Search results for: multi-element expression pattern

Authors: Meng-Hui Chen, Chen-Yu Kao, Chia-Yu Hsu, Pei-Chann Chang

Abstract:

The main idea in this paper is using sequential pattern mining to find the information which is helpful for finding high performance solutions. By combining this information, it is defined as blocks. Using the blocks to generate artificial chromosomes (ACs) could improve the structure of solutions. Estimation of Distribution Algorithms (EDAs) is adapted to solve the combinatorial problems. Nevertheless many of these approaches are advantageous for this application, but only some of them are used to enhance the efficiency of application. Generating ACs uses patterns and EDAs could increase the diversity. According to the experimental result, the algorithm which we proposed has a better performance to solve the permutation flow-shop problems.

Keywords: combinatorial problems, sequential pattern mining, estimationof distribution algorithms, artificial chromosomes

Procedia PDF Downloads 611

Authors: Gizem Buldum, Alexander Bismarck, Athanasios Mantalaris

Abstract:

Cellulose is the most abundant biopolymer on earth and it is currently being utilised in a multitude of industrial applications. Over the last 30 years, attention has been paid to the bacterial cellulose (BC), since BC exhibits unique physical, chemical and mechanical properties when compared to plant-based cellulose, including high purity and biocompatibility. Although Acetobacter xylinum is the most efficient producer of BC, it’s long doubling time results in insufficient yields of the cellulose production. This limits widespread and continued use of BC. In this study, E. coli BL21 (DE3) or E. coli HMS cells are selected as host organisms for the expression of bacterial cellulose synthase operon (bcs) of A.xylinum. The expression system is created based on pET-Duet1 and pCDF plasmid vectors, which carry bcs operon. The results showed that all bcs genes were successfully transferred and expressed in E.coli strains. The expressions of bcs proteins were shown by SDS and Native page analyses. The functionality of the bcs operon was proved by congo red binding assay. The effect of culturing temperature and the inducer concentration (IPTG) on cell growth and plasmid stability were monitored. The percentage of plasmid harboring cells induced with 0.025 mM IPTG was obtained as 85% at 22˚C in the end of 10-hr culturing period. It was confirmed that the high output cellulose production machinery of A.xylinum can be transferred into other organisms.

Keywords: bacterial cellulose, biopolymer, recombinant expression system, production

Procedia PDF Downloads 401

Authors: Garima Chaudhary

Abstract:

The gender of an individual in forensic DNA analysis is normally accessed by using the STR multiplexes with the incorporated gender based marker amelogenin or in other words by presence or absence of Y-Chromosome, but it may not be true in all the cases. We hereby report an interesting case of a phenotypic female carrying a male karyotype (46XY). In the alleged murder case, the deceased female with XY genotype was noticed. The expression of 18 Y-linked genes was studied to measure the extent of expression. Expression at 4 loci was observed that might have caused the misinterpretation in forensic casework. This clinical situation of the deceased in this case was diagnosed as testicular feminization syndrome, which characterize a female phenotype with a male karyotype (46, XY). Most of these cases have SRY (testis determining factor). The genetic explanation of this phenomenon is not very clear. Here, we are discussing the impact of such situations of genetic discrepancy in forensic interpretation of results. In the presented murder case of a phenotypic female, sexual assault was also suspected. For confirmation vaginal swabs and micro slides were also sent to us for DNA examination. After DNA analysis using STR markers, Y-chromosome was detected in the samples which supporting the suspicion of sexual assault before murder. When the reference blood sample of the deceased was analyzed, it was found to be case of testicular feminization syndrome. Interesting inferences were made from the results obtained.

Keywords: DNA profiling, forensic case study, Y chromosome, females

Procedia PDF Downloads 228

Authors: Precious Barnes, Abraham Mensah, Leonard Derkyi-Kwarteng, Benjamin Amoani, George Adjei, Ernest Adankwah, Faustina Pappoe, Kwabena Dankwah, Daniel Amoako-Sakyi, Samuel Victor Nuvor, Dorcas Obiri-Yeboah, Ewura Seidu Yahaya, Patrick Kafui Akakpo, Roland Osei Saahene

Abstract:

Context: Breast cancer is a prevalent and aggressive type of cancer among African women, with high mortality rates in Ghana. Nuclear factor kappa B (NF-kB) is a transcription factor that has been associated with tumor progression in breast cancer. However, there is a lack of published data on NF-kB in breast cancer patients in Ghana or other African countries. Research Aim: The aim of this study was to assess the prognostic significance of NF-kB (p65) expression and its association with various clinicopathological features in breast cancer patients at the Cape Coast Teaching Hospital in Ghana. Methodology: A total of 90 formalin-fixed breast cancer tissues and 15 normal breast tissues were used in this study. The expression level of NF-kB (p65) was examined using immunohistochemical techniques. Correlation analysis between NF-kB (p65) expression and clinicopathological features was performed using SPSS version 25. Findings: The study found that NF-kB (p65) was expressed in 86.7% of breast cancer tissues. There was a significant relationship between NF-kB (p65) expression and tumor grade, proliferation index (Ki67), and molecular subtype. High-level expression of NF-kB (p65) was more common in tumor grade 3 compared to grade 1, and Ki67 > 20 had higher expression of NF-kB (p65) compared to Ki67 ≤ 20. Triple-negative breast cancer patients had the highest overexpression of NF-kB (p65) compared to other molecular subtypes. There was no significant association between NF-kB (p65) expression and other clinicopathological parameters. Theoretical Importance: This study provides important insights into the expression of NF-kB (p65) in breast cancer patients in Ghana, particularly in relation to tumor grade and proliferation index. The findings suggest that NF-kB (p65) could serve as a potential biological marker for cancer stage, progression, prognosis and as a therapeutic target. Data Collection and Analysis Procedures: Formalin-fixed breast cancer tissues and normal breast tissues were collected and analyzed using immunohistochemical techniques. Correlation analysis between NF-kB (p65) expression and clinicopathological features was performed using SPSS version 25. Question Addressed: This study addressed the question of the prognostic significance of NF-kB (p65) expression and its association with clinicopathological features in breast cancer patients in Ghana. Conclusion: This study, the first of its kind in Ghana, demonstrates that NF-kB (p65) is highly expressed among breast cancer patients at the Cape Coast Teaching Hospital, especially in triple-negative breast cancer patients. The expression of NF-kB (p65) is associated with tumor grade and proliferation index. NF-kB (p65) could potentially serve as a biological marker for cancer stage, progression, prognosis, and as a therapeutic target.

