Search results for: genetic predisposition

Authors: Swati Gautam, Amita Jain, Shyampyari Jaiswar

Abstract:

Objective: To elucidate the role of (ApaI&TaqI) VDR gene polymorphism in the pathogenesis of female genital tuberculosis (FGTB) cases. Background: Female genital TB represents about 15-20% of total extra-pulmonary TB (EPTB). Female subjects with vitamin D deficiency have been shown to be at higher risk of pulmonary TB as well as FGTB. In same context few functional polymorphism in vitamin D receptor (VDR) gene has been considered as an important genetic risk factor that modulate the development of FGTB. Therefore we aimed, to elucidate the role of (ApaI&TaqI) VDR gene polymorphism in the pathogenesis of FGTB. Study design: Case-Control study. Sample size: Cases (60) and Controls (60). Study site: Department of Obstetrics & Gynecology & Department of Microbiology, K.G.M.U. Lucknow, (UP). Inclusion criteria: Cases: Women with age group 20-35 years, premenstrual endometrial aspiration collected and included in the study, those were positive with acid-fast bacilli (AFB)/ TB-PCR/ LJ culture/ liquid culture. Controls: Women with age group 20-35 years having no history of ATT and all test negative for TB recruited as control. Exclusion criteria: -Women with endometriosis, polycystic ovaries (PCOD), positive on Chlamydia & gonorrhea, already on anti-tubercular therapy (ATT) excluded. Materials and Methods: Blood samples were collected in EDTA tubes from cases and controls stored at -20ºC. Genomic DNA extraction was carried out by salting-out method. Genotyping of VDR gene (ApaI&TaqI) polymorphism was performed by using single amplification refractory mutation system (ARMS) PCR technique. PCR products were analyzed by electrophoresis on 2% agarose gel. Statistical analysis was done by SPSS16.3 software & computing odds ratio (OR) with 95% CI. Results: Increased risk of female genital tuberculosis was observed in AA genotype (OR =1.1419-6.212 95% CI, P*<0.036) and A allele (OR =1.255-3.518, 95% CI, P* < 0.006) in FGTB as compared to controls. Moreover A allele was found more frequent in FGTB patients. No significant difference was observed in TaqI gene polymorphism of VDR gene. Conclusion: The ApaI polymorphism is significantly associated with etiology of FGTB and plays an important role as a genetic risk factor in FGTB women.

Keywords: ARMS, ATT, EPTB, FGTB, VDR

Procedia PDF Downloads 275

Authors: O. Ekrami, P. Claes, S. Van Dongen

Abstract:

Fluctuating asymmetry (FA) has been studied for many years as an indicator of developmental stability or ‘genetic quality’ based on the assumption that perfect symmetry is ideally the expected outcome for a bilateral organism. Further studies have also investigated the possible link between FA and attractiveness or levels of masculinity or femininity. These hypotheses have been mostly examined using 2D images, and the structure of interest is usually presented using a limited number of landmarks. Such methods have the downside of simplifying and reducing the dimensionality of the structure, which will in return increase the error of the analysis. In an attempt to reach more conclusive and accurate results, in this study we have used high-resolution 3D scans of human faces and have developed an algorithm to measure and localize FA, taking a spatially-dense approach. A symmetric spatially dense anthropometric mask with paired vertices is non-rigidly mapped on target faces using an Iterative Closest Point (ICP) registration algorithm. A set of 19 manually indicated landmarks were used to examine the precision of our mapping step. The protocol’s accuracy in measurement and localizing FA is assessed using simulated faces with known amounts of asymmetry added to them. The results of validation of our approach show that the algorithm is perfectly capable of locating and measuring FA in 3D simulated faces. With the use of such algorithm, the additional captured information on asymmetry can be used to improve the studies of FA as an indicator of fitness or attractiveness. This algorithm can especially be of great benefit in studies of high number of subjects due to its automated and time-efficient nature. Additionally, taking a spatially dense approach provides us with information about the locality of FA, which is impossible to obtain using conventional methods. It also enables us to analyze the asymmetry of a morphological structures in a multivariate manner; This can be achieved by using methods such as Principal Components Analysis (PCA) or Factor Analysis, which can be a step towards understanding the underlying processes of asymmetry. This method can also be used in combination with genome wide association studies to help unravel the genetic bases of FA. To conclude, we introduced an algorithm to study and analyze asymmetry in human faces, with the possibility of extending the application to other morphological structures, in an automated, accurate and multi-variate framework.

Keywords: developmental stability, fluctuating asymmetry, morphometrics, 3D image processing

Procedia PDF Downloads 136

Authors: Samia A. El-Fiky, F. A. Abou-Zaid, Ibrahim M. Farag, Naira M. Efiky

Abstract:

