Search results for: genetic polymorphisms

Authors: Michael Aupetit, Mahmoud Al-ismail, Khaled Mohamed

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Cancer is a major public health problem all over the world. Breast cancer has the highest incidence rate over all cancers for women in Qatar making its study a top priority of the country. Human cancer is a dynamic disease that develops over an extended period through the accumulation of a series of genetic alterations. A Darwinian process drives the tumor cells toward higher malignancy growing the branches of a progression tree in the space of genes expression. Although it is not possible to track these genetic alterations dynamically for one patient, it is possible to reconstruct the progression tree from the aggregation of thousands of tumor cells’ genetic profiles from thousands of different patients at different stages of the disease. Analyzing the progression tree is a way to detect pivotal molecular events that drive the malignant evolution and to provide a guide for the development of cancer diagnostics, prognostics and targeted therapeutics. In this work we present the development of a Visual Analytic web platform CanVis enabling users to upload gene-expression data and analyze their progression tree. The server computes the progression tree based on state-of-the-art techniques and allows an interactive visual exploration of this tree and the gene-expression data along its branching structure helping to discover potential driver genes.

Keywords: breast cancer, progression tree, visual analytics, web platform

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Authors: Hamed K. Esfahani, Bithin Datta

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Transport of reactive chemical contaminant species in groundwater aquifers is a complex and highly non-linear physical and geochemical process especially for real life scenarios. Simulating this transport process involves solving complex nonlinear equations and generally requires huge computational time for a given aquifer study area. Development of optimal remediation strategies in aquifers may require repeated solution of such complex numerical simulation models. To overcome this computational limitation and improve the computational feasibility of large number of repeated simulations, Genetic Programming based trained surrogate models are developed to approximately simulate such complex transport processes. Transport process of acid mine drainage, a hazardous pollutant is first simulated using a numerical simulated model: HYDROGEOCHEM 5.0 for a contaminated aquifer in a historic mine site. Simulation model solution results for an illustrative contaminated aquifer site is then approximated by training and testing a Genetic Programming (GP) based surrogate model. Performance evaluation of the ensemble GP models as surrogate models for the reactive species transport in groundwater demonstrates the feasibility of its use and the associated computational advantages. The results show the efficiency and feasibility of using ensemble GP surrogate models as approximate simulators of complex hydrogeologic and geochemical processes in a contaminated groundwater aquifer incorporating uncertainties in historic mine site.

Keywords: geochemical transport simulation, acid mine drainage, surrogate models, ensemble genetic programming, contaminated aquifers, mine sites

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Authors: A. Mansouri, F. Krim

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This paper presents two techniques for DC motor parameters identification. We propose a numerical method using the adaptive extensive recursive least squares (AERLS) algorithm for real time parameters estimation. This algorithm, based on minimization of quadratic criterion, is realized in simulation for parameters identification of DC motor autoregressive moving average with extra inputs (ARMAX). As advanced technique, we use genetic algorithms (GA) identification with biased estimation for high dynamic performance speed regulation. DC motors are extensively used in variable speed drives, for robot and solar panel trajectory control. GA effectiveness is derived through comparison of the two approaches.

Keywords: ARMAX model, DC motor, AERLS, GA, optimization, parameter identification, PID speed regulation

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Authors: Benjamin A. Ha, Marco Morselli, Xinhui Paige Zhang, Elizabeth A. C. Heath-Heckman, Jonathan B. Puritz, David K. Jacobs

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Next-generation sequencing has enhanced the ability to acquire massive amounts of sequence data to address classic population genetic questions for non-model organisms. Targeted approaches allow for cost effective or more precise analyses of relevant sequences; although, many such techniques require a known genome and it can be costly to purchase probes from a company. This is challenging for non-model organisms with no published genome and can be expensive for large population genetic studies. Expressed exome capture sequencing (EecSeq) synthesizes probes in the lab from expressed mRNA, which is used to capture and sequence the coding regions of genomic DNA from a pooled suite of samples. A normalization step produces probes to recover transcripts from a wide range of expression levels. This approach offers low cost recovery of a broad range of genes in the genome. This research project expands on EecSeq to investigate if mRNA from one taxon may be used to capture relevant sequences from a series of increasingly less closely related taxa. For this purpose, we propose to use the endangered Northern Tidewater goby, Eucyclogobius newberryi, a non-model organism that inhabits California coastal lagoons. mRNA will be extracted from E. newberryi to create probes and capture exomes from eight other taxa, including the more at-risk Southern Tidewater goby, E. kristinae, and more divergent species. Captured exomes will be sequenced, analyzed bioinformatically and phylogenetically, then compared to previously generated phylogenies across this group of gobies. This will provide an assessment of the utility of the technique in cross-species studies and for analyzing low genetic variation within species as is the case for E. kristinae. This method has potential applications to provide economical ways to expand population genetic and evolutionary biology studies for non-model organisms.

