Search results for: β-tubulin-1 gene

Authors: M. Marjaneh, M. Y. Narazah, H. Shahrul

Abstract:

Array-based gene expression analysis is a powerful tool to profile expression of genes and to generate information on therapeutic effects of new anti-cancer compounds. Anti-apoptotic effect of thymoquinone was studied in MCF7 breast cancer cell line using gene expression profiling with cDNA micro array. The purity and yield of RNA samples were determined using RNeasyPlus Mini kit. The Agilent RNA 6000 Nano LabChip kit evaluated the quantity of the RNA samples. AffinityScript RT oligo-dT promoter primer was used to generate cDNA strands. T7 RNA polymerase was used to convert cDNA to cRNA. The cRNA samples and human universal reference RNA were labelled with Cy-3-CTP and Cy-5-CTP, respectively. Feature Extraction and GeneSpring software analysed the data. The single experiment analysis revealed involvement of 64 pathways with up-regulated genes and 78 pathways with down-regulated genes. The MAPK and p38-MAPK pathways were inhibited due to the up-regulation of PTPRR gene. The inhibition of p38-MAPK suggested up-regulation of TGF-ß pathway. Inhibition of p38 - MAPK caused up-regulation of TP53 and down-regulation of Bcl2 genes indicating involvement of intrinsic apoptotic pathway. Down-regulation of CARD16 gene as an adaptor molecule regulated CASP1 and suggested necrosis-like programmed cell death and involvement of caspase in apoptosis. Furthermore, down-regulation of GPCR, EGF-EGFR signalling pathways suggested reduction of ER. Involvement of AhR pathway which control cytochrome P450 and glucuronidation pathways showed metabolism of Thymoquinone. The findings showed differential expression of several genes in apoptosis pathways with thymoquinone treatment in estrogen receptor-positive breast cancer cells.

Keywords: cDNA microarray, thymoquinone, CARD16, PTPRR, CASP10

Procedia PDF Downloads 348

Authors: Agnieszka H. Ludwig-Slomczynska, Michal T. Seweryn, Przemyslaw Kapusta, Ewelina Pitera, Katarzyna Cyganek, Urszula Mantaj, Lucja Dobrucka, Ewa Wender-Ozegowska, Maciej T. Malecki, Pawel Wolkow

Abstract:

Obesity results from an imbalance between energy intake and its expenditure. Genome-Wide Association Study (GWAS) analyses have led to discovery of only about 100 variants influencing body mass index (BMI), which explain only a small portion of genetic variability. Analysis of gene epistasis gives a chance to discover another part. Since it was shown that interaction and communication between nuclear and mitochondrial genome are indispensable for normal cell function, we have looked for epistatic interactions between the two genomes to find their correlation with BMI. Methods: The analysis was performed on 366 T1DM patients using Illumina Infinium OmniExpressExome-8 chip and followed by imputation on Michigan Imputation Server. Only genes which influence mitochondrial functioning (listed in Human MitoCarta 2.0) were included in the analysis – variants of nuclear origin (MAF > 5%) in 1140 genes and 42 mitochondrial variants (MAF > 1%). Gene expression analysis was performed on GTex data. Association analysis between genetic variants and BMI was performed with the use of Linear Mixed Models as implemented in the package 'GENESIS' in R. Analysis of association between mRNA expression and BMI was performed with the use of linear models and standard significance tests in R. Results: Among variants involved in epistasis between mitochondria and nucleus we have identified one in mitochondrial transcription factor, TFB2M (rs6701836). It interacted with mitochondrial variants localized to MT-RNR1 (p=0.0004, MAF=15%), MT-ND2 (p=0.07, MAF=5%) and MT-ND4 (p=0.01, MAF=1.1%). Analysis of the interaction between nuclear variant rs6701836 (nuc) and rs3021088 localized to MT-ND2 mitochondrial gene (mito) has shown that the combination of the two led to BMI decrease (p=0.024). Each of the variants on its own does not correlate with higher BMI [p(nuc)=0.856, p(mito)=0.116)]. Although rs6701836 is intronic, it influences gene expression in the thyroid (p=0.000037). rs3021088 is a missense variant that leads to alanine to threonine substitution in the MT-ND2 gene which belongs to complex I of the electron transport chain. The analysis of the influence of genetic variants on gene expression has confirmed the trend explained above – the interaction of the two genes leads to BMI decrease (p=0.0308). Each of the mRNAs on its own is associated with higher BMI (p(mito)=0.0244 and p(nuc)=0.0269). Conclusıons: Our results show that nuclear-mitochondrial epistasis can influence BMI in T1DM patients. The correlation between transcription factor expression and mitochondrial genetic variants will be subject to further analysis.

Keywords: body mass index, epistasis, mitochondria, type 1 diabetes

Procedia PDF Downloads 175

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

Abstract:

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

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

Procedia PDF Downloads 376

Authors: Ali Aydin, Mert Sudagidan, Aysen Coban, Alparslan Kadir Devrim

Abstract:

Pseudomonas spp. (specifically, P. fluorescens and P. fragi) are considered the principal spoilage microorganisms of refrigerated poultry meats. The higher the level psychrophilic spoilage Pseudomonas spp. on carcasses at the end of processing lead to decrease the shelf life of the refrigerated product. The aim of the study was the identification of psychrophilic Pseudomonas spp. having proteolytic and lipolytic activities from poultry meats by 16S rRNA and rpoB gene sequencing, investigation of protease and lipase related genes and determination of proteolytic activity of Pseudomonas spp. In the of isolation procedure, collected chicken meat samples from local markets and slaughterhouses were homogenized and the lysates were incubated on Standard method agar and Skim Milk agar for selection of proteolytic bacteria and tributyrin agar for selection of lipolytic bacteria at +4 °C for 7 days. After detection of proteolytic and lipolytic colonies, the isolates were firstly analyzed by biochemical tests such as Gram staining, catalase and oxidase tests. DNA gene sequencing analysis and comparison with GenBank revealed that 126 strong enzyme Pseudomonas spp. were identified as predominantly P. fluorescens (n=55), P. fragi (n=42), Pseudomonas spp. (n=24), P. cedrina (n=2), P. poae (n=1), P. koreensis (n=1), and P. gessardi (n=1). Additionally, protease related aprX gene was screened in the strains and it was detected in 69/126 strains, whereas, lipase related lipA gene was found in 9 Pseudomonas strains. Protease activity was determined using commercially available protease assay kit and 5 strains showed high protease activity. The results showed that psychrophilic Pseudomonas strains were present in chicken meat samples and they can produce important levels of proteases and lipases for food spoilage to decrease food quality and safety.

