Search results for: gene regulatory network

Authors: Shahram Nanekarani, Majid Goodarzi, Majid Khosravi

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The present study aimed at analyzing of ovine major histocompatibility complex class II (Ovar II) DRB1 gene second exon in Lori Sheep breed. The MHC plays a central role in the control of disease resistance and immunological response. Genomic DNA from blood samples of 124 sheep was extracted and a 296 bp MHC exon 2 fragment was amplified using polymerase chain reaction. PCR products were characterized by the restriction fragment length polymorphism technique using Hin1I restriction enzyme. The PCRRFLP patterns showed three genotypes, AA, AB and BB with frequency of 0.282, 0.573 and 0.145, respectively. There was no significant (P > 0.05) deviation from Hardy–Weinberg equilibrium for this locus in this population. The results of the present study indicate that exon 2 of the Ovar-DRB1 gene is highly polymorphic in Lori sheep and could be considered as an important marker assisted selection, for improvement of immunity in sheep.

Keywords: MHC-DRB1 gene, polymorphism, PCR-RFLP, lori sheep

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Authors: Emine Şahin, Murat Soner Balcıoğlu

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The aim of this study was to determine the growth hormone (bGH) gene polymorphism in the Holstein cattle growing around Antalya in Turkey. In order to determine the bGH-AluI polymorphism, polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) method was performed. A 891 bp fragment of bGH was amplified and two types of alleles C and D for bGH were observed. In this study, the frequencies of C and D alleles were 0.8438 and 0.1562, respectively. The genotype frequencies for CC, CD and DD were 0.787, 0.191 and 0.022, respectively. According to the results of the chi-square test, a significant deviation from the Hardy-Weinberg equilibrium was not determined for the bGH locus in the population.

Keywords: Growth Hormone Gene, Holstein , Polymorphism, RFLP

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Authors: Tong Ming Liu

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Human mesenchymal stem cells (MSCs) represent the most used stem cells for clinical application, which have been used in over 1000 clinical trials to treat over 30 diseases due to multilineage differentiation potential, secretome and immunosuppression. Gene therapies of MSCs hold great promise in the treatment of many diseases due to enhanced MSC-based clinical outcomes. To identify genes for gene therapy of MSCs, by comparing gene expression profile before and after MSC differentiation following by functional screening, we have identified ZNF145 that regulated MSC differentiation. Forced expression of ZNF145 resulted in enhanced in vitro chondrogenesis of MSCs as an upstream factor of SOX9 and improved osteochondral repair upon implant into osteochondral defects in rodents. By comparing gene expression profile during differentiation of iPSCs toward MSCs, we also identified gene HOX regulating MSC stemness, which was much downregulated in late-passaged MSCs. Knockdown of this gene greatly compromised MSC stemness including abolished proliferation, decreased CFU-F, promoted senescence and reduced expression of cell surface antigens linked to the MSC phenotype. In addition, multi-linage differentiation was also greatly impaired. Notably, HOX overexpression resulted in improved multi-lineage differentiation. In the mechanism, HOX expression significantly deceased in late passage of MSCs compared with early passage of MSCs, correlating with MSC important genes. ChIP-seq data shown that HOX binds to genes related to MSC self-renewal and differentiation. Most importantly, most HOX binding sites are lost in late passage of MSCs. HOX exerts its effects by directing binding Twist1, one important gene of MSCs. The identification of the genes regulating MSC differentiation and stemness will provide and promising strategies for gene therapy of MSCs in regenerative medicine.

Keywords: mesenchymal stem cell, novel transcription factor, stemness, gene therapy, cartilage repair, signaling pathway

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Authors: Yasser M. Saad, Heba El-Sebaie Abd El-Sadek

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Some Metapenaeus monoceros cox1 gene fragments were isolated, purified, sequenced, and comparatively analyzed with some other Crustacean Cox1 gene sequences (obtained from National Center for Biotechnology Information). This work was designed for testing the efficiency of this system in reconstruction of phylogenetic relations among some Crustacean species belonging to four genera (Metapenaeus, Artemia, Daphnia and Calanus). The single nucleotide polymorphism and haplotype diversity were calculated for all estimated mt-DNA fragments. The genetic distance values were 0.292, 0.015, 0.151, and 0.09 within Metapenaeus species, Calanus species, Artemia species, and Daphnia species, respectively. The reconstructed phylogenetic tree is clustered into some unique clades. Cytochrome oxidase subunit 1 gene (cox1) was a powerful system in reconstruction of phylogenetic relations among evaluated crustacean species.

Keywords: crustaceans, genetics, Cox1, phylogeny

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Authors: Tety Hartatik, Dian Kurniawati, Adiarto

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The aim of the research was to determine the associations between polymorphism of the bovine growth hormone (GH) gene (Leu/Val, L/V) and milk production of Friesian Holstein Cattle. A total of 62 cows which consist of two Friesian Holstein groups (cattle from New Zealand are 19 heads and cattle from Australia are 43 heads). We perform the PCR and RFLP method for analyzing the genotype of the target gene GH 211 bp in the part of intron 4 and exon 5 of GH gene. The frequencies of genotypes LL were higher than genotype LV. The number of genotype LL in New Zealand and Australia groups are 84% and 79%, respectively. The number of genotype LV in New Zealand and Australia groups are 16% and 21%, respectively. The association between Leu/Val polymorphism on milk production, fat and protein content in both groups does not show the significant effect. However base on the groups (cows from New Zealand compare with those from Australia) show the significant effect on fat and protein content.