Clomipramine hydrochloride is one of the most used tricyclic antidepressant drug in Egypt. This drug contains in its chemical structure on two benzene rings. Benzene is considered to be toxic and clastogenic agent. So, the present study was designed to assess the genotoxic effect of Clomipramine hydrochloride on somatic and germ cells in mice. Three dose levels 0.195 (Low), 0.26 (Medium), and 0.65 (High) mg/kg.b.wt. were used. Seven groups of male mice were utilized in this work. The first group was employed as a control. In the remaining six groups, each of the above doses was orally administrated for two groups, one of them was treated for 5 days and the other group was given the same dose for 30 days. At the end of experiments, the animals were sacrificed for cytogenetic and sperm examination as well as histopathological investigations by using hematoxylin and eosin stains (H and E stains) and electron microscope. Concerning the sperm studies, these studies were confined to 5 days treatment with different dose levels. Moreover, the ultrastructural investigation by electron microscope was restricted to 30 days treatment with drug doses. The results of the dose dependent effect of Clomipramine showed that the treatment with three different doses induced increases of frequencies of chromosome aberrations in bone marrow and spermatocyte cells as compared to control. In addition, mitotic and meiotic activities of somatic and germ cells were declined. The treatments with medium or high doses were more effective for inducing significant increases of chromosome aberrations and significant decreases of cell divisions than treatment with low dose. The effect of high dose was more pronounced for causing such genetic deleterious in respect to effect of medium dose. Moreover, the results of the time dependent effect of Clomipramine observed that the treatment with different dose levels for 30 days led to significant increases of genetic aberrations than treatment for 5 days. Sperm examinations revealed that the treatment with Clomipramine at different dose levels caused significant increase of sperm shape abnormalities and significant decrease in sperm count as compared to control. The adverse effects on sperm shape and count were more obviousness by using the treatments with medium or high doses than those found in treatment with low dose. The group of mice treated with high dose had the highest rate of sperm shape abnormalities and the lowest proportion of sperm count as compared to mice received medium dose. In histopathological investigation, hematoxylin and eosin stains showed that, the using of low dose of Clomipramine for 5 or 30 days caused a little pathological changes in liver tissue. However, using medium and high doses for 5 or 30 days induced severe damages than that observed in mice treated with low dose. The treatment with high dose for 30 days gave the worst results of pathological changes in hepatic cells. Moreover, ultrastructure examination revealed, the mice treated with low dose of Clomipramine had little differences in liver histological architecture as compared to control group. These differences were confined to cytoplasmic inclusions. Whereas, prominent pathological changes in nuclei as well as dilated of rough Endoplasmic Reticulum (rER) were observed in mice treated with medium or high doses of Clomipramine drug. In conclusion, the present study adds evidence that treatments with medium or high doses of Clomipramine have genotoxic effects on somatic and germ cells of mice, as unwanted side effects. However, the using of low dose (especially for short time, 5 days) can be utilized as a therapeutic dose, where it caused relatively similar proportions of genetic, sperm, and histopathological changes as those found in normal control.

Keywords: clomipramine, mice, chromosome aberrations, sperm abnormalities, histopathology

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Authors: Fahad Alsharari, Mohd Salmi Md. Noorani

Abstract:

A Motzkin shift is a mathematical model for constraints on genetic sequences. In terms of the theory of symbolic dynamics, the Motzkin shift is nonsofic, and therefore, we cannot use the Perron-Frobenius theory to calculate its topological entropy. The Motzkin shift M(M,N) which comes from language theory, is defined to be the shift system over an alphabet A that consists of N negative symbols, N positive symbols and M neutral symbols. For an x in the full shift AZ, x is in M(M,N) if and only if every finite block appearing in x has a non-zero reduced form. Therefore, the constraint for x cannot be bounded in length. K. Inoue has shown that the entropy of the Motzkin shift M(M,N) is log(M + N + 1). In this paper, we find a new method of calculating the topological entropy of the Motzkin shift M(M,N) without any measure theoretical discussion.

Keywords: entropy, Motzkin shift, mathematical model, theory

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Authors: Sudha T., Naveen C.

Abstract:

Dengue is a serious public health issue that causes significant annual economic and welfare burdens on nations. However, enhanced optimization techniques and quantitative modeling approaches can predict the incidence of dengue. By advocating for a data-driven approach, public health officials can make informed decisions, thereby improving the overall effectiveness of sudden disease outbreak control efforts. The National Oceanic and Atmospheric Administration and the Centers for Disease Control and Prevention are two of the U.S. Federal Government agencies from which this study uses environmental data. Based on environmental data that describe changes in temperature, precipitation, vegetation, and other factors known to affect dengue incidence, many predictive models are constructed that use different machine learning methods to estimate weekly dengue cases. The first step involves preparing the data, which includes handling outliers and missing values to make sure the data is prepared for subsequent processing and the creation of an accurate forecasting model. In the second phase, multiple feature selection procedures are applied using various machine learning models and optimization techniques. During the third phase of the research, machine learning models like the Huber Regressor, Support Vector Machine, Gradient Boosting Regressor (GBR), and Support Vector Regressor (SVR) are compared with several optimization techniques for feature selection, such as Harmony Search and Genetic Algorithm. In the fourth stage, the model's performance is evaluated using Mean Square Error (MSE), Mean Absolute Error (MAE), and Root Mean Square Error (RMSE) as assistance. Selecting an optimization strategy with the least number of errors, lowest price, biggest productivity, or maximum potential results is the goal. In a variety of industries, including engineering, science, management, mathematics, finance, and medicine, optimization is widely employed. An effective optimization method based on harmony search and an integrated genetic algorithm is introduced for input feature selection, and it shows an important improvement in the model's predictive accuracy. The predictive models with Huber Regressor as the foundation perform the best for optimization and also prediction.

Keywords: deep learning model, dengue fever, prediction, optimization

Procedia PDF Downloads 54

Authors: Samia A. El-Fiky, Fouad A. Abou-Zaid, Ibrahim M. Farag, Naira M. El-Fiky

Abstract:

