Search results for: Ammonia monooxygenase α-subunit gene

Authors: Hajar Hosseini Khorami

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Porphyrins are organic, aromatic compounds found in heme, cytochrome, cobalamin, chlorophyll , and many other natural products with essential roles in biological processes that their cationic forms have been used as groups of favorable non-viral vectors recently. Cationic porphyrins are self-chromogenic reagents with a high capacity for modifications, great interaction with DNA and protection of DNA from nuclease during delivery of it into a cell with low toxicity. In order to have high efficient gene transfection into the cell while causing low toxicity, genetically manipulations of the non-viral vector, cationic porphyrin, would be useful. In this study newly modified cationic porphyrin derivative, 5, 10-dihexyl-15, 20bis (N-methyl-4-pyridyl) porphyrin was applied. Cytotoxicity of synthesized cationic porphyrin on Chinese Hamster Ovarian (CHO) cells was evaluated by using MTT assay. This cationic derivative is dose-dependent, with low cytotoxicity at the ranges from 100 μM to 0.01μM. It was uptake by cells at high concentration. Using direct non-viral gene transfection method and different concentration of cationic porphyrin were tested on transfection of CHO cells by applying derived transfection reagent with X-tremeGENE HP DNA as a positive control. However, no transfection observed by porphyrin derivative and the parameters tested except for positive control. Results of this study suggested that applying different protocol, and also trying other concentration of cationic porphyrins and DNA for forming a strong complex would increase the possibility of efficient gene transfection by using cationic porphyrins.

Keywords: cationic porphyrins, gene delivery, non-viral vectors, transfection reagents

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Authors: Ngoc Tu Truong, Nuong T. Bui, Ben Rao, Ya L. Shen

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Quorum sensing is a phenomenon present in many gram-negative bacteria that allows bacterial communication and controlled expression of a large suite of genes through quorum sensing signals - N-acyl homoserine lactones (AHLs). In order to investigate the ability of the rhlR/rhlI quorum sensing system in Pseudomonas aeruginosa to express the ß-Galactosidase reporter gene, an engineered E. coli strain EpHL02, was genetically engineered. This engineered E. coli strain EpHL02 responded to the presence of the N-butanoyl homoserine lactone and N-hexanoyl homoserine lactone to express the ß-Galactosidase reporter gene at a concentration limit of 5x10⁻⁸ M. This was also found to be comparable to AHLs extraction from Serratia marcescens H31. Moreover, we examined this ability of this engineered E. coli strain for respond of AHLs from extractions of Pseudomonas aeruginosa ATCC9027. The results demonstrated that the rhlR/rhlI quorum sensing system can express the ß-Galactosidase reporter gene by using the N-butanoyl homoserine lactone, N-hexanoyl homoserine lactone and AHLs from extractions of Serratia marcescens H31 and Pseudomonas aeruginosa ATCC9027 in the engineered E. coli strain EpHL02.

Keywords: N-butanoyl homoserine lactone, C4-HSL, N-hexanoyl homoserine lactone, C6-HSL, Pseudomonas aeruginosa, quorum sensing, Serratia marcescens, ß-galactosidase reporter gene

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Authors: Saad Mahmud Khan, Sarah El Hajj Chehadeh, Mehera Abdulrahman, Wael Osman, Habiba Al Safar

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Obesity is a non-communicable disease that is widely prevalent with approximately 600 million people classified as obese worldwide. Its etiology is multifactorial and involves a complex interplay between genes and the environment. Over the past few decades, obesity rates among the Emirati population have been increasing. The aim of this study was to investigate the association of candidate gene single nucleotide polymorphisms (SNPs), namely the fat mass and obesity associated (FTO) gene SNP rs9939609 and Vitamin D Receptor (VDR) gene SNP rs1544410, with obesity in the UAE population. Methods: This is a case-control study in which 414 individuals were enrolled during their routine visit to endocrinology clinics in Abu Dhabi, United Arab Emirates between the period of June 2012 and December 2013. Several biochemical tests and clinical assessments along with a lifestyle questionnaire for each participant were completed at the clinic. Genomic DNA was extracted from saliva samples of 201 obese, 114 overweight and 99 normal subjects. Genotyping for the variants was performed using TaqMan assay. Results: The mean Body Mass Index (BMI) ± SD for the obese, overweight, and normal subjects was 35.76 ± 4.54, 27.53 ± 1.45 and 22.69 ± 1.84 kg/m2, respectively. Increasing BMI values were associated with an increase in values for systolic blood pressure, diastolic blood pressure, HbA1c, and triglycerides. The SNP rs9939609 in the FTO gene was found to be significantly associated with the BMI (p=0.028), with the minor allele A having a clear additive effect on BMI values. No significant association was detected between BMI and rs1544410 of the VDR gene. Conclusions: Our study findings indicate that the minor allele A of the rs9939609 has a significant association with increasing BMI values. In addition, our findings support the fact that increasing BMI is associated with increasing risks of other comorbidities such as higher blood pressure, poorer glycemic control and higher triglycerides.

