Search results for: O-antigen gene cluster
2139 Functional Analysis of Thyroid Peroxidase Gene Mutations Detected in Patients with Thyroid Dyshormonogenesis
Authors: Biswabandhu Bankura, Srikanta Guria, Madhusudan Das
Abstract:
Purpose: Thyroid peroxidase (TPO) is the key enzyme in the biosynthesis of thyroid hormones. We aimed to identify the spectrum of mutations in the TPO gene leading to hypothyroidism in the population of West Bengal to establish the genetic etiology of the disease. Methods: 200 hypothyroid patients (case) and their corresponding sex and age matched 200 normal individuals (control) were screened depending on their clinical manifestations. Genomic DNA was isolated from peripheral blood samples and TPO gene (Exon 7 to Exon 14) was amplified by PCR. The PCR products were subjected to sequencing to identify mutations. Results: Single nucleotide changes such as Glu 641 Lys, Asp 668 Asn, Thr 725 Pro, Asp 620 Asn, Ser 398 Thr, and Ala 373 Ser were found. Changes in the TPO were assayed in vitro to compare mutant and wild-type activities. Five mutants were enzymatically inactive in the guaiacol and iodide assays. This is a strong indication that the mutations are present at crucial positions of the TPO gene, resulting in inactivated TPO. Key Findings: The results of this study may help to develop a genetic screening protocol for goiter and hypothyroidism in the population of West Bengal.Keywords: thyroid peroxidase, hypothyroidism, mutation, in vitro assay, transfection
Procedia PDF Downloads 3292138 A Deletion in Duchenne Muscular Dystrophy Gene Found Through Whole Exome Sequencing in Iran
Authors: Negin Parsamanesh, Saman Ameri-Mahabadi, Ali Nikfar, Mojdeh Mansouri, Hossein Chiti, Gita Fatemi Abhari
Abstract:
Duchenne muscular dystrophy (DMD) is a severe progressive X-linked neuromuscular illness that affects movement through mutations in dystrophin gene. The mutation leads to insufficient, lack of or dysfunction of dystrophin. The cause of DMD was determined in an Iranian family. Exome sequencing was carried out along with a complete physical examination of the family. In silico methods were applied to find the alteration in the protein structure. The homozygous variant in DMD gene (NM-004006.2) was defined as c.2732-2733delTT (p.Phe911CysfsX8) in exon 21. In addition, phylogenetic conservation study of the human dystrophin protein sequence revealed that phenylalanine 911 is one of the evolutionarily conserved amino acids. In conclusion, our study indicated a new deletion in the DMD gene in the affected family. This deletion with an X-linked inheritance pattern is new in Iran. These findings could facilitate genetic counseling for this family and other patients in the future.Keywords: duchenne muscular dystrophy, whole exome sequencing, iran, metabolic syndrome
Procedia PDF Downloads 642137 Determination of Genotypic Relationship among 12 Sugarcane (Saccharum officinarum) Varieties
Authors: Faith Eweluegim Enahoro-Ofagbe, Alika Eke Joseph
Abstract:
Information on genetic variation within a population is crucial for utilizing heterozygosity for breeding programs that aim to improve crop species. The study was conducted to ascertain the genotypic similarities among twelve sugarcane (Saccharum officinarum) varieties to group them for purposes of hybridizations for cane yield improvement. The experiment was conducted at the University of Benin, Faculty of Agriculture Teaching and Research Farm, Benin City. Twelve sugarcane varieties obtained from National Cereals Research Institute, Badeggi, Niger State, Nigeria, were planted in three replications in a randomized complete block design. Each variety was planted on a five-row plot of 5.0 m in length. Data were collected on 12 agronomic traits, including; the number of millable cane, cane girth, internode length, number of male and female flowers (fuss), days to flag leaf, days to flowering, brix%, cane yield, and others. There were significant differences, according to the findings among the twelve genotypes for the number of days to flag leaf, number of male and female flowers (fuss), and cane yield. The relationship between the twelve sugarcane varieties was expressed using hierarchical cluster analysis. The twelve genotypes were grouped into three major clusters based on hierarchical classification. Cluster I had five genotypes, cluster II had four, and cluster III had three. Cluster III was dominated by varieties characterized by higher cane yield, number of leaves, internode length, brix%, number of millable stalks, stalk/stool, cane girth, and cane length. Cluster II contained genotypes with early maturity characteristics, such as early flowering, early flag leaf development, growth rate, and the number of female and male flowers (fuss). The maximum inter-cluster distance between clusters III and I indicated higher genetic diversity between the two groups. Hybridization between the two groups could result in transgressive recombinants for agronomically important traits.Keywords: sugarcane, Saccharum officinarum, genotype, cluster analysis, principal components analysis
Procedia PDF Downloads 732136 Milk Yield and Fingerprinting of Beta-Casein Precursor (CSN2) Gene in Some Saudi Camel Breeds
Authors: Amr A. El Hanafy, Yasser M. Saad, Saleh A. Alkarim, Hussein A. Almehdar, Elrashdy M. Redwan
Abstract:
Camels are substantial providers of transport, milk, sport, meat, shelter, fuel, security and capital in many countries, particularly Saudi Arabia. Identification of animal breeds has progressed rapidly during the last decade. Advanced molecular techniques are playing a significant role in breeding or strain protection laws. On the other hand, fingerprinting of some molecular markers related to some productive traits in farm animals represents most important studies to our knowledge, which aim to conserve these local genetic resources, and to the genetic improvement of such local breeds by selective programs depending on gene markers. Milk records were taken two days in each week from female camels of Majahem, Safara, Wathaha, and Hamara breeds, respectively from different private farms in northern Jeddah, Riyadh and Alwagh governorates and average weekly yields were calculated. DNA sequencing for CSN2 gene was used for evaluating the genetic variations and calculating the genetic distance values among four Saudi camel populations which are Hamra(R), Safra(Y), Wadha(W) and Majaheim(M). In addition, this marker was analyzed for reconstructing the Neighbor joining tree among evaluating camel breeds. In respect to milk yield during winter season, result indicated that average weekly milk yield of Safara camel breed (30.05 Kg/week) is significantly (p < 0.05) lower than the other 3 breeds which ranged from 39.68 for Hamara to 42.42 Kg/week for Majahem, while there are not significant differences between these three breeds. The Neighbor Joining analysis that re-constructed based on DNA variations showed that samples are clustered into two unique clades. The first clade includes Y (from Y4 to Y18) and M (from M1, to M9). On the other hand, the second cluster is including all R (from R1 to R6) and W (from W1 to W6). The genetic distance values were equal 0.0068 (between the groups M&Y and R&W) and equal 0 (within each group).Keywords: milk yield, beta-casein precursor (CSN2), Saudi camel, molecular markers