Clomipramine hydrochloride is one of the most used tricyclic antidepressant drug in Egypt. This drug contains in its chemical structure on two benzene rings. Benzene is considered to be toxic and clastogenic agent. So, the present study was designed to assess the genotoxic effect of Clomipramine hydrochloride on somatic and germ cells in mice. Three dose levels 0.195 (Low), 0.26 (Medium), and 0.65 (High) mg/kg.b.wt. were used. Seven groups of male mice were utilized in this work. The first group was employed as a control. In the remaining six groups, each of the above doses was orally administrated for two groups, one of them was treated for 5 days and the other group was given the same dose for 30 days. At the end of experiments, the animals were sacrificed for cytogenetic and sperm examination as well as histopathological investigations by using hematoxylin and eosin stains (H and E stains) and electron microscope. Concerning the sperm studies, these studies were confined to 5 days treatment with different dose levels. Moreover, the ultrastructural investigation by electron microscope was restricted to 30 days treatment with drug doses. The results of the dose dependent effect of Clomipramine showed that the treatment with three different doses induced increases of frequencies of chromosome aberrations in bone marrow and spermatocyte cells as compared to control. In addition, mitotic and meiotic activities of somatic and germ cells were declined. The treatments with medium or high doses were more effective for inducing significant increases of chromosome aberrations and significant decreases of cell divisions than treatment with low dose. The effect of high dose was more pronounced for causing such genetic deleterious in respect to effect of medium dose. Moreover, the results of the time dependent effect of Clomipramine observed that the treatment with different dose levels for 30 days led to significant increases of genetic aberrations than treatment for 5 days. Sperm examinations revealed that the treatment with Clomipramine at different dose levels caused significant increase of sperm shape abnormalities and significant decrease in sperm count as compared to control. The adverse effects on sperm shape and count were more obviousness by using the treatments with medium or high doses than those found in treatment with low dose. The group of mice treated with high dose had the highest rate of sperm shape abnormalities and the lowest proportion of sperm count as compared to mice received medium dose. In histopathological investigation, hematoxylin and eosin stains showed that, the using of low dose of Clomipramine for 5 or 30 days caused a little pathological changes in liver tissue. However, using medium and high doses for 5 or 30 days induced severe damages than that observed in mice treated with low dose. The treatment with high dose for 30 days gave the worst results of pathological changes in hepatic cells. Moreover, ultrastructure examination revealed, the mice treated with low dose of Clomipramine had little differences in liver histological architecture as compared to control group. These differences were confined to cytoplasmic inclusions. Whereas, prominent pathological changes in nuclei as well as dilated of rough Endoplasmic Reticulum (rER) were observed in mice treated with medium or high doses of Clomipramine drug. In conclusion, the present study adds evidence that treatments with medium or high doses of Clomipramine have genotoxic effects on somatic and germ cells of mice, as unwanted side effects. However, the using of low dose (especially for short time, 5 days) can be utilized as a therapeutic dose, where it caused relatively similar proportions of genetic, sperm, and histopathological changes as those found in normal control.

Keywords: chromosome aberrations, clomipramine, mice, histopathology, sperm abnormalities

Procedia PDF Downloads 517

Authors: Roya Bakhtiar, Alireza Abdolmohammadi, Hadi Hajarian, Zahra Nikousefat, Davood, Kalantar-Neyestanaki

Abstract:

The objective of the present study was to determine the polymorphism in the leptin (332G>A) and its association with biometric traits in Sanjabi sheep. For this purpose, blood samples from 96 rams were taken, and tail length, width tail, circumference tail, body length, body width, and height were simultaneously recorded. PCR was performed using specific primer to amplify 463 bp fragment including exon 3 of leptin gene, and PCR products were digested by Cail restriction enzymes. The 332G>A (at 332th nucleotide of exon 3 leptin gene) that caused an amino acid change from Arg to Gln was detected by Cail (CAGNNNCTG) endonuclease, as the endonuclease cannot cut this region if G nucleotide is located in this position. Three genotypes including GG (463), GA (463, 360and 103 bp) and GG (360 bp and 103 bp) were identified after digestion by enzyme. The estimated frequencies of three genotypes including GG, GA, and AA for 332G>A locus were 0.68, 0.29 and 0.03 and those were 0.18 and 0.82 for A and G alleles, respectively. In the current study, chi-square test indicated that 332G>A positions did not deviate from the Hardy–Weinberg (HW) equilibrium. The most important reason to show HW equation was that samples used in this study belong to three large local herds with a traditional breeding system having random mating and without selection. Shannon index amount was calculated which represent an average genetic variation in Sanjabi rams. Also, heterozygosity estimated by Nei index indicated that genetic diversity of mutation in the leptin gene is moderate. Leptin gene polymorphism in the 332G>A had significant effect on body length (P<0.05) trait, and individuals with GA genotype had significantly the higher body length compared to other individuals. Although animals with GA genotype had higher body width, this difference was not statistically significant (P>0.05). This non-synonymous SNP resulted in different amino acid changes at codon positions111(R/Q). As leptin activity is localized, at least in part, in domains between amino acid residues 106-1406, it is speculated that the detected SNP at position 332 may affect the activity of leptin and may lead to different biological functions. Based to our results, due to significant effect of leptin gene polymorphism on body size traits, this gene may be used a candidate gene for improving these traits.

Keywords: body size, Leptin gene, PCR-RFLP, Sanjabi sheep

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Authors: Lethukuthula Ngobese, Abin Gupthar, Patrick Govender

Abstract:

The ability of yeast cell wall-derived mannoproteins (glycoproteins) to positively contribute to oenological properties has been a key factor that stimulates research initiatives into these industrially important glycoproteins. In addition, and from a fundamental research perspective, yeast cell wall glycoproteins are involved in a wide range of biological interactions. To date, and to the best of our knowledge, our understanding of the fine molecular structure of these mannoproteins is fairly limited. Generally, the amino acid sequences of their protein moieties have been established from structural and functional analysis of the genomic sequence of these yeasts whilst far less information is available on the glycosyl moieties of these mannoproteins. A novel strategy was devised in this study that entails the genetic engineering of yeast strains that over-express and release cell wall-associated glycoproteins into the liquid growth medium. To this end, the Flo1p mannoprotein was overexpressed in Saccharomyces cerevisiae laboratory strains bearing a specific deletion in KNR4 and GPI7 genes involved in cell wall biosynthesis that have been previously shown to extracellularly hyper-secrete cell wall-associated glycoproteins. A polymerase chain reaction (PCR) -based cloning strategy was employed to generate transgenic yeast strains in which the native cell wall FLO1 glycoprotein-encoding gene is brought under transcriptional control of the constitutive PGK1 promoter. The modified Helm’s flocculation assay was employed to assess flocculation intensities of a Flo1p over-expressing wild type and deletion mutant as an indirect measure of their abilities to release the desired mannoprotein. The flocculation intensities of the transformed strains were assessed and all the strains showed similar intensities (>98% flocculation). To assess if mannoproteins were released into the growth medium, the supernatant of each strain was subjected to the BCA protein assay and the transformed Δknr4 strain showed a considerable increase in protein levels. This study has the potential to produce mannoproteins in sufficient quantities that may be employed in future investigations to understand their molecular structures and mechanisms of interaction to the benefit of both fundamental and industrial applications.