Keywords: Friesian Holstein, fat content, growth hormone gene, milk production, PCR-RLFP, protein content

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Authors: Jacek Kabzinski, Karolina Przybylowska, Lukasz Dziki, Adam Dziki, Ireneusz Majsterek

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The incidence of colorectal cancer (CRC) is increasing from year to year. Despite intensive research CRC etiology remains unknown. Studies suggest that at the basis of the process of carcinogenesis can lie reduced efficiency of DNA repair mechanisms, often caused by polymorphisms in DNA repair genes. The aim of the study was to determine the relationship between gene polymorphisms Pro242Arg of PolB gene and Arg780His of Lig3 gene and modulation of the risk of colorectal cancer in the Polish population. Determination of the molecular basis of carcinogenesis process and predicting increased risk will allow qualifying patients to increased risk group and including them in preventive program. We used blood collected from 110 patients diagnosed with colorectal cancer. The control group consisted of equal number of healthy people. Genotyping was performed by TaqMan method. The obtained results indicate that the genotype 780Arg/His of Lig3 gene is associated with an increased risk of colorectal cancer. On the basis of these results, we conclude that Lig3 gene polymorphism Arg780His may be associated with an increased risk of colorectal cancer.

Keywords: BER, colorectal cancer, PolB, Lig3, polymorphisms

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Authors: W. Loongyai, N. Saengsawang, W. Danvilai, C. Kridtayopas, P. Sopannarath, C. Bunchasak

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Betong chicken is a slow growing and a lean strain of chicken, while the rapid growth of broiler is accompanied by increased fat. We investigated the growth performance, fat accumulations, lipid serum biochemical levels and lipoprotein lipase (LPL) gene expression of female Betong (KU line) at the age of 4 and 6 weeks. A total of 80 female Betong chickens (KU line) and 80 female broiler chickens were reared under open system (each group had 4 replicates of 20 chicks per pen). The results showed that feed intake and average daily gain (ADG) of broiler chicken were significantly higher than Betong (KU line) (P < 0.01), while feed conversion ratio (FCR) of Betong (KU line) at week 6 were significantly lower than broiler chicken (P < 0.01) at 6 weeks. At 4 and 6 weeks, two birds per replicate were randomly selected and slaughtered. Carcass weight did not significantly differ between treatments; the percentage of abdominal fat and subcutaneous fat yield was higher in the broiler (P < 0.01) at 4 and 6 week. Total cholesterol and LDL level of broiler were higher than Betong (KU line) at 4 and 6 weeks (P < 0.05). Abdominal fat samples were collected for total RNA extraction. The cDNA was amplified using primers specific for LPL gene expression and analysed using real-time PCR. The results showed that the expression of LPL gene was not different when compared between Betong (KU line) and broiler chickens at the age of 4 and 6 weeks (P > 0.05). Our results indicated that broiler chickens had high growth rate and fat accumulation when compared with Betong (KU line) chickens, whereas LPL gene expression did not differ between breeds.

Keywords: lipoprotein lipase gene, Betong (KU line), broiler, abdominal fat, gene expression

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Authors: Imran Hashmi, Sipkaduwa Arachchige Sashika Sureni Wickramasooriya

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Gene-drive technology has emerged as a promising tool for disease control by influencing the population dynamics of disease-carrying organisms. Various gene drive mechanisms, derived from global laboratory experiments, aim to strategically manage and prevent the spread of targeted diseases. One prominent strategy involves population replacement, wherein genetically modified mosquitoes are introduced to replace the existing local wild population. To enhance our understanding and aid in the design of effective release strategies, we employ a comprehensive mathematical model. The utilized approach employs agent-based modeling, enabling the consideration of individual mosquito attributes and flexibility in parameter manipulation. Through the integration of an agent-based model and a meta-population spatial approach, the dynamics of gene drive mosquito spreading in a released site are simulated. The model's outcomes offer valuable insights into future population dynamics, providing guidance for the development of informed release strategies. This research significantly contributes to the ongoing discourse on the responsible and effective implementation of gene drive technology for disease vector control.

Keywords: gene drive, agent-based modeling, disease-carrying organisms, malaria

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Authors: Omar S. Sharaf

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The mitochondrial 12s rRNA (mt-12s rDNA) gene for pig-specific was developed to detect material from pork species in different products collected from Jordanian market. The amplification PCR products of 359 bp and 531 bp were successfully amplified from the cyt b gene of pig the amplification product using mt-12S rDNA gene were successfully produced a single band with a molecular size of 456 bp. In the present work, the PCR amplification of mtDNA of cytochrome b has been shown as a suitable tool for rapid detection of pig DNA. 100 samples from different dairy, gelatin and chocolate based products and 50 samples from baby food formula were collected and tested to a presence of any pig derivatives. It was found that 10% of chocolate based products, 12% of gelatin and 56% from dairy products and 5.2% from baby food formula showed single band from mt-12S rDNA gene.

