Search results for: gene concordance factor confidence

Authors: Ahmad Ali Shahid, Mukhtar Ahmed

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The demand for long staple fiber having better strength and length is increasing with the introduction of modern spinning and weaving industry in Pakistan. Work on gene discovery from developing cotton fibers has helped to identify dozens of genes that take part in cotton fiber development and several genes have been characterized for their role in fiber development. Sucrose synthase (SuS) is a key enzyme in the metabolism of sucrose in a plant cell, in cotton fiber it catalyzes a reversible reaction, but preferentially converts sucrose and UDP into fructose and UDP-glucose. UDP-glucose (UDPG) is a nucleotide sugar act as a donor for glucose residue in many glycosylation reactions and is essential for the cytosolic formation of sucrose and involved in the synthesis of cell wall cellulose. The study was focused on successful Agrobacterium-mediated stable transformation of SuS gene in pCAMBIA 1301 into cotton under a CaMV35S promoter. Integration and expression of the gene were confirmed by PCR, GUS assay, and real-time PCR. Young leaves of SuS overexpressing lines showed increased total soluble sugars and plant biomass as compared to non-transgenic control plants. Cellulose contents from fiber were significantly increased. SEM analysis revealed that fibers from transgenic cotton were highly spiral and fiber twist number increased per unit length when compared with control. Morphological data from field plants showed that transgenic plants performed better in field conditions. Incorporation of genes related to cotton fiber length and quality can provide new avenues for fiber improvement. The utilization of this technology would provide an efficient import substitution and sustained production of long-staple fiber in Pakistan to fulfill the industrial requirements.

Keywords: agrobacterium-mediated transformation, cotton fiber, sucrose synthase gene, staple length

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Authors: Neda Menbari, Ramin Mehdiabadi

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Background: breast cancer remains a critical global health issue, constituting a leading cause of cancer-related mortality in women. MicroRNAs (miRs) are natural RNA molecules that play an important role in cellular processes and regulate post-transcriptional gene expression. MiR-216b-5p is a miR that acts as a tumor suppressor. The expression levels of FoxM1 and miR-216b-5p in malignant and control cells have been evaluated by quantitative polymerase chain reaction (qPCR) technique and flow cytometry. Results: the results of this study revealed a significant downregulation of miR-216b-5p in cancerous cells compared to the control MCF-10A cells (P=0.0004). Interestingly, the expression of miR-216b-5p exhibited an inverse relationship with key clinical indicators such as tumor size, grade, and lymph node invasion. Conclusion: The study's findings showed the prognostic value of miR-216b-5p levels in breast cancer, and its reduced expression correlates with unfavorable tumor characteristics. This research recommends performing more studies on the role of FoxM1 and miR-216b-5p in breast cancer pathology which potentially paving the way for targeted therapeutic interventions.

Keywords: breast cancer, gene expression, FOXM1, microRNA

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Authors: Iman Kamranfar, Gang-Ping Xue, Salma Balazadeh, Bernd Mueller-Roeber

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Adverse environmental conditions such as salinity stress, high temperature and drought limit plant growth and typically lead to precocious tissue degeneration and leaf senescence, a process by which nutrients from photosynthetic organs are recycled for the formation of flowers and seeds to secure reaching the next generation under such harmful conditions. In addition, abiotic stress affects developmental patterns that help the plant to withstand unfavourable environmental conditions. We discovered an NAC (for NAM, ATAF1, 2, and CUC2) transcription factor (TF), called RAF in the following, which plays a central role in abiotic drought stress-triggered senescence and the control of developmental adaptations to stressful environments. RAF is an ABA-responsive TF; RAF overexpressors are hypersensitive to abscisic acid (ABA) and exhibit precocious senescence while knock-out mutants show delayed senescence. To explore the RAF gene regulatory network (GRN), we determined its preferred DNA binding sites by binding site selection assay (BSSA) and performed microarray-based expression profiling using inducible RAF overexpression lines and chromatin immunoprecipitation (ChIP)-PCR. Our studies identified several direct target genes, including those encoding for catabolic enzymes acting during stress-induced senescence. Furthermore, we identified various genes controlling drought stress-related developmental changes. Based on our results, we conclude that RAF functions as a central transcriptional regulator that coordinates developmental programs with stress-related inputs from the environment. To explore the potential agricultural applications of our findings, we are currently extending our studies towards crop species.