Keywords: coastal lagoons, endangered species, non-model organism, target capture method

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Authors: Atefeh Esmailnejad, Gholam Reza Nikbakht Brujeni

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The major histocompatibility complex (MHC) is the best-characterized genetic region associated with susceptibility and/or resistance to a wide range of infectious diseases, autoimmune diseases and immune responses to vaccines. It has been demonstrated that there is an association between the MHC and resistance to Marek disease, Newcastle disease, Rous sarcoma tumor, Avian leucosis, Fowl cholera, Salmonellosis and Pasteurellosis in chicken. The present study evaluated the MHC polymorphism and its association with antibody response to Newcastle (ND) vaccine in Iranian native chickens. The MHC polymorphism was investigated using LEI0258 microsatellite locus by PCR-based fragment analysis. LEI0258 microsatellite marker is a genetic indicator for MHC, which is located on microchromosome 16 and strongly associated with serologically defined MHC haplotypes. Antibody titer against ND vaccine was measured by Haemaglutination Inhibition (HI) assay. Statistical analysis was performed using SPSS software (version 21). Total of 13 LEI0258 microsatellite alleles were identified in 72 samples which indicated a high genetic diversity in the population. The association study revealed a significant influence of MHC alleles on immune responses to Newcastle vaccine. 311 and 313 bp alleles were significantly associated with elevated immune responses to Newcastle vaccine (p<0.05). These results would be applicable in designing and improving the populations under selective breeding.

Keywords: chicken, LEI0258, MHC, Newcastle vaccine

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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 selected marine animal 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: marine genomics, evolutionary bioinformatics, human genome sequencing, genomic analyses

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Authors: Eisha Vienna M. Fernandez, Cristan Q. Cabanilla, Hiyasmin Lim, John Donnie A. Ramos

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Allergy is a multifactorial disease affecting a significant proportion of the population. It is developed through the interaction of allergens and the presence of certain polymorphisms in various susceptibility genes. In this study, the correlation of the 105A/C single nucleotide polymorphism (SNP) of the IL-18 gene and house dust mite-specific IgE among Filipino allergic and non-allergic population was investigated. Atopic status was defined by serum total IgE concentration of ≥100 IU/mL, while house dust mite allergy was defined by specific IgE value ≥ +1SD of IgE of nonatopic participants. Two hundred twenty match-paired Filipino cases and controls aged 6-60 were the subjects of this investigation. The level of total IgE and Specific IgE were measured using Enzyme-Linked Immunosorbent Assay (ELISA) while Polymerase Chain Reaction – Restriction Fragment Length Polymorphism (PCR-RFLP) analysis was used in the SNP detection. Sensitization profiles of the allergic patients revealed that 97.3% were sensitized to Blomia tropicalis, 40.0% to Dermatophagoides farinae, and 29.1% to Dermatophagoides pteronyssinus. Multiple sensitization to HDMs was also observed among the 47.27% of the atopic participants. Any of the allergy classes of the atopic triad were exhibited by the cases (allergic asthma: 48.18%; allergic rhinitis: 62.73%; atopic dermatitis: 19.09%), and two or all of these atopic states are concurrently occurring in 26.36% of the cases. A greater proportion of the atopic participants with allergic asthma and allergic rhinitis were sensitized to D. farinae, and D. pteronyssinus, while more of those with atopic dermatitis were sensitized to D. pteronyssinus than D. farinae. Results show that there is overrepresentation of the allele “A” of the 105A/C IL-18 gene SNP in both cases and control groups of the population. The genotype that predominate the population is the heterozygous “AC”, followed by the homozygous wild “AA”, and the homozygous variant “CC” being the least. The study confirmed a positive association between serum specific IgE against B. tropicalis and D. pteronyssinus and the allele “C” (Bt P=0.021, Dp P=0.027) and “AC” (Bt P=0.003, Dp P=0.026) genotype. Findings also revealed that the genotypes “AA” (OR:1.217; 95% CI: 0.701-2.113) and “CC” (OR, 3.5; 95% CI: 0.727-16.849) increase the risk of developing allergy. This indicates that the 105A/C IL-18 gene SNP is a candidate genetic marker for HDM allergy among Filipino patients.