Keywords: breast cancer, Ki67, NF-kB (p65), tumor grade

Procedia PDF Downloads 72

Authors: Yen-Ni Teng, Hsing-Yi Chen, Hsien-An Pan, Yung-Ming Lin, Hany A. Omar, Jui-Hsiang Hung

Abstract:

Leucine-rich repeats and WD repeat domain containing 1 (LRWD1) is highly expressed in the testes of healthy males. On the other hand, LRWD1 is significantly down-regulated in the testicular tissues of patients with severe spermatogenic defects. In our study, the downregulation of LRWD1 expression by shRNA caused a significant reduction of cell growth and mitosis and a noteworthy increase in the cell microtubule atrophy rate. Here, we used EMBOSS CpG plot analysis to explore the promoter region of LRWD1 gene. We found that CpG islands are located between positions -253 to +5 nucleotides upstream from the LRWD1 transcription start site. Luciferase reporter assay revealed that the hypermethylation of the LRWD1 promoter reduced the transcription activity in cells. In addition, quantitative methylation-specific PCR and immunostaining showed that the methylation inhibitor, 5-Aza-2'-deoxycytidine, increased LRWD1 promoter activity, LRWD1 mRNA, protein expression and cell viability. Whereas, the methylation activator, S-adenosylmethionine, caused opposite effects. The overexpression of p53 and Nrf2 in NT2/D1 cells increased LRWD1 promoter activity while 5-fluorodeoxyuridine decreased it. In conclusion, this study highlights evidence that the methylation status of LRWD1 promoter is associated with LRWD1 expression. Since the expression level of LRWD1 plays an important role in spermatogenesis, the methylation status of LRWD1 may serve as a novel molecular diagnostic or therapeutic approach in male's infertility.

Keywords: LRWD1, DNA methylation, p53, Nrf2

Procedia PDF Downloads 148

Authors: Z. Chekini, P. Afsharian, F. Ramezanali, A. A. Akhlaghi, R. Aflatoonian

Abstract:

Macrophage migration inhibitory factor (MIF) is a key pro-inflammatory cytokine that involves in pathophysiological events of endometriosis. We aimed to evaluate the association between mRNA expression levels and polymorphisms of MIF in endometriosis. Seventy endometriosis patients and 70 volunteer fertile women were recruited. RFLP was applied to determine -173G/C polymorphism. ORF polymorphisms and -794(CATT)5-8 were detected by sequencing. Q-PCR was used for expression study of 14 ectopic tissues of patients. Homozygote of CATT5 was observed only in controls. The CATT5/G haplotype related to controls (p=0.094, OR=0.61). Expression level of MIF with -794(CATT)6,7/-173GC was significantly more than the other haplotypes (p=0.00). We identified four SNPs including: +254rs2096525 (p=0.843), +626rs33958703 (p=0.029), +656rs2070766 (p=0.703) and +509rs182012324 (p=1.00). In conclusion, increased repeat of CATT and presence of C allele in promoter of MIF were significantly associated with mRNA level in patients. It seems that +509rs182012324 and +626rs33958703 SNPs were significantly correlated with susceptibility to endometriosis.

Keywords: endometriosis, haplotype, macrophage migration inhibitory factor, polymorphism

Procedia PDF Downloads 457

Authors: Mohammad Reza Ameri, Ali Massumi, Mohammad Haghbin

Abstract:

Non-linear static analysis, commonly referred to as pushover analysis, is a powerful tool for assessing the seismic response of structures. A suitable lateral load pattern for pushover analysis can bring the results of this simple, quick and low-cost analysis close to the realistic results of nonlinear dynamic analyses. In this research, four samples of 10- and 15 story (two- and four-bay) reinforced concrete frames were studied. The lateral load distribution patterns recommended in FEMA 273/356 guidelines were applied to the sample models in order to perform pushover analyses. The results were then compared to the results obtained from several nonlinear incremental dynamic analyses for a range of earthquakes. Finally, a lateral load distribution pattern was proposed for pushover analysis of medium-rise reinforced concrete buildings based on the results of nonlinear static and dynamic analyses.

Keywords: lateral load pattern, nonlinear static analysis, incremental dynamic analysis, medium-rise reinforced concrete frames, performance based design

Procedia PDF Downloads 476

Authors: Nina Doskocz, Katarzyna Affek, Magdalena Matczuk, Monika Załęska-Radziwiłł

Abstract:

Wastewater treatment is a critical environmental issue, especially in the face of increasing urbanization and industrialization. One of the emerging issues related to wastewater is the presence of nanoparticles (NPs) - tiny particles with dimensions measured in nanometers. These nanoparticles are widely used in various industries, including medicine, electronics, and consumer products. With technological advances, NPs are increasingly finding their way into water and wastewater systems, posing new environmental challenges that require urgent research and regulation. Therefore, research on the impact of nanoparticles on wastewater treatment processes is critical to protect environmental health and ensure sustainable development in the face of advancing nanotechnology. Traditional ecotoxicological tests are often inadequate for routine analysis as they do not provide insight into the mechanisms of toxicity of these compounds. The development of (geno)toxicity biomarkers for nanoparticles will greatly aid in the rapid assessment and prediction of the effects of current and emerging nanomaterials on various organisms. However, despite growing interest in gene expression responses to nanoparticle-induced stress, the toxic mechanisms of action and defense responses against nanoparticle toxicity remain poorly understood. The aim of our research was to investigate the expression of several molecular biomarkers related to essential cellular functions - such as oxidative stress, xenobiotic detoxification, and mitochondrial electron transport - in Pseudomonas putida in response to Al₂O₃ nanoparticles found in wastewater, both before and after biological treatment, as well as in their native form. Real-time PCR (qPCR) was used to assess gene expression changes after 1 hour and 16 hours of exposure to Al₂O₃ NPs and wastewater containing these nanoparticles, both before and after biological treatment. In addition, gene expression measurements were performed on P. putida in the presence of bulk Al₂O₃ (pristine and in wastewater). The results showed increased expression of ahpC, katE and ctaD genes, indicating oxidative stress, increased detoxification capacity and impaired mitochondrial function. Both untreated and treated wastewater containing nanoparticles caused significant changes in gene expression, demonstrating the persistent bioactivity and potential toxicity of these nanoparticles. Nanoparticles exhibited greater reactivity and bioavailability compared to their bulk counterparts.

