboratory capacity for diagnosis of TB and drug resistance testing and make these services available, affordable, and accessible to the patients who need them.

Keywords: drug resistance tuberculosis, genetic determinant, intensive phase, Nigeria

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Authors: Jun Su Park, Byung Kwan Oh, Jin Woo Hwang, Yousok Kim, Hyo Seon Park

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For the structural safety, the maximum stress calculated from the stress distribution of a structure is widely used. The stress distribution can be estimated by deformed shape of the structure obtained from measurement. Although the estimation of stress is strongly affected by the location and number of sensing points, most studies have conducted the stress estimation without reasonable basis on sensing plan such as the location and number of sensors. In this paper, an optimal sensing technique for estimating the stress distribution is proposed. This technique proposes the optimal location and number of sensing points for a 2-D frame structure while minimizing the error of stress distribution between analytical model and estimation by cubic smoothing splines using genetic algorithm. To verify the proposed method, the optimal sensor measurement technique is applied to simulation tests on 2-D steel frame structure. The simulation tests are performed under various loading scenarios. Through those tests, the optimal sensing plan for the structure is suggested and verified.

Keywords: genetic algorithm, optimal sensing, optimizing sensor placements, steel frame structure

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Authors: Saule Mussabekova

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Forensic investigation of human teeth plays an important role in detection of crime, particularly in cases of personal identification of dead bodies changed by putrefactive processes or skeletonized bodies as well as when finding bodies of unknown persons. 152 teeth have been investigated; 85 of them belonged to men and 67 belonged to women taken from alive people of different age. Teeth have been investigated after extraction. Two types of teeth have been investigated: teeth without integrity violation of dental crown and teeth with different degrees of its violation. Additionally, 517 teeth have been investigated that were collected from dead bodies, 252 of which belonged to women and 265 belonged to men, whatever the cause of death with death limitation from 1 month to 20 years. Isohemagglutinating serums and Coliclons of different series have been used for the research of tooth-group specificity by serological methods according to the AB0 system. Standard protocols of different techniques have been used for DNA purification from teeth (by reagent Chelex 100 produced by Bio-Rad using reagent kit 'DNA IQTM System' produced by Promega company (USA) and using columns 'QIAamp DNA Investigator Kit' produced by Qiagen company). Results of comparative forensic investigation of human teeth using serological and molecular genetic methods have shown that use of serological methods for forensic identification is sensible only in cases of preselection prior to the next molecular genetic investigation as well as in cases of impossibility of corresponding genetic investigation for different objective reasons. A number of advantages of methods of molecular genetics in the dental investigation have been marked, particularly in putrefactive changes, in personal identification. Key moments of modern condition of personal identification have been reflected according to dental state. Prospective directions of advance preparation of material have been emphasized for identification of teeth in forensic practice.

Keywords: dental state, forensic identification, molecular genetic analysis, teeth

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Authors: Bliss Singhal

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Machine learning (ML) is a branch of Artificial Intelligence (AI) where computers analyze data and find patterns in the data. The study focuses on the detection of metastatic cancer using ML. Metastatic cancer is the stage where cancer has spread to other parts of the body and is the cause of approximately 90% of cancer-related deaths. Normally, pathologists spend hours each day to manually classifying whether tumors are benign or malignant. This tedious task contributes to mislabeling metastasis being over 60% of the time and emphasizes the importance of being aware of human error and other inefficiencies. ML is a good candidate to improve the correct identification of metastatic cancer, saving thousands of lives and can also improve the speed and efficiency of the process, thereby taking fewer resources and time. So far, the deep learning methodology of AI has been used in research to detect cancer. This study is a novel approach to determining the potential of using preprocessing algorithms combined with classification algorithms in detecting metastatic cancer. The study used two preprocessing algorithms: principal component analysis (PCA) and the genetic algorithm, to reduce the dimensionality of the dataset and then used three classification algorithms: logistic regression, decision tree classifier, and k-nearest neighbors to detect metastatic cancer in the pathology scans. The highest accuracy of 71.14% was produced by the ML pipeline comprising of PCA, the genetic algorithm, and the k-nearest neighbor algorithm, suggesting that preprocessing and classification algorithms have great potential for detecting metastatic cancer.