Keywords: Pseudomonas, chicken meat, protease, lipase

Procedia PDF Downloads 388

Authors: Jarmila Bernasovska, Pavel Ružbarský, Ivan Bernasovsky, Regina Lohajová Behulová

Abstract:

The paper presents the results of the application of molecular genetics methods in sport research, with special emphasis on the most advanced methods and trends in diagnosing of motoric predispositions for the sake of identifying talented children. Genetic tests differ in principle from the traditional motoric tests, because the DNA of an individual does not change during life. Genetics is important in determining the capacity of an individual and for professional sport level. Genetic information can be used for individual genetic predispositions in early childhood. The phenotypes are influenced by a combination of genetic and environmental factors. The aim of the presented study was to examine physical condition, coordination skills, motoric docility and to determine the frequency of ACTN3 (R577X) gene in Romany children from Eastern Slovakia and compared their motoric performance with non-Romany children. This paper is not looking just for a performance, but also its association to genetic predispositions in relation to ACTN3 gene and its R577X polymorphism. Genotype data were obtained from 175 Romany children from 6 to 15 years old and 218 non-Romany children at the same age from Eastern Slovakia. Biological material for genetic analyses comprised samples of buccal swabs. Genotypes were determined using Real Time High resolution melting PCR method (Rotor Gene 6000 Corbett and LightCycler 480 Roche). Romany children of analyzed group legged to non-Romany children at the same age in all the compared tests. The % distribution of R and X alleles in children was different from controls. The frequency of XX genotype was 11,45% which is comparable to a frequency of an Indian population. Data were analysed with the ANOVA statistical programme and parametric and nonparametric tests. This work was supported by grants APVV-0716-10, ITMS 26220120023 and ITMS 26220120041.

Keywords: ACTN3 gene, R577X polymorphism, Romany children, sport performance, Slovakia

Procedia PDF Downloads 457

Authors: Emanuela Chiarella, Annamaria Aloisio, Nisticò Clelia, Maria Mesuraca

Abstract:

ZNF521 is a stem cell-associated transcription co-factor, that plays a crucial role in the homeostatic regulation of the stem cell compartment in the hematopoietic, osteo-adipogenic, and neural system. In normal hematopoiesis, primary human CD34+ hematopoietic stem cells display typically a high expression of ZNF521, while its mRNA levels rapidly decrease when these progenitors progress towards erythroid, granulocytic, or B-lymphoid differentiation. However, most acute myeloid leukemias (AMLs) and leukemia-initiating cells keep high ZNF521 expression. In particular, AMLs are often characterized by chromosomal translocations involving the Mixed Lineage Leukemia (MLL) gene, which MLL gene includes a variety of fusion oncogenes arisen from genes normally required during hematopoietic development; once they are fused, they promote epigenetic and transcription factor dysregulation. The chromosomal translocation t(9;11)(p21-22;q23), fusing the MLL gene with AF9 gene, results in a monocytic immune phenotype with an aggressive course, frequent relapses, and a short survival time. To better understand the dysfunctional transcriptional networks related to genetic aberrations, AML gene expression profile datasets were queried for ZNF521 expression and its correlations with specific gene rearrangements and mutations. The results showed that ZNF521 mRNA levels are associated with specific genetic aberrations: the highest expression levels were observed in AMLs involving t(11q23) MLL rearrangements in two distinct datasets (MILE and den Boer); elevated ZNF521 mRNA expression levels were also revealed in AMLs with t(7;12) or with internal rearrangements of chromosome 16. On the contrary, relatively low ZNF521 expression levels seemed to be associated with the t(8;21) translocation, that in turn is correlated with the AML1-ETO fusion gene or the t(15;17) translocation and in AMLs with FLT3-ITD, NPM1, or CEBPα double mutations. Invitro, we found that the enforced co-expression of ZNF521 in cord blood-derived CD34+ cells induced a significant proliferative advantage, improving MLL-AF9 effects on the induction of proliferation and the expansion of leukemic progenitor cells. Transcriptome profiling of CD34+ cells transduced with either MLL-AF9, ZNF521, or a combination of the two transgenes highlighted specific sets of up- or down-regulated genes that are involved in the leukemic phenotype, including those encoding transcription factors, epigenetic modulators, and cell cycle regulators as well as those engaged in the transport or uptake of nutrients. These data enhance the functional cooperation between ZNF521 and MA9, resulting in the development, maintenance, and clonal expansion of leukemic cells. Finally, silencing of ZNF521 in MLL-AF9-transformed primary CD34+ cells inhibited their proliferation and led to their extinction, as well as ZNF521 silencing in the MLL-AF9+ THP-1 cell line resulted in an impairment of their growth and clonogenicity. Taken together, our data highlight ZNF521 role in the control of self-renewal and in the immature compartment of malignant hematopoiesis, which, by altering the gene expression landscape, contributes to the development and/or maintenance of AML acting in concert with the MLL-AF9 fusion oncogene.

Keywords: AML, human zinc finger protein 521 (hZNF521), mixed lineage leukemia gene (MLL) AF9 (MLLT3 or LTG9), cord blood-derived hematopoietic stem cells (CB-CD34+)

Procedia PDF Downloads 112

Authors: Syed M. Shahid, Rozeena Shaikh, Syeda N. Nawab, Abid Azhar

Abstract:

Diabetes mellitus (DM) is a prevalent non-communicable disease worldwide. DM may lead to many vascular complications like hypertension, nephropathy, retinopathy, neuropathy and foot infections. Pathogenesis of diabetic nephropathy (DN) is implicated by the polymorphisms in genes encoding the specific components of renin angiotensin aldosterone system (RAAS) which include angiotensinogen (AGT), angiotensin-II receptor and angiotensin converting enzyme (ACE) genes. This study was designed to explore the possible association of AG (M268T) polymorphism in the patients of diabetes and nephropathy in Pakistan. Study subjects included 100 controls, 260 diabetic patients without renal insufficiency and 190 diabetic nephropathy patients with persistent albuminuria. Fasting blood samples were collected from all the subjects after getting institutional ethical approval and informed consent. The biochemical estimations, PCR amplification and direct sequencing for the specific region of AGT gene was carried out. A significantly high frequency of TT genotype and T allele of AGT (M268T) was observed in the patients of diabetes with nephropathy as compared to controls and diabetic patients without any known renal impairment. The TT genotype and T allele of AGT (M268T) polymorphism may be considered as a genetic risk factor for the development and progression of nephropathy in diabetes. Further cross sectional population studies would be of help to establish and confirm the observed possible association of AGT gene variations with development of nephropathy in diabetes.