Keywords: glycoproteins, genetic engineering, flocculation, over-expression

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Authors: Onder Turkmen, Musa Seymen, Sali Fidan, Mustafa Paksoy

Abstract:

There is a requirement for registered edible seed pumpkin suitable for eating in Turkey. A total of 81 genotypes collected from the researchers in 2005 originated from Eskisehir, Konya, Nevsehir, Tekirdag, Sakarya, Kayseri and Kirsehir provinces were utilized. The used genetic materials were brought to S5 generation by the research groups among 2006 and 2010 years. In this research, S5 stage reached in the genotype given some of the morphological features, and selection of promising genotypes generated scale were made. Results showed that the A-1 (420), A-7 (410), A-8 (420), A-32 (420), B-17 (410), B-24 (410), B-25 (420), B-33 (400), C-24 (420), C-25 (410), C-26 (410) and C-30 (420) genotypes are expected to be promising varieties.

Keywords: candidate cultivar, edible seed pumpkin, morphologic parameters, selection

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Authors: Konstantinos Metaxiotis, Konstantinos Liagkouras

Abstract:

The objective of this study is to examine the performance of three well-known multiobjective evolutionary algorithms for solving optimization problems. The first algorithm is the Non-dominated Sorting Genetic Algorithm-II (NSGA-II), the second one is the Strength Pareto Evolutionary Algorithm 2 (SPEA-2), and the third one is the Multiobjective Evolutionary Algorithms based on decomposition (MOEA/D). The examined multiobjective algorithms are analyzed and tested on the ZDT set of test functions by three performance metrics. The results indicate that the NSGA-II performs better than the other two algorithms based on three performance metrics.

Keywords: MOEAs, multiobjective optimization, ZDT test functions, evolutionary algorithms

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Authors: Abishek Rajkumar

Abstract:

Antibiotic resistance can occur naturally given the selective pressure placed on antibiotics. Within a large population of bacteria, there is a significant chance that some of those bacteria can develop resistance via mutations or genetic recombination. However, a growing public health concern has arisen over the fact that antibiotic resistance has increased significantly over the past few decades. This is because humans have been over-consuming and producing antibiotics, which has ultimately accelerated the antibiotic resistance seen in these bacteria. The product of all of this is an ongoing race between scientists and the bacteria as bacteria continue to develop resistance, which creates even more demand for an antibiotic that can still terminate the newly resistant strain of bacteria. This paper will focus on a myriad of aspects of antibiotic resistance in bacteria starting with how it occurs on a molecular level and then focusing on the antibiotic concentrations and how they affect the resistance and fitness seen in bacteria.

Keywords: antibiotic, molecular, mutation, resistance

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Authors: Selisha A. Sooklal, Phelelani Mpangase, Shaun Aron, Karl Rumbold

Abstract:

Organically bound fluorine (C-F bond) is extremely rare in nature. Despite this, the first fluorinated secondary metabolite, fluoroacetate, was isolated from the plant Dichapetalum cymosum (commonly known as Gifblaar). However, the enzyme responsible for fluorination (fluorinase) in Gifblaar was never isolated and very little progress has been achieved in understanding this process in higher plants. Fluorinated compounds have vast applications in the pharmaceutical, agrochemical and fine chemicals industries. Consequently, an enzyme capable of catalysing a C-F bond has great potential as a biocatalyst in the industry considering that the field of fluorination is virtually synthetic. As with any biocatalyst, a range of these enzymes are required. Therefore, it is imperative to expand the exploration for novel fluorinases. This study aimed to gain molecular insights into secondary metabolite biosynthesis in Gifblaar using a high-throughput sequencing-based approach. Mechanical wounding studies were performed using Gifblaar leaf tissue in order to induce expression of the fluorinase. The transcriptome of the wounded and unwounded plant was then sequenced on the Illumina HiSeq platform. A total of 26.4 million short sequence reads were assembled into 77 845 transcripts using Trinity. Overall, 68.6 % of transcripts were annotated with gene identities using public databases (SwissProt, TrEMBL, GO, COG, Pfam, EC) with an E-value threshold of 1E-05. Sequences exhibited the greatest homology to the model plant, Arabidopsis thaliana (27 %). A total of 244 annotated transcripts were found to be differentially expressed between the wounded and unwounded plant. In addition, secondary metabolic pathways present in Gifblaar were successfully reconstructed using Pathway tools. Due to lack of genetic information for plant fluorinases, a transcript failed to be annotated as a fluorinating enzyme. Thus, a local database containing the 5 existing bacterial fluorinases was created. Fifteen transcripts having homology to partial regions of existing fluorinases were found. In efforts to obtain the full coding sequence of the Gifblaar fluorinase, primers were designed targeting the regions of homology and genome walking will be performed to amplify the unknown regions. This is the first genetic data available for Gifblaar. It has provided novel insights into the mechanisms of metabolite biosynthesis and will allow for the discovery of the first eukaryotic fluorinase.

Keywords: biocatalyst, fluorinase, gifblaar, transcriptome

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Authors: Aidin Foroutan, David S. Wishart, Leluo L. Guan, Carolyn Fitzsimmons

Abstract:

Maximizing efficiency and growth potential of beef cattle requires not only genetic selection (i.e. residual feed intake (RFI)) but also adequate nutrition throughout all stages of growth and development. Nutrient restriction during gestation has been shown to negatively affect post-natal growth and development as well as fertility of the offspring. This, when combined with RFI may affect progeny traits. This study aims to investigate the impact of selection for divergent genetic potential for RFI and maternal nutrition during early- to mid-gestation, on bull calf traits such as fertility and muscle development using multiple ‘omics’ approaches. Comparisons were made between High-diet vs. Low-diet and between High-RFI vs. Low-RFI animals. An epigenetics experiment on semen samples identified 891 biomarkers associated with growth and development. A gene expression study on Longissimus thoracis muscle, semimembranosus muscle, liver, and testis identified 4 genes associated with muscle development and immunity of which Myocyte enhancer factor 2A [MEF2A; induces myogenesis and control muscle differentiation] was the only differentially expressed gene identified in all four tissues. An initial metabolomics experiment on serum samples using nuclear magnetic resonance (NMR) identified 4 metabolite biomarkers related to energy and protein metabolism. Once all the biomarkers are identified, bioinformatics approaches will be used to create a database covering all the ‘omics’ data collected from this project. This database will be broadened by adding other information obtained from relevant literature reviews. Association analyses with these data sets will be performed to reveal key biological pathways affected by RFI and maternal nutrition. Through these association studies between the genome and metabolome, it is expected that candidate biomarker genes and metabolites for feed efficiency, fertility, and/or muscle development are identified. If these gene/metabolite biomarkers are validated in a larger animal population, they could potentially be used in breeding programs to select superior animals. It is also expected that this work will lead to the development of an online tool that could be used to predict future traits of interest in an animal given its measurable ‘omics’ traits.