Keywords: abiotic stress, Arabidopsis, development, transcription factor

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Authors: Samira B. R. Prado, Paulo R. Melfi, Beatriz T. Minguzzi, João P. Fabi

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Fruit softening is the main change that occurs during papaya (Carica papaya L.) ripening. It is characterized by the depolymerization of cell wall polysaccharides, especially the pectic fractions, which causes cell wall disassembling. However, it is uncertain how the modification of the two main pectin polysaccharides fractions (water-soluble – WSF, and oxalate-soluble fractions - OSF) accounts for fruit softening. The aim of this work was to correlate molecular weight changes of WSF and OSF with the gene expression of pectin-solubilizing enzymes (pectinases) during papaya ripening. Papaya fruits obtained from a producer were harvest and storage under specific conditions. The fruits were divided in five groups according to days after harvesting. Cell walls from all groups of papaya pulp were isolated and fractionated (WSF and OSF). Expression profiles of pectinase genes were achieved according to the MIQE guidelines (Minimum Information for publication of Quantitative real-time PCR Experiments). The results showed an increased yield and a decreased molecular weight throughout ripening for WSF and OSF. Gene expression data support that papaya softening is achieved by polygalacturonases (PGs) up-regulation, in which their actions might have been facilitated by the constant action of pectinesterases (PMEs). Moreover, BGAL1 gene was up-regulated during ripening with a simultaneous galactose release, suggesting that galactosidases (GALs) could also account for pulp softening. The data suggest that a solubilization of galacturonans and a depolymerization of cell wall components were caused mainly by the action of PGs and GALs.

Keywords: carica papaya, fruit ripening, galactosidases, plant cell wall, polygalacturonases

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Authors: Ceyda Okudu, Secil Eroglu, Khandakar A. S. M. Saadat, Sibel O. Balci

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Ring Finger Protein 2 (RNF2) is a member of polycomb repressive complex 1 (PRC1), which is one of the epigenetic regulators in the genome. When RNF2 combines with other PRC1 members, it mediates the mono-ubiquitination of Histon2A (H2A). In breast cancer, RNF2 is commonly overexpressed, and also it promotes metastasis and invasion in other aggressive tumors like melanoma, prostate, and hepatocarcinoma. The role of RNF2 in the metastasis and invasion of breast cancer has not yet been elucidated. Our aim is to observe the role of RNF2 in metastasis and invasion in this study by miRNA mediated RNF2 gene silencing in breast cancer cell lines. We selected miRNAs, targeting to RNF2 by searching online databases. miR-17-5p, miR20a-5p, and miR-106b-5p were transfected to breast cancer cell lines (MCF-7, MDA-MB-231, SK-BR-3, and ZR-75-1), and also we used normal breast epithelial cell line (hTERT-HME1) to compare RNF2 gene expression level. After 48-72 hours post-transfection, mRNAs were isolated from the cells, and gene expressions were measured by RT-qPCR after from cDNA syntheses. We observed that RNF2 was highly expressed in SK-BR-3 and MDA-MB-231 cell lines opposite to MCF-7 and ZR-75-1 cell lines. RNF2 was downregulated 5, 5 and 7 fold by miR17-5p, miR20a-5p and miR106b-5p respectively in MCF-7. However, in SK-BR-3 and ZR-75-1 cell lines, miRNAs did not affect significantly RNF2 gene expression level. miR20a-5p decreased RNF2 3 fold and miR17-5p and miR106b-5p did not affect MDA-MB-231. After gene expression analysis, we performed metastasis and invasion assay in MCF-7 cells. For metastasis, we used both wound healing assay and Transwell Cell Migration Assay, and we used Transwell Cell Invasion Assay for invasion. The data of this assay showed that miR17-5p and miR20a-5p decreased both invasion and metastasis level, but miR106b-5p has no effect. We would like to conclude that RNF2 can be targeted by miR17-5p, miR20a-5p and miR106b-5p in MCF-7 cells and also RNF2, which is one of the upregulated genes in aggressive tumor, can be decreased by using these miRNAs. In future, we would like to confirm these results at the protein level and also whether these miRNAs are direct target of RNF2 or not.

Keywords: breast cancer, epigenetic, microRNAs, RNF2

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Authors: Mohsen Mousivand, Hesam Aminpour

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Soil slopes are usually located above the groundwater level that are largely unsaturated. It is possible that unsaturated soil of slope has expanded or collapsed as a result of wetting by rain or other factor that this type of soil behavior can cause serious problems including human and financial damage. The main factor causing this difference in behavior of saturated and unsaturated state of soil is matric suction that is created by interface of the soil and water in the soil pores. So far theoretical studies show that matric suction has important effect on the mechanical behavior of soil although the impact of this factor on slope stability has not been studied. This paper presents a numerical study of effect of matric suction on slope stability. The results of the study indicate that safety factor and stability of soil slope increase due to an increasing of matric suction and in view of matric suction leads to more accurate results and safety factor.

