Search results for: regional expression
3100 The Importance of including All Data in a Linear Model for the Analysis of RNAseq Data
Authors: Roxane A. Legaie, Kjiana E. Schwab, Caroline E. Gargett
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Studies looking at the changes in gene expression from RNAseq data often make use of linear models. It is also common practice to focus on a subset of data for a comparison of interest, leaving aside the samples not involved in this particular comparison. This work shows the importance of including all observations in the modeling process to better estimate variance parameters, even when the samples included are not directly used in the comparison under test. The human endometrium is a dynamic tissue, which undergoes cycles of growth and regression with each menstrual cycle. The mesenchymal stem cells (MSCs) present in the endometrium are likely responsible for this remarkable regenerative capacity. However recent studies suggest that MSCs also plays a role in the pathogenesis of endometriosis, one of the most common medical conditions affecting the lower abdomen in women in which the endometrial tissue grows outside the womb. In this study we compared gene expression profiles between MSCs and non-stem cell counterparts (‘non-MSC’) obtained from women with (‘E’) or without (‘noE’) endometriosis from RNAseq. Raw read counts were used for differential expression analysis using a linear model with the limma-voom R package, including either all samples in the study or only the samples belonging to the subset of interest (e.g. for the comparison ‘E vs noE in MSC cells’, including only MSC samples from E and noE patients but not the non-MSC ones). Using the full dataset we identified about 100 differentially expressed (DE) genes between E and noE samples in MSC samples (adj.p-val < 0.05 and |logFC|>1) while only 9 DE genes were identified when using only the subset of data (MSC samples only). Important genes known to be involved in endometriosis such as KLF9 and RND3 were missed in the latter case. When looking at the MSC vs non-MSC cells comparison, the linear model including all samples identified 260 genes for noE samples (including the stem cell marker SUSD2) while the subset analysis did not identify any DE genes. When looking at E samples, 12 genes were identified with the first approach and only 1 with the subset approach. Although the stem cell marker RGS5 was found in both cases, the subset test missed important genes involved in stem cell differentiation such as NOTCH3 and other potentially related genes to be used for further investigation and pathway analysis.Keywords: differential expression, endometriosis, linear model, RNAseq
Procedia PDF Downloads 4273099 Improving the Performance of Deep Learning in Facial Emotion Recognition with Image Sharpening
Authors: Ksheeraj Sai Vepuri, Nada Attar
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We as humans use words with accompanying visual and facial cues to communicate effectively. Classifying facial emotion using computer vision methodologies has been an active research area in the computer vision field. In this paper, we propose a simple method for facial expression recognition that enhances accuracy. We tested our method on the FER-2013 dataset that contains static images. Instead of using Histogram equalization to preprocess the dataset, we used Unsharp Mask to emphasize texture and details and sharpened the edges. We also used ImageDataGenerator from Keras library for data augmentation. Then we used Convolutional Neural Networks (CNN) model to classify the images into 7 different facial expressions, yielding an accuracy of 69.46% on the test set. Our results show that using image preprocessing such as the sharpening technique for a CNN model can improve the performance, even when the CNN model is relatively simple.Keywords: facial expression recognittion, image preprocessing, deep learning, CNN
Procedia PDF Downloads 1353098 A Robust Spatial Feature Extraction Method for Facial Expression Recognition
Authors: H. G. C. P. Dinesh, G. Tharshini, M. P. B. Ekanayake, G. M. R. I. Godaliyadda
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This paper presents a new spatial feature extraction method based on principle component analysis (PCA) and Fisher Discernment Analysis (FDA) for facial expression recognition. It not only extracts reliable features for classification, but also reduces the feature space dimensions of pattern samples. In this method, first each gray scale image is considered in its entirety as the measurement matrix. Then, principle components (PCs) of row vectors of this matrix and variance of these row vectors along PCs are estimated. Therefore, this method would ensure the preservation of spatial information of the facial image. Afterwards, by incorporating the spectral information of the eigen-filters derived from the PCs, a feature vector was constructed, for a given image. Finally, FDA was used to define a set of basis in a reduced dimension subspace such that the optimal clustering is achieved. The method of FDA defines an inter-class scatter matrix and intra-class scatter matrix to enhance the compactness of each cluster while maximizing the distance between cluster marginal points. In order to matching the test image with the training set, a cosine similarity based Bayesian classification was used. The proposed method was tested on the Cohn-Kanade database and JAFFE database. It was observed that the proposed method which incorporates spatial information to construct an optimal feature space outperforms the standard PCA and FDA based methods.Keywords: facial expression recognition, principle component analysis (PCA), fisher discernment analysis (FDA), eigen-filter, cosine similarity, bayesian classifier, f-measure
Procedia PDF Downloads 4223097 An Antidiabetic Dietary Defence Weapon: Oats and Milk Based Probiotic Fermented Product
Authors: Rameshwar Singh Seema
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In today’s world where diabetes has become an epidemic, our aim was to potentiate the effect of probiotics by integrating probiotics with cereals to formulate composite foods using Lactobacillus rhamnosus GG (LGG) and Lactobacillus casei NCDC19 against type 2 diabetes. After optimizing the product by Response Surface Methodology, it was studied for their effect on induction and progression of type 2 diabetes in HFD-fed Wistar rats. After 9 weeks study, best results were shown by the group fed with oat and milk based product fermented with LGG and L. casei NCDC19 which resulted in a significant decrease in blood glucose, HBA1c, improved OGTT, oxidative stress, cholesterol and triglycerides level during progression study of type 2 diabetes. During induction study also, there was significant reduction in blood glucose level, oxidative stress, cholesterol level and triglycerides level but slightly less as compared to progression study. Real time PCR gene expression studies were done for 5 genes (GLUT-4, IRS-2, ppar-γ, TNF-α, IL-6) whose expression is directly related to type 2 diabetes. The relative fold change expression was increased in case of GLUT-4, IRS-2, ppar-γ and decreased in case of TNF-α and IL-6 during both induction and progression study of diabetes but more significantly during progression study. Hence it was concluded that oat and milk based probiotic fermented product showed the synergistic effect of probiotics and oats especially in case of progression of type 2 diabetes. The benefits of these probiotic formulations may be further validated by clinical trials.Keywords: type 2 diabetes, LGG, L.casei NCDC19, food science