Keywords: biomarker, maternal nutrition, omics, residual feed intake

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Authors: Yazhi Huang, Jing Yang, Dingge Ying, Yan Zhang, Vorasuk Shotelersuk, Nattiya Hirankarn, Pak Chung Sham, Yu Lung Lau, Wanling Yang

Abstract:

Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT.

Keywords: human leukocyte antigens, next generation sequencing, whole exome sequencing, HLA typing

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Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati

Abstract:

Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.

Keywords: metabolic network, gene knockout, flux balance analysis, microarray data, integration

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Authors: Sandisiwe Mangali, Graeme Bradley

Abstract:

Genome is complete set of the organism's hereditary information encoded as either deoxyribonucleic acid or ribonucleic acid in most viruses. The three different types of genomes are nuclear, mitochondrial and the plastid genome and their sequences which are uncovered by genome sequencing are known as an archive for all genetic information and enable researchers to understand the composition of a genome, regulation of gene expression and also provide information on how the whole genome works. These sequences enable researchers to explore the population structure, genetic variations, and recent demographic events in threatened species. Particularly, genome sequencing refers to a process of figuring out the exact arrangement of the basic nucleotide bases of a genome and the process through which all the afore-mentioned genomes are sequenced is referred to as whole or complete genome sequencing. Gelidium pristoides is South African endemic Rhodophyta species which has been harvested in the Eastern Cape since the 1950s for its high economic value which is one motivation for its sequencing. Its endemism further motivates its sequencing for conservation biology as endemic species are more vulnerable to anthropogenic activities endangering a species. As sequencing, mapping and annotating the Gelidium pristoides genome is the aim of this study. To accomplish this aim, the genomic DNA was extracted and quantified using the Nucleospin Plank Kit, Qubit 2.0 and Nanodrop. Thereafter, the Ion Plus Fragment Library was used for preparation of a 600bp library which was then sequenced through the Ion S5 sequencing platform for two runs. The produced reads were then quality-controlled and assembled through the SPAdes assembler with default parameters and the genome assembly was quality assessed through the QUAST software. From this assembly, the plastid and the mitochondrial genomes were then sampled out using Gelidiales organellar genomes as search queries and ordered according to them using the Geneious software. The Qubit and the Nanodrop instruments revealed an A260/A280 and A230/A260 values of 1.81 and 1.52 respectively. A total of 30792074 reads were obtained and produced a total of 94140 contigs with resulted into a sequence length of 217.06 Mbp with N50 value of 3072 bp and GC content of 41.72%. A total length of 179281bp and 25734 bp was obtained for plastid and mitochondrial respectively. Genomic data allows a clear understanding of the genomic constituent of an organism and is valuable as foundation information for studies of individual genes and resolving the evolutionary relationships between organisms including Rhodophytes and other seaweeds.

Keywords: Gelidium pristoides, genome, genome sequencing and assembly, Ion S5 sequencing platform

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Authors: Huynh Viet Khai, Mitsuyasu Yabe

Abstract:

The study investigated the economic value of biodiversity attributes that could provide policy-makers reliable information to estimate welfare losses due to biodiversity reductions and analyse the trade-off between biodiversity and economics. In order to obtain the non-market benefits of biodiversity conservation, an indirect utility function and willingness to pay for biodiversity attributes were applied using the approach of choice modelling with the analysis of conditional logit model. The study found that Mekong Delta residents accepted their willingness to pay for VND 913 monthly for a one percent increase in healthy vegetation, VND 360 for an additional mammal species and VND 2,440 to avoid the welfare losses of 100 local farmers.

Keywords: choice modelling, genetic resources, wetland conservation, marginal willingness to pay

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Authors: Mustafa Ural, Can Bayseferogulari

Abstract:

In this work, radio frequency (RF) coupling between two HF antennas on a shipboard platform is minimized by determining an optimal antenna placement. Unlike the other works, the coupling is minimized not only at single frequency but over the whole frequency band of operation. Similarly, GAO and PSO, are used in order to determine optimal antenna placement. Throughout this work, outputs of two optimization techniques are compared with each other in terms of antenna placements and coupling results. At the end of the work, far-field radiation pattern performances of the antennas at their optimal places are analyzed in terms of directivity and coverage in order to see that.

Keywords: electromagnetic compatibility, antenna placement, optimization, genetic algorithm optimization, particle swarm optimization

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Authors: Debbarma Asis, Guha Chandan

Abstract:

Tumor Protein-53 (P53) is one of the tumor suppressor proteins. P53 regulates the cell cycle that conserves stability by preventing genome mutation. It is named so as it runs as 53-kilodalton (kDa) protein on Polyacrylamide gel electrophoresis although the actual mass is 43.7 kDa. Experimental evidence has indicated that P53 cancer mutants loses tumor suppression activity and subsequently gain oncogenic activities to promote tumourigenesis. Tumor-specific DNA has recently been detected in the plasma of breast cancer patients. Detection of tumor-specific genetic materials in cancer patients may provide a unique and valuable tumor marker for diagnosis and prognosis. Commercially available MDA-468 breast cancer cell line was used for the proposed study.

Keywords: tumor protein (P53), cancer mutants, MDA-468, tumor suppressor gene

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Authors: Tareg Belali, Mosleh Abomughaid, Muhanad Alhujaily

Abstract:

HNF4a is one of the steroid hormone receptor family of transcription factors with roles in the development of the liver and the regulation of several critical metabolic pathways, such as glycolysis, drug metabolism, and apolipoproteins and blood coagulation. The transcriptional potency of HNF4a is well known due to its involvement in diabetes and other metabolic diseases. However, recently HNF4a has been discovered to be closely associated with several haematological disorders, mainly because of genetic mutations, drugs, and hepatic disorders. We review HNF4a structure and function and its role in haematological disorders. We discuss possible good therapies that are based on targeting HNF4a.