Keywords: body mass index, FTO gene, obesity, rs9939609, United Arab Emirates

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Authors: Libo Jiang, Huan Li, Rongling Wu

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

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

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Authors: Piotr J. Balwierz, Mikhail Pachkov, Phil Arnold, Andreas J. Gruber, Mihaela Zavolan, Erik van Nimwegen

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Understanding the key players and interactions in the regulatory networks that control gene expression and chromatin state across different cell types and tissues in metazoans remains one of the central challenges in systems biology. Our laboratory has pioneered a number of methods for automatically inferring core gene regulatory networks directly from high-throughput data by modeling gene expression (RNA-seq) and chromatin state (ChIP-seq) measurements in terms of genome-wide computational predictions of regulatory sites for hundreds of transcription factors and micro-RNAs. These methods have now been completely automated in an integrated webserver called ISMARA that allows researchers to analyze their own data by simply uploading RNA-seq or ChIP-seq data sets and provides results in an integrated web interface as well as in downloadable flat form. For any data set, ISMARA infers the key regulators in the system, their activities across the input samples, the genes and pathways they target, and the core interactions between the regulators. We believe that by empowering experimental researchers to apply cutting-edge computational systems biology tools to their data in a completely automated manner, ISMARA can play an important role in developing our understanding of regulatory networks across metazoans.

Keywords: gene expression analysis, high-throughput sequencing analysis, transcription factor activity, transcription regulation

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Authors: Sabin Aslam, Sultan Habibullah Khan, James G. Thomson, Abhaya M. Dandekar

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Losses due to viral diseases are posing a serious threat to crop production. A quick breakdown of resistance to viruses like Cotton Leaf Curl Virus (CLCuV) demands the application of a proficient technology to engineer durable resistance. Gene stacking has recently emerged as a potential approach for integrating multiple genes in crop plants. In the present study, recombinase technology has been used for site-specific gene stacking. A target vector (pG-Rec) was designed for engineering a predetermined specific site in the plant genome whereby genes can be stacked repeatedly. Using Agrobacterium-mediated transformation, the pG-Rec was transformed into Coker-312 along with Nicotiana tabacum L. cv. Xanthi and Nicotiana benthamiana. The transgene analysis of target lines was conducted through junction PCR. The transgene positive target lines were used for further transformations to site-specifically stack two genes of interest using Bxb1 and PhiC31 recombinases. In the first instance, Cas9 driven by multiplex gRNAs (for Rep gene of CLCuV) was site-specifically integrated into the target lines and determined by the junction PCR and real-time PCR. The resulting plants were subsequently used to stack the second gene of interest (AVP3 gene from Arabidopsis for enhancing cotton plant growth). The addition of the genes is simultaneously achieved with the removal of marker genes for recycling with the next round of gene stacking. Consequently, transgenic marker-free plants were produced with two genes stacked at the specific site. These transgenic plants can be potential germplasm to introduce resistance against various strains of cotton leaf curl virus (CLCuV) and abiotic stresses. The results of the research demonstrate gene stacking in crop plants, a technology that can be used to introduce multiple genes sequentially at predefined genomic sites. The current climate change scenario highlights the use of such technologies so that gigantic environmental issues can be tackled by several traits in a single step. After evaluating virus resistance in the resulting plants, the lines can be a primer to initiate stacking of further genes in Cotton for other traits as well as molecular breeding with elite cotton lines.

Keywords: cotton, CRISPR/Cas9, gene stacking, genome editing, recombinases

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Authors: Amer A. Hasan, Mehri Igci, Ersin Borazan, Rozhgar A. Khailany, Emine Bayraktar, Ahmet Arslan

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Gastric cancer (GC) has high morbidity and fatality rate in various countries and is still one of the most frequent and deadly diseases. Novel mitogenic and motogenic Gastrokine1 (GKN1) and Gastrokine 2 (GKN2) genes that are highly expressed in the normal stomach epithelium and plays an important role in maintaining the integrity and homeostasis of stomach mucosal epithelial cells. Significant loss of copy number and mRNA transcript of GKN1 and GKN2 gene expression were frequently observed in all types of gastric cancer. In this study, 47 paired samples that were grouped according to the types of gastric cancer and the clinical characteristics of the patients, including gender and average of age were investigated with gene expression analysis and mutation screening by monetering RT-PCR, SSCP and nucleotide sequencing techniques. Both GKN1 and GKN2 genes were observed significantly reduced found by (Wilcoxon signed rank test; p<0.05). As a result of gene screening, no mutation (no different genotype) was detected. It is considered that gene mutations are not the cause of inactivation of gastrokines. In conclusion, the mRNA expression level of GKN1 and GKN2 genes statistically was decreased regardless the gender, age or cancer type of patients. Reduced of gastrokine genes seems to occur at the initial steps of cancer development. In order to understand the investigation between gastric cancer and diagnostic biomarker; further analysis is necessary.