Procedia PDF Downloads 2102135 Ribosomal Protein S4 Gene: Exploring the Presence in Syrian Strain of Leishmania Tropica Genome, Sequencing it and Evaluating Immune Response of pCI-S4 DNA Vaccine
Authors: Alyaa Abdlwahab
Abstract:
Cutaneous leishmaniasis represents a serious health problem in Syria; this problem has become noticeably aggravated after the civil war in the country. Leishmania tropica parasite is the main cause of cutaneous leishmaniasis in Syria. In order to control the disease, we need an effective vaccine against leishmania parasite. DNA vaccination remains one of the favorable approaches that have been used to face cutaneous leishmaniasis. Ribosomal protein S4 is responsible for important roles in Leishmania parasite life. DNA vaccine based on S4 gene has been used against infections by many species of Leishmania parasite but leishmania tropica parasite, so this gene represents a good candidate for DNA vaccine construction. After proving the existence of ribosomal protein S4 gene in a Syrian strain of Leishmania tropica (LCED Syrian 01), sequencing it and cloning it into pCI plasmid, BALB/C mice were inoculated with pCI-S4 DNA vaccine. The immune response was determined by monitoring the lesion progression in inoculated BALB/C mice for six weeks after challenging mice with Leishmania tropica (LCED Syrian 01) parasites. IL-12, IFN-γ, and IL-4 were quantified in draining lymph nodes (DLNa) of the immunized BALB/C mice by using the RT-qPCR technique. The parasite burden was calculated in the final week for the footpad lesion and the DLNs of the mice. This study proved the existence and the expression of the ribosomal protein S4 gene in Leishmania tropica (LCED Syrian 01) promastigotes. The sequence of ribosomal protein cDNA S4 gene was determined and published in Genbank; the gene size was 822 bp. Expression was also demonstrated at the level of cDNA. Also, this study revealed that pCI-S4 DNA vaccine induces TH1\TH2 response in immunized mice; this response prevents partially developing a dermal lesion of Leishmania.Keywords: ribosomal protein S4, DNA vaccine, Leishmania tropica, BALB\c
Procedia PDF Downloads 1282134 Efficacy of Teachers' Cluster Meetings on Teachers' Lesson Note Preparation and Teaching Performance in Oyo State, Nigeria
Authors: Olusola Joseph Adesina, Sunmaila Oyetunji Raimi, Olufemi Akinloye Bolaji, Abiodun Ezekiel Adesina
Abstract:
The quality of education and the standard of a nation cannot rise above the quality of the teacher (NPE, 2004). Efforts at improving the falling standard of education in the country call for the need-based assessment of the primary tier of education in Nigeria. It was revealed that the teachers’ standard of performance and pupils’ achievement was below average. Teachers’ cluster meeting intervention was therefore recommended as a step towards enhancing the teachers’ professional competency, efficient and effective proactive and interactive lesson presentation. The study thus determined the impact of the intervention on teachers’ professional performance (lesson note preparation and teaching performance) in Oyo State, Nigeria. The main and interaction effects of the gender of the teachers as moderator variable were also determined. Three null hypotheses guided the study. Pre-test, posttest control group quazi experimental design was adopted for the study. Three hundred intact classes from three hundred different schools were randomly selected into treatment and control groups. Two response instruments-Classroom Lesson Note Preparation Checklist (CLNPC; r = 0.89) Cluster Lesson Observation Checklist (CLOC; r = 0.86) were used for data collection. Mean, Standard deviation and Analysis of Covariance (ANCOVA) were used to analyse the collected data. The results showed that the teachers’ cluster meeting have significant impact on teachers’ lesson note preparation (F(1,295) = 31.607; p < 0.05; η2 = .097) and teaching performance (F(1,295) = 20.849; p < 0.05; η2 = .066) in the core subjects of primary schools in Oyo State, Nigeria. The study therefore recommended among others that teachers’ cluster meeting should be sustained for teachers’ professional development in the State.Keywords: teachers’ cluster meeting, teacher lesson note preparation, teaching performance, teachers’ gender, primary schools in Oyo state
Procedia PDF Downloads 3382133 Effect of SCN5A Gene Mutation in Endocardial Cell
Authors: Helan Satish, M. Ramasubba Reddy
Abstract:
The simulation of an endocardial cell for gene mutation in the cardiac sodium ion channel NaV1.5, encoded by SCN5A gene, is discussed. The characterization of Brugada Syndrome by loss of function effect on SCN5A mutation due to L812Q mutant present in the DII-S4 transmembrane region of the NaV1.5 channel protein and its effect in an endocardial cell is studied. Ten Tusscher model of human ventricular action potential is modified to incorporate the changes contributed by L812Q mutant in the endocardial cells. Results show that BrS-associated SCN5A mutation causes reduction in the inward sodium current by modifications in the channel gating dynamics such as delayed activation, enhanced inactivation, and slowed recovery from inactivation in the endocardial cell. A decrease in the inward sodium current was also observed, which affects depolarization phase (Phase 0) that leads to reduction in the spike amplitude of the cardiac action potential.Keywords: SCN5A gene mutation, sodium channel, Brugada syndrome, cardiac arrhythmia, action potential
Procedia PDF Downloads 1202132 Three-Dimensional Model of Leisure Activities: Activity, Relationship, and Expertise
Authors: Taekyun Hur, Yoonyoung Kim, Junkyu Lim
Abstract:
Previous works on leisure activities had been categorizing activities arbitrarily and subjectively while focusing on a single dimension (e.g. active-passive, individual-group). To overcome these problems, this study proposed a Korean leisure activities’ matrix model that considered multidimensional features of leisure activities, which was comprised of 3 main factors and 6 sub factors: (a) Active (physical, mental), (b) Relational (quantity, quality), (c) Expert (entry barrier, possibility of improving). We developed items for measuring the degree of each dimension for every leisure activity. Using the developed Leisure Activities Dimensions (LAD) questionnaire, we investigated the presented dimensions of a total of 78 leisure activities which had been enjoyed by most Koreans recently (e.g. watching movie, taking a walk, watching media). The study sample consisted of 1348 people (726 men, 658 women) ranging in age from teenagers to elderlies in their seventies. This study gathered 60 data for each leisure activity, a total of 4860 data, which were used for statistical analysis. First, this study compared 3-factor model (Activity, Relation, Expertise) fit with 6-factor model (physical activity, mental activity, relational quantity, relational quality, entry barrier, possibility of improving) fit by using confirmatory factor analysis. Based on several goodness-of-fit indicators, the 6-factor model for leisure activities was a better fit for the data. This result indicates that it is adequate to take account of enough dimensions of leisure activities (6-dimensions in our study) to specifically apprehend each leisure attributes. In addition, the 78 leisure activities were cluster-analyzed with the scores calculated based on the 6-factor model, which resulted in 8 leisure activity groups. Cluster 1 (e.g. group sports, group musical activity) and Cluster 5 (e.g. individual sports) had generally higher scores on all dimensions than others, but Cluster 5 had lower relational quantity than Cluster 1. In contrast, Cluster 3 (e.g. SNS, shopping) and Cluster 6 (e.g. playing a lottery, taking a nap) had low scores on a whole, though Cluster 3 showed medium levels of relational quantity and quality. Cluster 2 (e.g. machine operating, handwork/invention) required high expertise and mental activity, but low physical activity. Cluster 4 indicated high mental activity and relational quantity despite low expertise. Cluster 7 (e.g. tour, joining festival) required not only moderate degrees of physical activity and relation, but low expertise. Lastly, Cluster 8 (e.g. meditation, information searching) had the appearance of high mental activity. Even though clusters of our study had a few similarities with preexisting taxonomy of leisure activities, there was clear distinctiveness between them. Unlike the preexisting taxonomy that had been created subjectively, we assorted 78 leisure activities based on objective figures of 6-dimensions. We also could identify that some leisure activities, which used to belong to the same leisure group, were included in different clusters (e.g. filed ball sports, net sports) because of different features. In other words, the results can provide a different perspective on leisure activities research and be helpful for figuring out what various characteristics leisure participants have.Keywords: leisure, dimensional model, activity, relationship, expertise
Procedia PDF Downloads 3052131 DNA Barcoding of Tree Endemic Campanula Species From Artvi̇n, Türki̇ye
Authors: Hayal Akyildirim Beğen, Özgür Emi̇nağaoğlu
Abstract:
DNA barcoding is the method of description of species based on gene diversity. In current studies, registration, genetic identification and protection of especially endemic plants pecies are carried out by DNA barcoding techniques. Molecular studies are based on the amplification and sequencing of the barcode gene region by the PCR method. Endemic Campanula choruhensis Kit Tan & Sorger, Campanula troegera Damboldt and Campanula betulifolia K.Koch is widespread in Artvin, Erzurum and around Çoruh valley passing through it. Intense road and dam constructions are carried out in and around the distribution area of this species. This situation harms the habitat of the species and puts its extinction. In this study, the plastid matK barcode gene regions (650 bp) of three Campanula species were created. To make the identification of this species quickly and accurately, gene sequence compared with sequences of other Campanula L. species. As a result of phylogenetic analysis, C. choruhensis is close relative to C. betulifolia. Morphologically, these species were determined to be more similar to each other with flower and leaf characters. C. troegera formed a separate branch.Keywords: campanula, DNA barcoding, endemic, türkiye, artvin
Procedia PDF Downloads 642130 Two-Photon Ionization of Silver Clusters
Authors: V. Paployan, K. Madoyan, A. Melikyan, H. Minassian
Abstract:
Resonant two-photon ionization (TPI) is a valuable technique for the study of clusters due to its ultrahigh sensitivity. The comparison of the observed TPI spectra with results of calculations allows to deduce important information on the shape, rotational and vibrational temperatures of the clusters with high accuracy. In this communication we calculate the TPI cross-section for pump-probe scheme in Ag neutral cluster. The pump photon energy is chosen to be close to the surface plasmon (SP) energy of cluster in dielectric media. Since the interband transition energy in Ag exceeds the SP resonance energy, the main contribution into the TPI comes from the latter. The calculations are performed by separating the coordinates of electrons corresponding to the collective oscillations and the individual motion that allows to take into account the resonance contribution of excited SP oscillations. It is shown that the ionization cross section increases by two orders of magnitude if the energy of the pump photon matches the surface plasmon energy in the cluster.Keywords: resonance enhancement, silver clusters, surface plasmon, two-photon ionization
Procedia PDF Downloads 4212129 Estimation of Rare and Clustered Population Mean Using Two Auxiliary Variables in Adaptive Cluster Sampling
Authors: Muhammad Nouman Qureshi, Muhammad Hanif
Abstract:
Adaptive cluster sampling (ACS) is specifically developed for the estimation of highly clumped populations and applied to a wide range of situations like animals of rare and endangered species, uneven minerals, HIV patients and drug users. In this paper, we proposed a generalized semi-exponential estimator with two auxiliary variables under the framework of ACS design. The expressions of approximate bias and mean square error (MSE) of the proposed estimator are derived. Theoretical comparisons of the proposed estimator have been made with existing estimators. A numerical study is conducted on real and artificial populations to demonstrate and compare the efficiencies of the proposed estimator. The results indicate that the proposed generalized semi-exponential estimator performed considerably better than all the adaptive and non-adaptive estimators considered in this paper.Keywords: auxiliary information, adaptive cluster sampling, clustered populations, Hansen-Hurwitz estimation
Procedia PDF Downloads 2332128 Identification of a Novel Maize Dehydration-Responsive Gene with a Potential Role in Improving Maize Drought Tolerance
Authors: Kyle Phillips, Ndiko Ludidi