Procedia PDF Downloads 4123096 Relevance of Dosing Time for Everolimus Toxicity in Respect to the Circadian P-Glycoprotein Expression in Mdr1a::Luc Mice
Authors: Narin Ozturk, Xiao-Mei Li, Sylvie Giachetti, Francis Levi, Alper Okyar
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P-glycoprotein (P-gp, MDR1, ABCB1) is a transmembrane protein acting as an ATP-dependent efflux pump and functions as a biological barrier by extruding drugs and xenobiotics out of cells in healthy tissues especially in intestines, liver and brain as well as in tumor cells. The circadian timing system controls a variety of biological functions in mammals including xenobiotic metabolism and detoxification, proliferation and cell cycle events, and may affect pharmacokinetics, toxicity and efficacy of drugs. Selective mTOR (mammalian target of rapamycin) inhibitor everolimus is an immunosuppressant and anticancer drug that is active against many cancers, and its pharmacokinetics depend on P-gp. The aim of this study was to investigate the dosing time-dependent toxicity of everolimus with respect to the intestinal P-gp expression rhythms in mdr1a::Luc mice using Real Time-Biolumicorder (RT-BIO) System. Mdr1a::Luc male mice were synchronized with 12 h of Light and 12 h of Dark (LD12:12, with Zeitgeber Time 0 – ZT0 – corresponding Light onset). After 1-week baseline recordings, everolimus (5 mg/kg/day x 14 days) was administered orally at ZT1-resting period- and ZT13-activity period- to mdr1a::Luc mice singly housed in an innovative monitoring device, Real Time-Biolumicorder units which let us monitor real-time and long-term gene expression in freely moving mice. D-luciferin (1.5 mg/mL) was dissolved in drinking water. Mouse intestinal mdr1a::Luc oscillation profile reflecting P-gp gene expression and locomotor activity pattern were recorded every minute with the photomultiplier tube and infrared sensor respectively. General behavior and clinical signs were monitored, and body weight was measured every day as an index of toxicity. Drug-induced body weight change was expressed relative to body weight on the initial treatment day. Statistical significance of differences between groups was validated with ANOVA. Circadian rhythms were validated with Cosinor Analysis. Everolimus toxicity changed as a function of drug timing, which was least following dosing at ZT13, near the onset of the activity span in male mice. Mean body weight loss was nearly twice as large in mice treated with 5 mg/kg everolimus at ZT1 as compared to ZT13 (8.9% vs. 5.4%; ANOVA, p < 0.001). Based on the body weight loss and clinical signs upon everolimus treatment, tolerability for the drug was best following dosing at ZT13. Both rest-activity and mdr1a::Luc expression displayed stable 24-h periodic rhythms before everolimus and in both vehicle-treated controls. Real-time bioluminescence pattern of mdr1a revealed a circadian rhythm with a 24-h period with an acrophase at ZT16 (Cosinor, p < 0.001). Mdr1a expression remained rhythmic in everolimus-treated mice, whereas down-regulation was observed in P-gp expression in 2 of 4 mice. The study identified the circadian pattern of intestinal P-gp expression with an unprecedented precision. The circadian timing depending on the P-gp expression rhythms may play a crucial role in the tolerability/toxicity of everolimus. The circadian changes in mdr1a genes deserve further studies regarding their relevance for in vitro and in vivo chronotolerance of mdr1a-transported anticancer drugs. Chronotherapy with P-gp-effluxed anticancer drugs could then be applied according to their rhythmic patterns in host and tumor to jointly maximize treatment efficacy and minimize toxicity.Keywords: circadian rhythm, chronotoxicity, everolimus, mdr1a::Luc mice, p-glycoprotein
Procedia PDF Downloads 3393095 Targeting the EphA2 Receptor Tyrosine Kinases in Melanoma Cancer, both in Humans and Dogs
Authors: Shabnam Abdi, Behzad Toosi
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Background: Melanoma is the most lethal type of malignant skin cancer in humans and dogs since it spreads rapidly throughout the body. Despite significant advances in treatment, cancer at an advanced stage has a poor prognosis. Hence, more effective treatments are needed to enhance outcomes with fewer side effects. Erythropoietin-producing hepatocellular receptors are the largest family of receptor tyrosine kinases and are divided into two subfamilies, EphA and EphB, both of which play a significant role in disease, especially cancer. Due to their association with proliferation and invasion in many aggressive types of cancer, Eph receptor tyrosine kinases (Eph RTKs) are promising cancer therapy molecules. Because these receptors have not been studied in canine melanoma, we investigated how EphA2 influences survival and tumorigenicity of melanoma cells. Methods: Expression of EphA2 protein in canine melanoma cell lines and human melanoma cell line was evaluated by Western blot. Melanoma cells were transduced with lentiviral particles encoding Eph-targeting shRNAs or non-silencing shRNAs (control) for silencing the expression of EphA2 receptor, and silencing was confirmed by Western blotting and immunofluorescence. The effect of siRNA treatment on cellular proliferation, colony formation, tumorsphere assay, invasion was analyzed by Resazurin assay Matrigel invasion assay, respectively. Results: Expression of EphA2 was detected in canine and human melanoma cell lines. Moreover, stably silencing EphA2 by specific shRNAs significantly and consistently decreased the expression of EphA2 protein in both human and canine melanoma cells. Proliferation, colony formation, tumorsphere and invasion of melanoma cells were significantly decreased in EphA2 siRNA-treated cells compared to control. Conclusion: Our data provide the first functional evidence that the EphA2 receptor plays a critical role in the malignant cellular behavior of melanoma in both human and dogs.Keywords: ephA2, targeting, melanoma, human, canine
Procedia PDF Downloads 523094 Rooting Out Breast Cancer by Repressing ER Gene Expression: Correlating Bioactivity of Pomegranate Rind with Chemical Constituents Identified by HPLC-MS/MS
Authors: Alaa M. M. Badr Eldin, Marwa I. Ezzat, Mohammed S. Sedeek, Manal S. Afifi, Omar M. Sabry
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Cytotoxic activity of the total methanol extract against breast cancer cell line MCF-7 was amazing IC50 at 54 ug/ml. 130 polyphenolic compounds were tentatively identified in pomegranate peel (Punica granatum L.) methanol extract using HPLC-MS/MS technique. The antiestrogenic activity of the polyphenolic constituents found in pomegranate extract was confirmed experimentally in-vitro and by the in-silico molecular docking using gallagic acid, ellagic acid, and Punicalagin as these are considered model compounds confirmed in pomegranate peel extract. The methanolic extract was found to suppress ER, TGF-β, and NF-kB in-vitro gene expression strongly, and that was verified by qPCR and Western Blot gel electrophoresis techniques.Keywords: HPLC-MS/MS, pomegranate, breast cancer, ovarian cancer, ER, TGF-β, NF-kB