Keywords: nanoparticles, wastewater, gene expression, qPCR

Procedia PDF Downloads 17

Authors: Emad Heydarnia, Aref Sepasi, Nika Asefi, Sara Khakshournia, Javad Mohammadnejad

Abstract:

Background: Despite breakthrough therapeutics in breast cancer, it is one of the main causes of mortality among women worldwide. Thus, drug therapies for treating breast cancer have recently been developed by scientists. Metformin and Sorafenib are well-known therapeutic in breast cancer. In the present study, we combined Sorafenib and PCL-sorafenib with metformin to improve drug absorption and promote therapeutic efficiency. Methods: The MCF-7 cells were treated with Metformin, Sorafenib, or PCL-sorafenib. The growth inhibitory effect of these drugs and cell viability were assessed using MTT and flow cytometry assays, respectively. The expression of targeted genes involved in cell proliferation, signaling, and the cell cycle was measured by Real-time PCR. Results: The results showed that MCF-7 cells treated with Metformin/Sorafenib and PCL-sorafenib/Metformin co-treatment contributed to 50% viability compared to untreated group. Moreover, PI and Annexin V staining tests showed that the cells viability for Metformin/Sorafenib and PCL-sorafenib/Metformin was 38% and 17%, respectively. Furthermore, Sorafenib/Metformin and PCL-sorafenib/Metformin leads to p53 gene expression increase by which they can increase ROS, thereby decreasing GPX4 gene expression. In addition, they affected the expression of BCL2, and BAX genes and altered the cell cycle. Conclusion: Together, the combination of PCL-sorafenib/Metformin and Sorafenib/Metformin increased Sorafenib absorption at lower doses and also leads to apoptosis and oxidative stress increases in MCF-7 cells.

Keywords: breast cancer, metformin, nanotechnology, sorafenib

Procedia PDF Downloads 72

Authors: So Youn Park, Yi Sle Lee, Ki Whan Hong, Chi Dae Kim

Abstract:

The role of metabolism in the pathogenesis of osteoarthritis is an emerging field. Metabolic alterations may be a role in osteoarthritis (OA) pathogenesis, and these changes influence joint destruction via several cytokine. Especially, in OA patients, levels of IL-1β are elevated in the synovial fluid, synovial membrane, subchondral bone, and cartilage. The IL-1β is activated by NLRP3 inflammasomes, and NLRP3 inflammasomes are cytosolic complexes that drive the production of other inflammatory cytokines, including IL-1β. In this study, we examined that SIRT1 suppresses IL-1β through inhibiting NLRP3 inflammasomes and SIRT1 ameliorates osteoarthritis. OA fibroblasts were isolated from synovium of OA patients. IL-1β and NLRP3 were detected in synovium of OA patients by immunohistochemistry. Lipopolysaccharides (LPS) stimulated the expression of active IL-1β mRNA in OA fibroblasts and combination of LPS, and adenosine triphosphate increased more the expression of active IL-1β in OA fibroblasts. The level of IL-1β was measured by western blot and ELISA assay. NLRP3 inflammasomes complex were measured by western blot. SIRT1 did not inhibit expression of NLRP3 inflammasome. So caspase-1, apoptotic speck-like protein containing a caspase recruitment domain (ASC) and NLRP3 protein were expressed in OA fibroblasts. But SIRT1 suppressed activation of IL-1β by inhibiting activity of caspase-1 via NLRP3 inflammasome in OA fibroblasts under LPS plus ATP stimulation. These results suggest that SIRT1 is a modulator of NLRP3 inflammasomes in OA fibroblasts and ameliorate IL-1β, so expression of SIRT1 in OA fibroblast may be a potential strategy for OA inflammation treatment.

Keywords: osteoarthritis, inflammasome, SIRT1, IL-1beta

Procedia PDF Downloads 199

Authors: Hao-Su Liu, Jun-Qing Lei

Abstract:

This study introduces the theory of modified particle swarm optimizer and its application in time-domain expressions for bridge self-excited aerodynamic forces. Based on the indicial function expression and the rational function expression in time-domain expression for bridge self-excited aerodynamic forces, the characteristics of the two methods, i.e. the modified particle swarm optimizer and conventional search method, are compared in flutter derivatives’ fitting process. Theoretical analysis and numerical results indicate that adopting whether the indicial function expression or the rational function expression, the fitting flutter derivatives obtained by modified particle swarm optimizer have better goodness of fit with ones obtained from experiment. As to the flutter derivatives which have higher nonlinearity, the self-excited aerodynamic forces, using the flutter derivatives obtained through modified particle swarm optimizer fitting process, are much closer to the ones simulated by the experimental. The modified particle swarm optimizer was used to recognize the parameters of time-domain expressions for flutter derivatives of an actual long-span highway-railway truss bridge with double decks at the wind attack angle of 0°, -3° and +3°. It was found that this method could solve the bounded problems of attenuation coefficient effectively in conventional search method, and had the ability of searching in unboundedly area. Accordingly, this study provides a method for engineering industry to frequently and efficiently obtain the time-domain expressions for bridge self-excited aerodynamic forces.