Abstract:
Global climate change has resulted in altered rainfall patterns, which has resulted in annual losses in maize crop yields due to drought. Therefore it is important to produce maize cultivars that are more drought-tolerant, which is not an easily accomplished task as plants have a plethora of physical and biochemical adaptation methods. One such mechanism is the drought-induced expression of enzymatic and non-enzymatic proteins which assist plants to resist the effects of drought on their growth and development. One of these proteins is AtRD22 which has been identified in Arabidopsis thaliana. Using an in silico approach, a maize protein with 48% sequence homology to AtRD22 has been identified. This protein appears to be localized in the extracellular matrix, similarly to AtRD22. Promoter analysis of the encoding gene reveals cis-acting elements suggestive of induction of the gene’s expression by abscisic acid (ABA). Semi-quantitative transcriptomic analysis of the putative maize RD22 has revealed an increase in transcript levels after the exposure to drought. Current work elucidates the effect of up-regulation and silencing of the maize RD22 gene on the tolerance of maize to drought. The potential role of the maize RD22 gene in maize drought tolerance can be used as a tool to improve food security.Keywords: abscisic acid, drought-responsive cis-acting elements, maize drought tolerance, RD22
Procedia PDF Downloads 4532127 Identification and Validation of Co-Dominant Markers for Selection of the CO-4 Anthracnose Disease Resistance Gene in Common Bean Cultivar G2333
Authors: Annet Namusoke, Annet Namayanja, Peter Wasswa, Shakirah Nampijja
Abstract:
Common bean cultivar G2333 which offers broad resistance for anthracnose has been widely used as a source of resistance in breeding for anthracnose resistance. The cultivar is pyramided with three genes namely CO-4, CO-5 and CO-7 and of these three genes, the CO-4 gene has been found to offer the broadest resistance. The main aim of this work was to identify and validate easily assayable PCR based co-dominant molecular markers for selection of the CO-4 gene in segregating populations derived from crosses of G2333 with RWR 1946 and RWR 2075, two commercial Andean cultivars highly susceptible to anthracnose. Marker sequences for the study were obtained by blasting the sequence of the COK-4 gene in the Phaseolus gene database. Primer sequence pairs that were not provided from the Phaseolus gene database were designed by the use of Primer3 software. PCR conditions were optimized and the PCR products were run on 6% HPAGE gel. Results of the polymorphism test indicated that out of 18 identified markers, only two markers namely BM588 and BM211 behaved co-dominantly. Phenotypic evaluation for reaction to anthracnose disease was done by inoculating 21days old seedlings of three parents, F1 and F2 populations with race 7 of Colletotrichum lindemuthianum in the humid chamber. DNA testing of the BM588 marker onto the F2 segregating population of the crosses RWR 1946 x G 2333 and RWR 2075 x G2333 further revealed that the marker BM588 co-segregated with disease resistance with co-dominance of two alleles of 200bp and 400bp, fitting the expected segregation ratio of 1:2:1. The BM588 marker was significantly associated with disease resistance and gave promising results for marker assisted selection of the CO-4 gene in the breeding lines. Activities to validate the BM211 marker are also underway.Keywords: codominant, Colletotrichum lindemuthianum, MAS, Phaseolus vulgaris
Procedia PDF Downloads 2872126 Association of Brain-Derived Neurotrophic Factor (BDNF) Gene with Obesity and Metabolic Traits in Malaysian Adults
Authors: Yamunah Devi Apalasamy, Sanjay Rampal, Tin Tin Su, Foong Ming Moy, Hazreen Abdul Majid, Awang Bulgiba, Zahurin Mohamed
Abstract:
Obesity is a growing global health issue. Obesity results from a combination of environmental and genetics factors. Brain-derived neurotrophic factor (BDNF), a gene encodes the BDNF protein and the BDNF gene have been linked to regulation of body weight and appetite. Genome-wide association studies have identified the BDNF variants to be related to obesity among Caucasians, East Asians, and Filipinos. However, the role of BDNF in other ethnic groups remains inconclusive. This case control study aims to investigate the associations of BDNF gene polymorphisms with obesity and metabolic parameters in Malaysian Malays. BDNF rs4074134, BDNF rs10501087 and BDNF rs6265 were genotyped using Sequenom MassARRAY. Anthropometric, body fat, fasting lipids and glucose levels were measured. A total of 663 subjects (194 obese and 469 non-obese) were included in this study. There were no significant associations association between BDNF SNPs and obesity. The allelic and genotype frequencies of the BDNF SNPs were similar in the obese and non-obese groups. After adjustment for age and sex, the BDNF variants were not associated with obesity, body fat, fasting lipids and glucose levels. Haplotypes at the BDNF gene region, were not significantly associated with obesity. The BDNF rs4074134 was in strong LD with BDNF rs10501087 (D'=0.98) and BDNF rs6265 (D'=0.87). The BDNF rs10501087 was also in strong LD with BDNF rs6265 (D'=0.91). Our findings suggest that the BDNF variants and the haplotypes of BDNF gene were not associated with obesity and metabolic traits in this study population. Further research is needed to explore other BDNF variants with a larger sample size with gene-environment interactions in multi ethnic Malaysian population.Keywords: genomics of obesity, SNP, BMI, haplotypes
Procedia PDF Downloads 4292125 A Gene Selection Algorithm for Microarray Cancer Classification Using an Improved Particle Swarm Optimization
Authors: Arfan Ali Nagra, Tariq Shahzad, Meshal Alharbi, Khalid Masood Khan, Muhammad Mugees Asif, Taher M. Ghazal, Khmaies Ouahada
Abstract:
Gene selection is an essential step for the classification of microarray cancer data. Gene expression cancer data (DNA microarray) facilitates computing the robust and concurrent expression of various genes. Particle swarm optimization (PSO) requires simple operators and less number of parameters for tuning the model in gene selection. The selection of a prognostic gene with small redundancy is a great challenge for the researcher as there are a few complications in PSO based selection method. In this research, a new variant of PSO (Self-inertia weight adaptive PSO) has been proposed. In the proposed algorithm, SIW-APSO-ELM is explored to achieve gene selection prediction accuracies. This new algorithm balances the exploration capabilities of the improved inertia weight adaptive particle swarm optimization and the exploitation. The self-inertia weight adaptive particle swarm optimization (SIW-APSO) is used to search the solution. The SIW-APSO is updated with an evolutionary process in such a way that each particle iteratively improves its velocities and positions. The extreme learning machine (ELM) has been designed for the selection procedure. The proposed method has been to identify a number of genes in the cancer dataset. The classification algorithm contains ELM, K- centroid nearest neighbor (KCNN), and support vector machine (SVM) to attain high forecast accuracy as compared to the start-of-the-art methods on microarray cancer datasets that show the effectiveness of the proposed method.Keywords: microarray cancer, improved PSO, ELM, SVM, evolutionary algorithms