Keywords: halal food, baby infant formula, chocolate based products, PCR, Jordan

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Authors: Mahmoud Mabrok, Channarong Rodkhum

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Flavobacterium columanre is one of the devastating pathogen that causes noticeable economic losses in freshwater cultured fish. Like other filamentous bacteria, F. columanre tends to aggregate and fluctuate to all kind of media, thus revealing obstacles in recognition of its colonies. Since the molecular typing is the only fundamental tool for rapid and precise detection of this pathgen. The present study developed a species-specific PCR assay based on cslA unique gene of F. columnare. The cslA gene sequences of 13 F. columnare, strains retrieved from gene bank database, were aligned to identify a conserved homologous segment prior to primers design. The new primers yielded amplicons of 287 bp from F. columnare strains but not from relevant or other pathogens, unlike to other published set that showed no specificity and cross-reactivity with F. indicum. The primers were sensitive and detected as few as 7 CFUs of bacteria and 3 pg of gDNA template. The sensitivity was reduced ten times when using tissue samples. These primers precisely defined all field isolates in a double-blind study, proposing their applicable use for field detection.

Keywords: Columnaris infection, cslA gene, Flavobacterium columnare, PCR

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Authors: Gwenyth C. Eichfeld

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Variation in global COVID-19 spread is partly explained by social and behavioral factors. Many of these behaviors are linked to genetics. The short polymorphism of the 5-HTTLPR promoter region of the SLC6A4 gene is linked to collectivism. The seven-repeat polymorphism of the DRD4 gene is linked to risk-taking, migration, sensation-seeking, and impulsivity. Fewer CAG repeats in the androgen receptor gene are linked to impulsivity. This study investigates an association between the country-level frequency of these variants and early Covid-19 spread. Results of regression analysis indicate a significant association between increased country-wide prevalence of the short allele of the SLC6A4 gene and decreased COVID-19 spread when other factors that have been linked to COVID-19 are controlled for. Additionally, results show that the short allele of the SLC6A4 gene is associated with COVID-19 spread through GDP and percent urbanization rather than collectivism. Results showed no significant association between the frequency of the DRD4 polymorphism nor the androgen receptor polymorphism with early COVID-19 spread.

Keywords: neuroscience, genetics, population sciences, Covid-19

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Authors: Nihed Bahria El Asghar, Imen Jouili, Mounir Frikha

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Inter-datacenter transport network is very bandwidth and delay demanding. The data transferred over such a network is also highly QoS-exigent mostly because a huge volume of data should be transported transparently with regard to the application user. To avoid the data transfer failure, a backup path should be reserved. No re-routing delay should be observed. A dedicated 1+1 protection is however not applicable in inter-datacenter transport network because of the huge spare capacity. In this context, we propose a survivable virtual network with minimal backup based on network coding (1 ⊕ 1) and solve it using a modified Dijkstra-based heuristic.

Keywords: network coding, dedicated protection, spare capacity, inter-datacenters transport network

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Authors: Wissem Abdaoui, Nizar M. Mhaidat, Ilhem Mokhtari, Adel Gouri

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Colorectal cancer (CRC) is one of the most common tumors all over the world. Obesity, considered a risk factor of CRC, is characterized by a high level of secreted cytokines from adipose tissue. Among these inflammatory molecules, leptin is considered the key mediator for CRC cancer development and progression by activation of mitogenic and anti apoptotic signaling pathways. Gene expression can be significantly modulated by alterations in DNA methylation patterns. The aim of this study is to investigate the impact of leptin gene methylation on CRC prognosis and sensitivity to chemotherapy. The study involved 70 CRC tissue samples collected from King Abdullah University Hospital (KAUH) from which only 53 was analyzed because of bisulfate fragmentation and low yield of DNA extracted from FFPE tissues. A total of 22 blood samples were collected from healthy volunteers and enrolled as a control group. Leptin promoter methylation was analyzed by methylation specific PCR after bisulfate conversion. Results revealed that the incidence of leptin gene methylation was significantly higher in CRC patients in comparison to that of controls (P < 0.05). The correlation between patient’s demographics and leptin gene methylation was not significant (P < 0.05). However, a significant correlation between leptin gene methylation status and early cancer stages (I, II and III) was found in male but not in female (p < 0.05). Moreover, a significant correlation was found between leptin promoter methylation and early tumor localization T1-2 (p < 0.05). The correlation between epigenetic regulation of leptin and chemosensitivity was not significant. Taken together, these results suggest the possibility to use leptin gene methylation as a biomarker for the evaluation of CRC prognosis and metastasis.

Keywords: colorectal cancer, obesity, leptin, DNA methylation, disease prognosis, bisulfate conversion, chemoresistance

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Authors: Abigail Ekeigwe, Bethany McGowan, Loran C. Parker, Stephen Byrn, Kari L. Clase

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There are growing calls in the literature to develop and implement competency-based regulatory sciences education (CBRSE) in sub-Saharan Africa to expand and create a pipeline of a competent workforce of regulatory scientists. A defined competence framework is an essential component in developing competency-based education. However, such a competence framework is not available for regulatory scientists in sub-Saharan Africa. The purpose of this research is to identify entry-level competencies for inclusion in a competency framework for regulatory scientists in sub-Saharan Africa as a first step in developing CBRSE. The team systematically reviewed the literature following the PRISMA guidelines for systematic reviews and based on a pre-registered protocol on Open Science Framework (OSF). The protocol has the search strategy and the inclusion and exclusion criteria for publications. All included publications were coded to identify entry-level competencies for regulatory scientists. The team deductively coded the publications included in the study using the 'framework synthesis' model for systematic literature review. The World Health Organization’s conceptualization of competence guided the review and thematic synthesis. Topic and thematic codings were done using NVivo 12™ software. Based on the search strategy in the protocol, 2345 publications were retrieved. Twenty-two (n=22) of the retrieved publications met all the inclusion criteria for the research. Topic and thematic coding of the publications yielded three main domains of competence: knowledge, skills, and enabling behaviors. The knowledge domain has three sub-domains: administrative, regulatory governance/framework, and scientific knowledge. The skills domain has two sub-domains: functional and technical skills. Identification of competencies is the primal step that serves as a bedrock for curriculum development and competency-based education. The competencies identified in this research will help policymakers, educators, institutions, and international development partners design and implement competence-based regulatory science education in sub-Saharan Africa, ultimately leading to access to safe, quality, and effective medical products.