Procedia PDF Downloads 983093 Location Quotients Model in Turkey’s Provinces and Nuts II Regions
Authors: Semih Sözer
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One of the most common issues in economic systems is understanding characteristics of economic activities in cities and regions. Although there are critics to economic base models in conceptual and empirical aspects, these models are useful tools to examining the economic structure of a nation, regions or cities. This paper uses one of the methodologies of economic base models namely the location quotients model. Data for this model includes employment numbers of provinces and NUTS II regions in Turkey. Time series of data covers the years of 1990, 2000, 2003, and 2009. Aim of this study is finding which sectors are export-base and which sectors are import-base in provinces and regions. Model results show that big provinces or powerful regions (population, size etc.) mostly have basic sectors in their economic system. However, interesting facts came from different sectors in different provinces and regions in the model results.Keywords: economic base, location quotients model, regional economics, regional development
Procedia PDF Downloads 4193092 Examination of the Self-Expression Model with Reference to Luxury Watches with Particular Regard of the Buying-Reasons
Authors: Christopher Benedikt Jakob
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Human beings are intrigued by luxury watches for decades. It is fascinating that customers pay an enormous amount of money for specific wristwatch models. It is fascinating that customers of the luxury watch industry accept a yearly price increase. This behavior increases their desirability even more. Luxury watches are perceived as status symbols, but they are additionally accepted as a currency without the disadvantage of currency fluctuations. It is obvious that the symbolic value is more important as the functional value with reference to the buying-reasons as regards luxury watches. Nowadays human beings do not need a wristwatch to read the time. Tablets, notebooks, smartphones, the watch in the car and watches on public places are used to inform people about the current time. This is one of the reasons why there is a trend that people do not wear wristwatches anymore. Due to these facts, this study has the intention to give answers to the question why people invest an enormous amount of money on the consumption of luxury watches and why those watches are seen as a status symbol. The study examines why the luxury watch industry records significant growth rates. The self-expression model is used as an appropriate methodology to find reasons why human beings purchase specific luxury watches. This evaluative approach further discusses if human beings are aware of their current self and their ideal self and how they express them. Furthermore, the research critically evaluates the people’s social self and their ideal social self. One of the goals is to identify if customers know why they like specific luxury watches and dislike others although they have the same quality and cost comparable prices.Keywords: luxury watch, brand awareness, buying-behaviour, consumer, self-expression
Procedia PDF Downloads 1563091 A Research on the Coordinated Development of Chengdu-Chongqing Economic Circle under the Background of New Urbanization
Authors: Deng Tingting
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The coordinated and integrated development of regions is an inevitable requirement for China to move towards high-quality, sustainable development. As one of the regions with the best economic foundation and the strongest economic strength in western China, it is a typical area with national importance and strong network connection characteristics in terms of the comprehensive effect of linking the inland hinterland and connecting the western and national urban networks. The integrated development of the Chengdu-Chongqing economic circle is of great strategic significance for the rapid and high-quality development of the western region. In the context of new urbanization, this paper takes 16 urban units within the economic circle as the research object, based on the 5-year panel data of population, regional economy, and spatial construction and development from 2016 to 2020, using the entropy method and Theil index to analyze the three target layers, and cause analysis. The research shows that there are temporal and spatial differences in the Chengdu-Chongqing economic circle, and there are significant differences between the core city and the surrounding cities. Therefore, by reforming and innovating the regional coordinated development mechanism, breaking administrative barriers, and strengthening the "polar nucleus" radiation function to release the driving force for economic development, especially in the gully areas of economic development belts, not only promote the coordinated development of internal regions but also promote the coordinated and sustainable development of the western region and take a high-quality development path.Keywords: Chengdu-Chongqing economic circle, new urbanization, coordinated regional development, Theil Index
Procedia PDF Downloads 1133090 Anti-Inflammatory Effect of Myristic Acid through Inhibiting NF-κB and MAPK Signaling Pathways in Lipopolysaccharide-Stimulated RAW 264.7 Macrophage Cells
Authors: Hyun Ji Hyun, Hyo Sun Suh, Min Kook Kim, Yong Chan Kwon, Byung-Mu Lee
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Scope: This study is focused on the effect of myristic acid on LPS-induced inflammation in RAW 264.7 macrophage cells. Methods and results: For the experiment, RAW 264.7 mouse macrophage cell line was used. Results showed that treatment with myristic acid can attenuate LPS-induced inflammation. Moreover, myristic acid significantly suppressed expression of inflammatory mediators and down-regulating UVB-induced intracellular ROS generation. Furthermore, myristic acid reduced the expression of NF-κB by inhibiting degradation of IκB-α and ERK, JNK, and p38 pathways by inhibiting phosphorylation in RAW 264.7 macrophage cells. Conclusion: Overall, these data suggest that the myristic acid could reduce LPS-induced inflammation. Acknowledgment: This research was supported by the Ministry of Trade, Industry & Energy(MOTIE), Korea Institute for Advancement of Technology(KIAT) through the Encouragement Program for The Industries of Economic Cooperation RegionKeywords: anti-inflammation, myristic acid, ROS, ultraviolet light
Procedia PDF Downloads 1963089 Human C-Cbl and Cbl-b Proteins Are More Highly Expressed in the Thymus Compared to the Testis
Authors: Mazo Kone, Rachida Salah, Harir Noria