Procedia PDF Downloads 772124 Fruiting Body Specific Sc4 Hydrophobin Gene Plays a Role in Schizophyllum Commune Hyphal Attachment to Structured Glass Surfaces
Authors: Evans Iyamu
Abstract:
Genes encoding hydrophobins play distinct roles at different stages of the life cycle of fungi, and they foster hyphal attachment to surfaces. The hydrophobin Sc4 is known to provide a hydrophobic membrane lining of the gas channels within Schizophyllum commune fruiting bodies. Here, we cultivated non-fruiting, monokaryotic S. commune 12-43 on glass surfaces that could be verified by micrography. Differential gene expression profiling of nine hydrophobin genes and the hydrophobin-like sc15 gene by quantitative PCR showed significant up-regulation of sc4 when S. commune was attached to glass surfaces, also confirmed with RNA-Seq data analysis. Another silicate, namely quartz sand, was investigated, and induction of sc4 was seen as well. The up-regulation of the hydrophobin gene sc4 may indicate involvement in S. commune hyphal attachment to glass as well as quartz surfaces. We propose that the covering of hyphae by Sc4 allows for direct interaction with the hydrophobic surfaces of silicates and that differential functions of specific hydrophobin genes depend on the surface interface involved. This study could help with the clarification of the biological functions of hydrophobins in natural surroundings, including hydrophobic surface attachment. Therefore, the analysis of growth on glass serves as a basis for understanding S. commune interaction with glass surfaces while providing the possibility to visualize the interaction microscopically.Keywords: hydrophobin, structured glass surfaces, differential gene expression, quartz sand
Procedia PDF Downloads 1102123 Quantitative Evaluation of Endogenous Reference Genes for ddPCR under Salt Stress Using a Moderate Halophile
Authors: Qinghua Xing, Noha M. Mesbah, Haisheng Wang, Jun Li, Baisuo Zhao
Abstract:
Droplet digital PCR (ddPCR) is being increasingly adopted for gene detection and quantification because of its higher sensitivity and specificity. According to previous observations and our lab data, it is essential to use endogenous reference genes (RGs) when investigating gene expression at the mRNA level under salt stress. This study aimed to select and validate suitable RGs for gene expression under salt stress using ddPCR. Six candidate RGs were selected based on the tandem mass tag (TMT)-labeled quantitative proteomics of Alkalicoccus halolimnae at four salinities. The expression stability of these candidate genes was evaluated using statistical algorithms (geNorm, NormFinder, BestKeeper and RefFinder). There was a small fluctuation in cycle threshold (Ct) value and copy number of the pdp gene. Its expression stability was ranked in the vanguard of all algorithms, and was the most suitable RG for quantification of expression by both qPCR and ddPCR of A. halolimnae under salt stress. Single RG pdp and RG combinations were used to normalize the expression of ectA, ectB, ectC, and ectD under four salinities. The present study constitutes the first systematic analysis of endogenous RG selection for halophiles responding to salt stress. This work provides a valuable theory and an approach reference of internal control identification for ddPCR-based stress response models.Keywords: endogenous reference gene, salt stress, ddPCR, RT-qPCR, Alkalicoccus halolimnae
Procedia PDF Downloads 962122 Spatial Cluster Analysis of Human Cases of Crimean Congo Hemorrhagic Fever Reported in Pakistan
Authors: Tariq Abbas, Younus Muhammad, Sayyad Aun Muhammad
Abstract:
Background : Crimean Congo hemorrhagic fever (CCHF) is a tick born viral zoonotic disease that has been notified from almost all regions of Pakistan. The aim of this study was to investigate spatial distribution of CCHF cases reported to National Institue of Health , Islamabad during year 2013. Methods : Spatial statistics tools were applied to detect extent spatial auto-correlation and clusters of the disease based on adjusted cumulative incidence per million population for each district. Results : The data analyses revealed a large multi-district cluster of high values in the uplands of Balochistan province near Afghanistan border. Conclusion : The cluster included following districts: Pishin; Qilla Abdullah; Qilla Saifullah; Quetta, Sibi; Zhob; and Ziarat. These districts may be given priority in CCHF surveillance, control programs, and further epidemiological research . The location of the cluster close to border of Afghanistan and Iran highlight importance of the findings for organizations dealing with disease at national, regional and global levels.Keywords: Crimean Congo hemorrhagic fever, Pakistan, spatial autocorrelation, clusters , adjusted cumulative incidence
Procedia PDF Downloads 4042121 Gene Expression Profile Reveals Breast Cancer Proliferation and Metastasis
Authors: Nandhana Vivek, Bhaskar Gogoi, Ayyavu Mahesh
Abstract:
Breast cancer metastasis plays a key role in cancer progression and fatality. The present study examines the potential causes of metastasis in breast cancer by investigating the novel interactions between genes and their pathways. The gene expression profile of GSE99394, GSE1246464, and GSE103865 was downloaded from the GEO data repository to analyze the differentially expressed genes (DEGs). Protein-protein interactions, target factor interactions, pathways and gene relationships, and functional enrichment networks were investigated. The proliferation pathway was shown to be highly expressed in breast cancer progression and metastasis in all three datasets. Gene Ontology analysis revealed 11 DEGs as gene targets to control breast cancer metastasis: LYN, DLGAP5, CXCR4, CDC6, NANOG, IFI30, TXP2, AGTR1, MKI67, and FTH1. Upon studying the function, genomic and proteomic data, and pathway involvement of the target genes, DLGAP5 proved to be a promising candidate due to it being highly differentially expressed in all datasets. The study takes a unique perspective on the avenues through which DLGAP5 promotes metastasis. The current investigation helps pave the way in understanding the role DLGAP5 plays in metastasis, which leads to an increased incidence of death among breast cancer patients.Keywords: genomics, metastasis, microarray, cancer