Keywords: house dust mite allergy, interleukin-18 (IL-18), single nucleotide polymorphism,

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Authors: Yessengali Ussenbekov, Valery Terletskiy, Orik Zhanserkenova, Shynar Kasymbekova, Indira Beyshova, Aitkali Imanbayev, Almas Serikov

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Currently, there are 46 hereditary diseases afflicting cattle with known molecular genetic diagnostic methods developed for them. Genetic anomalies frequently occur in the Holstein cattle breeds from American and Canadian bloodlines. The data on the incidence of BLAD, CVM, DUMPS and BC autosomal recessive lethal mutations in pedigree animals are discordant, the detrimental allele incidence rates are high for the Holstein cattle breed, whereas the incidence rates of these mutations are low in some breeds or they are completely absent. Data were obtained on the basis of frozen semen of stud bulls. DNA was extracted from the semen with the DNA-Sorb-B extraction kit. The lethal mutation in the genes CD18, SLC35A3, UMP and ASS of Alatau stud bulls (N=124) was detected by polymerase chain reaction and RFLP analysis. It was established that stud bulls of the local Alatau breed were not carriers of the BLAD, CVM, DUMPS, and BC detrimental mutations. However, with a view to preventing the dissemination of hereditary diseases it is recommended to monitor the pedigree stock using molecular genetic methods.

Keywords: PCR, autosomal recessive point mutation, BLAD, CVM, DUMPS, BC, stud bulls

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Authors: Mary Rose Eunice S. Gundayao, Manolo M. Fernandez

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Metachromatic leukodystrophy (MLD) is a rare lysosomal storage disorder with an autosomal recessive inheritance pattern. Lysosomal storage disorders are often severe, follow a progressively neurodegenerative path, and may result in multi-organ failure, potentially leading to death within 5 to 6 years in cases of early-onset forms. There are limited data regarding cases of MLD in Filipino children. This is the case of a 2-year-old Filipino girl who presented with progressive neurological deterioration and was diagnosed with metachromatic leukodystrophy by molecular genetic testing. This case report aims to present this patient’s clinical history, neurological findings, diagnosis and novel genetic mutations causing MLD. A concise review of updated literature on MLD will be discussed.

Keywords: metachromatic leukodystrophy, ARSA gene, peripheral neuropathy, case report, demyelinating disease

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Authors: Xiao Zhang, Wensheng Xiao, Junguo Cui, Hongmin Wang

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Submersible permanent magnet linear synchronous motors (SPMLSMs) are electromagnetic devices, which can directly drive plunger pump to obtain the crude oil. Those motors have been gradually applied in oil fields due to high thrust force density and high efficiency. Since the force performance closely depends on the concrete structural parameters, the seven different structural parameters are investigated in detail. This paper presents an optimum design of an SPMLSM to minimize the detent force and maximize the thrust by using design of experiment (DOE) and genetic algorithm (GA). The three significant structural parameters (air-gap length, slot width, pole-arc coefficient) are separately screened using 27 1/16 fractional factorial design (FFD) to investigate the significant effect of seven parameters used in this research on the force performance. Response surface methodology (RSM) is well adapted to make analytical model of thrust and detent force with constraints of corresponding significant parameters and enable objective function to be easily created, respectively. GA is performed as a searching tool to search for the Pareto-optimal solutions. By finite element analysis, the proposed PMLSM shows merits in improving thrust and reducing the detent force dramatically.

Keywords: optimization, force performance, design of experiment (DOE), genetic algorithm (GA)

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Authors: Toshinori Nawata

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In this paper a nonlinear feedback control called augmented automatic choosing control (AACC) for a class of nonlinear systems with constrained input is presented. When designing the control, a constant term which arises from linearization of a given nonlinear system is treated as a coefficient of a stable zero dynamics. Parameters of the control are suboptimally selected by maximizing the stable region in the sense of Lyapunov with the aid of a genetic algorithm. This approach is applied to a field excitation control problem of power system to demonstrate the splendidness of the AACC. Simulation results show that the new controller can improve performance remarkably well.

Keywords: augmented automatic choosing control, nonlinear control, genetic algorithm, zero dynamics

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Authors: Surekha Tony, Roshan Mevada

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Wiskott-Aldrich syndrome (WAS) is a primary immunodeficiency disease resulting in recurrent infections, eczema, and microthrombocytopenia. In its classical form, significant combined immune deficiency, autoimmune complications, and risk of hematological malignancy necessitate early correction, preferably before 2 years of age, with hematopoietic stem cell transplant (HSCT) or gene therapy. Clinical features and severity are varied, making the diagnosis difficult in milder cases. We report an Omani boy diagnosed in early infancy with WAS based on clinical presentation and confirmed by genetic diagnosis with cure by HSCT from an HLA-identical sibling donor.

Keywords: genetic diagnosis, hematopoietic stem cell transplant, infant, Wiskott-Aldrich syndrome

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Authors: D. Mohammadzadeh S., J. Bolouri Bazaz

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This paper presents a new prediction model for compression index of fine-grained soils using multi-gene genetic programming (MGGP) technique. The proposed model relates the soil compression index to its liquid limit, plastic limit and void ratio. Several laboratory test results for fine-grained were used to develop the models. Various criteria were considered to check the validity of the model. The parametric and sensitivity analyses were performed and discussed. The MGGP method was found to be very effective for predicting the soil compression index. A comparative study was further performed to prove the superiority of the MGGP model to the existing soft computing and traditional empirical equations.