Keywords: RAAS, AGT (M268T), diabetes, nephropathy

Procedia PDF Downloads 528

Authors: Mahbuba Rahman, Sabri Boughorbel, Scott Presnell, Charlie Quinn, Darawan Rinchai, Damien Chaussabel, Nico Marr

Abstract:

Collections of large-scale datasets made available in public repositories can be used to identify and fill gaps in biomedical knowledge. But first, these data need to be made readily accessible to researchers for analysis and interpretation. Here a collection of transcriptome datasets was made available to investigate the functional programming of human hematopoietic cells in early life. Thirty two datasets were retrieved from the NCBI Gene Expression Omnibus (GEO) and loaded in a custom, interactive web application called the Gene Expression browser (GXB), designed for visualization and query of integrated large-scale data. Multiple sample groupings and gene rank lists were created based on the study design and variables in each dataset. Web links to customized graphical views can be generated by users and subsequently be used to graphically present data in manuscripts for publication. The GXB tool also enables browsing of a single gene across datasets, which can provide information on the role of a given molecule across biological systems. The dataset collection is available online. As a proof-of-principle, one of the datasets (GSE25087) was re-analyzed to identify genes that are differentially expressed by regulatory T cells in early life. Re-analysis of this dataset and a cross-study comparison using multiple other datasets in the above mentioned collection revealed that PMCH, a gene encoding a precursor of melanin-concentrating hormone (MCH), a cyclic neuropeptide, is highly expressed in a variety of other hematopoietic cell types, including neonatal erythroid cells as well as plasmacytoid dendritic cells upon viral infection. Our findings suggest an as yet unrecognized role of MCH in immune regulation, thereby highlighting the unique potential of the curated dataset collection and systems biology approach to generate new hypotheses which can be tested in future mechanistic studies.

Keywords: early-life, GEO datasets, PMCH, interactive query, systems biology

Procedia PDF Downloads 297

Authors: Nan Deng, Zhenqiu Liu

Abstract:

Thousands of patients with metastatic tumors were diagnosed with cancers of unknown primary sites each year. The inability to identify the primary cancer site may lead to inappropriate treatment and unexpected prognosis. Nowadays, a large amount of genomics and transcriptomics cancer data has been generated by next-generation sequencing (NGS) technologies, and The Cancer Genome Atlas (TCGA) database has accrued thousands of human cancer tumors and healthy controls, which provides an abundance of resource to differentiate cancer types. Meanwhile, deep convolutional neural networks (CNNs) have shown high accuracy on classification among a large number of image object categories. Here, we utilize 25 cancer primary tumors and 3 normal tissues from TCGA and convert their RNA-Seq gene expression profiling to color images; train, validate and test a CNN classifier directly from these images. The performance result shows that our CNN classifier can archive >80% test accuracy on most of the tumors and normal tissues. Since the gene expression pattern of distant metastases is similar to their primary tumors, the CNN classifier may provide a potential computational strategy on identifying the unknown primary origin of metastatic cancer in order to plan appropriate treatment for patients.

Keywords: bioinformatics, cancer, convolutional neural network, deep leaning, gene expression pattern

Procedia PDF Downloads 301

Authors: K. R. Thabethe, G. A. Adefolaju, M. J. Hosie

Abstract:

Cervical cancer is the third most commonly diagnosed cancer globally and it is one of three AIDS defining malignancies. Highly active antiretroviral therapy (HAART) is a combination of three or more antiretroviral drugs and has been shown to play a significant role in reducing the incidence of some AIDS defining malignancies, although its effect on cervical cancer is still unclear. The aim of this study was to investigate the relationship between cervical cancer and HAART. This was achieved by studying the expression of two signalling molecules expressed in cervical cancer; MUC1 and P65. Following the 24 hour treatment of a cervical cancer cell line, HCS-2, with drugs which are commonly used as part of HAART at their clinical plasma concentrations, real-time qPCR and immunofluorescence were used in order to study gene and protein expression. A one way ANOVA followed by a Tukey Kramer Post Hoc test was conducted using JMP 11 software on both sets of data. The drug classified as a protease inhibitor (PI) (i.e. LPV/r) reduced MUC1 and P65 gene and protein expression more than the other drug tested. PIs are known to play a significant role in cell death, therefore the cells were thought to be more susceptible to cell death following treatment with PIs. In conclusion, the drugs used, especially the PI showed some anticancer effects by facilitating cell death through decreased gene and protein expression of MUC1 and P65 and present promising agents for cancer treatment.

Keywords: cervical cancer, haart, MUC1, P65

Procedia PDF Downloads 333

Authors: Dalia. G. Aseel

Abstract:

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

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

Procedia PDF Downloads 150

Authors: Alina Smalinskiene Janina Petkeviciene, Jurate Klumbiene, Vilma Kriaucioniene, Vaiva Lesauskaite

Abstract:

The worldwide prevalence of obesity has been increasing dramatically in the last few decades, and Lithuania is no exception. In 2012, every fifth adult (19% of men and 20.5 % of women) was obese and every third was overweight Association studies have highlighted the influence of SNPs in obesity, with particular focus on FTO rs9939609. Thus far, no data on the possible association of this SNP to obesity in the adult Lithuanian population has been reported. Here, for the first time, we demonstrate an association between the FTO rs9939609 homozygous AA genotype and increased BMI when compared to homozygous TT. Furthermore, a positive association was determined between the FTO rs9939609 variant and risk of metabolic syndrome. Background: This study aimed to examine the associations between the fat mass and obesity associated (FTO) gene rs9939609 variant with obesity and metabolic syndrome in Lithuanian adult population. Materials and Methods: A cross-sectional health survey was carried out in randomly selected municipalities of Lithuania. The random sample was obtained from lists of 25–64 year-old inhabitants. The data from 1020 subjects were analysed. The rs9939609 SNP of the FTO gene was assessed using TaqMan assays (Applied Biosystems, Foster City, CA, USA). The Applied Biosystems 7900HT Real-Time Polymerase Chain Reaction System was used for detecting the SNPs. Results: The carriers of the AA genotype had the highest mean values of BMI and waist circumference (WC) and the highest risk of obesity. Interactions ‘genotype x age’ and ‘genotype x physical activity’ in determining BMI and WC were shown. Neither lipid and glucose levels, nor blood pressure were associated with the rs9939609 independently of BMI. In the age group of 25-44 years, association between the FTO genotypes and metabolic syndrome was found. Conclusion: The FTO rs9939609 variant was significantly associated with BMI and WC, and with the risk of obesity in Lithuanian population. The FTO polymorphism might have a greater influence on weight status in younger individuals and in subjects with a low level of physical activity.