Procedia PDF Downloads 932120 An Investigative Study on the Use of Online Marketing Methods in Hungary
Authors: E. Happ, Zs. Ivancsone Horvath
Abstract:
With the development of the information technology, IT, sector, all industry of the world has a new path, dealing with digitalisation. Tourism is the most rapidly increasing industry in the world. Without digitalisation, tourism operators would not be competitive enough with foreign destinations or other experience-based service providers. Digitalisation is also necessary to enable organizations, which are interested in tourism to meet the growing expectations of consumers. With the help of digitalisation, tourism providers can also obtain information about tourists, changes in consumer behaviour, and the use of online services. The degree of digitalisation in tourism is different for different services. The research is based on a questionnaire survey conducted in 2018 in Hungary. The sample with more than 500 respondents was processed by the SPSS program, using a variety of analysis methods. The following two variables were observed from more aspects: frequency of travel and the importance of services related to online travel. With the help of these variables, a cluster analysis was performed among the participants. The sample can be divided into two groups using K-mean cluster analysis. Cluster ‘1’ is a positive group; they can be called the “most digital tourists.” They agree in most things, with low standard deviation, and for them, digitalisation is a starting point. To the members of Cluster ‘2’, digitalisation is important, too. The results show what is important (accommodation, information gathering) to them, but also what they are not interested in at all within the digital world (e.g., car rental or online sharing). Interestingly, there is no third negative cluster. This result (that there is no result) proves that tourism uses digitalisation, and the question is only the extent of the use of online tools and methods. With the help of the designed consumer groups, the characteristics of digital tourism segments can be identified. The help of different variables characterised these groups. One of them is the frequency of travel, where there is a significant correlation between travel frequency and cluster membership. The shift is clear towards Cluster ‘1’, which means, those who find services related to online travel more important, are more likely to travel as well. By learning more about digital tourists’ consumer behaviour, the results of this research can help the providers in what kind of marketing tools could be used to influence the consumer choices of the different consumer groups created using digital devices, furthermore how to conduct more detailed and effective marketing activities. The main finding of the research was that most of the people have digital tools which are important to be able to participate in e-tourism. Of these, mobile devices are increasingly preferred. That means the challenge for service providers is no longer the digital presence but having optimised application for different devices.Keywords: cluster analysis, digital tourism, marketing tool, tourist behaviour
Procedia PDF Downloads 1222119 Mutational Analysis of DNase I Gene in Diabetic Patients
Authors: Hateem Zafar Kayani, Nageen Hussain
Abstract:
The main aim is to analyze the mutations of DNASE I gene in diabetic patients. A total of 120 diabetes patients and 120 controls were sampled. The total number of male diabetic patients included in the study was 79 (66%) while female patients were 41 (34%) in number. Exon 8 of the DNASE I gene was amplified by using thermo cycler. The possible band of interest was located at 165 base pairs. Two samples showed similar missense mutations at 127th position of exon 8 which replaced amino acid Arginine (Arg) to Glutamine (Gln). All controls showed no mutations. The association of diabetes with different levels of blood pressure and body mass index (BMI) were found to be significant.Keywords: deoxyribonuclease I, polymerase chain reaction, insulin-dependent diabetes mellitus, non-insulin dependent diabetes mellitus
Procedia PDF Downloads 3182118 A Minimum Spanning Tree-Based Method for Initializing the K-Means Clustering Algorithm
Authors: J. Yang, Y. Ma, X. Zhang, S. Li, Y. Zhang
Abstract:
The traditional k-means algorithm has been widely used as a simple and efficient clustering method. However, the algorithm often converges to local minima for the reason that it is sensitive to the initial cluster centers. In this paper, an algorithm for selecting initial cluster centers on the basis of minimum spanning tree (MST) is presented. The set of vertices in MST with same degree are regarded as a whole which is used to find the skeleton data points. Furthermore, a distance measure between the skeleton data points with consideration of degree and Euclidean distance is presented. Finally, MST-based initialization method for the k-means algorithm is presented, and the corresponding time complexity is analyzed as well. The presented algorithm is tested on five data sets from the UCI Machine Learning Repository. The experimental results illustrate the effectiveness of the presented algorithm compared to three existing initialization methods.Keywords: degree, initial cluster center, k-means, minimum spanning tree
Procedia PDF Downloads 4032117 Prognostic Implication of Nras Gene Mutations in Egyptian Adult Acute Myeloid Leukemia
Authors: Doaa M. Elghannam, Nashwa Khayrat Abousamra, Doaa A. Shahin, Enas F. Goda, Hanan Azzam, Emad Azmy, Manal Salah El-Din
Abstract:
Background: The pathogenesis of acute myeloid leukemia (AML) involves the cooperation of mutations promoting proliferation/survival and those impairing differentiation. Point mutations of the NRAS gene are the most frequent somatic mutations causing aberrant signal-transduction in acute myeloid leukemia (AML). Aim: The present work was conducted to study the frequency and prognostic significance of NRAS gene mutations (NRASmut) in de novo Egyptian adult AML. Material and methods: Bone marrow specimens from 150 patients with de novo acute myeloid leukemia and controls were analyzed by genomic PCR-SSCP at codons 12, 13 (exon 1), and 61 (exon 2) for NRAS mutations. Results: NRAS gene mutations was found in 19/150 (12.7%) AML cases, represented more frequently in the FAB subtype M4eo (P = 0.028), and at codon 12, 13 (14of 19; 73.7%). Patients with NRASmut had a significant lower peripheral marrow blasts (P = 0.004, P=0.03) and non significant improved clinical outcome than patients without the mutation. Complete remission rate was (63.2% vs 56.5%; p=0.46), resistant disease (15.8% vs 23.6%; p=0.51), three years overall survival (44% vs 42%; P = 0.85) and disease free survival (42.1% vs 38.9%, P = 0.74). Multivariate analysis showed that age was the strongest unfavorable factor for overall survival (relative risk [RR], 1.9; P = .002), followed by cytogenetics (P = .004). FAB types, NRAS mutation, and leukocytosis were less important. Conclusions: NRAS gene mutation frequency and spectrum differ between biologically distinct subtypes of AML but do not significantly influence prognosis and clinical outcome.Keywords: NRAS Gene, egyptian adult, acute myeloid leukemia, cytogenetics