Keywords: time-domain expressions, bridge self-excited aerodynamic forces, modified particle swarm optimizer, long-span highway-railway truss bridge

Procedia PDF Downloads 314

Authors: Nathalie Baeza-Kallee, Raphaël Bergès, Victoria Hein, Stéphanie Cabaret, Jeremy Garcia, Abigaëlle Gros, Emeline Tabouret, Aurélie Tchoghandjian, Carole Colin, Dominique Figarella-Branger

Abstract:

Glioblastoma (GBM) contains cancer stem cells that are resistant to treatment. GBM cancer stem cell expresses glycolipids recognized by the A2B5 antibody. A2B5, induced by the enzyme ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyl transferase 3 (ST8Sia3), plays a crucial role in the proliferation, migration, clonogenicity, and tumorigenesis of GBM cancer stem cells. Our aim was to characterize the resulting effects of neuraminidase that remove A2B5 in order to target GBM cancer stem cells. To this end, we set up a GBM organotypic slice model; quantified A2B5 expression by flow cytometry in U87-MG, U87-ST8Sia3, and GBM cancer stem cell lines, treated or not by neuraminidase; performed RNAseq and DNA methylation profiling; and analyzed the ganglioside expression by liquid chromatography-mass spectrometry in these cell lines, treated or not with neuraminidase. Results demonstrated that neuraminidase decreased A2B5 expression, tumor size, and regrowth after surgical removal in the organotypic slice model but did not induce a distinct transcriptomic or epigenetic signature in GBM CSC lines. RNAseq analysis revealed that OLIG2, CHI3L1, TIMP3, TNFAIP2, and TNFAIP6 transcripts were significantly overexpressed in U87-ST8Sia3 compared to U87-MG. RT-qPCR confirmed these results and demonstrated that neuraminidase decreased gene expression in GBM cancer stem cell lines. Moreover, neuraminidase drastically reduced ganglioside expression in GBM cancer stem cell lines. Neuraminidase, by its pleiotropic action, is an attractive local treatment against GBM.

Keywords: cancer stem cell, ganglioside, glioblastoma, targeted treatment

Procedia PDF Downloads 75

Authors: Assem I. El-Ansary

Abstract:

This paper illustrates the event-oriented Behavioral Pattern Analysis (BPA) modeling approach in developing an Multi-Agent Railway Control System (MARCS). The Event defined in BPA is a real-life conceptual entity that is unrelated to any implementation. The major contributions of this research are the Behavioral Pattern Analysis (BPA) modeling methodology, and the development of an interactive software tool (DECISION), which is based on a combination of the Analytic Hierarchy Process (AHP) and the ELECTRE Multi-Criteria Decision Making (MCDM) methods.

Keywords: analysis, multi-agent, railway control, modeling methodology, software modeling, event-oriented, behavioral pattern, use cases

Procedia PDF Downloads 545

Authors: Ho Seong Shin

Abstract:

Introduction: A research in relation to wound healing also showed that platelet-rich plasma (PRP) was effective on normal tissue regeneration. Nonetheless, there is no evidence that when platelet-rich plasma was applied on diabetic wound, it normalize diabetic wound healing process. In this study, we have analyzed matrix metalloproteinase-2 (MMP-2), matrix metalloproteinase-9 (MMP-9) expression to know the effect of PRP on diabetic wounds using Reverse transcription-polymerase chain reaction (RT-PCR) of MMP-2, MMP-9 mRNA. Materials and Methods: Platelet-rich plasma (PRP) was prepared from blood of 6 rats. The whole 120-mL was added immediately to an anticoagulant. Citrate phosphonate dextrose(CPD) buffer (0.15 mg CPDmL) in a ratio of 1 mL of CPD buffer to 5 mL of blood. The blood was then centrifuged at 220g for 20minutes. The supernatant was saved to produce fibrin glue. The participate containing PRP was used for second centrifugation at 480g for 20 minutes. The pellet from the second centrifugation was saved and diluted with supernatant until the platelet concentration became 900,000/μL. Twenty male, 4week-old OLETF rats were underwent operation; each rat had two wounds created on left and right sides. The each wound of left side was treated with PRP gel, the wound of right side was treated with physiologic saline gauze. Results: RT-PCR analysis; The levels of MMP-2 mRNA in PRP applied tissues were positively related to postwounding days, whereas MMP-2 mRNA expression in saline-applied tissues remained in 5day after treatment. MMP-9 mRNA was undetectable in saline-applied tissues for either tissue, except 3day after treatment. Following PRP-applied tissues, MMP-9 mRNA expression was detected, with maximal expression being seen at third day. The levels of MMP-9 mRNA in PRP applied tissues were reported high intensity of optical density related to saline applied tissues.

Keywords: diabetes, MMP-2, MMP-9, OLETF, PRP, wound healing MMP-9

Procedia PDF Downloads 273

Authors: Yingxu Wang

Abstract:

The base 6 structure and properties of mirror primes are discovered in this work towards the proof of Goldbach Conjecture. This paper reveals a fundamental pattern on pairs of mirror primes adjacent to any even number nₑ > 2 with symmetrical distances on both sides determined by a methodology of Mirror Prime Decomposition (MPD). MPD leads to a formal proof of the Goldbach conjecture, which states that the conjecture holds because any pivot even number, nₑ > 2, is a sum of at least an adjacent pair of primes divided by 2. This work has not only revealed the analytic pattern of base 6 primes but also proven the infinitive validation of the Goldbach conjecture.

Keywords: number theory, primes, mirror primes, double recursive patterns, Goldbach conjecture, formal proof, mirror-prime decomposition, applications

Procedia PDF Downloads 50

Authors: Nagat M. Saeed, Mabruka S. Elashheb, Fatma M. Ben Rabaha, Aisha M Edrah

Abstract:

The aim of the study was to determine the type and pattern of antibiotic susceptibility of the pathogenic microorganisms causing chronic suppurative otitis media (CSOM), which could lead to better therapeutic decisions and consequently avoidance of appearance of resistance to specific antibiotics. Most frequently isolated agents were Pseudomonas aeruginosa 28.5%; followed by Staphylococcus aureus 18.2%; proteus mirabilis 13.9%; Providencia stuartti 6.7%; Bacteroides melaninogenicus, Aspergillus sp., candida sp., 4.2% each; and other microorganisms were represented in 3-0.2%. Drug sensitivities pattern of Pseudomonas aeruginosa showed that ciprofloxacin was active against the majority of isolates (93.9%) followed by ceftazidime 86.2%, amikacin 76.2% and gentamicin 40.8%. However, Staphylococcus aureus isolates were resistant to penicillin 72.7%, erythromycin 28.6%, cephalothin 18.2%, cloxacillin 8.3% and ciprofloxacin was active against 96.2% of isolates. The resistance pattern of proteus mirabilis was 55.6% to ampicillin, 47.1% to carbencillin, 29.4% to cephalothin, 14.3% to gentamicin and 4.8% to amikacin while 100% were sensitive to ciprofloxacin. We conclude that ciprofloxacin is the best drug of choice in the treatment of CSOM caused by the common microorganisms.