Keywords: hepatocyte nuclear factor 4 alpha, HNF4a nuclear receptor, steroid hormone receptor family of transcription factors, hematological disorders

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Authors: Ran Vir Singh, Anuj Chauhan, Subhodh Kumar, Rajesh Rathore, Satish Kumar, B Gopi, Sushil Kumar, Tarun Kumar, Ramji Yadav, Donna Phangchopi, Shoor Vir Singh

Abstract:

Paratuberculosis caused by Mycobacterium avium subspecies paratuberculosis (MAP) is a chronic granulomatous enteritis affecting ruminants. It is responsible for significant economic losses in livestock industry worldwide. This organism is also of public health concern due to an unconfirmed link to Crohn’s disease. Susceptibility to paratuberculosis has been suggested to have genetic component with low to moderate heritability. Number of SNPs in various candidates genes have been observed to be affecting the susceptibility toward paratuberculosis. The objective of this study was to explore the association of various SNPs in the candidate genes and QTL region with MAP. A total of 117 SNPs from SLC11A1, IFNG, CARD15, TLR2, TLR4, CLEC7A, CD209, SP110, ANKARA2, PGLYRP1 and one QTL were selected for study. A total of 1222 cattle from various organized herds, gauhsalas and farmer herds were screened for MAP infection by Johnin intradermal skin test, AGID, serum ELISA, fecal microscopy, fecal culture and IS900 blood PCR. Based on the results of these tests, a case and control population of 200 and 183 respectively was established for study. A total of 117 SNPs from 10 candidate genes and one QTL were selected and validated/tested in our case and control population by PCR-RFLP technique. Data was analyzed using SAS 9.3 software. Statistical analysis revealed that, 107 out of 117 SNPs were not significantly associated with occurrence of MAP. Only SNP rs55617172 of TLR2, rs8193046 and rs8193060 of TLR4, rs110353594 and rs41654445 of CLEC7A, rs208814257of CD209, rs41933863 of ANKRA2, two loci {SLC11A1(53C/G)} and {IFNG (185 G/r) } and SNP rs41945014 in QTL region was significantly associated with MAP. Six SNP from 10 significant SNPs viz., rs110353594 and rs41654445 from CLEC7A, rs8193046 and rs8193060 from TLR4, rs109453173 from SLC11A1 rs208814257 from CD209 were validated in new case and control population. Out of these only one SNP rs8193046 of TLR4 gene was found significantly associated with occurrence of MAP in cattle. ODD ratio indicates that animals with AG genotype were more susceptible to MAP and this finding is in accordance with the earlier report. Hence it reaffirms that AG genotype can serve as a reliable genetic marker for indentifying more susceptible cattle in future selection against MAP infection in cattle.

Keywords: SNP, candidate genes, paratuberculosis, cattle

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Authors: Rachel Danielson, Brendan Bohannan, S.M. Tsai, Kyle Meyer, Jorge L.M. Rodrigues

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The Amazon Rainforest is a global diversity hotspot and crucial carbon sink, but approximately 20% of its total extent has been deforested- primarily for the establishment of cattle pasture. Understanding the impact of this large-scale disturbance on soil microbial community composition and activity is crucial in understanding potentially consequential shifts in nutrient or greenhouse gas cycling, as well as adding to the body of knowledge concerning how these complex communities respond to human disturbance. In this study, surface soils (0-10cm) were collected from three forests and three 45-year-old pastures in Rondonia, Brazil (the Amazon state with the greatest rate of forest destruction) in order to determine the impact of forest conversion on microbial communities involved in nitrogen fixation. Soil chemical and physical parameters were paired with measurements of microbial activity and genetic profiles to determine how community composition and process rates relate to environmental conditions. Measuring both the natural abundance of 15N in total soil N, as well as incorporation of enriched 15N2 under incubation has revealed that conversion of primary forest to cattle pasture results in a significant increase in the rate of nitrogen fixation by free-living diazotrophs. Quantification of nifH gene copy numbers (an essential subunit encoding the nitrogenase enzyme) correspondingly reveals a significant increase of genes in pasture compared to forest soils. Additionally, genetic sequencing of both nifH genes and transcripts shows a significant increase in the diversity of the present and metabolically active diazotrophs within the soil community. Levels of both organic and inorganic nitrogen tend to be lower in pastures compared to forests, with ammonium rather than nitrate as the dominant inorganic form. However, no significant or consistent differences in total, extractable, permanganate-oxidizable, or loss-on-ignition carbon are present between the two land-use types. Forest conversion is associated with a 0.5- 1.0 unit pH increase, but concentrations of many biologically relevant nutrients such as phosphorus do not increase consistently. Increases in free-living diazotrophic community abundance and activity appear to be related to shifts in carbon to nitrogen pool ratios. Furthermore, there may be an important impact of transient, low molecular weight plant-root-derived organic carbon on free-living diazotroph communities not captured in this study. Preliminary analysis of nitrogenase gene variant composition using NovoSeq metagenomic sequencing indicates that conversion of forest to pasture may significantly enrich vanadium-based nitrogenases. This indication is complemented by a significant decrease in available soil molybdenum. Very little is known about the ecology of diazotrophs utilizing vanadium-based nitrogenases, so further analysis may reveal important environmental conditions favoring their abundance and diversity in soil systems. Taken together, the results of this study indicate a significant change in nitrogen cycling and diazotroph community composition with the conversion of the Amazon Rainforest. This may have important implications for the sustainability of cattle pastures once established since nitrogen is a crucial nutrient for forage grass productivity.