Keywords: breast cancer, principal component analysis, genetic algorithm, k-nearest neighbors, decision tree classifier, logistic regression

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Authors: Libo Jiang, Huan Li, Rongling Wu

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Ordinary differentiation equations (ODE) have proven to be powerful for reconstructing precise and informative gene regulatory networks (GRNs) from dynamic gene expression data. However, joint modeling and analysis of all genes, essential for the systematical characterization of genetic interactions, are challenging due to high dimensionality and a complex pattern of genetic regulation including activation, repression, and antitermination. Here, we address these challenges by unifying variable selection and game theory through ODE. Each gene within a GRN is co-expressed with its partner genes in a way like a game of multiple players, each of which tends to choose an optimal strategy to maximize its “fitness” across the whole network. Based on this unifying theory, we designed and conducted a real experiment to infer salt tolerance-related GRNs for Euphrates poplar, a hero tree that can grow in the saline desert. The pattern and magnitude of interactions between several hub genes within these GRNs were found to determine the capacity of Euphrates poplar to resist to saline stress.

Keywords: gene regulatory network, ordinary differential equation, game theory, LASSO, saline resistance

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Authors: Babak H. Tabrizi, Seyed Farid Ghaderi

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Concurrent planning of the resource constraint project scheduling and material ordering problems have received significant attention within the last decades. Hence, the issue has been investigated here with the aim to minimize total project costs. Furthermore, the presented model considers different discount options in order to approach the real world conditions. The incorporated alternatives consist of all-unit and incremental discount strategies. On the other hand, a modified version of the genetic algorithm is applied in order to solve the model for larger sizes, in particular. Finally, the applicability and efficiency of the given model is tested by different numerical instances.

Keywords: genetic algorithm, material ordering, project management, project scheduling

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Authors: Karen Fang

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Investigative genetic genealogy has attracted much interest in both the field of ethics and the public eye due to its global application in criminal cases. Arguments have been made regarding privacy and informed consent, especially with law enforcement using consumer genetic testing results to convict individuals. In the case of public interest, DNA databases have the strong potential to significantly reduce crime, which in turn leads to safer communities and better futures. With the advancement of genetic technologies, the integration of a universal forensic DNA database in violent crimes, crimes against children, and missing person cases is expected to deter crime while protecting one’s privacy. Rather than collecting whole genomes from the whole population, STR profiles can be used to identify unrelated individuals without compromising personal information such as physical appearance, disease risk, and geographical origin, and additionally, reduce cost and storage space. STR DNA profiling is already used in the forensic science field and going a step further benefits several areas, including the reduction in recidivism, improved criminal court case turnaround time, and just punishment. Furthermore, adding individuals to the database as early as possible prevents young offenders and first-time offenders from participating in criminal activity. It is important to highlight that DNA databases should be inclusive and tightly governed, and the misconception on the use of DNA based on crime television series and other media sources should be addressed. Nonetheless, deterrent effects have been observed in countries like the US and Denmark with DNA databases that consist of serious violent offenders. Fewer crimes were reported, and fewer people were convicted of those crimes- a favorable outcome, not even the death penalty could provide. Currently, there is no better alternative than a universal forensic DNA database made up of STR profiles. It can open doors for investigative genetic genealogy and fostering better communities. Expanding the appropriate use of DNA databases is ethically acceptable and positively impacts the public.

Keywords: bioethics, deterrent effects, DNA database, investigative genetic genealogy, privacy, public interest

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Authors: Masoud Sheidai

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Biologists with a special field of population genetics and phylogeny have different research tasks such as populations’ genetic variability and divergence, species relatedness, the evolution of genetic and morphological characters, and identification of DNA SNPs with adaptive potential. To tackle these problems and reach a concise conclusion, they must use the proper and efficient statistical and bioinformatic methods as well as suitable genetic and morphological characteristics. In recent years application of different bioinformatic and statistical methods, which are based on various well-documented assumptions, are the proper analytical tools in the hands of researchers. The species delineation is usually carried out with the use of different clustering methods like K-means clustering based on proper distance measures according to the studied features of organisms. A well-defined species are assumed to be separated from the other taxa by molecular barcodes. The species relationships are studied by using molecular markers, which are analyzed by different analytical methods like multidimensional scaling (MDS) and principal coordinate analysis (PCoA). The species population structuring and genetic divergence are usually investigated by PCoA and PCA methods and a network diagram. These are based on bootstrapping of data. The Association of different genes and DNA sequences to ecological and geographical variables is determined by LFMM (Latent factor mixed model) and redundancy analysis (RDA), which are based on Bayesian and distance methods. Molecular and morphological differentiating characters in the studied species may be identified by linear discriminant analysis (DA) and discriminant analysis of principal components (DAPC). We shall illustrate these methods and related conclusions by giving examples from different edible and medicinal plant species.