Keywords: obesity metabolic syndrome, FTO gene, polymorphism, Lithuania

Procedia PDF Downloads 430

Authors: T. C. C. Soo, S. Bhassu

Abstract:

Unlike the common presence of both innate and adaptive immunity in vertebrates, crustaceans, in particular, shrimps, have been discovered to possess only innate immunity. This further emphasizes the importance of innate immunity within shrimps in pathogenic resistance. Under the study of pathogenic immune challenge, different shrimp species actually exhibit varying degrees of immune resistance towards the same pathogen. Furthermore, even within the same shrimp species, different batches of challenged shrimps can have different strengths of immune defence. Several important pathways are activated within shrimps during pathogenic infection. One of them is JAK-STAT pathway that is activated during bacterial, viral and fungal infections by which STAT(Signal Transducer and Activator of Transcription) gene is the core element of the pathway. Based on theory of Central Dogma, the genomic information is transmitted in the order of DNA, RNA and protein. This study is focused in uncovering the important evolutionary patterns present within the DNA (non-coding region) and RNA (coding region). The three shrimp species involved are Macrobrachium rosenbergii, Penaeus monodon and Litopenaeus vannamei which all possess commercial significance. The shrimp species were challenged with a famous penaeid shrimp virus called white spot syndrome virus (WSSV) which can cause serious lethality. Tissue samples were collected during time intervals of 0h, 3h, 6h, 12h, 24h, 36h and 48h. The DNA and RNA samples were then extracted using conventional kits from the hepatopancreas tissue samples. PCR technique together with designed STAT gene conserved primers were utilized for identification of the STAT coding sequences using RNA-converted cDNA samples and subsequent characterization using various bioinformatics approaches including Ramachandran plot, ProtParam and SWISS-MODEL. The varying levels of immune STAT gene activation for the three shrimp species during WSSV infection were confirmed using qRT-PCR technique. For one sample, three biological replicates with three technical replicates each were used for qRT-PCR. On the other hand, DNA samples were important for uncovering the structural variations within the genomic region of STAT gene which would greatly assist in understanding the STAT protein functional variations. The partially-overlapping primers technique was used for the genomic region sequencing. The evolutionary inferences and event predictions were then conducted through the Bayesian Inference method using all the acquired coding and non-coding sequences. This was supplemented by the construction of conventional phylogenetic trees using Maximum likelihood method. The results showed that adaptive evolution caused STAT gene sequence mutations between different shrimp species which led to evolutionary divergence event. Subsequently, the divergent sites were correlated to the differing expressions of STAT gene. Ultimately, this study assists in knowing the shrimp species innate immune variability and selection of disease resistant shrimps for breeding purpose. The deeper understanding of STAT gene evolution from the perspective of both purifying and adaptive approaches not only can provide better immunological insight among shrimp species, but also can be used as a good reference for immunological studies in humans or other model organisms.

Keywords: gene evolution, JAK-STAT pathway, immunology, STAT gene

Procedia PDF Downloads 151

Authors: Danna Jia, Bin Li

Abstract:

Background: Atopic dermatitis (AD) is a chronic and refractory inflammatory skin disease characterized by relapsing eczematous and pruritic skin lesions. The global prevalence of AD ranges from 1~ 20%, and its incidence rates are increasing. It affects individuals from infancy to adulthood, significantly impacting their daily lives and social activities. Despite its major health burden, the precise mechanisms underlying AD remain unknown. Understanding the genetic differences associated with AD is crucial for advancing diagnosis and targeted treatment development. This study aims to identify candidate genes of AD by using bioinformatics analysis. Methods: We conducted a comprehensive analysis of four pooled transcriptomic datasets (GSE16161, GSE32924, GSE130588, and GSE120721) obtained from the Gene Expression Omnibus (GEO) database. Differential gene expression analysis was performed using the R statistical language. The differentially expressed genes (DEGs) between AD patients and normal individuals were functionally analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Furthermore, a protein-protein interaction (PPI) network was constructed to identify candidate genes. Results: Among the patient-level gene expression datasets, we identified 114 shared DEGs, consisting of 53 upregulated genes and 61 downregulated genes. Functional analysis using GO and KEGG revealed that the DEGs were mainly associated with the negative regulation of transcription from RNA polymerase II promoter, membrane-related functions, protein binding, and the Human papillomavirus infection pathway. Through the PPI network analysis, we identified eight core genes: CD44, STAT1, HMMR, AURKA, MKI67, and SMARCA4. Conclusion: This study elucidates key genes associated with AD, providing potential targets for diagnosis and treatment. The identified genes have the potential to contribute to the understanding and management of AD. The bioinformatics analysis conducted in this study offers new insights and directions for further research on AD. Future studies can focus on validating the functional roles of these genes and exploring their therapeutic potential in AD. While these findings will require further verification as achieved with experiments involving in vivo and in vitro models, these results provided some initial insights into dysfunctional inflammatory and immune responses associated with AD. Such information offers the potential to develop novel therapeutic targets for use in preventing and treating AD.

Keywords: atopic dermatitis, bioinformatics, biomarkers, genes

Procedia PDF Downloads 84

Authors: Ali̇ Bayram, Semih Dalkilic, Remzi Yigiter

Abstract:

N-methyl-D-aspartate (NMDA) receptor is a subtype of glutamate receptor and plays a pivotal role in learning, memory, neuronal plasticity, neurotoxicity and synaptic mechanisms. Animal experiments were suggested that glutamate-induced excitotoxic injuriy and NMDA receptor blockage lead to amnesia and other neurodegenerative diseases including Alzheimer’s disease (AD), Huntington’s disease, amyotrophic lateral sclerosis. Aim of this study is to investigate association between NMDA receptor coding gene GRIN2B expression level and Alzheimer disease. The study was approved by the local ethics committees, and it was conducted according to the principles of the Declaration of Helsinki and guidelines for the Good Clinical Practice. Peripheral blood was collected 50 patients who diagnosed AD and 49 healthy control individuals. Total RNA was isolated with RNeasy midi kit (Qiagen) according to manufacturer’s instructions. After checked RNA quality and quantity with spectrophotometer, GRIN2B expression levels were detected by quantitative real time PCR (QRT-PCR). Statistical analyses were performed, variance between two groups were compared with Mann Whitney U test in GraphpadInstat algorithm with 95 % confidence interval and p < 0.05. After statistical analyses, we have determined that GRIN2B expression levels were down regulated in AD patients group with respect to control group. But expression level of this gene in each group was showed high variability. İn this study, we have determined that NMDA receptor coding gene GRIN2B expression level was down regulated in AD patients when compared with healthy control individuals. According to our results, we have speculated that GRIN2B expression level was associated with AD. But it is necessary to validate these results with bigger sample size.