Keywords: competence-based regulatory science education, competencies, systematic review, sub-Saharan Africa

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Authors: Katharina Ninaus, Ralf Terlutter, Sandra Diehl

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Information and communication technologies (ICT) have become pervasive in all areas of modern life, both in work and leisure. Technological developments and particularly the ubiquity of smartphones have made it possible for ICT consumers to be constantly connected to work, fostering an always-on mentality and increasing the pressure to be accessible at all times. However, performing work tasks outside of working hours using ICT results in a lack of mental detachment and recovery from work. It is, therefore, necessary to develop effective behavioral interventions to increase risk awareness of a constant connection to the workplace in the employed population. Drawing on regulatory focus theory, this study aims to investigate the persuasiveness of tailoring messages to individuals’ chronic regulatory focus in order to encourage ICT consumers to set boundaries by defining fixed times for professional accessibility outside of working hours in order to contribute to the well-being of ICT consumers with high ICT involvement in their work life. The experimental study examines the interaction effect between consumers’ chronic regulatory focus (i.e. promotion focus versus prevention focus) and positive or negative message framing (i.e. gain frame versus loss frame) on consumers’ intention to perform the advocated behavior. Based on the assumption that congruent messages create regulatory fit and increase message effectiveness, it is hypothesized that behavioral intention will be higher in the condition of regulatory fit compared to regulatory non-fit. It is further hypothesized that ad believability and attitude toward the ad will mediate the effect of regulatory fit on behavioral intention given that ad believability and ad attitude both determine consumer behavioral responses. Results confirm that the interaction between regulatory focus and message frame emerged as a predictor of behavioral intention such as that consumers’ intentions to set boundaries by defining fixed times for professional accessibility outside of working hours increased as congruency with their regulatory focus increased. The loss-framed ad was more effective for consumers with a predominant prevention focus, while the gain-framed ad was more effective for consumers with a predominant promotion focus. Ad believability and attitude toward the ad both emerged as predictors of behavioral intention. Mediation analysis revealed that the direct effect of the interaction between regulatory focus and message frame on behavioral intention was no longer significant when including ad believability and ad attitude as mediators in the model, indicating full mediation. However, while the indirect effect through ad believability was significant, the indirect effect through attitude toward the ad was not significant. Hence, regulatory fit increased ad believability, which then increased behavioral intention. Ad believability appears to have a superior effect indicating that behavioral intention does not depend on attitude toward the ad, but it depends on whether or not the ad is perceived as believable. The study shows that the principle of regulatory fit holds true in the context of ICT consumption and responds to calls for more research on mediators of health message framing effects.

Keywords: always-on mentality, Information and communication technologies (ICT) consumption, message framing, regulatory focus

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Authors: Jing Zhang

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To reduce the carbon footprint of mankind and become more sustainable is one of the major challenges in our era. Internet of Things (IoT) mainly resolves three problems: Things to Things (T2T), Human to Things, H2T), and Human to Human (H2H). Borrowing the classification of IoT, we can find carbon prints of industries also can be divided in these three ways. Therefore, monitoring the routes of generation and circulation of products may help calculate product carbon print. This paper does not consider any technique used by IoT itself, but the ideas of it look at the connection of products. Carbon prints are like a gene or mark of a product from raw materials to the final products, which never leave the products. The contribution of this paper is to combine the characteristics of IoT and the methodology of network science to find a way to calculate the product's carbon footprint. Life cycle assessment, LCA is a traditional and main tool to calculate the carbon print of products. LCA is a traditional but main tool, which includes three kinds.

Keywords: product carbon footprint, Internet of Things, network science, life cycle assessment

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Authors: Saeedeh Salimi, Farzaneh Farajian- Mashhadi, Ehsan Tabatabaei, Mahnaz Shahrakipoor, Minoo Yaghmaei, Mojgan Mokhtari

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Purpose: Estrogen receptor-α (ERα) plays an essential role in the adaptation of increased uterine blood flow during gestation. Therefore ERα gene could be a possible candidate for preeclampsia(PE) susceptibility. In the current study, we aimed to investigate the association of the ERα gene polymorphisms and PE in an Iranian population. Methods: One hundred ninety-two pregnant women with PE and 186 normotensive women were genotyped for ERα gene (PvuII and XbaI) polymorphisms by PCR-RFLP method. Results: The frequency of alleles and genotypes of ERα PvuII and XbaI polymorphisms were not different between PE and normotensive control women. However, higher frequency of GG genotype was observed in women with severe PE compared to mild PE (OR, 1.8 [95% CI, 1.1 to 3]; P = 0.02) and in severe PE compared to normotensive women [OR= 1.8(1.1-3), P=0.02] after adjusting for age, ethnicity and primiparity. Conclusions: The GG genotype of ERα XbaI polymorphism could be a genetic risk factor for PE predisposition.