Procedia PDF Downloads 892116 Verification & Validation of Map Reduce Program Model for Parallel K-Mediod Algorithm on Hadoop Cluster
Authors: Trapti Sharma, Devesh Kumar Srivastava
Abstract:
This paper is basically a analysis study of above MapReduce implementation and also to verify and validate the MapReduce solution model for Parallel K-Mediod algorithm on Hadoop Cluster. MapReduce is a programming model which authorize the managing of huge amounts of data in parallel, on a large number of devices. It is specially well suited to constant or moderate changing set of data since the implementation point of a position is usually high. MapReduce has slowly become the framework of choice for “big data”. The MapReduce model authorizes for systematic and instant organizing of large scale data with a cluster of evaluate nodes. One of the primary affect in Hadoop is how to minimize the completion length (i.e. makespan) of a set of MapReduce duty. In this paper, we have verified and validated various MapReduce applications like wordcount, grep, terasort and parallel K-Mediod clustering algorithm. We have found that as the amount of nodes increases the completion time decreases.Keywords: hadoop, mapreduce, k-mediod, validation, verification
Procedia PDF Downloads 3612115 Variation in Carboxylesterase Activity in Spodoptera litura Fabricious (Noctuidae: Lepidoptera) Populations from India
Authors: V. Karuppaiah, J. C. Padaria, C. Srivastava
Abstract:
The tobacco caterpillar, Spodoptera litura Fab (Lepidoptera: Noctuidae) is a polyphagous pest various field and horticulture crops in India. Pest had virtually developed resistance to all commonly used insecticides. Enhanced detoxification is the prime mechanism that is dictated by detoxification different enzymes and carboxylesterase is one of the major enzyme responsible development of resistance. In India, insecticide resistance studies on S. litura are mainly deployed on detoxification enzymes activity and investigation at gene level alteration i.e. at nucleotide level is very merger. In the present study, we collected the S. litura larvae from three different cauliflower growing belt viz., IARI, New Delhi (Delhi), Palari, Sonepat (Haryana) and Varanasi (Uttar Pradesh) to study the role of carboxylesterase activity and its gene level variation The CarE activity was measured using UV-VIS spectrophotometer with 3rd instar larvae of S. litura. The elevated activity of CarE was observed in Sonepat strain (28.09 ± 0.09 µmol/min/mg of protein) followed by Delhi (26.72 ± 0.04 µmol/min/mg of protein) and Varanasi strain (10.00 ± 0.44 µmol/min/mg of protein) of S. litura. The genomic DNA was isolated from 3rd instar larvae and CarE gene was amplified using a primer sequence, F:5’tccagagttccttgtcaggcac3’; R:5’ctgcatcaagcatgtctc3. CarE gene, about 500bp was partially amplified, sequenced and submitted to NCBI (Accession No. KF835886, KF835887 and KF835888). The sequence data revealed polymorphism at nucleotide level in all the three strains and gene found to have 88 to 97% similarity with previous available nucleotide sequences of S. litura, S. littoralis and S. exiqua. The polymorphism at the nucleotide level could be a reason for differential activity of carboxylesterase enzymes among the strains. However, investigation at gene expression level would be useful to analyze the overproduction of carboxylesterase enzyme.Keywords: carboxylesterase, CarE gene, nucleotide polymorphism, insecticide resistance, spodoptera litura
Procedia PDF Downloads 9162114 Analysing Industry Clustering to Develop Competitive Advantage for Wualai Silver Handicraft
Authors: Khanita Tumphasuwan
Abstract:
The Wualai community of Northern Thailand represents important intellectual and social capital and their silver handicraft products are desirable tourist souvenirs within Chiang Mai Province. This community has been in danger of losing this social and intellectual capital due to the application of an improper tool, the Scottish Enterprise model of clustering. This research aims to analyze and increase its competitive advantages for preventing the loss of social and intellectual capital. To improve the Wualai’s competitive advantage, analysis is undertaken using a Porterian cluster approach, including the diamond model, five forces model and cluster mapping. Research results suggest that utilizing the community’s Buddhist beliefs can foster collaboration between community members and is the only way to improve cluster effectiveness, increase competitive advantage, and in turn conserve the Wualai community.Keywords: industry clustering, silver handicraft, competitive advantage, intellectual capital, social capital
Procedia PDF Downloads 5572113 Gene Distribution of CB1 Receptor rs2023239 in Thailand Cannabis Patients
Authors: Tanyaporn Chairoch
Abstract:
Introduction: Cannabis is a drug to treat patients with many diseases such as Multiple sclerosis, Alzheimer’s disease, and Epilepsy, where theycontain many active compounds such as delta-9 tetrahydrocannabinol (THC) and cannabidiol (CBD). Especially, THC is the primary psychoactive ingredient in cannabis and binds to cannabinoid 1 (CB1) receptors. Moreover, CB1 is located on the neocortex, hippocampus, basal ganglia, cerebellum, and brainstem. In previous study, we found the association between the variant of CB1recptors gene (rs2023239) and decreased effect of nicotine reinforcement in patients. However, there are no data describing whether the distribution of CB1 receptor gene is a genetic marker for Thai patients who are treated with cannabis. Objective: Thus, the aim of this study we want to investigate the frequency of the CB1 receptor gene in Thai patients. Materials and Methods: All of sixty Thai patients received the medical cannabis for treatment who were recruited in this study. DNA will be extracted from EDTA whole blood by Genomic DNA Mini Kit. The genotyping of CNR1 gene (rs 2023239) was genotyped by the TaqMan real time PCR assay (ABI, Foster City, CA, USA).and using the real-time PCR ViiA7 (ABI, Foster City, CA, USA). Results: We found thirty-eight (63.3%) Thai patients were female, and twenty-two (36.70%) were male in this study with median age of 45.8 (range19 – 87 ) years. Especially, thirty-two (53.30%) medical cannabis tolerant controls were female ( 55%) and median age of52.1 (range 27 – 79 ) years. The most adverse effects for medical cannabis treatment was tachycardia. Furthermore, the number of rs 2023239 (TT) carriers was 26 of 27 (96.29%) in medical cannabis-induced adverse effects and 32 of 33 (96.96%) in tolerant controls. Additionally, rs 2023239 (CT) variant was found just only one of twenty-seven (3.7%) in medical cannabis-induced adverse effects and 1 of 33 (3.03%) in tolerant controls. Conclusions: The distribution of genetic variant in CNR1 gene might serve as a pharmacogenetics markers for screening before initiating the therapy with medical cannabis in Thai patients.Keywords: cannabis, pharmacogenetics, CNR1 gene, thai patient