Keywords: new prediction model, compression index soil, multi-gene genetic programming, MGGP

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Authors: Garima Anand, Rupam Kapoor

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Alternaria leaf spot caused by Alternaria carthami is one of the most devastating diseases of safflower. It has resulted in huge losses in crop production and cultivation leading to a fall out of India’s rank as the leading producer of safflower in the world. Understanding the diversity of any pathogen is essential for its management and for the development of disease control strategies. The diversity of A. carthami was therefore analysed on the basis of biochemical, pathogenicity and genetic lines using ISSR markers. Collections and isolations of 95 isolates of A. carthami were made from major safflower producing states of India. Virulence was analysed to evaluate the pathogenic potential of these isolates. The isolates from Bijapur, Dharwad districts (Karnataka), and Parbhani and Solapur districts (Maharashtra) were found to be highly virulent. The virulence assays showed low virulence levels (42%) for the largest part of the population. Biochemical characterization to assess aggressiveness of these isolates was done by estimating the activity of cell wall degrading enzymes where isolates from districts Dharwad, Bijapur of Karnataka and districts Parbhani and Latur of Maharashtra were found to be most aggressive. Genetic diversity among isolates of A. carthami was determined using eighteen ISSR markers. Distance analysis using neighbour joining method and PCoA analysis of the ISSR profiles divided the isolates into three sub-populations. The most virulent isolates clustered in one group in the dendrogram. The study provided no evidence for geographical clustering indicating that isolates are randomly spread across the states, signifying the high potential of the fungus to adapt to diverse regions. The study can, therefore, aid in the breeding and deployment of A. carthami resistant safflower varieties and in the management of Alternaria leaf spot disease.

Keywords: alternaria leaf spot, genetic diversity, pathogenic potential, virulence

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Authors: Rujia Chen, Ajit Narayanan

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Convolutional neural networks (CNN), as typically applied in deep learning, use layer-wise backpropagation (BP) to construct filters and kernels for feature extraction. Such filters are 2D or 3D groups of weights for constructing feature maps at subsequent layers of the CNN and are shared across the entire input. BP as a gradient descent algorithm has well-known problems of getting stuck at local optima. The use of genetic algorithms (GAs) for evolving weights between layers of standard artificial neural networks (ANNs) is a well-established area of neuroevolution. In particular, the use of crossover techniques when optimizing weights can help to overcome problems of local optima. However, the application of GAs for evolving the weights of filters and kernels in CNNs is not yet an established area of neuroevolution. In this paper, a GA-based filter development algorithm is proposed. The results of the proof-of-concept experiments described in this paper show the proposed GA algorithm can find filter weights through evolutionary techniques rather than BP learning. For some simple classification tasks like geometric shape recognition, the proposed algorithm can achieve 100% accuracy. The results for MNIST classification, while not as good as possible through standard filter learning through BP, show that filter and kernel evolution warrants further investigation as a new subarea of neuroevolution for deep architectures.

Keywords: neuroevolution, convolutional neural network, genetic algorithm, filters, kernels

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Authors: Lesley Northrop, Justin DeGrazia, Jessica Greenwood

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ASPIRA Labs now offers an en-suit and ready-to-implement technology transfer solution to enable labs and hospitals that lack the resources to build it themselves to offer in-house genetic testing. This unique platform employs a patented Molecular Inversion Probe (MIP) technology that combines the specificity of a hybrid capture protocol with the ease of an amplicon-based protocol and utilizes an advanced bioinformatics analysis pipeline based on machine learning. To demonstrate its efficacy, two independent genetic tests were validated on this technology transfer platform: expanded carrier screening (ECS) and hereditary cancer testing (HC). The analytical performance of ECS and HC was validated separately in a blinded manner for calling three different types of variants: SNVs, short indels (typically, <50 bp), and large indels/CNVs defined as multi-exonic del/dup events. The reference set was constructed using samples from Coriell Institute, an external clinical genetic testing laboratory, Maine Molecular Quality Controls Inc. (MMQCI), SeraCare and GIAB Consortium. Overall, the analytical performance showed a sensitivity and specificity of >99.4% for both ECS and HC in detecting SNVs. For indels, both tests reported specificity of 100%, and ECS demonstrated a sensitivity of 100%, whereas HC exhibited a sensitivity of 96.5%. The bioinformatics pipeline also correctly called all reference CNV events resulting in a sensitivity of 100% for both tests. No additional calls were made in the HC panel, leading to a perfect performance (specificity and F-measure of 100%). In the carrier panel, however, three additional positive calls were made outside the reference set. Two of these calls were confirmed using an orthogonal method and were re-classified as true positives leaving only one false positive. The pipeline also correctly identified all challenging carrier statuses, such as positive cases for spinal muscular atrophy and alpha-thalassemia, resulting in 100% sensitivity. After confirmation of additional positive calls via long-range PCR and MLPA, specificity for such cases was estimated at 99%. These performance metrics demonstrate that this tech-transfer solution can be confidently internalized by clinical labs and hospitals to offer mainstream ECS and HC as part of their test catalog, substantially increasing access to quality germline genetic testing for labs of all sizes and resources levels.