Keywords: estrogen receptor-α, polymorphism, gene, preeclampsia

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Authors: Thelma Maria Melo Pinheiro, Guilherme Raposo Diniz Vieira, Sidney Matos da Silva, Leonardo Mendonça de Oliveira Queiroz, Mateus Sousa Pinheiro, Danyllo Wenceslau de Oliveira Lopes

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The present article has the objective to describe the regulatory impact analysis (RIA) of the contracting efficiency of the Brazilian transmission system usage. This contracting is made by users connected to the main transmission network and is used to guide necessary investments to supply the electrical energy demand. Therefore, an inefficient contracting of this energy amount distorts the real need for grid capacity, affecting the sector planning accuracy and resources optimization. In order to provide this efficiency, the Brazilian Electricity Regulatory Agency (ANEEL) homologated the Normative Resolution (NR) No. 666, from July 23th of 2015, which consolidated the procedures for the contracting of transmission system usage and the contracting efficiency verification. Aiming for a more efficient and rational transmission system contracting, the resolution established economic incentives denominated as Inefficiency installment for excess (IIE) and inefficiency installment for over-contracting (IIOC). The first one, IIE, is verified when the contracted demand exceeds the established regulatory limit; it is applied to consumer units, generators, and distribution companies. The second one, IIOC, is verified when the distributors over-contract their demand. Thus, the establishment of the inefficiency installments IIE and IIOC intends to avoid the agent contract less energy than necessary or more than it is needed. Knowing that RIA evaluates a regulatory intervention to verify if its goals were achieved, the results from the application of the above-mentioned normative resolution to the Brazilian transmission sector were analyzed through indicators that were created for this RIA to evaluate the contracting efficiency transmission system usage, using real data from before and after the homologation of the normative resolution in 2015. For this, indicators were used as the efficiency contracting indicator (ECI), excess of demand indicator (EDI), and over-contracting of demand indicator (ODI). The results demonstrated, through the ECI analysis, a decrease of the contracting efficiency, a behaviour that was happening even before the normative resolution of 2015. On the other side, the EDI showed a considerable decrease in the amount of excess for the distributors and a small reduction for the generators; moreover, the ODI notable decreased, which optimizes the usage of the transmission installations. Hence, with the complete evaluation from the data and indicators, it was possible to conclude that IIE is a relevant incentive for a more efficient contracting, indicating to the agents that their contracting values are not adequate to keep their service provisions for their users. The IIOC also has its relevance, to the point that it shows to the distributors that their contracting values are overestimated.

Keywords: contracting, electricity regulation, evaluation, regulatory impact analysis, transmission power system

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Authors: Gülçin Akbas Uslu

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Honor cultures put importance on the sexual purity of women. Women are expected to avoid acts that may spoil their honor. The emphasis on honor leads to the subordination of women and the dominance of men. In order to protect and clean honor, women are exposed to physical and psychological violence. Therefore, understanding the motivations driving people to endorse honor bears importance. For this purpose, this study aims to explore honor endorsement from the joint perspective of System Justification Theory (SJT) and Regulatory Focus Theory (RFT). SJT asserts that people have a tendency to support and rationalize the system. The motivation to maintain the system may be a factor in the endorsement of honor. RFT proposes two distinct regulatory processes, namely promotion and prevention focus. Having a dominant prevention focus, such as a deep concern for responsibilities, risk avoidance, and minimizing negative outcomes, may have a role in honor. Data were collected conveniently from 366 participants (216 women; 150 men). Participants filled out Honor Endorsement Index, Honor Based System Justification Scale and Regulatory Focus Orientation Scale Results revealed that both regulatory focus and system justification play a role in understanding honor. One-way ANOVA findings showed that individuals with a dominant prevention focus endorse honor beliefs more than individuals with a dominant promotion focus. Besides, regression analysis revealed that prevention focus and system justification significantly and positively predict honor. Results provide clarifications for why honor has an important meaning in individuals’ life and why honor-based violence is approved. These findings bear great importance in Turkey, where emphasis on honor is high and can be used in reducing people’s adherence to honor, which is based on women’s sexuality and men’s power over women.

Keywords: honor, system justification theory, regulatory focus theory, prevention focus

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Authors: Narayan Moger, Divya B., Preethi Jambagi, Krishnaveni C. K., Apsana M. R., B. R. Patil, Basvaraj Bagewadi

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Salinity is one of the major threats to world food security. Considering the requirement for salt tolerant crop plants in the present study was undertaken to clone and transferred the salt tolerant ectA gene from marine ecosystem into agriculture crop system to impart salinity tolerance. Ectoine is the compatible solute which accumulates in the cell membrane, is known to be involved in salt tolerance activity in most of the Halophiles. The present situation is insisting to development of salt tolerant transgenic lines to combat abiotic stress. In this background, the investigation was conducted to develop transgenic tomato lines by cloning and transferring of ectA gene is an ectoine derivative capable of enzymatic action for the production of acetyl-diaminobutyric acid. The gene ectA is involved in maintaining the osmotic balance of plants. The PCR amplified ectA gene (579bp) was cloned into T/A cloning vector (pTZ57R/T). The construct pDBJ26 containing ectA gene was sequenced by using gene specific forward and reverse primers. Sequence was analyzed using BLAST algorithm to check similarity of ectA gene with other isolates. Highest homology of 99.66 per cent was found with ectA gene sequences of isolates Halomonas elongata with the available sequence information in NCBI database. The ectA gene was further sub cloned into pRI101-AN plant expression vector and transferred into E. coli DH5α for its maintenance. Further pDNM27 was mobilized into A. tumefaciens LBA4404 through tri-parental mating system. The recombinant Agrobacterium containing pDNM27 was transferred into tomato plants through In planta plant transformation method. Out of 300 seedlings, co-cultivated only twenty-seven plants were able to well establish under the greenhouse condition. Among twenty-seven transformants only twelve plants showed amplification with gene specific primers. Further work must be extended to evaluate the transformants at T1 and T2 generations for ectoine accumulation, salinity tolerance, plant growth and development and yield.