Keywords: Alzheimer’s disease, N-methyl-d-aspartate receptor, NR2B, GRIN2B, mRNA expression, RT-PCR

Procedia PDF Downloads 394

Authors: Seung-Hwa Baek, In-Jung Nam, Sang-Han Lee

Abstract:

The development of anti-melanogenic agents is important for the prevention of serious esthetic problem like a melasma, freckle, age spots, and chloasma. The aim of this study was to investigate the anti-melanogenic effect of sesamol, an active lignan isolated from sesame seed, by mushroom and cellular tyrosinase assay, melanin content and the analysis of melanogensis-related mRNA expressions in melana cells. Sesamol showed strong inhibitory activity against the mushroom tyrosinase in a dose-dependent manner. Intracellular tyrosinase inhibition activity was also confirmed by zymography. At a concentration of 50 μM, sesamol inhibited melanin production in melan-a cells with no cytoxicity while those of phenylthiourea (PTU) as a positive control were the same condition. Sesamol significantly inhibited the expression of melanogensis-related genes, such as tyrosinase, tyrosinase-related protein-1 (TRP-1), dopachrome tautomerase (Dct), microphthalmia-associated transcription factor (MITF) and melanocortin 1 receptor (MC1R). These findings indicate that sesamol could reduce melanin biosynthesis via the downregulation of tyrosinase activity and melanin production via subsequent gene expression of melanogenesis-related proteins. Together, these results suggest that the sesamol have strong potential in inhibiting melanin biosynthesis, in that the substance may be used as a new skin-whitening agent of cosmetic materials.

Keywords: sesamol, sesame seed, melanin biosynthesis, melanogenesis-related gene, skin-whitening agent

Procedia PDF Downloads 391

Authors: Özlem Ateş Sönmezoğlu, Begüm Terzi, Ahmet Yıldırım, Ramazan Özbey

Abstract:

The basic criteria which determine durum wheat quality is its suitability for pasta processing that is pasta making quality. Bright yellow color is a desired property in pasta products. Durum wheat pasta making quality is affected by grain pigment content and oxidative enzymes which affect adversely bright yellow color. Of the oxidative enzymes, lipoxygenase LOX is the most effective one on oxidative bleaching of yellow pigments in durum wheat products. Thus, wheat cultivars that are high in yellow pigments but low in LOX enzyme activity should be preferred for the production of pasta with high color quality. The aim of this study was to reduce lipoxygenase activities of the backcross durum wheat lines that were previously improved for their protein quality. For this purpose, two advanced lines with different parents (TMB2 and TMB3) were used recurrent parents. Also, Gediz-75 wheat with low LOX enzyme activity was used as the gene source. In all of the generations, backcrossed plants carrying the targeted gene region (Lpx-B1.1) were selected using SSR markers by marker assisted selection method. As a result, the study will be completed in three years instead of six years required in a classical backcross breeding study, leading to the development of high-quality candidate varieties. This research has been financially supported by TÜBİTAK (Project No: 112T910).

Keywords: durum wheat, lipoxygenase, LOX, Lpx-B1.1, MAS, Triticum durum

Procedia PDF Downloads 308

Authors: Mansur Abdulrasheed, Hussein I. Ibrahim, Ahmed F. Umar

Abstract:

Nitrification, the microbial oxidation of ammonia to nitrate (NO3-) via nitrite (NO2-) is a vital process in the biogeochemical nitrogen cycle and is performed by two distinct functional groups; ammonia oxidisers (comprised of ammonia oxidising bacteria (AOB) and ammonia oxidising archaea (AOA)) and nitrite oxidising bacteria. Autotrophic nitrification is said to occur in acidic soils, even though most laboratory cultures of isolated ammonia and nitrite oxidising bacteria fail to grow below neutral pH. Published studies revealed that soil pH is a major driver for determining the distribution and abundance of AOB and AOA. To determine whether distinct populations of nitrite oxidising bacteria within the lineages of Nitrospira and Nitrobacter are adapted to a particular range of pH as observed in ammonia oxidising organisms, the community structure of Nitrospira-like and Nitrobacter-like NOB were examined across a pH gradient (4.5–7.5) by amplifying nitrite oxido-reductase (nxrA) and 16S rRNA genes followed by denaturing gradient gel electrophoresis (DGGE). The community structure of both Nitrospira and Nitrobacter changed with soil pH, with distinct populations observed in acidic and neutral soils. The abundance of Nitrospira-like 16S rRNA and Nitrobacter-like nxrA gene copies contrasted across the pH gradient. Nitrobacter-like nxrA gene abundance decreased with increasing soil pH, whereas Nitrospira-like 16S rRNA gene abundance increased with increasing pH. Findings indicated that abundance and distributions of soil NOB is influence by soil pH.

Keywords: nitrospira, nitrobacter, nitrite-oxidizing bacteria, nitrification, pH, soil

Procedia PDF Downloads 303

Authors: Abtehal Y. Anaas, Mohd. Nazmi Bin Abd. Manap

Abstract:

Meat Tenderness is one of the most important factors affecting consumers' assessment of meat quality. Variation in meat tenderness is genetically controlled and varies among breeds, and it is also influenced by environmental factors that can affect its creation during rigor mortis and postmortem. The final postmortem meat tenderization relies on the extent of proteolysis of myofibrillar proteins caused by the endogenous activity of the proteolytic calpain system. This calpain system includes different calcium-dependent cysteine proteases, and an inhibitor, calpastatin. It is widely accepted that in farm animals including chickens, the μ-calpain gene (CAPN1) is a physiological candidate gene for meat tenderness. This study aimed to identify the association of single nucleotide polymorphism (SNP) markers in the CAPN1 gene with the tenderness of chicken breast meat from two Malaysian native and commercial broiler breed crosses. Ten, five months old native chickens and ten, 42 days commercial broilers were collected from the local market and breast muscles were removed two hours after slaughter, packed separately in plastic bags and kept at -20ºC for 24 h. The tenderness phenotype for all chickens’ breast meats was determined by Warner-Bratzler Shear Force (WBSF). Thawing and cooking losses were also measured in the same breast samples before using in WBSF determination. Polymerase chain reaction (PCR) was used to identify the previously reported C7198A and G9950A SNPs in the CAPN1 gene and assess their associations with meat tenderness in the two breeds. The broiler breast meat showed lower shear force values and lower thawing loss rates than the native chickens (p<0.05), whereas there were similar in the rates of cooking loss. The study confirms some previous results that the markers CAPN1 C7198A and G9950A were not significantly associated with the variation in meat tenderness in chickens. Therefore, further study is needed to confirm the functional molecular mechanism of these SNPs and evaluate their associations in different chicken populations.