Keywords: clinical genetics, genetic testing, molecular genetics, technology transfer

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: okra leaf curl virus, AV1 gene, sequencing, phylogenetic, cloning, purified protein, genetic diversity and viral proteins

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Authors: G. Bhushan, S. Dhingra, K. K. Dubey

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This paper presents the evaluation of performance (BSFC and BTE), combustion (P_max) and emission (CO, NO_x, HC and smoke opacity) parameters of karanja biodiesel in a single cylinder, four stroke, direct injection diesel engine by considering significant engine input parameters (blending ratio, compression ratio and load torque). Multi-objective optimization of performance, combustion and emission parameters is also carried out in a karanja biodiesel engine using hybrid RSM-NSGA-II technique. The pareto optimum solutions are predicted by running the hybrid RSM-NSGA-II technique. Each pareto optimal solution is having its own importance. Confirmation tests are also conducted at randomly selected few pareto solutions to check the authenticity of the results.

Keywords: genetic algorithm, rsm, biodiesel, karanja

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Authors: Zinhle Cindi, Collet Dandara, Mpiko Ntsekhe, Edson Makambwa, Miguel Larceda

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Background: Warfarin is the most commonly used drug in the management of thromboembolic disease. However, there is a huge variability in the time, number of doses or starting doses for patients to achieve the required international normalised ratio (INR) which is compounded by a narrow therapeutic index. Many genetic-association studies have reported on European and Asian populations which have led to the designing of specific algorithms that are now being used to assist in warfarin dosing. However, very few or no studies have looked at the pharmacogenetics of warfarin in African populations, yet, huge differences in dosage requirements to reach the same INR have been observed. Objective: We set out to investigate the distribution of 3 SNPs CYP4F2 c.1347C > T, VKORC1 g.-1639G > A and VKORC1 c.1173C > T among South African Mixed Ancestry (MA) and Black African patients. Methods: DNA was extracted from 383 participants and subsequently genotyped using PCR/RFLP for the CYP4F2 c.1347 (V433M) (rs2108622), VKORC1 g.-1639 (rs9923231) and VKORC1 c.1173 (rs9934438) SNPs. Results: Comparing the Black and MA groups, significant differences were observed in the distribution of the following genotypes; CYP4F2 c.1347C/T (23% vs. 39% p=0.03). All VKORC1 g.-1639G > A genotypes (p < 0.006) and all VKORC1 c.1173C > T genotypes (p < 0.007). Conclusion: CYP4F2 c.1347T (V433M) reduces CYP4F2 protein levels and therefore expected to affect the amount of warfarin needed to block vitamin k recycling. The VKORC1 g-1639A variant alters transcriptional regulation therefore affecting the function of vitamin k epoxide reductase in vitamin k production. The VKORC1 c.1173T variant reduces the enzyme activity of VKORC1 consequently enhancing the effectiveness of warfarin. These are preliminary results; more genetic characterization is required to understand all the genetic determinants affecting how patients respond to warfarin.

Keywords: algorithms, pharmacogenetics, thromboembolic disease, warfarin

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Authors: Jan Busch, Peter Nyhuis

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Considering the challenges of short product life cycles and growing variant diversity, cost minimization and manufacturing flexibility increasingly gain importance to maintain a competitive edge in today’s global and dynamic markets. In this context, an aerodynamic part feeding system for high-speed industrial assembly applications has been developed at the Institute of Production Systems and Logistics (IFA), Leibniz Universitaet Hannover. The aerodynamic part feeding system outperforms conventional systems with respect to its process safety, reliability, and operating speed. In this paper, a multi-objective optimisation of the aerodynamic feeding system regarding the orientation rate, the feeding velocity and the required nozzle pressure is presented.

Keywords: aerodynamic feeding system, genetic algorithm, multi-objective optimization, workpiece orientation

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Authors: V. Agostini, S. Gino, S. Inturri, A. Piccinini