Keywords: free-living diazotrophs, land use change, metagenomic sequencing, nitrogen fixation

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Authors: Bale Baidi Blaise, Gilles Marckmann, Liman Kaoye, Talaka Dya, Moustapha Bachirou, Gambo Betchewe, Tibi Beda

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This work highlights the capabilities of particles swarm optimization (PSO) method to identify parameters of hyperelastic models. The study compares this method with Genetic Algorithm (GA) method, Least Squares (LS) method, Pattern Search Algorithm (PSA) method, Beda-Chevalier (BC) method and the Levenberg-Marquardt (LM) method. Four classic hyperelastic models are used to test the different methods through parameters identification. Then, the study compares the ability of these models to reproduce experimental Treloar data in simple tension, biaxial tension and pure shear.

Keywords: particle swarm optimization, identification, hyperelastic, model

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Authors: Vassilios Moussas, Dimos N. Pantazis, Panagioths Stratakis

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The aim of this paper is to present the optimization methodology developed in the frame of a Coastal Transport Information System. The system will be used for the effective design of coastal transportation lines and incorporates subsystems that implement models, tools and techniques that may support the design of improved networks. The role of the optimization and decision subsystem is to provide the user with better and optimal scenarios that will best fulfill any constrains, goals or requirements posed. The complexity of the problem and the large number of parameters and objectives involved led to the adoption of an evolutionary method (Genetic Algorithms). The problem model and the subsystem structure are presented in detail, and, its support for simulation is also discussed.

Keywords: coastal transport, modeling, optimization

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Authors: Marija Milašinović-Šeremešić, Valentina Semenčenko, Milica Radosavljević, Dušanka Terzić, Ljiljana Mojović, Ljubica Dokić

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Maize (Zea mays L.) is one of the most important cereal crops, and as such, one of the most significant naturally renewable carbohydrate raw materials for the production of energy and multitude of different products. The main goal of the present study was to investigate a suitability of selected maize hybrids of different genetic background produced in Maize Research Institute ‘Zemun Polje’, Belgrade, Serbia, for starch, bioethanol and animal feed production. All the hybrids are commercial and their detailed characterization is important for the expansion of their different uses. The starches were isolated by using a 100-g laboratory maize wet-milling procedure. Hydrolysis experiments were done in two steps (liquefaction with Termamyl SC, and saccharification with SAN Extra L). Starch hydrolysates obtained by the two-step hydrolysis of the corn flour starch were subjected to fermentation by S. cerevisiae var. ellipsoideus under semi-anaerobic conditions. The digestibility based on enzymatic solubility was performed by the Aufréré method. All investigated ZP maize hybrids had very different physical characteristics and chemical composition which could allow various possibilities of their use. The amount of hard (vitreous) and soft (floury) endosperm in kernel is considered one of the most important parameters that can influence the starch and bioethanol yields. Hybrids with a lower test weight and density and a greater proportion of soft endosperm fraction had a higher yield, recovery and purity of starch. Among the chemical composition parameters only starch content significantly affected the starch yield. Starch yields of studied maize hybrids ranged from 58.8% in ZP 633 to 69.0% in ZP 808. The lowest bioethanol yield of 7.25% w/w was obtained for hybrid ZP 611k and the highest by hybrid ZP 434 (8.96% w/w). A very significant correlation was determined between kernel starch content and the bioethanol yield, as well as volumetric productivity (48h) (r=0.66). Obtained results showed that the NDF, ADF and ADL contents in the whole maize plant of the observed ZP maize hybrids varied from 40.0% to 60.1%, 18.6% to 32.1%, and 1.4% to 3.1%, respectively. The difference in the digestibility of the dry matter of the whole plant among hybrids (ZP 735 and ZP 560) amounted to 18.1%. Moreover, the differences in the contents of the lignocelluloses fraction affected the differences in dry matter digestibility. From the results it can be concluded that genetic background of the selected maize hybrids plays an important part in estimation of the technological value of maize hybrids for various purposes. Obtained results are of an exceptional importance for the breeding programs and selection of potentially most suitable maize hybrids for starch, bioethanol and animal feed production.

Keywords: bioethanol, biomass quality, maize, starch

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Authors: Rebecca Richards Steed, James Van Derslice, Ken Smith, Richard Medina, Amanda Bakian

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Elucidating gene-environment interactions for heritable disease outcomes is an emerging area of disease research, with genetic studies informing hypotheses for environment and gene interactions underlying some of the most confounding diseases of our time, like autism spectrum disorder (ASD). Geography has thus far played a key role in identifying environmental factors contributing to disease, but its use can be broadened to include genetic and environmental factors that have a synergistic effect on disease. Through the use of family pedigrees and disease outcomes with life-course residential histories, space-time clustering of generations at critical developmental windows can provide further understanding of (1) environmental factors that contribute to disease patterns in families, (2) susceptible critical windows of development most impacted by environment, (3) and that are most likely to lead to an ASD diagnosis. This paper introduces a retrospective case-control study that utilizes pedigree data, health data, and residential life-course location points to find space-time clustering of ancestors with a grandchild/child with a clinical diagnosis of ASD. Finding space-time clusters of ancestors at critical developmental windows serves as a proxy for shared environmental exposures. The authors refer to geographic life-course exposures as geographic legacies. Identifying space-time clusters of ancestors creates a bridge for researching exposures of past generations that may impact modern-day progeny health. Results from the space-time cluster analysis show multiple clusters for the maternal and paternal pedigrees. The paternal grandparent pedigree resulted in the most space-time clustering for birth and childhood developmental windows. No statistically significant clustering was found for adolescent years. These results will be further studied to identify the specific share of space-time environmental exposures. In conclusion, this study has found significant space-time clusters of parents, and grandparents for both maternal and paternal lineage. These results will be used to identify what environmental exposures have been shared with family members at critical developmental windows of time, and additional analysis will be applied.

Keywords: family pedigree, environmental exposure, geographic legacy, medical geography, transgenerational inheritance

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Authors: Zelikha Labbani

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The in vitro isolated microspore culture is the most powerful androgenic pathway to produce doubled haploid plants in the short time. To deviate a microspore toward embryogenesis, a number of factors, different for each species, must concur at the same time and place. Once induced, the microspore undergoes numerous changes at different levels, from overall morphology to gene expression. Induction of microspore embryogenesis not only implies the expression of an embryogenic program, but also a stress-related cellular response and a repression of the gametophytic program to revert the microspore to a totipotent status. As haploid single cells, microspore became a strategy to achieve various objectives particularly in genetic engineering. In this communication we would show the most recent advances in the producing haploid embryos via in vitro isolated microspore culture.