Keywords: CAPNl, chicken, meat tenderness, meat quality, SNPs

Procedia PDF Downloads 246

Authors: Mohamed Abdel-Hamid, Olfat Gamil Shaker, Doha El-Sayed Ellakwa, Eman Fathy Abdel-Maksoud

Abstract:

Introduction: Despite advances in the knowledge of the molecular virology of hepatitis C virus (HCV), the mechanisms of hepatocellular injury in HCV infection are not completely understood. Hepatitis C viral infection (HCV) influences the susceptibility to apoptosis. This could lead to insufficient antiviral immune response and persistent viral infection. Aim of this study: was to examine whether BCL-2 gene polymorphism at codon 43 (+127G/A or Ala43Thr) has an impact on development of hepatocellular carcinoma caused by chronic hepatitis C Egyptian patients. Subjects and Methods: The study included three groups; group 1: composing of 30 patients with hepatocellular carcinoma (HCC), group 2 composing of 30 patients with HCV, group 3 composing of 30 healthy subjects matching the same age and socioeconomic status were taken as a control group. Gene polymorphism of BCL2 (Ala43Thr) were evaluated by PCR-RFLP technique and measured for all patients and controls. Results: The summed 43Thr genotype was more frequent and statistically significant in HCC patients as compared to control group. This genotype of BCL2 gene may inhibit the programmed cell death which leads to disturbance in tissue and cells homeostasis and reduction in immune regulation. This result leads to viral replication and HCV persistence. Moreover, virus produces variety of mechanisms to block genes participated in apoptosis. This mechanism proves that HCV patients who have 43Thr genotype are more susceptible to HCC. Conclusion: The data suggest for the first time that the BCL2 polymorphism is associated with the susceptibility to HCC in Egyptian populations and might be used as molecular markers for evaluating HCC risk. This study clearly demonstrated that Chronic HCV exhibit a deregulation of apoptosis with the disease progression. This provides an insight into the pathogenesis of chronic HCV infection, and may contribute to the therapy.

Keywords: BCL2 gene, Hepatitis C Virus, Hepatocellular carcinoma, sensitivity, specificity, apoptosis

Procedia PDF Downloads 508

Authors: Zainab S. Ahmed, Mohammed S. Ali, Nadia A. Elshiekh, Sami Adam Ibrahim, Ghada M. El-Tayeb, Ahmed H. Elsadig, Rihab A. Omer, Sofia B. Mohamed

Abstract:

Maple syrup urine (MSUD) is an autosomal recessive disease that causes a deficiency in the enzyme branched-chain alpha-keto acid (BCKA) dehydrogenase. The development of disease has been associated with SNPs in the DBT gene. Despite that, the computational analysis of SNPs in coding and noncoding and their functional impacts on protein level still remains unknown. Hence, in this study, we carried out a comprehensive in silico analysis of missense that was predicted to have a harmful influence on DBT structure and function. In this study, eight different in silico prediction algorithms; SIFT, PROVEAN, MutPred, SNP&GO, PhD-SNP, PANTHER, I-Mutant 2.0 and MUpo were used for screening nsSNPs in DBT including. Additionally, to understand the effect of mutations in the strength of the interactions that bind protein together the ELASPIC servers were used. Finally, the 3D structure of DBT was formed using Mutation3D and Chimera servers respectively. Our result showed that a total of 15 nsSNPs confirmed by 4 software (R301C, R376H, W84R, S268F, W84C, F276C, H452R, R178H, I355T, V191G, M444T, T174A, I200T, R113H, and R178C) were found damaging and can lead to a shift in DBT gene structure. Moreover, we found 7 nsSNPs located on the 2-oxoacid_dh catalytic domain, 5 nsSNPs on the E_3 binding domain and 3 nsSNPs on the Biotin Domain. So these nsSNPs may alter the putative structure of DBT’s domain. Furthermore, we detected all these nsSNPs are on the core residues of the protein and have the ability to change the stability of the protein. Additionally, we found W84R, S268F, and M444T have high significance, and they affected Leucine, Isoleucine, and Valine, which reduces or disrupt the function of BCKD complex, E2-subunit which the DBT gene encodes. In conclusion, based on our extensive in-silico analysis, we report 15 nsSNPs that have possible association with protein deteriorating and disease-causing abilities. These candidate SNPs can aid in future studies on Maple Syrup Urine Disease type II base in the genetic level.

Keywords: DBT gene, ELASPIC, in silico analysis, UCSF chimer

Procedia PDF Downloads 201

Authors: Rasheed F. G., Hassan H. A., Shehu F. A., Mukhtar M. M., Muhammad Y. Y., Ibrahim S. S., Shehu D., Abdulsalam K., N. Abdullahi

Abstract:

A cross sectional randomized, descriptive cross sectional study was conducted on the frequency of GSTT1 null alleles in patients diagnosed with type-2-diabetes mellitus (T2DM). A total of 40 patients with T2DM and 10 non-diabetic controls were included in the study. GSTT1 null-alleles genotyping was carried out using multiplex PCR amplification to amplify GSTT1 gene (460bp) while using β-globulin (250bp) as an internal control. The results showed that 55% of T2DM patients had BMI within reference limits, 13% are overweight. Additionally, patients with T2DM were found to have significantly higher (p<0.05) serum levels of glucose, total cholesterol, triglyceride and low density lipoprotein. Furthermore, the presence of null genotype of GSTT1 (deletion in GSTT1) was observed in 28% of diabetic patients. Subjects with GSTT1 deletion have significantly higher (p<0.05) levels of serum glucose, low-density lipoprotein and total cholesterol when compared with individuals without deletion (diabetic and non-diabetic). This results suggests that the deletion of GSTT1 gene might serve as a predisposing factor in the development of T2DM and dyslipideamia

Keywords: diabetes, glutathione-S-transferase, lipid profile, PCR, polymorphism.

Procedia PDF Downloads 98

Authors: Sun Gang

Abstract:

A variety of functional spaces are distributed on the vast mountain waterfront. Their functional positioning presents a spontaneous form of settlement space, and the construction features show a passive impact on the natural environment. As the precious heritage of inheriting human civilization and promoting historical culture, the traditional settlement space in mountainous areas is also the local expression of landscape pattern pattern gene. Under the impact of rapid urban construction and the stimulation of the transformation of social consumption demand, the original texture, scale and ecology of the traditional mountain settlement space, especially the historical and cultural settlement space, have been affected, and the decline of characteristics hinders the development. This paper selects Anju Ancient Town, the fourth largest ancient city in China, which is located in the city of mountains and waters as the research object, and combines spatial analysis and other methods to study the characteristics and causes of its spatial morphology, analyze the internal logic in its formation and development process, build a genetic analysis map, explore the possibility of settlement inheritance and development, and provide reference for the construction, protection and inheritance of traditional mountain settlements.