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In cases of corpse identification or parental testing performed on exhumed alleged dead father, usually, we seek and acquire organic samples as bones and/or bone fragments, teeth, nails and muscle’s fragments. The DNA analysis of these cadaveric matrices usually leads to identifying success, but it often happens that the results of the typing are not satisfactory with highly degraded, partial or even non-interpretable genetic profiles. To aggravate the interpretative panorama deriving from the analysis of such 'classical' organic matrices, we must add a long and laborious treatment of the sample that starts from the mechanical fragmentation up to the protracted decalcification phase. These steps greatly increase the chance of sample contamination. In the present work, instead, we want to report the use of 'unusual' cadaveric matrices, demonstrating that their forensic genetics analysis can lead to better results in less time and with lower costs of reagents. We report six case reports, result of on-field experience, in which eyeswabs and cartilage were sampled and analyzed, allowing to obtain clear single genetic profiles, useful for identification purposes. In all cases we used the standard DNA tissue extraction protocols (as reported on the user manuals of the manufacturers such as QIAGEN or Invitrogen- Thermo Fisher Scientific), thus bypassing the long and difficult phases of mechanical fragmentation and decalcification of bones' samples. PCR was carried out using PowerPlex® Fusion System kit (Promega), and capillary electrophoresis was carried out on an ABI PRISM® 310 Genetic Analyzer (Applied Biosystems®), with GeneMapper ID v3.2.1 (Applied Biosystems®) software. The software Familias (version 3.1.3) was employed for kinship analysis. The genetic results achieved have proved to be much better than the analysis of bones or nails, both from the qualitative and quantitative point of view and from the point of view of costs and timing. This way, by using the standard procedure of DNA extraction from tissue, it is possible to obtain, in a shorter time and with maximum efficiency, an excellent genetic profile, which proves to be useful and can be easily decoded for later paternity tests and/or identification of human remains.

Keywords: DNA, eye swabs and cartilage, identification human remains, paternity testing

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Authors: S. Ahmad, C. Yuan, Q. Zhang

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The assorted architectural plasticity of a plant is majorly specified by stooling, a phenomenon tackled by a combination of developmental, environmental and hormonal accelerators of lateral buds. Chrysanthemums (Chrysanthemum morifolium) are one of the most economically important ornamental plants worldwide on the account of having plentiful architectural patterns, diverse shapes and attractive colors. Side branching is the major determinant guaranteeing the consistent demand of cut chrysanthemum in flower industry. Presence of immense number of axillary branches devalues the economic importance of this imperative plant and is a major challenge for mum growers to hold a stake in the cut flower market. Restricting branches to a minimum level, or no branches at all, is the dire need of the day in order to introducing novelty in cut chrysanthemums. Temperature is a potent factor which affects largely the escalation, development of chrysanthemum, and also the genetic expression of various vegetative traits like branching. It affects differently the developmental characteristics and phenotypic expressions of inherent qualities, thereby playing a significant role in differentiating the developmental responses in different cultivars of chrysanthemum. A detailed study pertaining to the affect of temperature on branching in chrysanthemum is a clear lacking throughout the literature on mums. Therefore, searching with temperature as an effective means of reducing side branching to a desired level could be an influencing extension of struggles about how to nullify stooling. This requires plenty of research in order to reveal the extended penetration of temperature in manipulating the genetic control of various important traits like branching, which is a burning issue now a days in producing cut flowers in chrysanthemum. The present review will highlight the impact of temperature on branching control mechanism in chrysanthemum at morpho-physiological, hormonal and molecular levels.

Keywords: branching, chrysanthemum, genetic control, hormonal, morpho-physiological, temperature

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Authors: Junghwa An, Sungkyoung Choi, Eun Ye, San Hoon Han, Young-Gun Choi, Chul Oun Jung

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The copper-winged bat (Myotis rufoniger) is the widely distributed medium body-sized bat in Asia, including Korea. This bat population has been decreasing because of habitat loss. This study reported the isolation and characterization of ten polymorphic microsatellite loci in endangered M. rufoniger. To do genetic studies, we use saliva DNA of bats during winter sleep period. The number of alleles per locus ranged from 2 to 9, and the observed and expected heterozygosities ranged from 0.063 to 0.750 and from 0.063 to 0.865, respectively. The average polymorphic information content (PIC) value of these markers was 0.37. Two loci of M. rufoniger showed departure from Hardy-Weinberg equilibrium(HWE). This demonstrated that the ten microsatellite loci can be used as genetic markers for further investigation of the copper-winged bat.

Keywords: copper-winged bat, microsatellite, population genetics, South Korea

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Authors: S. Neelima, P. S. Subramanyam

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A distribution system is an interface between the bulk power system and the consumers. Among these systems, radial distributions system is popular because of low cost and simple design. In distribution systems, the voltages at buses reduces when moved away from the substation, also the losses are high. The reason for a decrease in voltage and high losses is the insufficient amount of reactive power, which can be provided by the shunt capacitors. But the placement of the capacitor with an appropriate size is always a challenge. Thus, the optimal capacitor placement problem is to determine the location and size of capacitors to be placed in distribution networks in an efficient way to reduce the power losses and improve the voltage profile of the system. For this purpose, in this paper, two stage methodologies are used. In the first stage, the load flow of pre-compensated distribution system is carried out using ‘dimension reducing distribution load flow algorithm (DRDLFA)’. On the basis of this load flow the potential locations of compensation are computed. In the second stage, Genetic Algorithm (GA) technique is used to determine the optimal location and size of the capacitors such that the cost of the energy loss and capacitor cost to be a minimum. The above method is tested on IEEE 9 and 34 bus system and compared with other methods in the literature.