Keywords: otitis media, chronic suppurative otitis media (CSOM), microorganisms, drug sensitivity

Procedia PDF Downloads 345

Authors: JiYoung Park, SueGoo Rhee, HyunAe Woo

Abstract:

In liver regeneration, quiescent hepatocytes need to be primed to fully respond to growth factors such as hepatocyte growth factor. To understand the priming process, it is necessary to analyze patterns of gene expression that occur during liver regeneration after partial hepatectomy (PHx). Recently, tyrosine phosphorylation of signal transducer and activator of transcription 3 (pYSTAT3) has been shown to play an important role in initiating liver regeneration. In order to evaluate the role of pYSTAT3 on liver regeneration after PHx, we used an intrabody which can selectively inhibit pYSTAT3. In our previous studies, an intrabody had been shown that it bound specifically to the pYSTAT3. Adenovirus-mediated expression of the intrabody in HepG2 cells, as well as mouse liver, blocked both accumulation of pYSTAT3 in the nucleus and downstream target of pYSTAT3. In this study, PHx was performed on intrabody-expressing mice and the expression levels of liver regeneration-related genes were analyzed. We also measured liver/body weight ratios and the related cellular signaling pathways were analyzed. Acute phase response genes were reduced in an intrabody-expressing mice during liver regeneration than in control virus-injected mice. However, the time course of liver mass restoration in intrabody-expressing mice was similar to that observed in control virus-injected mice. We also observed that the expression levels of anti-apoptotic genes, such as Bcl2 and Bcl-xL were decreased in intrabody-expressing mice whereas the expression of cell cycle-related genes such as cyclin D1, and c-myc was increased. Liver regeneration after PHx was partially impaired by the selective inhibition of pYSTAT3 with a phosphorylation site-specific intrabody and these results indicated that pYSTAT3 might have limited role in liver mass recovery.

Keywords: STAT3, pYSTAT3, liver regeneration, intrabody

Procedia PDF Downloads 312

Authors: Vijay Kumar Singh, Pooja Kushwaha, Prabhat Ranjan, Krishna Kumar Ojha, Jitendra Kumar

Abstract:

Present day high-throughput genomic technologies, NGS/microarrays, are producing large volume of data that require improved analysis methods to make sense of the data. The correlation between genes and samples has been regularly used to gain insight into many biological phenomena including, but not limited to, co-expression/co-regulation, gene regulatory networks, clustering and pattern identification. However, presence of outliers and violation of assumptions underlying Pearson correlation is frequent and may distort the actual correlation between the genes and lead to spurious conclusions. Here, we report a method to measure the strength of association between genes. The method assumes that the expression values of a gene are Bernoulli random variables whose outcome depends on the sample being probed. The method considers the two genes as uncorrelated if the number of sample with same outcome for both the genes (Ns) is equal to certainly expected number (Es). The extent of correlation depends on how far Ns can deviate from the Es. The method does not assume normality for the parent population, fairly unaffected by the presence of outliers, can be applied to qualitative data and it uses the binomial distribution to assess the significance of association. At this stage, we would not claim about the superiority of the method over other existing correlation methods, but our method could be another way of calculating correlation in addition to existing methods. The method uses binomial distribution, which has not been used until yet, to assess the significance of association between two variables. We are evaluating the performance of our method on NGS/microarray data, which is noisy and pierce by the outliers, to see if our method can differentiate between spurious and actual correlation. While working with the method, it has not escaped our notice that the method could also be generalized to measure the association of more than two variables which has been proven difficult with the existing methods.

Keywords: binomial distribution, correlation, microarray, outliers, transcriptome

Procedia PDF Downloads 415

Authors: M. Błoch, P. Karpiński, P. Gasperowicz, R. Płoski, A. Lebioda, P. Skiba, A. Rozensztrauch, D. Patkowski, R. Śmigiel

Abstract:

Introduction: The cause of the isolated form of esophageal atresia has been yet unknown. Objectives: The primary objective of this study was to indicate epigenetic factors which may play an important role in the etiopathogenesis of esophageal atresia. Methods: We recruited a group of 6 pairs of twins, among whom one of the twins developed EA. The selection of such a group for testing allows for excluding external factors (e.g., infections, drugs, toxins) as the cause of the birth defect. The analyzes were performed with the use of genetic material isolated from the whole blood and esophagus tissue of a patient with EA. The reduced representation bisulphite sequencing (RRBS) technique was used to study the change in the genomic imprinting -a change in the expression of genes, which may be the epigenetic cause of EA. Results: In the course of the analyzes, significant hypomethylation and hypermethylation regions were identified. 65 genes with probably increased expression and 65 with decreased expression were selected. These genes have not been marked in literature as possibly pathogenic in esophageal atresia. However, their participation in the pathogenesis of esophageal atresia cannot be clearly excluded. Conclusion: We suggest a role of hypomethylation or hypermethylation of selected genes as one of the possible epigenetic factors in EA pathogenesis. The use of the RRBS technique in the search for the cause of EA is pioneer research; therefore, it seems necessary to extend the research group to new patients with EA. Acknowledgment: The work was supported by the National Science Centre, Poland, under research project 2016/21/N/NZ5/01927.

Keywords: esophageal atresia, epigenetics, embryonic development, surgery, genes expression, twins

Procedia PDF Downloads 75

Authors: Petra Borilova Linhartova, Michaela Ruckova, Sabina Sevcikova, Natalie Mlcuchova, Jan Bohm, Katerina Zukalova, Monika Vlachova, Jiri Dolina, Lumir Kunovsky, Radek Kroupa, Zdenek Pavlovsky, Zdenek Danek, Tereza Deissova, Lydie Izakovicova Holla, Ondrej Slaby, Zdenek Kala

Abstract:

Esophageal adenocarcinoma (EAC) is a highly aggressive malignancy that frequently develops from Barrett's esophagus (BE), a premalignant pathologic change occurring in the lower end of the esophagus. Specific microRNAs (miRNAs), small non-coding RNAs that function as posttranscriptional regulators of gene expression, were repeatedly proved to play key roles in the pathogenesis of these diseases. This pilot study aimed to analyze four selected miRNAs in esophageal tissues from healthy controls (HC) and patients with reflux esophagitis (RE)/BE/EAC, as well as to compare expression at the site of Barrett's mucosa/adenocarcinoma and healthy esophageal tissue outside the area of the main pathology in patients with BE/EAC. In this pilot study, 22 individuals (3 HC, 8 RE, 5 BE, 6 EAC) were included and endoscopically examined. RNA was isolated from the fresh-frozen esophageal tissue (stored in the RNAlater™ Stabilization Solution −70°C) using the AllPrep DNA/RNA/miRNA Universal Kit. Subsequent RT-qPCR analysis was performed using selected TaqMan MicroRNA Assays for miR-21, miR-34a, miR-196a, miR-196b, and endogenous control (RNU44). While the expression of miR-21 in the esophageal tissue with the main pathology was decreased in BE and EAC patients in comparison to the group of HC and RE patients (p=0.01), the expression of miR-196a was increased in the BE and EAC patients (p<0.01). Correlations between those miRNAs expression in tissue and severity of diagnosis were observed (p<0.05). In addition, miR-196a was significantly more expressed at the site with the main pathology than in paired adjacent esophageal tissue in BE and EAC patients (p<0.01). In conclusion, our pilot results showed that miR-196a, which regulates the proliferation, invasion, and migration (and was previously associated with esophageal squamous cell carcinoma and marked as a potential therapeutic target), could be a diagnostic tissue biomarker for BE and EAC as well.

Keywords: microRNA, barrett´s esophagus, esophageal adenocarcinoma, biomarker

Procedia PDF Downloads 112

Authors: Zhang Zhenzhen

Abstract:

Valproate (VPA) is commonly used in the treatment of bipolar disorder and epilepsy. The mechanism is complicated, including its ability to inhibit histone deacetylases (HDACs). Here, we show that VPA attenuated VEGF gene expression and the morphological changes in choroidal neovascularization (CNV) induced by photocoagulation in retina. C57BL/6 mice were injected subcutaneously at 300mg/kg twice daily with VPA before insult. Vascular endothelial growth factor (VEGF)-A and VEGF-B were examined in the eyes of VPA-treated mice and in human retinal pigment epithelial cell lines (ARPE-19) exposed to VPA. In addition, CNV was induced by photocoagulation in mice injected with VPA, and the volume of CNV was compared by fluorescence-labeled choroidal flat mount. Morphological changes were analyzed on stained histological sections. Western blot analysis was used to determine protein levels of VEGF-A and VEGF-B, and acetylation of histone H3 in each group. VPA injected intraperitoneally attenuated the VEGF-A and VEGF-B expression in the retina, accompanied by the hyperacetylation of retina tissue, indicating that VPA acts directly on retina tissues through acetylation to reduce the expression of VEGF. VPA also attenuated the VEGF-A mRNA expression in the retinal pigment epithelium showed by immunohistochemistry. Moreover, the administration of VPA significantly attenuated photocoagulation-induced CNV in mice. These results demonstrate that VPA attenuated VEGF production in retina associated with choroidal neovascularization possibly via the HDAC inhibition.

Keywords: retina, acetylation, chorodial neovascularization, vascular endothelial growth factor

Procedia PDF Downloads 204

Authors: Natasha Petrovska, Mirjana Pavlovic, Maria M. Larrondo-Petrie

Abstract:

Neural stem cells (NSCs) are multi-potent, self-renewing cells that generate new neurons. Three subtypes of NSCs can be separated regarding the stages of NSC lineage: quiescent neural stem cells (qNSCs), activated neural stem cells (aNSCs) and neural progenitor cells (NPCs), but their gene expression signatures are not utterly understood yet. Single-cell examinations have started to elucidate the complex structure of NSC populations. Nevertheless, there is a lack of thorough molecular interpretation of the NSC lineage heterogeneity and an increasing need for tools to analyze and improve the efficiency and correctness of single-cell sequencing data. Feature selection and ordering can identify and classify the gene expression signatures of these subtypes and can discover novel subpopulations during the NSCs activation and differentiation processes. The aim here is to review the implementation of the feature selection technique on NSC subtypes and the classification techniques that have been used for the identification of gene expression signatures.

Keywords: feature selection, feature similarity, neural stem cells, genes, feature selection methods

Procedia PDF Downloads 152

Authors: Ng Liang Shen, Hau Yuan Wen

Abstract:

Arrhythmia analysis of ECG signal plays a major role in diagnosing most of the cardiac diseases. Therefore, a single arrhythmia detection of an electrocardiographic (ECG) record can determine multiple pattern of various algorithms and match accordingly each ECG beats based on Machine Learning supervised learning. These researchers used different features and classification methods to classify different arrhythmia types. A major problem in these studies is the fact that the symptoms of the disease do not show all the time in the ECG record. Hence, a successful diagnosis might require the manual investigation of several hours of ECG records. The point of this paper presents investigations cardiovascular ailment in Electrocardiogram (ECG) Signals for Cardiac Arrhythmia utilizing examination of ECG irregular wave frames via heart beat as correspond arrhythmia which with Machine Learning Pattern Recognition.

Keywords: electrocardiogram, ECG, classification, machine learning, pattern recognition, detection, QRS

Procedia PDF Downloads 376

Authors: Bineet Kumar

Abstract:

Many civil engineering infrastructures frequently encounter repetitive loading during their service life. Due to the inherent complexity observed in concrete, like quasi-brittle materials, understanding the fatigue behavior in concrete still posesa challenge. Moreover, the fracture process zone characteristics ahead of the crack tip have been observed to be different in fatigue loading than in the monotonic cases. Therefore, it is crucial to comprehend the energy dissipation associated with the fracture process zone (FPZ) due to repetitive loading. It is well known that stiffness degradation due to cyclic loadingprovides a better understanding of the fracture behavior of concrete. Under repetitive load cycles, concrete members exhibit a two-stage stiffness degradation process. Experimentally it has been observed that the stiffness decreases initially with an increase in crack length and subsequently increases. In this work, an attempt has been made to propose an analytical expression to predict energy dissipation and later the stiffness degradation as a function of crack length. Three-point bend specimens have been considered in the present work to derive the formulations. In this approach, the expression for the resultant stress distribution below the neutral axis has been derived by correlating the bending stress with the cohesive stresses developed ahead of the crack tip due to the existence of the fracture process zone. This resultant stress expression is utilized to estimate the dissipated energydue to crack propagation as a function of crack length. Further, the formulation for the stiffness degradation has been developed by relating the dissipated energy with the work done. It can be used to predict the critical crack length and fatigue life. An attempt has been made to understand the influence of stress amplitude on the damage pattern by using the information on the rate of stiffness degradation. It has been demonstrated that with the increase in the stress amplitude, the damage/FPZ proceeds more in the direction of crack propagation compared to the damage in the direction parallel to the span of the beam, which causes a lesser rate of stiffness degradation for the incremental crack length. Further, the effect of loading frequency has been investigated in terms of stiffness degradation. Under low-frequency loading cases, the damage/FPZ has been found to spread more in the direction parallel to the span, in turn reducing the critical crack length and fatigue life. In such a case, a higher rate of stiffness degradation has been observed in comparison to the high-frequency loading case.