Keywords: GWAS analysis, K-Means clustering, LFMM, multidimensional scaling, redundancy analysis

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Authors: Ezio Bassi, Francesco Vercesi, Francesco Benzi

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The aim of this study is to evaluate the potentiality of synchronous reluctance motors for lift systems by also evaluating the vibroacoustic behaviour of the motor. Two types of synchronous machines are designed, analysed, and compared with an equivalent induction motor, which is the more common solution in such gearbox applications. The machines' performance are further improved with optimization procedures based on multiobjective optimization genetic algorithm (MOGA). The difference between the two synchronous motors consists in the rotor geometry; a symmetric and an asymmetric rotor design were investigated. The evaluation of the vibroacoustic performance has been conducted with a multi-variable model and finite element software taking into account electromagnetic, mechanical, and thermal features of the motor, therefore carrying out a multi-physics analysis of the electrical machine.

Keywords: synchronous reluctance motor, vibro-acoustic, lift systems, genetic algorithm

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Authors: Amr A. El Hanafy, Yasser M. Saad, Saleh A. Alkarim, Hussein A. Almehdar, Elrashdy M. Redwan

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Camels are substantial providers of transport, milk, sport, meat, shelter, fuel, security and capital in many countries, particularly Saudi Arabia. Identification of animal breeds has progressed rapidly during the last decade. Advanced molecular techniques are playing a significant role in breeding or strain protection laws. On the other hand, fingerprinting of some molecular markers related to some productive traits in farm animals represents most important studies to our knowledge, which aim to conserve these local genetic resources, and to the genetic improvement of such local breeds by selective programs depending on gene markers. Milk records were taken two days in each week from female camels of Majahem, Safara, Wathaha, and Hamara breeds, respectively from different private farms in northern Jeddah, Riyadh and Alwagh governorates and average weekly yields were calculated. DNA sequencing for CSN2 gene was used for evaluating the genetic variations and calculating the genetic distance values among four Saudi camel populations which are Hamra(R), Safra(Y), Wadha(W) and Majaheim(M). In addition, this marker was analyzed for reconstructing the Neighbor joining tree among evaluating camel breeds. In respect to milk yield during winter season, result indicated that average weekly milk yield of Safara camel breed (30.05 Kg/week) is significantly (p < 0.05) lower than the other 3 breeds which ranged from 39.68 for Hamara to 42.42 Kg/week for Majahem, while there are not significant differences between these three breeds. The Neighbor Joining analysis that re-constructed based on DNA variations showed that samples are clustered into two unique clades. The first clade includes Y (from Y4 to Y18) and M (from M1, to M9). On the other hand, the second cluster is including all R (from R1 to R6) and W (from W1 to W6). The genetic distance values were equal 0.0068 (between the groups M&Y and R&W) and equal 0 (within each group).

Keywords: milk yield, beta-casein precursor (CSN2), Saudi camel, molecular markers

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Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo

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Availability of different genetic tests after completion of Human Genome Project increases the physicians’ responsibility to keep themselves update on the potential implementation of these genetic tests in their daily practice. However, due to numbers of barriers, still many of physicians are not either aware of these tests or are not willing to offer or refer their patients for genetic tests. This study was conducted an anonymous, cross-sectional, mailed-based survey to develop a primary data of Malaysian physicians’ level of knowledge and perception of gene profiling. Questionnaire had 29 questions. Total scores on selected questions were used to assess the level of knowledge. The highest possible score was 11. Descriptive statistics, one way ANOVA and chi-squared test was used for statistical analysis. Sixty three completed questionnaires was returned by 27 general practitioners (GPs) and 36 medical specialists. Responders’ age range from 24 to 55 years old (mean 30.2 ± 6.4). About 40% of the participants rated themselves as having poor level of knowledge in genetics in general whilst 60% believed that they have fair level of knowledge. However, almost half (46%) of the respondents felt that they were not knowledgeable about available genetic tests. A majority (94%) of the responders were not aware of any lab or company which is offering gene profiling services in Malaysia. Only 4% of participants were aware of using gene profiling for detection of dosage of some drugs. Respondents perceived greater utility of gene profiling for breast cancer (38%) compared to the colorectal familial cancer (3%). The score of knowledge ranged from 2 to 8 (mean 4.38 ± 1.67). Non-significant differences between score of knowledge of GPs and specialists were observed, with score of 4.19 and 4.58 respectively. There was no significant association between any demographic factors and level of knowledge. However, those who graduated between years 2001 to 2005 had higher level of knowledge. Overall, 83% of participants showed relatively high level of perception on value of gene profiling to detect patient’s risk of disease. However, low perception was observed for both statements of using gene profiling for general population in order to alter their lifestyle (25%) as well as having the full sequence of a patient genome for the purpose of determining a patient’s best match for treatment (18%). The lack of clinical guidelines, limited provider knowledge and awareness, lack of time and resources to educate patients, lack of evidence-based clinical information and cost of tests were the most barriers of ordering gene profiling mentioned by physicians. In conclusion Malaysian physicians who participate in this study had mediocre level of knowledge and awareness in gene profiling. The low exposure to the genetic questions and problems might be a key predictor of lack of awareness and knowledge on available genetic tests. Educational and training workshop might be useful in helping Malaysian physicians incorporate genetic profiling into practice for eligible patients.

Keywords: gene profiling, knowledge, Malaysia, physician

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Authors: Ismail El Gayar, Ossama Ismail, Yousri El Gamal

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This paper presented a technique to solve one of the transportation problems that faces us in real life which is the Bus Scheduling Problem. Most of the countries using buses in schools, companies and traveling offices as an example to transfer multiple passengers from many places to specific place and vice versa. This transferring process can cost time and money, so we build a decision support system that can solve this problem. In this paper, a genetic algorithm with the shortest path technique is used to generate a competitive solution to other well-known techniques. It also presents a comparison between our solution and other solutions for this problem.

Keywords: bus scheduling problem, decision support system, genetic algorithm, shortest path

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Authors: Jiawen Wang, Qijun Chen

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The performance of most machine-learning methods for image inpainting depends on the quantity and quality of the training samples. However, it is very expensive or even impossible to obtain a great number of training samples in many scenarios. In this paper, an image inpainting model based on a generative adversary network (GAN) is constructed for the cases when the number of training samples is small. Firstly, a feature extraction network (F-net) is incorporated into the GAN network to utilize the available information of the inpainting image. The weighted sum of the extracted feature and the random noise acts as the input to the generative network (G-net). The proposed network can be trained well even when the sample size is very small. Secondly, in the phase of the completion for each damaged image, a genetic algorithm is designed to search an optimized noise input for G-net; based on this optimized input, the parameters of the G-net and F-net are further learned (Once the completion for a certain damaged image ends, the parameters restore to its original values obtained in the training phase) to generate an image patch that not only can fill the missing part of the damaged image smoothly but also has visual semantics.

Keywords: image inpainting, generative adversary nets, genetic algorithm, small-sample size

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Authors: D. Leibman, D. Wolf, A. Gal-On

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Viral diseases of tomato crops result in heavy yield losses and may even jeopardize the production of these crops. Classical tomato breeding for disease resistance against Tomato yellow leaf curl virus (TYLCV), leads to partial resistance associated with a number of recessive genes. To author’s best knowledge Pepino mosaic virus (PepMV) genetic resistance is not yet available. The generation of viral resistance by means of genetic engineering was reported and implemented for many crops, including tomato. Transgenic resistance against viruses is based, in most cases, on Post Transcriptional Gene Silencing (PTGS), an endogenous mechanism which destroys the virus genome. In this work, we developed immunity against PepMV and TYLCV in a tomato based on a PTGS mechanism. Tomato plants were transformed with a hairpin-construct-expressed transgene-derived double-strand-RNA (tr-dsRNA). In the case of PepMV, the binary construct harbored three consecutive fragments of the replicase gene from three different PepMV strains (Italian, Spanish and American), to provide resistance against a range of virus strains. In the case of TYLCV, the binary vector included three consecutive fragments of the IR, V2 and C2 viral genes constructed in a hairpin configuration. Selected transgenic lines (T0) showed a high accumulation of transgene siRNA of 21-24 bases, and T1 transgenic lines showed complete immunity to PepMV and TYLCV. Graft inoculation displayed immunity of the transgenic scion against PepMV and TYLCV. The study presents the engineering of resistance in tomato against two serious diseases, which will help in the production of high-quality tomato. However, unfortunately, these resistant plants have not been implemented due to public ignorance and opposition against breeding by genetic engineering.