Keywords: gastric cancer, diagnostic biomarker, nucleotide sequencing, semi-quantitative RT-PCR

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Authors: Valeriy M. Kondratev, Ekaterina A. Vyacheslavova, Talgat Shugabaev, Alexander S. Gudovskikh, Alexey D. Bolshakov

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Modern sensorics imposes strict requirements on the biosensors characteristics, especially technological feasibility, and selectivity. There is a growing interest in the analysis of human health biological markers, which indirectly testifying the pathological processes in the body. Such markers are acids and alkalis produced by the human, in particular - ammonia and hydrochloric acid, which are found in human sweat, blood, and urine, as well as in gastric juice. Biosensors based on modern nanomaterials, especially low dimensional, can be used for this markers detection. Most classical adsorption sensors based on metal and silicon oxides are considered non-selective, because they identically change their electrical resistance (or impedance) under the action of adsorption of different target analytes. This work demonstrates a feasible frequency-resistive method of electrical impedance spectroscopy data analysis. The approach allows to obtain of selectivity in adsorption sensors of a resistive type. The method potential is demonstrated with analyzis of impedance spectra of silicon nanowires in the presence of NH3 and HCl vapors with concentrations of about 125 mmol/L (2 ppm) and water vapor. We demonstrate the possibility of unambiguous distinction of the sensory signal from NH3 and HCl adsorption. Moreover, the method is found applicable for analysis of the composition of ammonia and hydrochloric acid vapors mixture without water cross-sensitivity. Presented silicon sensor can be used to find diseases of the gastrointestinal tract by the qualitative and quantitative detection of ammonia and hydrochloric acid content in biological samples. The method of data analysis can be directly translated to other nanomaterials to analyze their applicability in the field of biosensory.

Keywords: electrical impedance spectroscopy, spectroscopy data analysis, selective adsorption sensor, nanotechnology

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

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

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

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Authors: Xiaoling Ren, Guidong Yang

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Ammonia, as one of the largest-volume industrial chemicals, is mostly produced by century-old Haber-Bosch process with extreme conditionsand high-cost. Under the circumstance, researchersarededicated in finding new ways to replace the Haber-Bosch process. Photocatalytic nitrogen fixation is a promising sustainable, clear and green strategy for ammonia synthesis, butit is still a big challenge due to the high activation energy for nitrogen. It is essential to develop an efficient photocatalyst for making this approach industrial application. Constructing chemisorption active sites through defect engineering can be defined as an effective and reliable means to improve nitrogen activation by forming the extraordinary coordination environment and electronic structure. Besides, the construction of three-dimensionally orderdmacroporous (3DOM) structured photocatalyst is considered to be one of effectivestrategiesto improve the activity due to it canincrease the diffusion rate of reactants in the interior, which isbeneficial to the mass transfer process of nitrogen molecules in photocatalytic nitrogen reduction. Herein, Fe doped 3DOM WO₃(Fe-3DOM WO₃) without noble metal cocatalysts is synthesized by a polystyrene-template strategy, which is firstly used for photocatalytic nitrogen fixation. To elucidate the chemical nature of the dopant, the X-ray diffraction (XRD) analysiswas conducted. The pure 3DOM WO₃ has a monoclinic type crystal structure. And no additional peak is observed in Fe doped 3DOM WO₃, indicating that the incorporation of Fe atoms did not result in a secondary phase formation. In order to confirm the morphologies of Fe-3DOM WO₃and 3DOM WO₃, scanning electron microscopy (SEM) was employed. The synthesized Fe-3DOM WO₃and 3DOM WO₃ both exhibit a highly ordered three dimensional inverse opal structure with interconnected pores. From high-resolution TEM image of Fe-3DOM WO₃, the ordered lattice fringes with a spacing of 3.84 Å can be assigned to the (001) plane of WO₃, which is consistent with the XRD results. Finally, the photocatalytic nitrogen reduction performance of 3DOM WO₃ and Fe doped 3DOM WO₃with various Fe contents were examined. As a result, both Fe-3DOM WO₃ samples achieve higher ammonia production rate than that of pure 3DOM WO₃, indicating that the doped Fe plays a critical role in the photocatalytic nitrogen fixation performance. To verify the reaction process upon N2 reduction on the Fe-3DOM WO₃, in-situ diffuse reflectance infrared Fourier-transform spectroscopy was employed to monitor the intermediates. The in-situ DRIFTS spectra of Fe-3DOM WO₃ exhibit the increased signals with the irradiation time from 0–60min in the N2 atmosphere. The above results prove that nitrogen is gradually hydrogenated to produce ammonia over Fe-3DOM WO₃. Thiswork would enrich our knowledge in designing efficient photocatalystsfor photocatalytic nitrogen reduction.

Keywords: ammonia, photocatalytic, nitrogen fixation, Fe doped 3DOM WO₃

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Authors: Kazem Bashirnezhad, Seyed Ahmad Kebriyaee, saeed hoseyngholizadeh moghadam

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The urea–SCR catalyst system has the advantages of high NOx conversion efficiency and a wide range of operating conditions. The key factors for successful implementation of urea–SCR technology is good mixing of urea (ammonia) and gas to reduce ammonia slip. Urea mixer components are required to facilitate evaporation and mixing, because it is difficult to evaporate urea in the liquid state; the injection parameters are the most critical factors affecting mixer performance. In this study, The effect of urea injection on NOx emissions in a six-cylinder, four-stroke internal combustion engine fueled with B80 biodiesel has been experimentally investigated. The results reveal that urea injection leads to a reduction of NOx emissions of B80 biodiesel fuel. Moreover, the influence of injection parameters on NOx reductions has been studied. The findings show that by increasing the injection temperature, more reduction in NOx emissions has been occurred. Also, urea mass flow rate increment leads to more NOx reduction. The same result has been obtained by an increase in spray angle.