Procedia PDF Downloads 1012112 Modeling of CREB Pathway Induced Gene Induction: From Stimulation to Repression
Authors: K. Julia Rose Mary, Victor Arokia Doss
Abstract:
Electrical and chemical stimulations up-regulate phosphorylaion of CREB, a transcriptional factor that induces its target gene production for memory consolidation and Late Long-Term Potentiation (L-LTP) in CA1 region of the hippocampus. L-LTP requires complex interactions among second-messenger signaling cascade molecules such as cAMP, CAMKII, CAMKIV, MAPK, RSK, PKA, all of which converge to phosphorylate CREB which along with CBP induces the transcription of target genes involved in memory consolidation. A differential equation based model for L-LTP representing stimulus-mediated activation of downstream mediators which confirms the steep, supralinear stimulus-response effects of activation and inhibition was used. The same was extended to accommodate the inhibitory effect of the Inducible cAMP Early Repressor (ICER). ICER is the natural inducible CREB antagonist represses CRE-Mediated gene transcription involved in long-term plasticity for learning and memory. After verifying the sensitivity and robustness of the model, we had simulated it with various empirical levels of repressor concentration to analyse their effect on the gene induction. The model appears to predict the regulatory dynamics of repression on the L-LTP and agrees with the experimental values. The flux data obtained in the simulations demonstrate various aspects of equilibrium between the gene induction and repression.Keywords: CREB, L-LTP, mathematical modeling, simulation
Procedia PDF Downloads 2882111 Bean in Turkey: Characterization, Inter Gene Pool Hybridization Events, Breeding, Utilizations
Authors: Faheem Shahzad Baloch, Muhammad Azhar Nadeem, Muhammad Amjad Nawaz, Ephrem Habyarimana, Gonul Comertpay, Tolga Karakoy, Rustu Hatipoglu, Mehmet Zahit Yeken, Vahdettin Ciftci
Abstract:
Turkey is considered a bridge between Europe, Asia, and Africa and possibly played an important role in the distribution of many crops including common bean. Hundreds of common bean landraces can be found in Turkey, particularly in farmers’ fields, and they consistently contribute to the overall production. To investigate the existing genetic diversity and hybridization events between the Andean and Mesoamerican gene pools in the Turkish common bean, 188 common bean accessions (182 landraces and 6 modern cultivars as controls) were collected from 19 different Turkish geographic regions. These accessions were characterized using phenotypic data (growth habit and seed weight), geographic provenance, 12557 high-quality whole-genome DArTseq markers, and 3767 novel DArTseq loci were also identified. The clustering algorithms resolved the Turkish common bean landrace germplasm into the two recognized gene pools, the Mesoamerican and Andean gene pools. Hybridization events were observed in both gene pools (14.36% of the accessions) but mostly in the Mesoamerican (7.97% of the accessions), and was low relative to previous European studies. The lower level of hybridization witnessed the existence of Turkish common bean germplasm in its original form as compared to Europe. Mesoamerican gene pool reflected a higher level of diversity, while the Andean gene pool was predominant (56.91% of the accessions), but genetically less diverse and phenotypically more pure, reflecting farmers greater preference for the Andean gene pool. We also found some genetically distinct landraces and overall, a meaningful level of genetic variability which can be used by the scientific community in breeding efforts to develop superior common bean strains.Keywords: bean germplasm, DArTseq markers, genotyping by sequencing, Turkey, whole genome diversity
Procedia PDF Downloads 2392110 Dwindling the Stability of DNA Sequence by Base Substitution at Intersection of COMT and MIR4761 Gene
Authors: Srishty Gulati, Anju Singh, Shrikant Kukreti
Abstract:
The manifestation of structural polymorphism in DNA depends on the sequence and surrounding environment. Ample of folded DNA structures have been found in the cellular system out of which DNA hairpins are very common, however, are indispensable due to their role in the replication initiation sites, recombination, transcription regulation, and protein recognition. We enumerate this approach in our study, where the two base substitutions and change in temperature embark destabilization of DNA structure and misbalance the equilibrium between two structures of a sequence present at the overlapping region of the human COMT gene and MIR4761 gene. COMT and MIR4761 gene encodes for catechol-O-methyltransferase (COMT) enzyme and microRNAs (miRNAs), respectively. Environmental changes and errors during cell division lead to genetic abnormalities. The COMT gene entailed in dopamine regulation fosters neurological diseases like Parkinson's disease, schizophrenia, velocardiofacial syndrome, etc. A 19-mer deoxyoligonucleotide sequence 5'-AGGACAAGGTGTGCATGCC-3' (COMT19) is located at exon-4 on chromosome 22 and band q11.2 at the intersection of COMT and MIR4761 gene. Bioinformatics studies suggest that this sequence is conserved in humans and few other organisms and is involved in recognition of transcription factors in the vicinity of 3'-end. Non-denaturating gel electrophoresis and CD spectroscopy of COMT sequences indicate the formation of hairpin type DNA structures. Temperature-dependent CD studies revealed an unusual shift in the slipped DNA-Hairpin DNA equilibrium with the change in temperature. Also, UV-thermal melting techniques suggest that the two base substitutions on the complementary strand of COMT19 did not affect the structure but reduces the stability of duplex. This study gives insight about the possibility of existing structurally polymorphic transient states within DNA segments present at the intersection of COMT and MIR4761 gene.Keywords: base-substitution, catechol-o-methyltransferase (COMT), hairpin-DNA, structural polymorphism
Procedia PDF Downloads 117