Keywords: mountain traditional settlement, historical and cultural settlement space, spatial form, spatial gene

Procedia PDF Downloads 91

Authors: Azar Sharafianpor, Hossein Rassi, Fahimeh Nemati Mansur

Abstract:

Cardiovascular diseases (CVD) are the most important cause of death in industrialized and developing countries such as Iran. The most important risk factors for the CVD, genetic factors and chronic infectious agents, such as Helicobacter pylori, can be mentioned. The TNFα gene is one of the most important anti-inflammatory cytokines that can affect the sensitivity, efficacy, and ability of the immune response to chronic infections. Some TNF-α gene polymorphisms, including the replacement of the G nucleotide G with A at position 308 in the promoter region of TNF-α, increase the transcription of cytokines in the target cells and thus predispose a person to chronic infections. This study examines the TNF-α 308 polymorphism and its association with Helicobacter pylori infection in this disease. This study was a case-control study in which 154 patients were examined as cases or patients with symptoms of myocardial infarction or angina and 160 as controls or healthy subjects. All of the subjects at different ages were given venous blood and age, BMI, cholesterol, LDL, and HDL were determined. DNA was extracted from the specimens, and the cagA gene from H. pylori and the TNF-α-308 polymorphism were determined by PCR in patients and healthy subjects. Statistical analysis was performed with Epi Info software. The results showed that the frequency of H. pylori infection in the patients and healthy group were 53.23% (82 out of 154) and 47.5% (76 out of 160). There was no significant difference in H. pylori outbreak between the two groups. The frequencies of TNF-α-308 genotype for GG, GA, and AA in patients were 0.17, 0.49, and 0.34, respectively, whereas for controls 0.47, 0.35, and 0.18 for GG, GA, and AA, respectively. The frequency of genotype analysis of TNF-α-308 polymorphisms in both patients and healthy groups showed that there was a significant difference in the frequency of genotypes and the AA genotype was higher in the affected individuals. Also, there was a significant relationship between the genotype and the contamination with H. pylori and changes in cholesterol, LDL, and HDL levels were observed. The results of the study indicate that H. pylori detection in individuals with AA genotype in people under 50 years of age can play an important role in early diagnosis and treatment of cardiovascular disease.

Keywords: Helicobacter pylori, TNFα gene, cardiovascular diseases, TNFα-308 polymorphism

Procedia PDF Downloads 154

Authors: Agumah N. B. Orji, M. U., Oru C. M., Ugbo, E. N., Onwuliri E. A Nwakaeze, E. A.,

Abstract:

ERG11 gene has been reported to be one of the genes whose expression is responsible for resistance of Candida to various triazole drugs, which are first line treatment for candidiasis. This study was carried out to determine the prevalence of Triazole (Fluconazole and voriconazole) resistant Candida albicans expressing ERG11 gene from adult females in Abakaliki. Urine and vaginal swab samples were randomly collected from volunteers after obtaining their consent to participate in the study. A total of 565 adult females participated in the study. A total of 340 urine specimens and 288 vaginal swab specimens were collected. Direct wet mount technique, as well as culture in Trichomonas broth, were used to examine the urine and vaginal swab specimens for the presence of motile Trichomonads. The Trichomonas broth used was selective for both T. vaginalis and C. albicans. Broths that yielded budding yeast cells after microscopy were subcultured on to Sabouraud dextrose agar, after which Germ tube test was carried out to confirm the presence of C. albicans. Biochemical tests, including carbohydrate fermentation and urease utilization, were also performed. Antibiogram of C. albicans isolates obtained from this study was carried out using commercially available azole drugs. Fluconazole and voriconazole were selected as Triazole drugs used for this study. Nystatin was used as a tangential control. An MIC test was carried out with E-strips on some of the resistant C. albicans isolates A total of 6 isolates that resisted all the azole drugs were selected and screened for the presence of ERG11 gene using Reverse transcriptase polymerase chain reaction technique. The total prevalence recorded for C. albicans was 13.0%. Frequency was statistically higher in Pregnant (7.96%) than non pregnant (5.09%) volunteers (X2=0.94 at P=0.05). With respect to clinical samples, frequency was higher in vaginal swabs samples (7.96%) than Urine samples (5.09%) (X2=9.05 at P=0.05). Volunteers within the age group 26-30 years recorded the highest prevalence (4.46%), while those within the age group 36-40 years recorded the lowest at 1.27%(X2=4.34 at P=0.05). In pregnant female participants, the highest frequency was recorded with those in their 3rd trimester (4.14%), while lowest incidence was recorded for those in their first trimester (0.80%). Antibiogram results from this study showed that C. albicans isolates obtained from this study resisted Fluconazole (72%) more than Voriconazole (57%). Only one out of the six selected isolates yielded resistance in the MIC test. Results obtained from the RT-PCR showed that there was no expression of ERG11 gene among the fluconazole resistant isolates of C. albicans. Observed resistance may be due to other factors other than expression of ERG11 gene.

Keywords: candida, ERG11, triazole, nigeria

Procedia PDF Downloads 150

Authors: Nazira B. Bekenova, Lydia A. Mukovozova, Andrej M. Grjibovski, Alma Z. Tokayeva, Yerbol M. Smail, Nurlan E. Aukenov

Abstract:

Erysipelas is an infectious disease with socio-economic significance and prone to prolonged recurrent course (30%). Contribution of genetic factors, in particular the gene polymorphism of cytokines, can be essential in disease etiology and pathogenesis. Interleukin – 17 A are produced by T helpers of 17 type and plays a key role in development of local inflammation process. Local inflammatory process is a dominant in the clinic of erysipelas. Established that the skin and mucosas are primary areas of migration (homing) Th17-cell and their cytokines are stimulate the barrier function of the epithelium. We studied associations between gene polymorphism of IL-17A (C737T) rs 8193036 and IL-17A level in patients with erysipelas Kazakh population. Altogether, 90 cases with erysipelas and 90 healthy controls from an ethnic Kazakh population comprised the sample. Cases were identified at Clinical Infectious Diseases Hospital of Semey (Kazakhstan). The IL-17A (rs8193036) polymorphism was analyzed by a real time polymerase chain reaction. Plasma levels of IL-17 A were assessed by immuneenzyme analysis method using ‘Vector-Best’ test-system (Russia). Differences in levels of IL-17 A between CC, TT, CT groups were studied using Kruskal — Wallis test. Pairwise comparisons were performed using Mann-Whitney tests with Bonferroni correction (New significance level was set to 0.025). We found, that in patients with erysipelas with CC genotype the level of IL-17 A was higher (p= 0, 010) compared to the carriers of CT genotype. When compared the level of IL – 17 A between the patients with TT genotype and patients with CC genotype, also between the patients with CT genotype and patients with TT genotype statistically significant differences are not revealed (p = 0.374 and p = 0.043, respectively). Comparisons of IL-17 A plasma levels between the CC and CT genotypes, between the CC and TT genotypes, and between the TT and CT in healthy patients did not reveal significant differences (p = 0, 291). Therefore, we are determined the associations of gene polymorphism of IL-17 A (C737T) with its level in patients erysipelas carriers CC genotype.