Keywords: urea, NOx emissions, diesel engines, biodiesels

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Authors: Sadaf Ilyas

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Recombinant cytokines have been employed successfully as potential therapeutic agent. Some cytokine therapies are already used as a part of clinical practice, ranging from early exploratory trials to well established therapies that have already received approval. Interleukin 15 is a pleiotropic cytokine having multiple roles in peripheral innate and adaptive immune cell function. It regulates the activation, proliferation and maturation of NK cells, T-cells, monocytes/macrophages and granulocytes, and the interactions between them thus acting as a bridge between innate and adaptive immune responses. Unraveling the biology of IL-15 has revealed some interesting surprises that may point toward some of the first therapeutic applications for this cytokine. In this study, the human interleukin 15 gene was isolated, amplified and ligated to a TA vector which was then transfected to a bacterial host, E. coli Top10F’. The sequence of cloned gene was confirmed and it showed 100% homology with the reported sequence. The confirmed gene was then subcloned in pET Expression system to study the IPTG induced expression of IL-15 gene. Positive expression was obtained for number of clones that showed 15 kd band of IL-15 in SDS-PAGE analysis, indicating the successful strain development that can be studied further to assess the potential therapeutic intervention of this cytokine in relevance to human diseases.

Keywords: Interleukin 15, pET expression system, immune therapy, protein purification

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Authors: Andi Setiawan, Annisa Ulfah Pristya

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Indonesian rubber plant area reached 2.9 million hectares with productivity reached 1.38 million. High rubber productivity is directly proportional to the amount of waste produced rubber processing industry. Rubber industry would produce a negative impact on the rubber industry in the form of environmental pollution caused by waste that has not been treated optimally. Rubber industrial wastewater containing high-nitrogen compounds (nitrate and ammonia) and phosphate compounds which cause water pollution and odor problems due to the high ammonia content. On the other hand, demand for NPK fertilizers in Indonesia continues to increase from year to year and in need of ammonia and phosphate as raw material. Based on domestic demand, it takes a year to 400,000 tons of ammonia and Indonesia imports 200,000 tons of ammonia per year valued at IDR 4.2 trillion. As well, the lack of phosphoric acid to be imported from Jordan, Morocco, South Africa, the Philippines, and India as many as 225 thousand tons per year. During this time, the process of wastewater treatment is generally done with a rubber on the tank to contain the waste and then precipitated, filtered and the rest released into the environment. However, this method is inefficient and thus require high energy costs because through many stages before producing clean water that can be discharged into the river. On the other hand, Indonesia has the potential of pineapple fruit can be harvested throughout the year in all of Indonesia. In 2010, production reached 1,406,445 tons of pineapple in Indonesia or about 9.36 percent of the total fruit production in Indonesia. Increased productivity is directly proportional to the amount of pineapple waste pineapple leaves are kept continuous and usually just dumped in the ground or disposed of with other waste at the final disposal. Through Eco-Nanofiltration Membrane-Based Fiber Pineapple leaves Waste so that environmental problems can be solved efficiently. Nanofiltration is a process that uses pressure as a driving force that can be either convection or diffusion of each molecule. Nanofiltration membranes that can split water to nano size so as to separate the waste processed residual economic value that N and P were higher as a raw material for the manufacture of NPK fertilizer to overcome the crisis in Indonesia. The raw materials were used to manufacture Eco-Nanofiltration Membrane is cellulose from pineapple fiber which processed into cellulose acetate which is biodegradable and only requires a change of the membrane every 6 months. Expected output target is Green eco-technology so with nanofiltration membranes not only treat waste rubber industry in an effective, efficient and environmentally friendly but also lowers the cost of waste treatment compared to conventional methods.

Keywords: biodegradable, cellulose diacetate, fertilizers, pineapple, rubber

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Authors: Chaiwat Boonkaewwan, Anutian Suklek, Jatuporn Rattanasrisomporn, Autchara Kayan

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Toll-like receptors (TLR) are conserved microbial sensing receptors located on cell surface that are able to detect different pathogens. The aim of the present study is to examine the expression of TLR gene in peripheral blood mononuclear cell of Betong (KU line) chicken. Blood samples were collected from healthy 12 Betong (KU line) chicken. PBMCs were isolated and maintained in RPMI1640 with 10% FBS, penicillin and streptomycin. Cell viability was determined by trypan blue dye exclusion test. The expression of TLRs gene was investigated by polymerase chain reaction (PCR) technique. Results showed that PBMCs viability from Betong (KU line) chicken was 95.38 ± 1.06%. From the study of TLRs gene expression, results indicated that there are expressions of TLR1.1 TLR1.2 TLR2.1 TLR2.2 TLR3 TLR4 TLR5 TLR 7 TLR15 and TLR21 in PBMCs of Betong (KU line) chicken. In conclusion, PBMCs isolated from blood of Betong (KU line) chicken had a high cell viability ( > 95%). The expression of TLRs in chicken was all found in PBMCs, which indicated that PBMC isolated from the blood of Betong (KU line) chicken can be used as an in vitro immune responses study.