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Background and objectives: c-Cbl and Cbl-b are two members of the Cbl family proteins, with a crucial role of downregulation of tyrosine kinase receptors. They act as E3 ubiquitin ligases and are multivalent adaptor proteins, making them important in maintaining homeostasis in the body. This study investigated the expression level in thymus and testis in normal conditions. Methods: The expression level was assessed by immunochemistry of tissue microarrays of normal thymus and testis biopsies. Results: Cbl-b and c-Cbl proteins were found to be highly expressed in normal testis and thymus, indicated as yellowish brown granules in the cytomembrane and cytoplasm compared to controls. The c-Cbl appears to be more highly expressed than the Cbl-b in the thymus, while c-Cbl appears slightly stronger than Cbl-b in the testis. The thymus was found with a higher grade compared to the testis. Conclusion: In this work we concluded, that in normal condition, thymus tissue expresses more Cbl family proteins(c-Cbl and Cbl-b) than the testis tissue in humans.Keywords: Human C-Cbl proteins, Human Cbl-b protein, Testis, Thymus
Procedia PDF Downloads 2243088 Interferon-Induced Transmembrane Protein-3 rs12252-CC Associated with the Progress of Hepatocellular Carcinoma by Up-Regulating the Expression of Interferon-Induced Transmembrane Protein 3
Authors: Yuli Hou, Jianping Sun, Mengdan Gao, Hui Liu, Ling Qin, Ang Li, Dongfu Li, Yonghong Zhang, Yan Zhao
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Background and Aims: Interferon-induced transmembrane protein 3 (IFITM3) is a component of ISG (Interferon-Stimulated Gene) family. IFITM3 has been recognized as a key signal molecule regulating cell growth in some tumors. However, the function of IFITM3 rs12252-CC genotype in the hepatocellular carcinoma (HCC) remains unknown to author’s best knowledge. A cohort study was employed to clarify the relationship between IFITM3 rs12252-CC genotype and HCC progression, and cellular experiments were used to investigate the correlation of function of IFITM3 and the progress of HCC. Methods: 336 candidates were enrolled in study, including 156 with HBV related HCC and 180 with chronic Hepatitis B infections or liver cirrhosis. Polymerase chain reaction (PCR) was employed to determine the gene polymorphism of IFITM3. The functions of IFITM3 were detected in PLC/PRF/5 cell with different treated:LV-IFITM3 transfected with lentivirus to knockdown the expression of IFITM3 and LV-NC transfected with empty lentivirus as negative control. The IFITM3 expression, proliferation and migration were detected by Quantitative reverse transcription polymerase chain reaction (qRT-PCR), QuantiGene Plex 2.0 assay, western blotting, immunohistochemistry, Cell Counting Kit(CCK)-8 and wound healing respectively. Six samples (three infected with empty lentiviral as control; three infected with LV-IFITM3 vector lentiviral as experimental group ) of PLC/PRF/5 were sequenced at BGI (Beijing Genomics Institute, Shenzhen,China) using RNA-seq technology to identify the IFITM3-related signaling pathways and chose PI3K/AKT pathway as related signaling to verify. Results: The patients with HCC had a significantly higher proportion of IFITM3 rs12252-CC compared with the patients with chronic HBV infection or liver cirrhosis. The distribution of CC genotype in HCC patients with low differentiation was significantly higher than that in those with high differentiation. Patients with CC genotype found with bigger tumor size, higher percentage of vascular thrombosis, higher distribution of low differentiation and higher 5-year relapse rate than those with CT/TT genotypes. The expression of IFITM3 was higher in HCC tissues than adjacent normal tissues, and the level of IFITM3 was higher in HCC tissues with low differentiation and metastatic than high/medium differentiation and without metastatic. Higher RNA level of IFITM3 was found in CC genotype than TT genotype. In PLC/PRF/5 cell with knockdown, the ability of cell proliferation and migration was inhibited. Analysis RNA sequencing and verification of RT-PCR found out the phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin(PI3K/AKT/mTOR) pathway was associated with knockdown IFITM3.With the inhibition of IFITM3, the expression of PI3K/AKT/mTOR signaling pathway was blocked and the expression of vimentin was decreased. Conclusions: IFITM3 rs12252-CC with the higher expression plays a vital role in the progress of HCC by regulating HCC cell proliferation and migration. These effects are associated with PI3K/AKT/mTOR signaling pathway.Keywords: IFITM3, interferon-induced transmembrane protein 3, HCC, hepatocellular carcinoma, PI3K/ AKT/mTOR, phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin
Procedia PDF Downloads 1193087 Analysis of the Content of Sugars, Vitamin C, Preservatives, Synthetic Dyes, Sweeteners, Sodium and Potassium and Microbiological Purity in Selected Products Made From Fruit and Vegetables in Small Regional Factories and in Large Food Corporations
Authors: Katarzyna Miśkiewicz, Magdalena Lasoń-Rydel, Małgorzata Krępska, Katarzyna Sieczyńska, Iwona Masłowska-Lipowicz, Katarzyna Ławińska
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The aim of the study was to analyse a selection of 12 pasteurised products made from fruit and vegetables, such as fruit juices, fruit drinks, jams, marmalades and jam produced by small regional factories as well as large food corporations. The research was carried out as part of the project "Innovative system of healthy and regional food distribution", funded by the Ministry of Education and Science (Poland), which aims to create an economically and organisationally strong agri-food industry in Poland through effective cooperation between scientific and socio-economic actors. The main activities of the project include support for the creation of new distribution channels for regional food products and their easy access to a wide group of potential customers while maintaining the highest quality standards. One of the key areas of the project is food quality analyses conducted to indicate the competitive advantage of regional products. Presented here are studies on the content of sugars, vitamin C, preservatives, synthetic colours, sweeteners, sodium and potassium, as well as studies on the microbiological purity of selected products made from fruit and vegetables. The composition of products made from fruit and vegetables varies greatly and depends on both the type of raw material and the way it is processed. Of the samples tested, fruit drinks contained the least amount of sugars, and jam and marmalade made by large producers and bought in large chain stores contained the most. However, the low sugar content of some fruit drinks is due to the presence of the sweetener sucralose in their composition. The vitamin C content of the samples varied, being higher in products where it was added during production. All products made in small local factories were free of food additives such as preservatives, sweeteners and synthetic colours, indicating their superiority over products made by large producers. Products made in small local factories were characterised by a relatively high potassium content. The microbiological purity of commercial products was confirmed - no Salmonella spp. were detected, and the number of mesophilic bacteria, moulds, yeasts, and β-glucuronidase-positive E. coli was below the limit of quantification.Keywords: fruit and vegetable products, sugars, food additives, HPLC, ICP-OES
Procedia PDF Downloads 833086 Expression Profiling and Immunohistochemical Analysis of Squamous Cell Carcinoma of Head and Neck (Tumor, Transition Zone, Normal) by Whole Genome Scale Sequencing
Authors: Veronika Zivicova, Petr Broz, Zdenek Fik, Alzbeta Mifkova, Jan Plzak, Zdenek Cada, Herbert Kaltner, Jana Fialova Kucerova, Hans-Joachim Gabius, Karel Smetana Jr.