Keywords: dimension reducing distribution load flow algorithm, DRDLFA, genetic algorithm, electrical distribution network, optimal capacitors placement, voltage profile improvement, loss reduction

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Authors: Fekadu Gadissa, Kassahun Tesfaye, Kifle Dagne, Mulatu Geleta

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‘Ethiopian dinich’ also called ‘Ethiopian potato’ is one of the economically important ‘orphan’ edible tuber crops indigenous to Ethiopia. We evaluated the morphological and agronomic traits performances of 174 samples from Ethiopia at multiple locations using 12 qualitative and 16 quantitative traits, recorded at the correct growth stages. We observed several morphotypes and phenotypic variations for qualitative traits along with a wide range of mean performance values for all quantitative traits. Analysis of variance for each quantitative trait showed a highly significant (p<0.001) variation among the collections with eventually non-significant variation for environment-traits interaction for all but flower length. A comparatively high phenotypic and genotypic coefficient of variation was observed for plant height, days to flower initiation, days to 50% flowering and tuber number per hill. Moreover, the variability and coefficients of variation due to genotype-environment interaction was nearly zero for all the traits except flower length. High genotypic coefficients of variation coupled with a high estimate of broad sense heritability and high genetic advance as a percent of collection mean were obtained for tuber weight per hill, number of primary branches per plant, tuber number per hill and number of plants per hill. Association of tuber yield per hectare of land showed a large magnitude of positive phenotypic and genotypic correlation with those traits. Principal components analysis revealed 76% of the total variation for the first six principal axes with high factor loadings again from tuber number per hill, number of primary branches per plant and tuber weight. The collections were grouped into four clusters with the weak region (zone) of origin based pattern. In general, there is high genetic-based variability for ‘Ethiopian dinich’ improvement and conservation. DNA based markers are recommended for further genetic diversity estimation for use in breeding and conservation.

Keywords: agro-morphological traits, Ethiopian dinich, genetic diversity, variance components

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Authors: Ghada Badr, Manar Hosny, Nuha Bintayyash, Eman Albilali, Souad Larabi Marie-Sainte

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The median problem is significantly applied to derive the most reasonable rearrangement phylogenetic tree for many species. More specifically, the problem is concerned with finding a permutation that minimizes the sum of distances between itself and a set of three signed permutations. Genomes with equal number of genes but different order can be represented as permutations. In this paper, an algorithm, namely BeamGA median, is proposed that combines a heuristic search approach (local beam) as an initialization step to generate a number of solutions, and then a Genetic Algorithm (GA) is applied in order to refine the solutions, aiming to achieve a better median with the smallest possible reversal distance from the three original permutations. In this approach, any genome rearrangement distance can be applied. In this paper, we use the reversal distance. To the best of our knowledge, the proposed approach was not applied before for solving the median problem. Our approach considers true biological evolution scenario by applying the concept of common intervals during the GA optimization process. This allows us to imitate a true biological behavior and enhance genetic approach time convergence. We were able to handle permutations with a large number of genes, within an acceptable time performance and with same or better accuracy as compared to existing algorithms.

Keywords: median problem, phylogenetic tree, permutation, genetic algorithm, beam search, genome rearrangement distance

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Authors: Hesham Abdin, Mohamed Zakaria, Talaat Abd-Elmonaem, Alaa El-Din Sayed Hafez

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Kalman filter algorithm is an estimator known as the workhorse of estimation. It has an important application in missile guidance, especially in lack of accurate data of the target due to noise or uncertainty. In this paper, a Kalman filter is used as a tracking filter in a simulated target-interceptor scenario with noise. It estimates the position, velocity, and acceleration of the target in the presence of noise. These estimations are needed for both proportional navigation and differential geometry guidance laws. A Kalman filter has a good performance at low noise, but a large noise causes considerable errors leads to performance degradation. Therefore, a new technique is required to overcome this defect using tuning factors to tune a Kalman filter to adapt increasing of noise. The values of the tuning factors are between 0.8 and 1.2, they have a specific value for the first half of range and a different value for the second half. they are multiplied by the estimated values. These factors have its optimum values and are altered with the change of the target heading. A genetic algorithm updates these selections to increase the maximum effective range which was previously reduced by noise. The results show that the selected factors have other benefits such as decreasing the minimum effective range that was increased earlier due to noise. In addition to, the selected factors decrease the miss distance for all ranges of this direction of the target, and expand the effective range which leads to increase probability of kill.