Keywords: toll-like receptor, Betong (KU line) chicken, peripheral blood mononuclear cells

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Authors: Yijun Lai, Saber Khederzadeh, Lingshaung Han

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Species in Thunnus are organized due to the similarity between them. The closeness between T. maccoyii, T. thynnus, T. Tonggol, T. atlanticus, T. albacares, T. obsesus, T. alalunga, and T. orientails are in different degrees. However, the genetic pattern of differentiation has not been presented based on individuals yet, to the author’s best knowledge. Hence, we aimed to analyze the difference in individuals level of tuna species to identify the factors that contribute to the maternal lineage variety using Cytochrome c oxidase subunit I (COXI) gene sequences. Our analyses provided evidence of sharing lineages in the Thunnus. A phylogenetic analysis revealed that these lineages are basal to the other sequences. We also showed a close connection between the T. tonggol, T. thynnus, and T. albacares populations. Also, the majority of the T. orientalis samples were clustered with the T. alalunga and, then, T. atlanticus populations. Phylogenetic trees and migration modeling revealed high proximity of T. thynnus sequences to a few T. orientalis and suggested possible gene flow with T. tonggol and T. albacares lineages, while all T. obsesus samples indicated unique clustering with each other. Our results support the presence of old maternal lineages in Thunnus, as a legacy of an ancient wave of colonization or migration.

Keywords: Thunnus Tuna, phylogeny, maternal lineage, COXI gene

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Authors: Muhammad Ihsan Andi Dagong, Cece Sumantri, Ronny Rachman Noor, Rachmat Herman, Mohamad Yamin

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Calpastatin involved in various physiological processes in the body such as the protein turnover, growth, fusion and mioblast migration. Thus, allegedly Calpastatin gene diversity (CAST) have an association with growth and potential use as candidate genes for growth trait. This study aims to identify the association between the genetic diversity of CAST gene with some growth properties such as body dimention (morphometric), body weight and daily weight gain in sheep. A total of 157 heads of Thin Tail Sheep (TTS) reared intensively for fattening purposes in the uniform environmental conditions. Overall sheep used were male, and maintained for 3 months. The parameters of growth properties were measured among others: body weight gain (ADG) (g/head / day), body weight (kg), body length (cm), chest circumference (cm), height (cm). All the sheep were genotyped by using PCR-SSCP (single strand conformational polymorphism) methods. CAST gene in locus fragment intron 5 - exon 6 were amplified with a predicted length of about 254 bp PCR products. Then the sheep were stratified based on their CAST genotypes. The result of this research showed that no association were found between the CAST gene variations with morphometric body weight, but there was a significant association with daily body weight gain (ADG) in sheep observed. CAST-23 and CAST-33 genotypes has higher average daily gain than other genotypes. CAST-23 and CAST-33 genotypes that carrying the CAST-2 and CAST-3 alleles potential to be used in the selection of the nature of the growth trait of the TTS sheep.

Keywords: body weight, calpastatin, genotype, growth trait, thin tail sheep

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Authors: Youcef Sehili, Khaled Loubar, Lyes Tarabet, Mahfoudh Cerdoun, Clement Lacroix

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As emissions regulations grow more stringent and traditional fuel sources become increasingly scarce, incorporating carbon-free fuels in the transportation sector emerges as a key strategy for mitigating the impact of greenhouse gas emissions. While the utilization of hydrogen (H2) presents significant technological challenges, as evident in the engine limitation known as knocking, ammonia (NH3) provides a viable alternative that overcomes this obstacle and offers convenient transportation, storage, and distribution. Moreover, the implementation of a dual-fuel engine using ammonia as the primary gas is promising, delivering both ecological and economic benefits. However, when employing this combustion mode, the substitution of ammonia at high rates adversely affects combustion performance and leads to elevated emissions of unburnt NH3, especially under high loads, which requires special treatment of this mode of combustion. This study aims to simulate combustion in a common rail direct injection (CRDI) dual-fuel engine, considering the fundamental geometry of the combustion chamber as well as fifteen (15) alternative proposed geometries to determine the configuration that exhibits superior engine performance during high-load conditions. The research presented here focuses on improving the understanding of the equations and mechanisms involved in the combustion of finely atomized jets of liquid fuel and on mastering the CONVERGETM code, which facilitates the simulation of this combustion process. By analyzing the effect of piston bowl shape on the performance and emissions of a diesel engine operating in dual fuel mode, this work combines knowledge of combustion phenomena with proficiency in the calculation code. To select the optimal geometry, an evaluation of the Swirl, Tumble, and Squish flow patterns was conducted for the fifteen (15) studied geometries. Variations in-cylinder pressure, heat release rate, turbulence kinetic energy, turbulence dissipation rate, and emission rates were observed, while thermal efficiency and specific fuel consumption were estimated as functions of crankshaft angle. To maximize thermal efficiency, a synergistic approach involving the enrichment of intake air with oxygen (O2) and the enrichment of primary fuel with hydrogen (H2) was implemented. Based on the results obtained, it is worth noting that the proposed geometry (T8_b8_d0.6/SW_8.0) outperformed the others in terms of flow quality, reduction of pollutants emitted with a reduction of more than 90% in unburnt NH3, and an impressive improvement in engine efficiency of more than 11%.