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The possibility to determine genome-wide expression profiles of cells and tissues opens a new level of analysis in the quest to define dysregulation in malignancy and thus identify new tumor markers. Toward this long-term aim, we here address two issues on this level for head and neck cancer specimen: i) defining profiles in different regions, i.e. the tumor, the transition zone and normal control and ii) comparing complete data sets for seven individual patients. Special focus in the flanking immunohistochemical part is given to adhesion/growth-regulatory galectins that upregulate chemo- and cytokine expression in an NF-κB-dependent manner, to these regulators and to markers of differentiation, i.e. keratins. The detailed listing of up- and down-regulations, also available in printed form (1), not only served to unveil new candidates for testing as marker but also let the impact of the tumor in the transition zone become apparent. The extent of interindividual variation raises a strong cautionary note on assuming uniformity of regulatory events, to be noted when considering therapeutic implications. Thus, a combination of test targets (and a network analysis for galectins and their downstream effectors) is (are) advised prior to reaching conclusions on further perspectives.Keywords: galectins, genome scale sequencing, squamous cell carcinoma, transition zone
Procedia PDF Downloads 2323085 Quorum-Sensing Driven Inhibitors for Mitigating Microbial Influenced Corrosion
Authors: Asma Lamin, Anna H. Kaksonen, Ivan Cole, Paul White, Xiao-Bo Chen
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Microbiologically influenced corrosion (MIC) is a process in which microorganisms initiate, facilitate, or accelerate the electrochemical corrosion reactions of metallic components. Several reports documented that MIC accounts for about 20 to 40 % of the total cost of corrosion. Biofilm formation due to the presence of microorganisms on the surface of metal components is known to play a vital role in MIC, which can lead to severe consequences in various environmental and industrial settings. Quorum sensing (QS) system plays a major role in regulating biofilm formation and control the expression of some microbial enzymes. QS is a communication mechanism between microorganisms that involves the regulation of gene expression as a response to the microbial cell density within an environment. This process is employed by both Gram-positive and Gram-negative bacteria to regulate different physiological functions. QS involves production, detection, and responses to signalling chemicals, known as auto-inducers. QS controls specific processes important for the microbial community, such as biofilm formation, virulence factor expression, production of secondary metabolites and stress adaptation mechanisms. The use of QS inhibitors (QSIs) has been proposed as a possible solution to biofilm related challenges in many different applications. Although QSIs have demonstrated some strength in tackling biofouling, QSI-based strategies to control microbially influenced corrosion have not been thoroughly investigated. As such, our research aims to target the QS mechanisms as a strategy for mitigating MIC on metal surfaces in engineered systems.Keywords: quorum sensing, quorum quenching, biofilm, biocorrosion
Procedia PDF Downloads 803084 Effect of Different Muscle Contraction Mode on the Expression of Myostatin, IGF-1, and PGC-1 Alpha Family Members in Human Vastus Lateralis Muscle
Authors: Pejman Taghibeikzadehbadr
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Muscle contraction stimulates a transient change of myogenic factors, partly related to the mode of contractions. Here, we assessed the response of Insulin-like growth factor 1Ea (IGF-1Ea), Insulin-like growth factor 1Eb (IGF-1Eb), Insulin-like growth factor 1Ec (IGF-1Ec), Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α-1), Peroxisome proliferator-activated receptor gamma coactivator 4-alpha (PGC1α-4), and myostatin to the eccentric Vs the concentric contraction in human skeletal muscle. Ten healthy males were performed an acute eccentric and concentric exercise bout (n = 5 per group). For each contraction type, participants performed 12 sets of 10 repetitions knee extension by the dominant leg. Baseline and post-exercise muscle biopsy were taken 4 weeks before and immediately after experimental sessions from Vastus Lateralis muscle. Genes expression was measured by real-time PCR technique. There was a significant increase in PGC1α-1, PGC1α-4, IGF-1Ea and, IGF-1Eb mRNA after concentric contraction (p ≤ 0.05), while the PGC1α-4 and IGF-1Ec significantly increased after eccentric contraction (p ≤ 0.05). It is intriguing to highlight that; no significant differences between groups were evident for changes in any variables following exercise bouts (p ≥ 0.05). Our results found that concentric and eccentric contractions presented different responses in PGC1α-1, IGF-1Ea, IGF-1Eb, and IGF-1Ec mRNA. However, a similar significant increase in mRNA content was observed in PGC1α-4. Further, no apparent differences could be found between the response of genes to eccentric and concentric contraction.Keywords: eccentric contraction, concentric contraction, gene expression, PGC-1 alpha, IGF-1 Myostatin
Procedia PDF Downloads 1543083 Activation of Caspase 3 by Terpenoids and Flavonoids in Cancer Cell Lines
Authors: Nusrat Masood, Vijaya Dubey, Suaib Luqman
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Caspase 3, a member of cysteine-aspartic acid protease family, is an imperative indicator for cell death particularly when substantiating apoptosis. Thus, caspase 3 is an interesting target for the discovery and development of anticancer agent. We adopted a four level assessment of both terpenoids and flavonoids and thus experimentally performed the enzymatic assay in cell free system as well as in cancer cell line which was validated through real time expression and molecular interaction studies. A significant difference was observed with both the class of natural products indicating terpenoids as better activators of caspase 3 compared to flavonoids both in the cell free system as well as in cell lines. The expression analysis, activation constant and binding energy also correlate well with the enzyme activity. Overall, terpenoids had an unswerving effect on caspase 3 in all the tested system while flavonoids indirectly affect enzyme activity.Keywords: Caspase 3, terpenoids, flavonoids, activation constant, binding energy
Procedia PDF Downloads 2343082 BRG1 and Ep300 as a Transcriptional Regulators of Breast Cancer Growth
Authors: Maciej Sobczak, Julita Pietrzak, Tomasz Płoszaj, Agnieszka Robaszkiewicz