Keywords: in vitro isolated microspore culture, success, haploid cells, bioinformatics, biomedicine

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Authors: Elif Gencturk, Ekin Yurdakul, Ahmet Y. Celik, Senol Mutlu, Kutlu O. Ulgen

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Yeast cells are generally used as a model system of eukaryotes due to their complex genetic structure, rapid growth ability in optimum conditions, easy replication and well-defined genetic system properties. Thus, yeast cells increased the knowledge of the principal pathways in humans. During fermentation, carbohydrates (hexoses and pentoses) degrade into some toxic by-products such as 5-hydroxymethylfurfural (5-HMF or HMF) and furfural. HMF influences the ethanol yield, and ethanol productivity; it interferes with microbial growth and is considered as a potent inhibitor of bioethanol production. In this study, yeast single cell behavior under HMF application was monitored by using a continuous flow single phase microfluidic platform. Microfluidic device in operation is fabricated by hot embossing and thermo-compression techniques from cyclo-olefin polymer (COP). COP is biocompatible, transparent and rigid material and it is suitable for observing fluorescence of cells considering its low auto-fluorescence characteristic. The response of yeast cells was recorded through Red Fluorescent Protein (RFP) tagged Nop56 gene product, which is an essential evolutionary-conserved nucleolar protein, and also a member of the box C/D snoRNP complexes. With the application of HMF, yeast cell proliferation continued but HMF slowed down the cell growth, and after HMF treatment the cell proliferation stopped. By the addition of fresh nutrient medium, the yeast cells recovered after 6 hours of HMF exposure. Thus, HMF application suppresses normal functioning of cell cycle but it does not cause cells to die. The monitoring of Nop56 expression phases of the individual cells shed light on the protein and ribosome synthesis cycles along with their link to growth. Further computational study revealed that the mechanisms underlying the inhibitory or inductive effects of HMF on growth are enriched in functional categories of protein degradation, protein processing, DNA repair and multidrug resistance. The present microfluidic device can successfully be used for studying the effects of inhibitory agents on growth by single cell tracking, thus capturing cell to cell variations. By metabolic engineering techniques, engineered strains can be developed, and the metabolic network of the microorganism can thus be manipulated such that chemical overproduction of target metabolite is achieved along with the maximum growth/biomass yield.  

Keywords: COP, HMF, ribosome biogenesis, thermoplastic microbioreactor, yeast

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Authors: Kostas Metaxiotis, Kostas Liagkouras

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This study presents an Expert System specially designed to be used with Multiobjective Evolutionary Algorithms (MOEAs) for the solution of the portfolio selection problem. The validation of the proposed hybrid System is done by using data sets from Hang Seng 31 in Hong Kong, DAX 100 in Germany and FTSE 100 in UK. The performance of the proposed system is assessed in comparison with the Non-dominated Sorting Genetic Algorithm II (NSGAII). The evaluation of the performance is based on different performance metrics that evaluate both the proximity of the solutions to the Pareto front and their dispersion on it. The results show that the proposed hybrid system is efficient for the solution of this kind of problems.

Keywords: expert systems, multi-objective optimization, evolutionary algorithms, portfolio selection

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Authors: Danni Cheng

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Background: Preclinical and epidemiological studies have reported potential protective effects of low-density lipoprotein cholesterol (LDL-C) lowering drugs on head and neck squamous cell cancer (HNSCC) survival, but the causality was not consistent. Genetic variants associated with LDL-C lowering drug targets can predict the effects of their therapeutic inhibition on disease outcomes. Objective: We aimed to evaluate the causal association of genetically proxied cholesterol-lowering drug targets and circulating lipid traits with cancer survival in HNSCC patients stratified by human papillomavirus (HPV) status using two-sample Mendelian randomization (MR) analyses. Method: Single-nucleotide polymorphisms (SNPs) in gene region of LDL-C lowering drug targets (HMGCR, NPC1L1, CETP, PCSK9, and LDLR) associated with LDL-C levels in genome-wide association study (GWAS) from the Global Lipids Genetics Consortium (GLGC) were used to proxy LDL-C lowering drug action. SNPs proxy circulating lipids (LDL-C, HDL-C, total cholesterol, triglycerides, apoprotein A and apoprotein B) were also derived from the GLGC data. Genetic associations of these SNPs and cancer survivals were derived from 1,120 HPV-positive oropharyngeal squamous cell carcinoma (OPSCC) and 2,570 non-HPV-driven HNSCC patients in VOYAGER program. We estimated the causal associations of LDL-C lowering drugs and circulating lipids with HNSCC survival using the inverse-variance weighted method. Results: Genetically proxied HMGCR inhibition was significantly associated with worse overall survival (OS) in non-HPV-drive HNSCC patients (inverse variance-weighted hazard ratio (HR IVW), 2.64[95%CI,1.28-5.43]; P = 0.01) but better OS in HPV-positive OPSCC patients (HR IVW,0.11[95%CI,0.02-0.56]; P = 0.01). Estimates for NPC1L1 were strongly associated with worse OS in both total HNSCC (HR IVW,4.17[95%CI,1.06-16.36]; P = 0.04) and non-HPV-driven HNSCC patients (HR IVW,7.33[95%CI,1.63-32.97]; P = 0.01). A similar result was found that genetically proxied PSCK9 inhibitors were significantly associated with poor OS in non-HPV-driven HNSCC (HR IVW,1.56[95%CI,1.02 to 2.39]). Conclusion: Genetically proxied long-term HMGCR inhibition was significantly associated with decreased OS in non-HPV-driven HNSCC and increased OS in HPV-positive OPSCC. While genetically proxied NPC1L1 and PCSK9 had associations with worse OS in total and non-HPV-driven HNSCC patients. Further research is needed to understand whether these drugs have consistent associations with head and neck tumor outcomes.

Keywords: Mendelian randomization analysis, head and neck cancer, cancer survival, cholesterol, statin

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