Keywords: salinity, computable solutes, ectA, transgenic, in planta transformation

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Authors: Felice Elefant, Akanksha Bhatnaghar, Keegan Krick, Elizabeth Heller

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Context: The severity of Alzheimer’s Disease (AD) progression involves an interplay of genetics, age, and environmental factors orchestrated by histone acetyltransferase (HAT) mediated neuroepigenetic mechanisms. While disruption of Tip60 HAT action in neural gene control is implicated in AD, alternative mechanisms underlying Tip60 function remain unexplored. Altered RNA splicing has recently been highlighted as a widespread hallmark in the AD transcriptome that is implicated in the disease. Research Aim: The aim of this study was to identify a novel RNA binding/splicing function for Tip60 in human hippocampus and impaired in brains from AD fly models and AD patients. Methodology/Analysis: The authors used RNA immunoprecipitation using RNA isolated from 200 pooled wild type Drosophila brains for each of the 3 biological replicates. To identify Tip60’s RNA targets, they performed genome sequencing (DNB-SequencingTM technology, BGI genomics) on 3 replicates for Input RNA and RNA IPs by Tip60. Findings: The authors' transcriptomic analysis of RNA bound to Tip60 by Tip60-RNA immunoprecipitation (RIP) revealed Tip60 RNA targets enriched for critical neuronal processes implicated in AD. Remarkably, 79% of Tip60’s RNA targets overlap with its chromatin gene targets, supporting a model by which Tip60 orchestrates bi-level transcriptional regulation at both the chromatin and RNA level, a function unprecedented for any HAT to date. Since RNA splicing occurs co-transcriptionally and splicing defects are implicated in AD, the authors investigated whether Tip60-RNA targeting modulates splicing decisions and if this function is altered in AD. Replicate multivariate analysis of transcript splicing (rMATS) analysis of RNA-Seq data sets from wild-type and AD fly brains revealed a multitude of mammalian-like AS defects. Strikingly, over half of these altered RNAs were bonafide Tip60-RNA targets enriched for in the AD-gene curated database, with some AS alterations prevented against by increasing Tip60 in fly brain. Importantly, human orthologs of several Tip60-modulated spliced genes in Drosophila are well characterized aberrantly spliced genes in human AD brains, implicating disruption of Tip60’s splicing function in AD pathogenesis. Theoretical Importance: The authors' findings support a novel RNA interaction and splicing regulatory function for Tip60 that may underlie AS impairments that hallmark AD etiology. Data Collection: The authors collected data from RNA immunoprecipitation experiments using RNA isolated from 200 pooled wild type Drosophila brains for each of the 3 biological replicates. They also performed genome sequencing (DNBSequencingTM technology, BGI genomics) on 3 replicates for Input RNA and RNA IPs by Tip60. Questions: The question addressed by this study was whether Tip60 has a novel RNA binding/splicing function in human hippocampus and whether this function is impaired in brains from AD fly models and AD patients. Conclusions: The authors' findings support a novel RNA interaction and splicing regulatory function for Tip60 that may underlie AS impairments that hallmark AD etiology.

Keywords: Alzheimer's disease, cognition, aging, neuroepigenetics

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Authors: Feng Zhang

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Kashin-Beck disease (KBD) is a chronic osteochondropathy. The mechanism of hand growth and development failure of KBD remains elusive now. In this study, we conducted a two-stage genome-wide association study (GWAS) of palmar length-width ratio (LWR) of KBD, totally involving 493 Chinese Han KBD patients. Affymetrix Genome Wide Human SNP Array 6.0 was applied for SNP genotyping. Association analysis was conducted by PLINK software. Imputation analysis was performed by IMPUTE against the reference panel of the 1000 genome project. In the GWAS, the most significant association was observed between palmar LWR and rs2071358 of COL2A1 gene (P value = 4.68×10-8). Imputation analysis identified 3 SNPs surrounding rs2071358 with significant or suggestive association signals. Replication study observed additional significant association signals at both rs2071358 (P value = 0.017) and rs4760608 (P value = 0.002) of COL2A1 gene after Bonferroni correction. Our results suggest that COL2A1 gene was a novel susceptibility gene involved in the growth and development failure of hand of KBD.

Keywords: Kashin-Beck disease, genome-wide association study, COL2A1, hand

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Authors: Takumi Shindo, Koji Okamura

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The first generation of the wide area network was circuit centric network. How the optimal circuit can be signed was the most important issue to get the best performance. This architecture had succeeded for line based telephone system. The second generation was host centric network and Internet based on this architecture has very succeeded world widely. And Internet became as new social infrastructure. Currently the architecture of the network is based on the location of the information. This future network is called Information centric network (ICN). The information-centric network (ICN) has being researched by many projects and different architectures for implementation of ICN have been proposed. The goal of this study is to compare performances of those ICN architectures. In this paper, the authors propose general ICN model which can represent two typical ICN architectures and compare communication performances using request routing. Finally, simulation results are shown. Also, we assume that this network architecture should be adapt to energy on-demand routing.