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Brg1, a member of SWI/SNF complex, plays a role in chromatin remodeling, therefore, regulates expression of many genes. Brg1 is an ATPase of SWI/SNF complex, thus its activity requires ATP. Through its bromodomain recognizes acetylated histone residues and evicts them, thus promoting transcriptionally active state of chromatin. One of the enzymes that is responsible for acetylation of histone residues is Ep300. It was previously shown in the literature that cooperation of Brg1 and Ep300 occurs at the promoter regions that have binding sites for E2F-family transcription factors as well as CpG islands. According to literature, approximately 20% of human cancer possess mutation in Brg1 or any other crucial SWI/SNF subunit. That phenomenon makes Brg1-Ep300 a very promising target for anti-cancer therapy. Therefore in our study, we investigated if physical interaction between Brg1 and Ep300 exists and what impact those two proteins have on key for breast cancer cells processes such as DNA damage repair and cell proliferation. Bioinformatical analysis pointed out, that genes involved in cell proliferation and DNA damage repair are overexpressed in MCF7 and MDA-MB-231 cells. Moreover, promoter regions of these genes are highly acetylated, which suggests high transcriptional activity of those sites. Notably, many of those gene possess within their promoters an E2F, Brg1 motives, as well as CpG islands and acetylated histones. Our data show that Brg1 physically interacts with Ep300, and together they regulate expression of genes involved in DNA damage repair and cell proliferation. Upon inhibiting Brg1 or Ep300, expression of vital for cancer cell survival genes such as CDK2/4, BRCA1/2, PCNA, and XRCC1 is decreased in MDA-MB-231 and MCF7 cells. Moreover, inhibition or silencing of either Brg1 or Ep300 leads to cell cycle arrest in G1. After inhibition of BRG1 or Ep300 on tested gene promoters, the repressor complex including Rb, HDAC1, and EZH2 is formed, which inhibits gene expression. These results highlight potentially significant target for targeted anticancer therapy to be introduced as a supportive therapy.Keywords: brg1, ep300, breast cancer, epigenetics
Procedia PDF Downloads 1733081 Identification of Watershed Landscape Character Types in Middle Yangtze River within Wuhan Metropolitan Area
Authors: Huijie Wang, Bin Zhang
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In China, the middle reaches of the Yangtze River are well-developed, boasting a wealth of different types of watershed landscape. In this regard, landscape character assessment (LCA) can serve as a basis for protection, management and planning of trans-regional watershed landscape types. For this study, we chose the middle reaches of the Yangtze River in Wuhan metropolitan area as our study site, wherein the water system consists of rich variety in landscape types. We analyzed trans-regional data to cluster and identify types of landscape characteristics at two levels. 55 basins were analyzed as variables with topography, land cover and river system features in order to identify the watershed landscape character types. For watershed landscape, drainage density and degree of curvature were specified as special variables to directly reflect the regional differences of river system features. Then, we used the principal component analysis (PCA) method and hierarchical clustering algorithm based on the geographic information system (GIS) and statistical products and services solution (SPSS) to obtain results for clusters of watershed landscape which were divided into 8 characteristic groups. These groups highlighted watershed landscape characteristics of different river systems as well as key landscape characteristics that can serve as a basis for targeted protection of watershed landscape characteristics, thus helping to rationally develop multi-value landscape resources and promote coordinated development of trans-regions.Keywords: GIS, hierarchical clustering, landscape character, landscape typology, principal component analysis, watershed
Procedia PDF Downloads 2213080 The Convention Refugee Definition-from Universal to Regional: A Systematic Review
Authors: Wen Jiayuan
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This article traces the broadening of the refugee definition from the early 1970s onwards. It first discusses Article 1A(1), the core universal legal definition of ‘refugee’ provided by the 1951 Geneva Convention. It then focuses on Article 1A(2), read together with the 1967 Protocol, which without time or geographical limits, offers a general definition of the refugee as including any person who is outside their country or origin and unable or unwilling to return there or to avail themselves of its protection, owing to a well-founded fear of persecution for reasons of race, religion, nationality, social group or political opinion. It then shifts to the contemporary alternative refugee definitions adopted in regional areas, namely Africa, Latin America, and Europe. By looking deeply into the 1969 OAU Convention, the 1984 Cartagena Declaration, and ECtHR, the assertation is that while the appearance of new definitions may lead to a more responsive international environment, it may also undermine the consistency of the international refugee regime.Keywords: refugee definition, 1951 Geneva Convention, 1969 OAU Convention, 1984 Cartagena Declaration
Procedia PDF Downloads 1263079 Dimethyl fumarate Alleviates Valproic Acid-Induced Autism in Wistar Rats via Activating NRF-2 and Inhibiting NF-κB Pathways
Authors: Sandy Elsayed, Aya Mohamed, Noha Nassar
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Introduction: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social deficits and repetitive behavior. Multiple studies suggest that oxidative stress and neuroinflammation are key factors in the etiology of ASD and often associated with worsening of ASD-related behaviors. Nuclear factor erythroid 2-related factor 2 (NRF-2) is a transcription factor that promotes expression of antioxidant response element genes in oxidative stress. In ASD subjects, decreased expression of NRF-2 in frontal cortex shifted the redox homeostasis towards oxidative stress, and resulted in inflammation evidenced by elevation of nuclear factor kappa B (NF-κB) transcriptional activity. Dimethyl fumarate (DMF) is a NRF-2 activator that is used in the treatment of psoriasis and multiple sclerosis. It participates in the transcriptional control of inflammatory factors via inhibition of NF-κB and its downstream targets. This study aimed to investigate the role of DMF in alleviating the cognitive impairments and behavior deficits associated with ASD through mitigation of oxidative stress and inflammation in prenatal valproic acid (VPA) rat model of autism. Methods: Pregnant female Wistar rats received a single intraperitoneal injection of VPA (600 mg/kg) to induce autistic-like-behavioral and neurobiological alterations in their offspring. Chronic oral gavage of DMF (150mg/kg/day) started from postnatal day (PND) 24 till PND62 (39 days). Prenatal VPA exposure elicited autistic behaviors including decreased social interaction and stereotyped behavior. Social interaction was evaluated using three-chamber sociability test and calculation of sociability index (SI), while stereotyped repetitive behavior and anxiety associated with ASD were assessed using marble burying test (MBT). Biochemical analyses were done on prefrontal cortex homogenates including NRF-2, and NF-κB expression. Moreover, inducible nitric oxide synthase (iNOS) gene expression and tumor necrosis factor (TNF-) protein expression were evaluated as markers of inflammation. Results: Prenatal VPA elicited decreased social interaction shown by decreased SI compared to control group (p < 0.001) and DMF enhanced SI (p < 0.05). In MBT, prenatal injection of VPA manifested stereotyped behavior and enhanced number of buried marbles compared to control (p < 0.05) and DMF reduced the anxiety-related behavior in rats exhibiting ASD-like behaviors (p < 0.05). In prefrontal cortex, NRF-2 expression was downregulated in prenatal VPA model (p < 0.0001) and DMF reversed this effect (p < 0.0001). The inflammatory transcription factor NF-κB was elevated in prenatal VPA model (p < 0.0001) and reduced (p < 0.0001) upon NRF-2 activation by DMF. Prenatal VPA expressed higher levels of proinflammatory cytokine TNF- compared to control group (p < 0.0001) and DMF reduced it (p < 0.0001). Finally, the gene expression of iNOS was downregulated upon NRF-2 activation by DMF (p < 0.01). Conclusion: This study proposes that DMF is a potential agent that can be used to ameliorate autistic-like-changes through NRF-2 activation along with NF-κB downregulation and therefore, it is a promising novel therapy for ASD.Keywords: autism spectrum disorders, dimethyl fumarate, neuroinflammation, NRF-2