Keywords: proportional navigation, differential geometry, Kalman filter, genetic algorithm

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Authors: Hasrat Arjjumend, Sabiha Alam

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The Nagoya Protocol is landmark international legislation governing access to genetic resources and benefit sharing from utilization of genetic resource and traditional knowledge. The field implications of the international law have been assessed by surveying academic/ research institutions, civil society organizations (CSOs) and concerned individuals, who gave their opinions on whether the provider parties (usually developing countries) would ensure effective participation of Indigenous people and local communities (ILCs) in establishing the mechanisms to inform the potential users of traditional knowledge (TK) about their obligations under art. 12.2 of Nagoya Protocol. First of all, involvement and participation of ILCs in suggested clearing-house mechanisms of the Parties are seldom witnessed. Secondly, as respondents expressed, it is doubtful that developing countries would ensure effective participation of ILCs in establishing the mechanisms to inform the potential users of TK about their obligations. Yet, as most of ILCs speak and understand local or indigenous languages, whether the Nagoya Protocol provides or not, it is a felt need that the Parties should disclose information in a language understandable to ILCs. Alternative opinions indicate that if TK held by ILCs is disclosed, the value is gone. Therefore, it should be protected by the domestic law first and should be disclosed then.

Keywords: genetic resources, indigenous people, language, Nagoya protocol, participation, traditional knowledge

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Authors: Monika Szymańska-Czerwińsk, Kinga Zaręba-Marchewka, Krzysztof Niemczuk

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Chlamydiaceae are Gram-negative bacteria distributed worldwide in animals and humans. One of them is Chlamydia gallinacea recently discovered. Available data show that C. gallinacea is dominant chlamydial agent found in poultry in European and Asian countries. The aim of the studies was screening of poultry flocks in order to evaluate frequency of C. gallinacea shedding and genetic diversity. Sampling was conducted in different regions of Poland in 2019-2020. Overall, 1466 cloacal/oral swabs were collected in duplicate from 146 apparently healthy poultry flocks including chickens, turkeys, ducks, geese and quails. Dry swabs were used for DNA extraction. DNA extracts were screened using a Chlamydiaceae 23S rRNA real-time PCR assay. To identify Chlamydia species, specific real-time PCR assays were performed. Furthermore, selected samples were used for sequencing based on ompA gene fragments and variable domains (VD1-2, VD3-4). In total, 10.3% of the tested flocks were Chlamydiaceae-positive (15/146 farms). The presence of Chlamydiaceae was confirmed mainly in chickens (13/92 farms) but also in turkey (1/19 farms) and goose (1/26 farms) flocks. Eleven flocks were identified as C. gallinacea-positive while four flocks remained unclassified. Phylogenetic analysis revealed at least 16 genetic variants of C. gallinacea. Research showed that Chlamydiaceae occur in a poultry flock in Poland. The strains of C. gallinacea as dominant species show genetic variability.

Keywords: C. gallinacea, emerging agent, poultry, real-time PCR

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Authors: Abu S. Mustafa, Mohammad W. Khan, Faraz Shaheed Khan, Nazima Habibi

Abstract:

Brucellosis is a zoonotic disease of worldwide prevalence. There are at least four species and several strains of Brucella that cause human disease. Brucella genomes have very limited variation across strains, which hinder strain identification using classical molecular techniques, including PCR and 16 S rDNA sequencing. The aim of this study was to perform whole genome sequencing of clinical isolates of Brucella and perform bioinformatics and comparative genomics analyses to determine the existence of genetic differences across the isolates of a single Brucella species and strain. The draft sequence data were generated from 15 clinical isolates of Brucella melitensis (biovar 2 strain 63/9) using MiSeq next generation sequencing platform. The generated reads were used for further assembly and analysis. All the analysis was performed using Bioinformatics work station (8 core i7 processor, 8GB RAM with Bio-Linux operating system). FastQC was used to determine the quality of reads and low quality reads were trimmed or eliminated using Fastx_trimmer. Assembly was done by using Velvet and ABySS softwares. The ordering of assembled contigs was performed by Mauve. An online server RAST was employed to annotate the contigs assembly. Annotated genomes were compared using Mauve and ACT tools. The QC score for DNA sequence data, generated by MiSeq, was higher than 30 for 80% of reads with more than 100x coverage, which suggested that data could be utilized for further analysis. However when analyzed by FastQC, quality of four reads was not good enough for creating a complete genome draft so remaining 11 samples were used for further analysis. The comparative genome analyses showed that despite sharing same gene sets, single nucleotide polymorphisms and insertions/deletions existed across different genomes, which provided a variable extent of diversity to these bacteria. In conclusion, the next generation sequencing, bioinformatics, and comparative genome analysis can be utilized to find variations (point mutations, insertions and deletions) across different genomes of Brucella within a single strain. This information could be useful in surveillance and epidemiological studies supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: brucella, bioinformatics, comparative genomics, whole genome sequencing

Procedia PDF Downloads 379