Keywords: fatigue life, fatigue, fracture, concrete

Procedia PDF Downloads 95

Authors: Paola Modesto, Floriana Fruscione, Isabella Martini, Simona Perga, Federica Riccardo, Mariateresa Camerino, Davide Giacobino, Cecilia Gola, Luca Licenziato, Elisabetta Razzuoli, Katia Varello, Lorella Maniscalco, Elena Bozzetta, Angelo Ferrari

Abstract:

Canine and human melanoma, osteosarcoma (OSA), and mammary carcinomas are aggressive tumors with common characteristics making dogs a good model for comparative oncology. Novel therapeutic strategies against these tumors could be useful to both species. In humans, chondroitin sulphate proteoglycan 4 (CSPG4) is a marker involved in tumor progression and could be a candidate target for immunotherapy. The anti-CSPG4 DNA electrovaccination has shown to be an effective approach for canine malignant melanoma (CMM) [1]. An immunohistochemistry evaluation of CSPG4 expression in tumour tissue is generally performed prior to electrovaccination. To assess the possibility to perform a rapid molecular evaluation and in order to validate these spontaneous canine tumors as the model for human studies, we investigate the CSPG4 gene expression by RT qPCR in CMM, OSA, and canine mammary tumors (CMT). The total RNA was extracted from RNAlater stored tissue samples (CMM n=16; OSA n=13; CMT n=6; five paired normal tissues for CMM, five paired normal tissues for OSA and one paired normal tissue for CMT), retro-transcribed and then analyzed by duplex RT-qPCR using two different TaqMan assays for the target gene CSPG4 and the internal reference gene (RG) Ribosomal Protein S19 (RPS19). RPS19 was selected from a panel of 9 candidate RGs, according to NormFinder analysis following the protocol already described [2]. Relative expression was analyzed by CFX Maestro™ Software. Student t-test and ANOVA were performed (significance set at P<0.05). Results showed that gene expression of CSPG4 in OSA tissues is significantly increased by 3-4 folds when compared to controls. In CMT, gene expression of the target was increased from 1.5 to 19.9 folds. In melanoma, although an increasing trend was observed, no significant differences between the two groups were highlighted. Immunohistochemistry analysis of the two cancer types showed that the expression of CSPG4 within CMM is concentrated in isles of cells compared to OSA, where the distribution of positive cells is homogeneous. This evidence could explain the differences in gene expression results.CSPG4 immunohistochemistry evaluation in mammary carcinoma is in progress. The evidence of CSPG4 expression in a different type of canine tumors opens the way to the possibility of extending the CSPG4 immunotherapy marker in CMM, OSA, and CMT and may have an impact to translate this strategy modality to human oncology.

Keywords: canine melanoma, canine mammary carcinomas, canine osteosarcoma, CSPG4, gene expression, immunotherapy

Procedia PDF Downloads 174

Authors: Nahush Modak, Meena Pangarkar, Anand Pathak, Ankita Tamhane

Abstract:

Background: Breast cancer is the prominent cause of cancer and mortality among women. This study was done to show the statistical analysis of a cohort of over 250 patients detected with breast cancer diagnosed by oncologists using Immunohistochemistry (IHC). IHC was performed by using ER; PR; HER2; Ki-67 antibodies. Materials and methods: Formalin fixed Paraffin embedded tissue samples were obtained by surgical manner and standard protocol was followed for fixation, grossing, tissue processing, embedding, cutting and IHC. The Ventana Benchmark XT machine was used for automated IHC of the samples. Antibodies used were supplied by F. Hoffmann-La Roche Ltd. Statistical analysis was performed by using SPSS for windows. Statistical tests performed were chi-squared test and Correlation tests with p<.01. The raw data was collected and provided by National Cancer Insitute, Jamtha, India. Result: Luminal B was the most prevailing molecular subtype of Breast cancer at our institute. Chi squared test of homogeneity was performed to find equality in distribution and Luminal B was the most prevalent molecular subtype. The worse prognostic indicator for breast cancer depends upon expression of Ki-67 and her2 protein in cancerous cells. Our study was done at p <.01 and significant dependence was observed. There exists no dependence of age on molecular subtype of breast cancer. Similarly, age is an independent variable while considering Ki-67 expression. Chi square test performed on Human epidermal growth factor receptor 2 (HER2) statuses of patients and strong dependence was observed in percentage of Ki-67 expression and Her2 (+/-) character which shows that, value of Ki depends upon Her2 expression in cancerous cells (p<.01). Surprisingly, dependence was observed in case of Ki-67 and Pr, at p <.01. This shows that Progesterone receptor proteins (PR) are over-expressed when there is an elevation in expression of Ki-67 protein. Conclusion: We conclude from that Luminal B is the most prevalent molecular subtype at National Cancer Institute, Jamtha, India. There was found no significant correlation between age and Ki-67 expression in any molecular subtype. And no dependence or correlation exists between patients’ age and molecular subtype. We also found that, when the diagnosis is Luminal A, out of the cohort of 257 patients, no patient shows >14% Ki-67 value. Statistically, extremely significant values were observed for dependence of PR+Her2- and PR-Her2+ scores on Ki-67 expression. (p<.01). Her2 is an important prognostic factor in breast cancer. Chi squared test for Her2 and Ki-67 shows that the expression of Ki depends upon Her2 statuses. Moreover, Ki-67 cannot be used as a standalone prognostic factor for determining breast cancer.