Keywords: ammonia, hydrogen, combustion, dual-fuel engine, emissions

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Authors: Aran Abd Al Rahman

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Joubert syndrome regards as a congenital cerebellar ataxia caused by autosomal recessive carried on X chromosome. The disease diagnosed by brain imaging—the so-called molar tooth sign. Neurological signs were present from the neonatal period and include hypotonia progressing to ataxia, global developmental delay, ocular motor apraxia, and breathing dysregulation. These signs are variably associated with multiorgan involvement, mainly of the retina, kidneys, skeleton, and liver. 30 causative genes have been identified so far, all of which encode for proteins of the primary cilium or its apparatus, The purpose of our project was to detect the mutant gene (INPP5E gene) which cause Joubert syndrome. There were many methods used for diagnosis such as MRI and CT- scan and molecular diagnosis by doing ARMS PCR for detection of mutant gene that we were used in this research project. In this research for individual family which reported, the two children with parents, the two children were affected and were carrier.

Keywords: Joubert syndrome, genetic disease, Kurdistan region, Sulaimani

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Authors: H. Merhni, A. Sbiti, I. Ratbi, A. Sefiani

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The proximal spinal muscular atrophy (SMA) is a group of neuromuscular disorders characterized by progressive muscle weakness due to the degeneration and loss of anterior motor neurons of the spinal cord. Depending on the age of onset of symptoms and their evolution, four types of SMA, varying in severity, result in a mutations of the SMN gene (survival of Motor neuron). We have analyzed the DNA of 295 patients referred to our genetic counseling; since January 1996 until October 2014; for suspected SMA. The homozygous deletion of exon 7 of the SMN gene was found in 133 patients; of which, 40.6% were born to consanguineous parents. In countries like Morocco, where the frequency of heterozygotes for SMA is high, genetic testing should be offered as first-line and, after careful clinical assessment, especially in newborns and infants with congenital hypotonia unexplained and prognosis compromise. The molecular diagnosis of SMA allows a quick and certainly diagnosis, provide adequate genetic counseling for families at risk and suggest, for couples who want prenatal diagnosis. The analysis of the SMN gene is a perfect example of genetic testing with an excellent cost/benefit ratio that can be of great interest in public health, especially in low-income countries. We emphasize in this work for the benefit of the generalization of molecular diagnosis of SMA by the technique of PCR-enzymatic digestion in other centers in Morocco.

Keywords: Exon7, PCR-digestion, SMA, SMN gene

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Authors: Tahira Hussain, Ilhom Rahamkulov, Muhammad Aasim, Ugur Pirlak, Emre Aksoy, Mehmet Emin Caliskan, Allah Bakhsh

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RNA interference (RNAi) has proved its usefulness in functional genomic research on insects recently and is considered potential strategy in crop improvement for the control of insect pests. The different insect pests incur significant losses to potato yield worldwide, Colorado Potato Beetle (CPB) being most notorious one. The present study focuses to knock down highly specific 20-hydroxyecdysone hormone-receptor complex interaction by using RNAi approach to silence Ecdysone receptor (EcR) gene of CPB in transgenic potato plants expressing dsRNA of EcR gene. The partial cDNA of Ecdysone receptor gene of CPB was amplified using specific primers in sense and anti-sense orientation and cloned in pRNAi-GG vector flanked by an intronic sequence (pdk). Leaf and internodal explants of Lady Olympia, Agria and Granola cultivars of potato were infected with Agrobacterium strain LBA4404 harboring plasmid pRNAi-CPB, pRNAi-GFP (used as control). Neomycin phosphotransferase (nptII) gene was used as a plant selectable marker at a concentration of 100 mg L⁻¹. The primary transformants obtained have shown proper integration of T-DNA in plant genome by standard molecular analysis like polymerase chain reaction (PCR), real-time PCR, Sothern blot. The transgenic plants developed out of these cultivars are being evaluated for their efficacy against larvae as well adults of CPB. The transgenic lines are expected to inhibit expression of EcR protein gene, hindering their molting process, hence leading to increased potato yield.