Keywords: ICN, information centric network, CCN, energy

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Authors: Han-Qin Zheng, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Wen-Chi Chang

Abstract:

As the most important non-vascular plants, algae have many research applications, including high species diversity, biofuel sources, adsorption of heavy metals and, following processing, health supplements. With the increasing availability of next-generation sequencing (NGS) data for algae genomes and transcriptomes, an integrated resource for retrieving gene expression data and metabolic pathway is essential for functional analysis and systems biology in algae. However, gene expression profiles and biological pathways are displayed separately in current resources, and making it impossible to search current databases directly to identify the cellular response mechanisms. Therefore, this work develops a novel AlgaePath database to retrieve gene expression profiles efficiently under various conditions in numerous metabolic pathways. AlgaePath, a web-based database, integrates gene information, biological pathways, and next-generation sequencing (NGS) datasets in Chlamydomonasreinhardtii and Neodesmus sp. UTEX 2219-4. Users can identify gene expression profiles and pathway information by using five query pages (i.e. Gene Search, Pathway Search, Differentially Expressed Genes (DEGs) Search, Gene Group Analysis, and Co-Expression Analysis). The gene expression data of 45 and 4 samples can be obtained directly on pathway maps in C. reinhardtii and Neodesmus sp. UTEX 2219-4, respectively. Genes that are differentially expressed between two conditions can be identified in Folds Search. Furthermore, the Gene Group Analysis of AlgaePath includes pathway enrichment analysis, and can easily compare the gene expression profiles of functionally related genes in a map. Finally, Co-Expression Analysis provides co-expressed transcripts of a target gene. The analysis results provide a valuable reference for designing further experiments and elucidating critical mechanisms from high-throughput data. More than an effective interface to clarify the transcript response mechanisms in different metabolic pathways under various conditions, AlgaePath is also a data mining system to identify critical mechanisms based on high-throughput sequencing.

Keywords: next-generation sequencing (NGS), algae, transcriptome, metabolic pathway, co-expression

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Authors: Shima Behzadi

Abstract:

Background: In many human malignant tumors, microRNA expression is aberrant. This study investigates miR-141 as a prognostic marker in colorectal cancer with K-Ras mutation. Materials and methods: In this case-control study, 100 patients, mostly over the age of 50, who were diagnosed with colorectal cancer were selected. The pathology department of the Mostoufi Pathobiology and Genetics Laboratory in Tehran confirmed the presence of colorectal cancer in samples of paraffin-embedded colon tissue. The case group was composed of patients with codon 12 and 13 mutations in exon 2 of the K-Ras gene, while tumor samples of individuals without these mutations in exon 2 of the K-Ras gene were selected as the control group, with patient consent. The changes in the expression of miR-141 were examined in both groups. Results: The study found that 20% of the patients tested positive for codon 12 mutation, and 10% of patients had codon 13 mutation. As a result, in 30 cases, there was a higher level of miR-141 expression. The miR-141 gene expression level in K-Ras positive tumor samples was 1.5 times higher than its expression level in K-Ras negative samples. This increase in expression was statistically significant, with a p-value of less than 0.001, indicating that the observed results are highly statistically significant. Conclusion: The study revealed that the incidence of typical K-Ras gene mutations among the colorectal cancer patients in the sample matches the national average in Iran. Additionally, the expression of miR-141 can serve as a useful biomarker to aid in the prognosis of colorectal cancer.

Keywords: colorectal cancer, K-Ras gene, miR-141 marker, real time PCR, electrophoresis

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Authors: Anida Causevic-Ramosevac, Sabina Semiz

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The aim of this study was to investigate the association of four single nucleotide polymorphisms (SNPs) - rs673548, rs693 in ApoB gene, rs1800775 in CETP gene and rs4846914 in GALNT2 gene with parameters of type 2 diabetes (T2D) and diabetic dyslipidemia in the population of Bosnia and Herzegovina (BH). Materials and methods: Our study involved 352 patients with T2D and 156 healthy subjects. Biochemical and anthropometric parameters were measured in all participants. DNA was extracted from the peripheral blood for the purpose of genetic testing. Polymorphisms in ApoB (rs673548, rs693), CETP (rs1800775) and GALNT2 (rs4846914) genes were analyzed by using Sequenom IPLEX platform. Results: Our results demonstrated significant associations for rs180075 polymorphism in CETP gene with levels of fasting insulin (p = 0.020; p = 0.027; p = 0.044), triglycerides (p = 0.046) and ALT (p = 0.031) activity in control group. In group of diabetic patients, results showed a significant association of rs673548 in ApoB gene with levels of fasting insulin (p = 0.008), HOMA-IR (p = 0.013), VLDL-C (p = 0.037) and CRP (p = 0.029) and rs693 in ApoB gene with BMI (p = 0.025), systolic blood pressure (p = 0.027), fasting insulin (p = 0.037) and HOMA-IR (p = 0.023) levels. Significant associations were also observed for rs1800775 in CETP gene with triglyceride (p = 0.023) levels and rs4846914 in GALNT2 gene with HbA1C (p = 0.013) and triglyceride (p = 0.043) levels. Conclusion: In conclusion, this is the first study that examined the impact of variations of candidate genes on a wide range of metabolic parameters in BH population. Our results suggest an association of variations of ApoB, CETP and GALNT2 genes with specific markers of T2D and dyslipidemia. Further studies would be needed in order to confirm these genetic effects in other ethnic groups as well.