Procedia PDF Downloads 323078 Research on the Conservation Strategy of Territorial Landscape Based on Characteristics: The Case of Fujian, China
Authors: Tingting Huang, Sha Li, Geoffrey Griffiths, Martin Lukac, Jianning Zhu
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Territorial landscapes have experienced a gradual loss of their typical characteristics during long-term human activities. In order to protect the integrity of regional landscapes, it is necessary to characterize, evaluate and protect them in a graded manner. The study takes Fujian, China, as an example and classifies the landscape characters of the site at the regional scale, middle scale, and detailed scale. A multi-scale approach combining parametric and holistic approaches is used to classify and partition the landscape character types (LCTs) and landscape character areas (LCAs) at different scales, and a multi-element landscape assessment approach is adopted to explore the conservation strategies of the landscape character. Firstly, multiple fields and multiple elements of geography, nature and humanities were selected as the basis of assessment according to the scales. Secondly, the study takes a parametric approach to the classification and partitioning of landscape character, Principal Component Analysis, and two-stage cluster analysis (K-means and GMM) in MATLAB software to obtain LCTs, combines with Canny Operator Edge Detection Algorithm to obtain landscape character contours and corrects LCTs and LCAs by field survey and manual identification methods. Finally, the study adopts the Landscape Sensitivity Assessment method to perform landscape character conservation analysis and formulates five strategies for different LCAs: conservation, enhancement, restoration, creation, and combination. This multi-scale identification approach can efficiently integrate multiple types of landscape character elements, reduce the difficulty of broad-scale operations in the process of landscape character conservation, and provide a basis for landscape character conservation strategies. Based on the natural background and the restoration of regional characteristics, the results of landscape character assessment are scientific and objective and can provide a strong reference in regional and national scale territorial spatial planning.Keywords: parameterization, multi-scale, landscape character identify, landscape character assessment
Procedia PDF Downloads 903077 Study on the Expression of Drought Tolerant Genes in Water-Stressed Basella Alba and Basella Rubra
Authors: T. O. Ajewole, K. S. Olorunmiaye, D. A. Animasaun, M. Okpeku
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Drought impact on the production of food crops for the benefit of mankind cannot be overemphasized. This study shows the different kind of genes expressed at various level of drought regimes on Basella alba and rubra using a real-time PCR machine. The planting was done in the screen house while the gene expression study was carried out in the laboratory. Sandy-loamy soil was collected and four levels of drought regime was used as treatment and a control experiment was set up for the two vegetables. Drought interval of 5, 10, 15 and 20 days were used as treatments while a control experiment which was not starved of water at any point was also set up, five replicates were set up for each treatment. Stress was introduced at 12 Weeks after planting (WAP). From the result of this study, Basella alba shows the highest amplicon size of 34.6 and 52.32 for GmPCS5 and HVA1 respectively which by implication means these genes were expressed the more as the stress period interval increases.Keywords: water stress, basella alba, basella rubra, HVA1
Procedia PDF Downloads 363076 Effect of Miconazole Nitrate on Immunological Response and Its Preventive Efficacy in Labeo rohita Fingerlings against Oomycetes Saprolegnia parasitica
Authors: Mukta Singh, Ratan Kumar Saha, Himadri Saha, Paramveer Singh
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The present study evaluated the effect of sub-lethal doses of antifungal drug miconazole nitrate (MCZ) on immunological responses including immune-related gene expression and its role as a prophylactic drug against S. parasitica in Labeo rohita fingerlings. Fish were fed with sub lethal doses of MCZ i.e., T1- 6.30 mg MCZ kgBW⁻¹, T2- 12.61 mg MCZ kgBW⁻¹ and T3- 25.22 mg MCZ kgBW⁻¹ and sampling was done at different time intervals for 240 h. Immunological parameters viz. lysozyme activity, oxygen radical production and plasma anti-protease activity showed significant enhancement (p < 0.05) in fish fed with T2 and T3 doses. Significant reduction in plasma protein content was observed in all the dietary groups as compared to control. Expression of immune-relevant genes like TLR-22 and β2-M showed significantly higher expression at six h and 24 h of sampling in both liver and head-kidney. However, these genes showed a down-regulation after 120 h of sampling in both the tissues. Preventive efficacy study showed that single dose of MCZ provides protection against oomycetes up to the fourth day of infection. Significantly higher mortality was observed in control diet-fed fish as compared to fish fed with MCZ medicated diet. Thus, from the study, it can be concluded that the MCZ can act as a potent antifungal agent for preventing oomycetes infection as well as to enhance the immune response.Keywords: antifungal, immune gene, immunological, miconazole nitrate, prophylactic
Procedia PDF Downloads 2423075 Hyaluronan and Hyaluronan-Associated Genes in Human CD8 T Cells
Authors: Emily Schlebes, Christian Hundhausen, Jens W. Fischer