Keywords: plant mediated RNAi, molecular strategy, ecdysone receptor, insect metamorphosis

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Authors: Kang-Hyun Leem, Myung-Gyou Kim, Hye Kyung Kim

Abstract:

Deer antler, traditionally used as a tonic and valuable drug in oriental medicine, has been considered to possess bone-strengthening activity. The upper section, mid section, and base of the antler has been known to exhibit different biological properties. Present study was performed to examine the effects of different parts of deer antler extract (DH) on osteogenic gene expressions in MG-63 cells and longitudinal bone growth in adolescent male rats. The expressions of osteogenic genes, collagen, alkaline phosphatase, osteocalcin, and osteopontin, were measured by quantitative real-time PCR. Longitudinal bone growth was measured in 3-week-old male Sprague-Dawley rats using fluorescence microscopy. To examine the effects on the growth plate metabolism, the total height of growth plate and bone morphogenetic protein-2 (BMP-2) were measured. Collagen and osteocalcin mRNA expressions were increased by all three parts of the DH treatment while osteopontin gene expression was not affected by any of the DH treatment. Alkaline phosphatase gene expression was increased by upper and mid part of DH while base part of DH fails to affect alkaline phosphatase gene expression. The upper and mid parts of the DH treatment enhanced longitudinal bone growth and total height of growth plate. The induction of BMP-2 protein expression in growth plate assessed by immunostaining was also promoted by upper and mid parts of the DH treatment. These results suggest that DH, especially upper and mid parts, stimulate osteogenic gene expressions and have the effect on bone growth in adolescent rats and might be used for the growth delayed adolescent and inherent growth failure patient.

Keywords: bone morphogenetic protein-2, deer antler, longitudinal bone growth, osteogenic genes

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Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo

Abstract:

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

Keywords: gene profiling, knowledge, Malaysia, physician

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Authors: Shivani Sharma, Prashant Saxena, Inamul Hasan Madar

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Since the time of Darwin, it has been considered that genetic change is the direct indicator of variation in phenotype. But a few studies in system biology in the past years have proposed that epigenetic developmental processes also affect the phenotype thus shifting the focus from a linear genotype-phenotype map to a non-linear G-P map. In this paper, we attempt at explaining the evolution of colour vision in mammals by taking LWS/ Long-wave sensitive gene under consideration.

Keywords: evolution, phenotypes, epigenetics, LWS gene, G-P map

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Authors: Maria Alekxandra B. Sison, Reginald C. Mallare, Joseph Albert M. Mendoza

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Ammonia (NH₃) is the alternative carbon-free fuel of the future for its promising applications. Investigations on NH₃-fuel blends recommend using hydrogen (H₂) to increase the heating value of NH3, promote combustion performance, and improve NOx efflux mitigation. To further examine the effects of this concept, the study analyzed the combustion performance, in terms of turbulence, combustion efficiency (CE), and NOx emissions, of NH3/fuel with variations of combustor diameter ratio, H2 fuel mole fraction, and fuel mass flow rate (ṁ). The simulations were performed using Computational Fluid Dynamics (CFD) modeling to represent a non-premixed (NP) and partially premixed (PP) combustion under a two-dimensional ultra-low NOx Rich-Burn, Quick-Quench, Lean-Burn (RQL) combustor. Governed by the Detached Eddy Simulation model, it was found that the diameter ratio greatly affects the turbulence in PP and NP mode, whereas ṁ in PP should be prioritized when increasing CE. The NOx emission is minimal during PP combustion, but NP combustion suggested modifying ṁ to achieve higher CE and Reynolds number without sacrificing the NO generation from the reaction.

Keywords: combustion efficiency, turbulence, dual-stage combustor, NOx emission

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Authors: Bopit Puyati, Anchittha Kaewchana, Nuntita Ruksachat

Abstract:

In January 2018, a male wild elephant, approximately 2 years old, was found dead in Phu Luang Wildlife Sanctuary, Loei province. The elephant was likely to die around 2 weeks earlier. The carcass was decayed without any signs of attack or bullet. No organs were removed. A deadly viral disease was suspected. Different organs including lung, liver, intestine and tongue were collected and submitted to the veterinary research and development center, Surin province for viral detection. The samples were then examined with real-time PCR for detecting U41 Major DNA binding protein (MDBP) gene and with conventional PCR for the presence of specific polymerase gene. We used tumor necrosis factor (TNF) gene as the internal control. In our real-time PCR, elephant endotheliotropic herpesvirus (EEHV) was recovered from lung, liver, and tongue whereas only tongue provided a positive result in the conventional PCR. All samples were positive with TNF gene detection. To our knowledge, this is the first report of EEHV detection in wild elephant in Thailand. EEHV surveillance in this wild population is strongly suggested. Linkage between EEHV in wild and domestic elephants should be further explored.

Keywords: elephant endotheliotropic herpes virus, PCR, Thailand, wild Asian elephant

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Authors: Jayesh Mahitkar, V. K. Singh, Surendra Singh Kachhwaha

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Wire Mesh Heat Pipe (WMHP) as an effective component of thermal control system in the payload of spacecraft, utilizing ammonia to transfer efficient amount of heat. One dimensional generic and robust mathematical model with partial-analytical hydraulic approach (PAHA) is developed to study inside behaviour of WMHP. In this model, inside performance during operation is investigated like mass flow rate, and velocity along the wire mesh as well as vapour core is modeled respectively. This numerical model investigate heat flow along length, pressure drop along wire mesh as well as vapour line in axial direction. Furthermore, WMHP is modeled into equivalent resistance network such that total thermal resistance of heat pipe, temperature drop across evaporator end and condenser end is evaluated. This numerical investigation should be carried out for single layer and double layer wire mesh each with heat input at evaporator section is 10W, 20 W and 30 W at condenser temperature maintained at 20˚C.