Keywords: ApoB, CETP, dyslipidemia, GALNT2, type 2 diabetes

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Authors: Sharon Yunger, Liat Altman, Yuval Garini, Yaron Shav-Tal

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Understanding the dynamics of transcription in living cells has improved since the development of quantitative fluorescence-based imaging techniques. We established a method for following transcription from a single copy gene in living cells. A gene tagged with MS2 repeats, used for mRNA tagging, in its 3' UTR was integrated into a single genomic locus. The actively transcribing gene was detected and analyzed by fluorescence in situ hybridization (FISH) and live-cell imaging. Several cell clones were created that differed in the promoter regulating the gene. Thus, comparative analysis could be obtained without the risk of different position effects at each integration site. Cells in S/G2 phases could be detected exhibiting two adjacent transcription sites on sister chromatids. A sharp reduction in the transcription levels was observed as cells progressed along the cell cycle. We hypothesized that a change in chromatin structure acts as a general mechanism during the cell cycle leading to down-regulation in the activity of some genes. We addressed this question by treating the cells with chromatin decondensing agents. Quantifying and imaging the treated cells suggests that chromatin structure plays a role both in regulating transcriptional levels along the cell cycle, as well as in limiting an active gene from reaching its maximum transcription potential at any given time. These results contribute to understanding the role of chromatin as a regulator of gene expression.

Keywords: cell cycle, living cells, nucleus, transcription

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Authors: Sezin Ekşioğlu

Abstract:

Multilabel classification has a huge importance for several applications, it is also a challenging research topic. It is a kind of supervised learning that contains binary targets. The distance between multilabel and binary classification is having more than one class in multilabel classification problems. Features can belong to one class or many classes. There exists a wide range of applications for multi label prediction such as image labeling, text categorization, gene functionality. Even though features are classified in many classes, they may not always be properly classified. There are many ensemble methods for the classification. However, most of the researchers have been concerned about better multilabel methods. Especially little ones focus on both efficiency of classifiers and pairwise relationships at the same time in order to implement better multilabel classification. In this paper, we worked on modified ensemble methods by getting benefit from k-Nearest Neighbors and neural network structure to address issues within a beneficial way and to get better impacts from the multilabel classification. Publicly available datasets (yeast, emotion, scene and birds) are performed to demonstrate the developed algorithm efficiency and the technique is measured by accuracy, F1 score and hamming loss metrics. Our algorithm boosts benchmarks for each datasets with different metrics.

Keywords: multilabel, classification, neural network, KNN

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Authors: Debora P. Arce, Flavia J. Krsticevic, Marco R. Bertolaccini, Joaquín Ezpeleta, Estela M. Valle, Sergio D. Ponce, Elizabeth Tapia

Abstract:

Small Heat Shock Proteins (sHSPs) are low molecular weight chaperones that play an important role during stress response and development in all living organisms. Fruit maturation and oxidative stress can induce sHSP synthesis both in Arabidopsis and tomato plants. RNA-Seq technology is becoming widely used in various transcriptomics studies; however, analyzing and interpreting the RNA-Seq data face serious challenges. In the present work, we de novo assembled the Solanum lycopersicum transcriptome for three different maturation stages (mature green, breaker and red ripe). Differential gene expression analysis was carried out during tomato fruit development. We identified 12 sHSPs differentially expressed that might be involved in breaker and red ripe fruit maturation. Interestingly, these sHSPs have different subcellular localization and suggest a complex regulation of the fruit maturation network process.

Keywords: sHSPs, maturation, tomato, RNA-Seq, assembly

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Authors: Chia-Jung Li, Li-Te Lin, Kuan-Hao Tsui

Abstract:

The study identifies SPP1 as a potential gene associated with ovarian aging, revealing a significant decline in its expression in aged ovaries. SPP1, also known as osteopontin (OPN), is a multifunctional glycoprotein involved with regulatory proteins and pro-inflammatory immune chemokines. However, its genetic links to ovarian aging have not been extensively explored. Spatial transcriptomic analyses were conducted on ovaries from young and aged female mice, along with a sample from a 73-year-old individual. Additionally, single-cell RNA sequencing analysis was performed to identify associations between SPP1 and key genes. The study focused on crucial genes, including ITGAV, ITGB1, CD44, MMP3, and FN1, with a particular emphasis on the correlation between SPP1 and ITGB1. The findings indicate a significant decline in SPP1 expression in aged ovaries, which was consistent in the 73-year-old sample. Single-cell RNA sequencing unveiled associations between SPP1 and key genes, emphasizing a strong co-expression correlation between SPP1 and ITGB1. While the study provides valuable insights, further research is necessary to understand the broader implications and potential applications of SPP1 in ovarian aging. Translating these findings to clinical settings requires careful consideration. The identification of SPP1 as a gene implicated in ovarian aging opens new avenues for advancing precision medicine and refining treatment strategies for conditions related to ovarian aging.

Keywords: SPP1, ovarian aging, spatial transcriptomic, single-cell RNA sequencing

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