Keywords: breast cancer molecular subtypes , correlation, immunohistochemistry, Ki-67 and HR, statistical analysis

Procedia PDF Downloads 123

Authors: Faizah Almalki, Simeon Gill, Steve G. Hayes, Lisa Taylor

Abstract:

A core element of cultural identity is the traditional costumes that provide insight into the heritage that has been acquired over time. This heritage is apparent in the use of colour, the styles and the functions of the clothing and it also reflects the skills of those who created the items and the time taken to produce them. Modern flat pattern drafting methods for making garment patterns are simple in comparison to the relatively laborious traditional approaches that would require personal interaction with the wearer throughout the production process. The current study reflects on the main elements of the pattern cutting system and how this has evolved in Saudi Arabia to affect the design of the Sawan garment. Analysis of the traditional methods for constructing Sawan garments was undertaken through observation of the practice and the garments and consulting documented guidance. This provided a foundation through which to explore how modern technology can be applied to improve the process. In this research, modern methods are proposed for producing traditional Saudi garments more efficiently while retaining elements of the conventional style and design. The current study has documented the vital aspects of Sawan garment style. The result showed that the method had been used to take the body measurements and pattern making was elementary and offered simple geometric shape and the Sawan garment is composed of four pieces. Consequently, this research allows for classical pattern shapes to be embedded in garments now worn in Saudi Arabia and for the continuation of cultural heritage.

Keywords: traditional Sawan garment technique, modern pattern cutting technique, the shape of the garment and software, Lectra Modaris

Procedia PDF Downloads 132

Authors: Jer-Yuh Liu, Je-Chiuan Ye, Jin-Ming Hwang

Abstract:

Protein kinase C alpha (PKCα) is a key signaling molecule in human cancer development. As a therapeutic strategy, targeting PKCα is difficult because the molecule is ubiquitously expressed in non-malignant cells. PKCα is regulated by the cooperative interaction of the transcription factors myeloid zinc finger 1 (MZF-1) and Ets-like protein-1 (Elk-1) in human cancer cells. By conducting tissue array analysis, herein, we determined the protein expression of MZF-1/Elk-1/PKCα in various cancers. The data show that the expression of MZF-1/Elk-1 is correlated with that of PKCα in hepatocellular carcinoma (HCC), but not in bladder and lung cancers. In addition, the PKCα down-regulation by shRNA Elk-1 was only observed in the HCC SK-Hep-1 cells. Blocking the interaction between MZF-1 and Elk-1 through the transfection of their binding domain MZF-160–72 decreased PKCα expression. This step ultimately depressed the epithelial-mesenchymal transition potential of the HCC cells. These findings could be used to develop an alternative therapeutic strategy for patients with the PKCα-derived HCC.

Keywords: protein kinase C alpha, myeloid zinc finger 1, ets-like protein-1, hepatocellular carcinoma

Procedia PDF Downloads 227

Authors: F. Saleh, F. Lyall, A. Abdulsid, L. Marks

Abstract:

Background: Labour in human is a complex biological process that involves interactions of neurological, hormonal and inflammatory pathways, with the placenta being a key regulator of these pathways. It is known that uterine contractions and labour pain cause physiological changes in gene expression in maternal and fetal blood, and in placenta during labour. Oxidative and inflammatory stress pathways are implicated in labour and they may cause alteration of placental gene expression. Additionally, in placental tissues, labour increases the expression of genes involved in placental oxidative stress, inflammatory cytokines, angiogenic regulators and apoptosis. Recently, Hydrogen Sulphide (H2S) has been considered as an endogenous gaseous mediator which promotes vasodilation and exhibits cytoprotective anti-inflammatory properties. The endogenous H2S is synthesised predominantly by two enzymes: cystathionine β-synthase (CBS) and cystathionine γ-lyase (CSE). As the H2S pathway has anti-oxidative and anti-inflammatory characteristics thus, we hypothesised that the expression of CBS and CSE in placental tissues would alter during labour. Methods: CBS and CSE expressions were examined in placentas using western blotting and RT-PCR in inner, middle and outer placental zones in placentas obtained from healthy non labouring women who delivered by caesarian section. These were compared with the equivalent zone of placentas obtained from women who had uncomplicated labour and delivered vaginally. Results: No differences in CBS and CSE mRNA or protein levels were found between the different sites within placentas in either the labour or non-labour group. There were no significant differences in either CBS or CSE expression between the two groups at the inner site and middle site. However, at the outer site there was a highly significant decrease in CBS protein expression in the labour group when compared to the non-labour group (p = 0.002). Conclusion: To the best of author’s knowledge, this is the first report to suggest that, CBS is expressed in a spatial manner within the human placenta. Further work is needed to clarify the precise function and mechanism of this spatial regulation although it is likely that inflammatory pathways regulation is a complex process in which this plays a role.

Keywords: anti-inflammatory, hydrogen sulphide, labour, oxidative stress

Procedia PDF Downloads 241

Authors: Elvira Hörandl

Abstract:

The term “Geographical parthenogenesis” describes the phenomenon that asexual organisms usually occupy larger and more northern distribution areas than their sexual relatives and tend to colonize previously glaciated areas. Several case studies in flowering plants confirm the geographical pattern, but the causal factors behind the phenomenon are still unclear. Previous authors regarded predominant polyploidy in asexual (apomictic) plants as the main factor. However, the geographical pattern is not the rule for sexual polyploids. Recent research confirmed a previous hypothesis of the author that a combination of factors is acting: Although uniparental reproduction provides better colonization abilities, it is most efficient in combination with polyploidy. I will present results on case studies in the genus Ranunculus of both autopolyploid and allopolyploid species and species complexes reproducing via facultative apomixis. Polyploidy seems to contribute mainly to a better tolerance of colder climates and temperate extremes, whereby epigenetic flexibility, changes in gene expression, and phenotypic plasticity play an important role in occupying ecological niches under harsh conditions. Phylogenomic studies entangle complex hybrid origins of asexual taxa, which increases intragenomic heterozygosity of asexual plants. Interestingly, our results suggest an association of sexuality with abiotic stresses, specifically with light stress, which might explain that still, most plants in high altitudes and in southern areas retain sexual reproduction despite other climatic conditions that would favor apomictic plants. We conclude that geographical parthenogenesis results from the complex interplay of the genomic constitution, mode of reproduction and environmental factors.

Keywords: apomixis, polyploidy, hybridization, abiotic stress, epigenetics, phylogenomics

Procedia PDF Downloads 74