Keywords: PepMV, PTGS, TYLCV, tr-dsRNA

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Authors: Sajjad Baghernezhad

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Meta-heuristic and hybrid algorithms have high adeer in modeling medical problems. In this study, a neural network was used to predict covid-19 among high-risk and low-risk patients. This study was conducted to collect the applied method and its target population consisting of 550 high-risk and low-risk patients from the Kerman University of medical sciences medical center to predict the coronavirus. In this study, the memetic algorithm, which is a combination of a genetic algorithm and a local search algorithm, has been used to update the weights of the neural network and develop the accuracy of the neural network. The initial study showed that the accuracy of the neural network was 88%. After updating the weights, the memetic algorithm increased by 93%. For the proposed model, sensitivity, specificity, positive predictivity value, value/accuracy to 97.4, 92.3, 95.8, 96.2, and 0.918, respectively; for the genetic algorithm model, 87.05, 9.20 7, 89.45, 97.30 and 0.967 and for logistic regression model were 87.40, 95.20, 93.79, 0.87 and 0.916. Based on the findings of this study, neural network models have a lower error rate in the diagnosis of patients based on individual variables and vital signs compared to the regression model. The findings of this study can help planners and health care providers in signing programs and early diagnosis of COVID-19 or Corona.

Keywords: COVID-19, decision support technique, neural network, genetic algorithm, memetic algorithm

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Authors: Manas Shah

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Black Scholes option pricing model is one of the most important concepts in modern world of computational finance. However, its practical use can be challenging as one of the input parameters must be estimated; implied volatility of the underlying security. The more precisely these values are estimated, the more accurate their corresponding estimates of theoretical option prices would be. Here, we present a novel model based on Cuckoo Search Optimization (CS) which finds more precise estimates of implied volatility than Particle Swarm Optimization (PSO) and Genetic Algorithm (GA).

Keywords: black scholes model, cuckoo search optimization, particle swarm optimization, genetic algorithm

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Authors: Amar Khoukhi, Mohamed Shahab

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This paper presents the optimal control problem of mobile robot motion as a nonlinear programming problem (NLP) and solved using a direct method of numerical optimal control. The NLP is initialized with a B-Spline for which node locations are optimized using a genetic search. The system acceleration inputs and sampling periods are considered as optimization variables. Different scenarios with different objectives weights are implemented and investigated. Interesting results are found in terms of complying with the expected behavior of a mobile robot system and time-energy minimization.

Keywords: multi-objective control, non-holonomic systems, mobile robots, nonlinear programming, motion planning, B-spline, genetic algorithm

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Authors: Wafa Al Jabri

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Background: In Middle Eastern Islamic Countries (MEICs), there is a high prevalence of genetic blood disorders (GBDs), particularly sickle cell disease and thalassemia. The GBDs are considered a major public health concern, especially with the increase in affected populations along with the associated psychological, social, and financial cost of management. Despite the availability of premarital screening services (PSS) that aim to identify the asymptomatic carriers of GBDs and provide genetic counseling to couples in order toreduce the prevalence of these diseases; yet, the success rate of PSS is very low due to religious and socio-cultural concerns. Purpose: This paper aims to highlight the factors that affect the success of PSS in MEICs. Methods: A literature review of articles located in CINAHL, PubMed, SCOPUS, and MedLinewas carried out using the following terms: “premarital screening,” “success,” “effectiveness,” and “ genetic blood disorders.” Second, a hand search of the reference lists and Google searches were conducted to find studies that did not exist in the primary database searches. Only studies which are conducted in MEICs countries and published in the last five years were included. Studies that were not published in English were excluded. Results: Fourteen articles were included in the review. The results showed that PSS in most of the MEICs was successful in achieving its objective of identifying high-risk marriages; however, the service failed to meetitsultimate goal of reducing the prevalence of GBDs. Various factors seem to hinder the success of PSS, including poor public awareness, late timing of the screening, culture and social stigma, religious beliefs, availability of prenatal diagnosis and therapeutic abortion, emotional factors, and availability of genetic counseling services. However, poor public awareness, late timing of the screening, and unavailability of adequate counseling services were the most common barriers identified. Conclusion: Overcoming the identified barriers by providing effective health education programs, offering the screening test to young adults at an earlier stage, and tailoring the genetic counseling would be crucial steps to provide a framework for an effective PSS in MEICs.