Keywords: erysipelas, interleukin – 17 A, Kazakh, polymorphism

Procedia PDF Downloads 436

Authors: Nadia A. Mohamed, Mehrevan M. Abdel-Moniem

Abstract:

Zingiber officinale (ginger) has been cultivated for medicinal purposes due to their various proprieties both in vitro and in vivo, so we designed to evaluate the ginger’s potential effect on nephrin m RNA expression in cisplatin-induced nephrotoxic rats. Method: Forty male albino rats were divided into group I was injected (IP) with one ml saline, group II(cisplatin) injected (IP) with a single dose of 12 mg/kg cisplatin, group III (ginger) received (PO) 310 mg/kg for 30 successive days, and group IV(cisplatin and ginger) rats received ginger extract (310 mg/kg) daily for 20 successive days (PO), and then on day 20 of ginger extract administration each rat was injected(IP) with a single dose of 12 mg/kg cisplatin. The blood was sampled to assess urea, creatinine (SC), while the levels of malondialdehyde (MDA), nitric oxide (NO) and paraoxonase (PON1) were measured in kidney tissue homogenate. Expression of urinary nephrin gene (nephrin mRNA) was detected using qRT-PCR. Results: Treatment with ginger significantly decreased the levels of kidney function parameters as well as MDA and NO elevated by cisplatin injection, while PON1 was significantly reduced in the cisplatin group. However, the protection of male rats with ginger significantly increased the levels of nephrin gene expression and PON1 compared with the cisplatin-treated group. Our results generated a proposal on the ameliorating effect of ginger on nephrin mRNA gene expression reduction in cisplatin-induced nephrotoxicity.

Keywords: nephrin mRNA, ginger, cisplatin, nephrotoxicity

Procedia PDF Downloads 145

Authors: Maryam Beiranvand, Sajad Yaghoubi

Abstract:

Background: Some microbes can colonize plants’ inner tissues without causing obvious damage and can even produce useful bioactive substances. In the present study, the diversity of the endophytic bacteria associated with medicinal plants from Iran was investigated by culturing techniques, molecular gene identification, as well as measuring them for antibacterial activity. Results: In the spring season from 2013 to 2014, 35 herb pharmacology samples were collected, sterilized, meshed, and then cultured on selective media culture. A total of 199 endophytic bacteria were successfully isolated from 35 tissue cultures of medical plants, and sixty-seven out of 199 bacterial isolates were subjected to identification by the 16S rRNA gene sequence analysis method. Based on the sequence similarity gene and phylogenetic analyses, these isolates were grouped into five classes, fourteen orders, seventeen families, twenty-one genera, and forty strains. The most abundant group of endophytic bacteria was actinobacterial, consisting of thirty-two (47%) out of 67 bacterial isolates. Ten (22.3%) out of 67 bacterial isolates remained unidentified and classified at the genus level. The signature of the 16S rRNA gene formed a distinct line in a phylogenetic tree showing that they might be new species of bacteria. One (5.2%) out of 67 bacterial isolates was still not well categorized. Forty-two out of 67 strains were candidates for antimicrobial activity tests. Nineteen (45%) out of 42 strains showed antimicrobial activity multidrug resistance (MDR); thirteen (68%) out of 19 strains were allocated to classes actinobacteria. Four (21%) out of 19 strains belonged to the Bacillaceae family, one (5.2%) out of 19 strains was the Paenibacillaceae family, and one (5.2%) out of 19 strains belonged to the Pseudomonadaceae family. The other twenty-three strains did not show inhibitory activities. Conclusions: Our research showed a high-level phylogenetic diversity and the intoxicating antibiotic activity of endophytic bacteria in the herb pharmacology of Iran.

Keywords: Antibacterial activity, endophytic bacteria, multidrug-resistant bacteria, whole genom sequencing

Procedia PDF Downloads 86

Authors: Mariam G. Eshak, Ahmed Abbas, M. I. El-Sabry, M. M. Mashaly

Abstract:

This investigation was conducted to determine the physiological response and evaluate the expression of inflammatory and cell death genes and DNA damage induced by endotoxic shock in laying hens. Endotoxic shock was induced by a single intravenous injection of 107 Escherichia coli (E. coli,) colony/hen. In the present study, 240 forty-week-old laying hens (H&N) were randomly assigned into 2 groups with 3 replicates of 40 birds each. Hens were reared in battery cages with wire floors in an open-sided housing system under natural conditions. Housing and general management practices were similar for all groups. At 42-wk of age, 45 hens from the first group (15 replicate) were infected with E. coli, while the same number of hens from the second group was injected with saline and served as a control. Heat shock protein-70 (HSP-70) expression, plasma corticosterone concentration, body temperature, and the gene expression of bax, caspase-3 activity, P38, Interlukin-1β (Il-1β), and tumor necrosis factor alpha (TNF-α) genes and DNA damage in the brain and liver were measured. Hens treated with E. coli showed significant (P≤0.05) increase of body temperature by 1.2 ᴼC and plasma corticosterone by 3 folds compared to the controls. Further, hens injected with E.Coli showed markedly over-expression of HSP-70 and increase DNA damage in brain and liver. These results were synchronized with activating cell death program since our data showed significant (P≤0.05) high expression of bax and caspase-3 activity genes in the brain and liver. These results were related to remarkable over-inflammation gene expression of P38, IL-1β, and TNF-α in brain and liver. In conclusion, our results indicate that endotoxic shock induces inflammatory physiological response and triggers cell death program by promoting P38, IL-1β, and TNF-α gene expression in the brain and liver.

Keywords: chicken, DNA damage, Escherichia coli, gene expression, inflammation

Procedia PDF Downloads 347

Authors: Sagri Sharma

Abstract:

Analysis of diseases integrating multi-factors increases the complexity of the problem and therefore, development of frameworks for the analysis of diseases is an issue that is currently a topic of intense research. Due to the inter-dependence of the various parameters, the use of traditional methodologies has not been very effective. Consequently, newer methodologies are being sought to deal with the problem. Supervised Learning Algorithms are commonly used for performing the prediction on previously unseen data. These algorithms are commonly used for applications in fields ranging from image analysis to protein structure and function prediction and they get trained using a known dataset to come up with a predictor model that generates reasonable predictions for the response to new data. Gene expression profiles generated by DNA analysis experiments can be quite complex since these experiments can involve hypotheses involving entire genomes. The application of well-known machine learning algorithm - Support Vector Machine - to analyze the expression levels of thousands of genes simultaneously in a timely, automated and cost effective way is thus used. The objectives to undertake the presented work are development of a methodology to identify genes relevant to Hepatocellular Carcinoma (HCC) from gene expression dataset utilizing supervised learning algorithms and statistical evaluations along with development of a predictive framework that can perform classification tasks on new, unseen data.

Keywords: artificial intelligence, biomarker, gene expression datasets, hepatocellular carcinoma, machine learning, supervised learning algorithms, support vector machine

Procedia PDF Downloads 429