Keywords: ammonia, heat transfer, modeling, wire mesh

Procedia PDF Downloads 252

Authors: N. Allouache, O. Rahli

Abstract:

Solar radiation is by far the largest and the most world’s abundant, clean, and permanent energy source. In recent years, many promising technologies have been developed to harness the sun's energy. These technologies help in environmental protection, economizing energy, and sustainable development, which are the major issues of the world. One of these important technologies is the solar refrigerating machines that make use of either absorption or adsorption technologies. In this present work, the adsorbent bed is modelized and optimized using different working pairs, such as zeolite-water, silica gel-water, activated carbon-ammonia, calcium chlorid-ammonia, activated carbon fiber- methanol and activated carbon AC35-methanol. The results show that the enhancement of the heat and mass transfer depends on the properties of the working pair; the performances of the adsorption cycle are essentially influenced by the choice of the adsorbent-adsorbate pair. The system can operate successfully for optimal parameters such as the evaporator, condenser, and generating temperatures. The activated carbon is the best adsorbent due to its high surface area and micropore volume.

Keywords: adsorbent bed, heat and mass transfer, numerical analysis, working pairs

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Authors: Azna Zuberi

Abstract:

Biofilm is a sessile bacterial accretion in which bacteria adapts different physiological and morphological behavior from planktonic form. It is the root cause of about 80% microbial infections in human. Among them, E. coli biofilms are most prevalent in medical devices associated nosocomial infections. The objective of this study was to inhibit biofilm formation by targeting LuxS gene, involved in quorum sensing using CRISPRi. luxS is a synthase, involved in the synthesis of Autoinducer-2(AI-2), which in turn guides the initial stage of biofilm formation. To implement CRISPRi system, we have synthesized complementary sgRNA to target gene sequence and co-expressed with dCas9. Suppression of luxS was confirmed through qRT-PCR. The effect of luxS gene on biofilm inhibition was studied through crystal violet assay, XTT reduction assay and scanning electron microscopy. We conclude that CRISPRi system could be a potential strategy to inhibit bacterial biofilm through mechanism base approach.

Keywords: biofilm, CRISPRi, luxS, microbial

Procedia PDF Downloads 162

Authors: Małgorzata Wrzosek, Nina Baruch, Beata Jabłonowska-Lietz

Abstract:

Background: The fat mass & obesity-associated (FTO) gene is linked to an increased risk of obesity. However, the relation between rs9939609 and eating behaviors or energy expenditure is not fully elucidated. The aim of this study was to investigate the relationship between the rs9939609 polymorphism of the FTO gene and the postprandial satiety, sweets intake, physical activity and depressive symptoms in patients with obesity. Methods: The study group consisted of 585 subjects with a BMI of 42.97.0 kg/m². The rs9939609 polymorphism of the FTO gene was examined using real time – PCR method. The severity of depressive symptoms was assessed with the Beck Depression Inventory (BDI-II). Information was obtained about demographics, eating habits and lifestyle. Results: More than half (63.5%) of the patients reported consumption of sweets between main meals and 30% declared high and very high postprandial satiety and the frequency of TA/AA carriers in rs9939609 (FTO) compared with TT carriers was similar. Significantly lower BDI-II scores were found in subjects with higher level of physical activity and it was seen amongst patients with the AA and AT genotypes of the FTO rs9939609 polymorphism. Conclusion: Obesity is a highly heritable trait, but eating habits also appear as major factors affecting obesity development.

Keywords: FTO polymorphism, physical activity, obesity, depression, postprandial satiety, sugary foods, sweets

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Authors: Ahmad Ali Shahid, M Shakil Shaukat

Abstract:

Agriculture is the backbone of economy of Pakistan and Cotton is the major agricultural export and supreme source of raw fiber for our textile industry. To combat against the developing resistance in the target insects and combating these challenges wholesomely, a novel combination of pyramided/stacked genes was conceptualized and later realized, through the means of biotechnology i.e., transformation of three genes namely, Cry1Ac, Cry2A, and EPSP synthase (glyphosate tolerant) genes in the locally cultivated cotton variety. The progenies of the transformed plants were successfully raised and screened under the tunnel conditions for two generations and the present study focused on the screening of plants which were confirmed for containing all of these three genes and their expressions. Initially, the screening was done through glyphosate spray assay and the plants which were healthy and showed no damage on leaves were selected after 07 days of spray. In the laboratory, the DNA of these plants were isolated and subjected to amplification of the three genes. Thus, seventeen out of twenty were confirmed positive for Cry1Ac gene and ten out of twenty were positive for Cry2A gene and all twenty were positive for presence of EPSP synthase gene. Then, the ten plant samples which were confirmed with presence of all three genes were subjected to expression analysis of these proteins through ELISA. The results showed that eight out of ten plants were actively expressing the three transgenes. Real-time PCR was also done to quantify the expression levels of the EPSP synthase gene. Finally, eight plants were confirmed for the presence and active expression of all three genes in T3 generation of the triple gene transformed cotton. These plants may be subjected to T4 generation to develop a new stable variety in due course of time.

Keywords: agriculture, cotton, transformation, cry genes, ELISA, PCR

Procedia PDF Downloads 372