Keywords: premarital screening, success, effectiveness, and genetic blood disorders

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Authors: Sammy Kibor, Filip Huyghe, Marc Kochzius, James Kairo

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Goldstripe Sardinella, Sardinella gibbosa, (Bleeker, 1849) is a commercially and ecologically important small pelagic fish common in the Western Indian Ocean region. The present study aimed to assess genetic diversity and population structure of the species in the Kenya-Tanzania transboundary area using mtDNA and msDNA markers. Some 630 bp sequence in the mitochondrial DNA (mtDNA) Cytochrome C Oxidase I (COI) and five polymorphic microsatellite DNA loci were analyzed. Fin clips of 309 individuals from eight locations within the transboundary area were collected between July and December 2018. The S. gibbosa individuals from the different locations were distinguishable from one another based on the mtDNA variation, as demonstrated with a neighbor-joining tree and minimum spanning network analysis. None of the identified 22 haplotypes were shared between Kenya and Tanzania. Gene diversity per locus was relatively high (0.271-0.751), highest Fis was 0.391. The structure analysis, discriminant analysis of Principal component (DAPC) and the pair-wise (FST = 0.136 P < 0.001) values after Bonferroni correction using five microsatellite loci provided clear inference on genetic differentiation and thus evidence of population structure of S. gibbosa along the Kenya-Tanzania coast. This study shows a high level of genetic diversity and the presence of population structure (Φst =0.078 P < 0.001) resulting to the existence of four populations giving a clear indication of minimum gene flow among the population. This information has application in the designing of marine protected areas, an important tool for marine conservation.

Keywords: marine connectivity, microsatellites, population genetics, transboundary

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Authors: Agostinho Antunes

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The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: adaptation, animals, evolution, genomics

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Authors: Gordana Branković, Dejan Dodig, Vesna Pajić, Vesna Kandić, Desimir Knežević, Nenad Đurić