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The glycosaminoglycan hyaluronan (HA) is a major component of the extracellular matrix, typically produced by fibroblasts of the connective tissue but also by immune cells. Here, we investigated the capacity of human peripheral blood CD8 T cells from healthy donors to produce HA and to express HA receptors as well as HA degrading enzymes. Further, we evaluated the effect of pharmacological HA inhibition on CD8 T cell function. Using immunocytochemistry together with quantitative PCR analysis, we found that HA synthesis is rapidly induced upon antibody-induced T cell receptor (TCR) activation and almost exclusively mediated by HA synthase 3 (HAS3). TCR activation also resulted in the upregulation of HA receptors CD44, hyaluronan-mediated motility receptor (HMMR), and layilin (LAYN), although kinetics and strength of expression varied greatly between subjects. The HA-degrading enzymes HYAL1 and HYAL2 were detected at low levels and induced by cell activation in some individuals. Interestingly, expression of HAS3, HA receptors, and hyaluronidases were modulated by the proinflammatory cytokines IL-6 and IL-1bβ in most subjects. To assess the functional role of HA in CD8 T cells, we performed carboxyfluorescein succinimidyl ester (CFSE) based proliferation assays and cytokine analysis in the presence of the HA inhibitor 4- Methylumbelliferone (4-MU). Despite significant inter-individual variation with regard to the effective dose, 4-MU resulted in the inhibition of CD8 T cell proliferation and reduced release of TNF-α and IFN-γ. Collectively, these data demonstrate that human CD8 T cells respond to TCR stimulation with a synthesis of HA and expression of HA-related genes. They further suggest that HA inhibition may be helpful in interfering with pathogenic T cell activation in human disease.Keywords: CD8 T cells, extracellular matrix, hyaluronan, hyaluronan synthase 3
Procedia PDF Downloads 943074 WT1 Exprassion in Malignant Surface Epithelial Ovarian Tumors
Authors: Mahmoodreza Tahamtan
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Background: Malignant surface epithelial ovarian tumors (SEOT) account for approximately 90% of primary ovarian cancer. Wilms tumor gene (WT1) product was defined as a tumor suppressor gene, but today it is considered capable of performing oncogenic functions. There seems to be differences in WT1 expression patterns among SEOT subtypes. We evaluate the immunohistochemical expression of WT1 protein among different histologic subtypes of SEOT. Materials and Methods: Immunohistochemistry for WT1 was done on 35 serous cystadenocarcinomas, 9 borderline serous tumors, 3 mucinous cystadenocarcinomas, 10 borderline mucinous tumors, 7 endometrioid ovarian carcinomas, 3 clear cell carcinomas, 1 malignant Brenner tumor, 2 metastatic adenocarcinomas, and 6 endometrial adenocarcinomas. A tumor was considered negative if < 1% of tumor cells were stained.Positive reactions were graded as follows:1+,1%-24%; 2+,25%-49%; 3+,50%-74%; 4+,75%-100%. Results: Of the 35 cases of ovarian serous cystadenocarcinoma, 30(85.7%) were diffusely positive (3+,4+),4 showed reactivity of < 50% of the tumor cells (1+,2+), and one were negative. All 9 borderline serous tumors showed immunoreactivity with WT1. All the mucinous tumors(n:13), endometrioid carcinomas (n: 7), clear cell carcinomas (n: 3), metastatic adenocarcinomas (n: 2) and primary endometrial carcinomas (n:6) were negative. The single malignant Brenner tumor showed a positive reaction for WT1(4+) Conclusion: WT1 is a good marker to distinguish primary ovarian serous carcinomas from other surface epithelial tumors (especially endometrioid subtype) and metastatic carcinomas (especially endometrial serous carcinoma), other than malignant mesothelioma. We cannot rely to the degree of expression inorder to separate high grade borderline serous tumors from low grade ones.Keywords: WT1, ovary, epithelial tumors, malignant
Procedia PDF Downloads 943073 Heritage Impact Assessment Policy within Western Balkans, Albania
Authors: Anisa Duraj
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As usually acknowledged, cultural heritage is the weakest component in EIA studies. The role of heritage impact assessment (HIA) in development projects is not often accounted for, and in those cases where it is, HIA is considered as a reactive response and not as a solutions provider. Because of continuous development projects, in most cases, heritage is unconsidered and often put under threat. Cultural protection and development challenges ask for prudent legal regulation and appropriate policy implementation. The challenges become even more peculiar in underdeveloped countries or endangered areas, which are generally characterized by numerous legal constraints. Therefore, the need for strategic proposals for HIA is of high importance. In order to trigger HIA as a proactive operation in the IA process and make sure to cover cultural heritage in the whole EIA framework, an appropriate system of evaluation of impacts should be provided. To obtain the required results for HIA, this last must be part of a regional policy, which will address and guide development projects toward a proper evaluation of their impacts affecting heritage. In order to get a clearer picture of existing gabs but also new possibilities for HIA, this paper will focus on the Western Balkans region and the undergoing changes that it faces. Concerning continuous development pressure in the region and within the aspiration of the Western Balkans countries to join the European Union (EU) as member states, attention should be paid to new development policies under the EU directives for conducting EIAs, and accurate support is required for the restructuration of existing policies as well as for the implementation of the UN Agenda for SDGs. In the framework of new emerging needs, if HIA is taken into account, the outcome would be an inclusive regional program that would help to overcome marginality issues of spaces and people.Keywords: cultural heritage, impact assessment, SDGs, urban development, western Balkans, regional policy, HIA, EIA
Procedia PDF Downloads 963072 Association of Nuclear – Mitochondrial Epistasis with BMI in Type 1 Diabetes Mellitus Patients
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
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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 1693071 Mechanical Properties of Young and Senescence Fibroblast Cells Using Passive Microrheology
Authors: Samira Khalaji, , Fenneke Klein Jan, Kay-E. Gottschalk, Eugenia Makrantonaki, Karin Scharffetter-Kochanek
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Biological aging is a multi-dimensional process that takes place over a whole range of scales from the nanoscopic alterations within individual cells, over transformations in tissues and organs and to changes of the whole organism. On the single cell level, aging involves mutation of genes, differences in gene expression levels as well as altered posttranslational modifications of proteins. A variety of proteins is affected, including proteins of the cell cytoskeleton and migration machinery. Previous work quantified the expression of cytoskeleton proteins on the gene and protein levels in senescent and young fibroblasts. Their results show that senescent skin fibroblasts have an upregulated expression of the intermediate filament (IF) protein vimentin in contrast to actin and tubulin, which are downregulated. IFs play an important role in providing mechanical stability of cells. However, the mechanical properties of IFs depending on cellular senescence or age of the donor has not been studied so far. Hence, we employed passive microrheology on primary human dermal fibroblasts from female donors with age of 28 years (young) and 86 years (old) as model of in vivo aging and human normal dermal fibroblast from 11-year old male with CPD 17-35 (young) and CPD 58-59 (senescence) as a model of in vitro replicative senescence. In contrast to the expectations, our primary results show no significant differences in the viscoelastic properties of fibroblasts depending on age of the donor or cellular replicative senescence.Keywords: aging, cytoskeleton, fibroblast, mechanical properties
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