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The wheat grain quality properties are influenced by genotype, environmental conditions and genotype × environment interaction (GEI). The increasing request of more nutritious wheat products will direct future breeding programmes. Therefore, the aim of investigation was to determine: i) variability of the protein content (PC), wet gluten content (WG) and Zeleny sedimentation volume (ZS); ii) components of variance, heritability in a broad sense (hb2), and expected genetic advance as percent of mean (GAM) for PC, WG, and ZS; iii) correlations between PC, WG, ZS, and most important agronomic traits; in order to assess expected breeding success versus environmental impact for these quality traits. The plant material consisted of 30 genotypes of bread wheat (Triticum aestivum L. ssp. aestivum) and durum wheat (Triticum durum Desf.). The trials were sown at the three test locations in Serbia: Rimski Šančevi, Zemun Polje and Padinska Skela during 2010-2011 and 2011-2012. The experiments were set as randomized complete block design with four replications. The plot consisted of five rows of 1 m2 (5 × 0.2 m × 1 m). PC, WG and ZS were determined by the use of Near infrared spectrometry (NIRS) with the Infraneo analyser (Chopin Technologies, France). PC, WG and ZS, in bread wheat, were in the range 13.4-16.4%, 22.8-30.3%, and 39.4-67.1 mL, respectively, and in durum wheat, in the range 15.3-18.1%, 28.9-36.3%, 37.4-48.3 mL, respectively. The dominant component of variance for PC, WG, and ZS, in bread wheat, was genotype with the genetic variance/GEI variance (VG/VG × E) relation of 3.2, 2.9 and 1.0, respectively, and in durum wheat was GEI with the VG/VG × E relation of 0.70, 0.69 and 0.49, respectively. hb2 and GAM values for PC, WG and ZS, in bread wheat, were 94.9% and 12.6%, 93.7% and 18.4%, and 86.2% and 28.1%, respectively, and in durum wheat, 80.7% and 7.6%, 79.7% and 10.2%, and 74% and 11.2%, respectively. The most consistent through six environments, statistically significant correlations, for bread wheat, were between PC and spike length (-0.312 to -0.637); PC, WG, ZS and grain number per spike (-0.320 to -0.620; -0.369 to -0.567; -0.301 to -0.378, respectively); PC and grain thickness (0.338 to 0.566), and for durum wheat, were between PC, WG, ZS and yield (-0.290 to -0.690; -0.433 to -0.753; -0.297 to -0.660, respectively); PC and plant height (-0.314 to -0.521); PC, WG and spike length (-0.298 to -0.597; -0.293 to -0.627, respectively); PC, WG and grain thickness (0.260 to 0.575; 0.269 to 0.498, respectively); PC, WG and grain vitreousness (0.278 to 0.665; 0.357 to 0.690, respectively). Breeding success can be anticipated for ZS in bread wheat due to coupled high values for hb2 and GAM, suggesting existence of additive genetic effects, and also for WG in bread wheat, due to very high hb2 and medium high GAM. The small, and medium, negative correlations between PC, WG, ZS, and yield or yield components, indicate difficulties to select simultaneously for high quality and yield, depending on linkage for particular genetic arrangements to be broken by recombination.

Keywords: bread and durum wheat, genetic advance, protein and wet gluten content, Zeleny sedimentation volume

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Authors: Paromik Bhattacharyya, Vijay Kumar, Johannes Van Staden

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Micropropagation is an important tool for the conservation of threatened and commercially important plant species of which orchids deserve special attention. Ansellia africana is one such medicinally important orchid species having much commercial significance. Thus, development of regeneration protocols for producing clonally stable regenerates using axillary buds is of much importance. However, for large-scale micropropagation to become not only successful but also acceptable by end-users, somaclonal variations occurring in the plantlets need to be eliminated. In the light of the various factors (genotype, ploidy level, in vitro culture age, explant and culture type, etc.) that may account for the somaclonal variations of divergent genetic changes at the cellular and molecular levels, genetic analysis of micropropagated plants using a multidisciplinary approach is of utmost importance. In the present study, the clonal integrity of the long term micropropagated A. africana plants were assessed using advanced molecular marker system i.e. Start Codon Targeted Polymorphism (SCoT). Our studies recorded a clonally stable regeneration protocol for A. africana with a very high degree of clonal fidelity amongst the regenerates. The results obtained from these molecular analyses could help in modifying the regeneration protocols for obtaining clonally stable true to type plantlets for sustainable commercial use.

Keywords: medicinal orchid micropropagation, start codon targeted polymorphism (SCoT), RAP), traditional African pharmacopoeia, genetic fidelity

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Authors: Minjung Kim, Hyunkoo Kang, Jinkoo Kim

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In this study, a seismic retrofit scheme for a reinforced concrete shear wall structure using steel slit dampers was presented. The stiffness and the strength of the slit damper used in the retrofit were verified by cyclic loading test. A genetic algorithm was applied to find out the optimum location of the slit dampers. The effects of the slit dampers on the seismic retrofit of the model were compared with those of jacketing shear walls. The seismic performance of the model structure with optimally positioned slit dampers was evaluated by nonlinear static and dynamic analyses. Based on the analysis results, the simple procedure for determining required damping ratio using capacity spectrum method along with the damper distribution pattern proportional to the inter-story drifts was validated. The analysis results showed that the seismic retrofit of the model structure using the slit dampers was more economical than the jacketing of the shear walls and that the capacity spectrum method combined with the simple damper distribution pattern led to satisfactory damper distribution pattern compatible with the solution obtained from the genetic algorithm.

Keywords: seismic retrofit, slit dampers, genetic algorithm, jacketing, capacity spectrum method

Procedia PDF Downloads 275