Keywords: slope, unsaturated soil, matric suction, stability

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Authors: Dana Gabriková, Martin Mistrík, Jarmila Bernasovská, Iveta Tóthová, Jana Kisková

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The Roma (Gypsies) is a transnational minority with a high degree of consanguineous marriages. Similar to other genetically isolated founder populations, the Roma harbor a number of unique or rare genetic disorders. This paper discusses about a rare form of Charcot-Marie-Tooth disease – type 4G (CMT4G), also called Hereditary Motor and Sensory Neuropathy type Russe, an autosomal recessive disease caused by mutation private to Roma characterized by abnormally increased density of non-myelinated axons. CMT4G was originally found in Bulgarian Roma and in 2009 two putative causative mutations in the HK1 gene were identified. Since then, several cases were reported in Roma families mainly from Bulgaria and Spain. Here we present a Slovak Roma family in which CMT4G was diagnosed on the basis of clinical examination and genetic testing. This case is a further proof of the role of the HK1 gene in pathogenesis of the disease. It confirms that mutation in the HK1 gene is a common cause of autosomal recessive CMT disease in Roma and should be considered as a common part of a diagnostic procedure.

Keywords: gypsies, HK1, HSMN-Russe, rare disease

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Authors: Edwin Hidayat, Redi Yulianto, Disi Hanafiah

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On the one hand, parameters which are used for determining the number of lane on the new road construction are average annual average daily traffic (AADT) and peak hour factor (K-factor). On the other hand, the value of K-factor listed in the guidelines and manual for road planning in Indonesia is a value of adoption or adaptation from foreign guidelines or manuals. Thus, the value is less suitable for Indonesian condition due to differences in road conditions, vehicle type, and driving behavior. The purpose of this study is to provide an example on how to determine k-factor values at a road segment with particular conditions in north coast road, West Java. The methodology is started with collecting traffic volume data for 24 hours over 365 days using PLATO (Automated Traffic Counter) with the approach of video image processing. Then, the traffic volume data is divided into per hour and analyzed by comparing the peak traffic volume in the 30th hour (or other) with the AADT in the same year. The analysis has resulted that for the 30th peak hour the K-factor is 0.97. This value can be used for planning road geometry or evaluating the road capacity performance for the 4/2D interurban road.

Keywords: road geometry, K-factor, annual average daily traffic, north coast road

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Authors: Xiaoping Su, Gabriel G. Malouf

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Introduction: Breast cancer is a heterogeneous disease that can be classified in 4 subgroups using transcriptional profiling. The role of lncRNA expression in human breast cancer biology, prognosis, and molecular classification remains unknown. Methods and results: Using an integrative comprehensive analysis of lncRNA, mRNA and DNA methylation in 900 breast cancer patients from The Cancer Genome Atlas (TCGA) project, we unraveled the molecular portraits of 1,700 expressed lncRNA. Some of those lncRNAs (i.e, HOTAIR) are previously reported and others are novel (i.e, HOTAIRM1, MAPT-AS1). The lncRNA classification correlated well with the PAM50 classification for basal-like, Her-2 enriched and luminal B subgroups, in contrast to the luminal A subgroup which behaved differently. Importantly, estrogen receptor (ESR1) expression was associated with distinct lncRNA networks in lncRNA clusters III and IV. Gene set enrichment analysis for cis- and trans-acting lncRNA showed enrichment for breast cancer signatures driven by breast cancer master regulators. Almost two third of those lncRNA were marked by enhancer chromatin modifications (i.e., H3K27ac), suggesting that lncRNA expression may result in increased activity of neighboring genes. Differential analysis of gene expression profiling data showed that lncRNA HOTAIRM1 was significantly down-regulated in basal-like subtype, and DNA methylation profiling data showed that lncRNA HOTAIRM1 was highly methylated in basal-like subtype. Thus, our integrative analysis of gene expression and DNA methylation strongly suggested that lncRNA HOTAIRM1 should be a tumor suppressor in basal-like subtype. Conclusion and significance: Our study depicts the first lncRNA molecular portrait of breast cancer and shows that lncRNA HOTAIRM1 might be a novel tumor suppressor.

Keywords: lncRNA profiling, breast cancer, HOTAIRM1, tumor suppressor

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Authors: Rabiul Islam

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The study was in order to assess soil erosion at plot scale Universal Soil Loss Equation (USLE) erosion model and Geographic Information System (GIS) technique have been used for the study 8 plots in Guthrie Corridor Expressway, Selangor, Malaysia. The USLE model estimates an average soil loss soil integrating several factors such as rainfall erosivity factor(R ), Soil erodibility factor (K), slope length and steepness factor (LS), vegetation cover factor as well as conservation practice factor (C &P) and Results shows that the four plots have very low rates of soil loss, i.e. NLDNM, NDNM, PLDM, and NDM having an average soil loss of 0.059, 0.106, 0.386 and 0.372 ton/ha/ year, respectively. The NBNM, PLDNM and NLDM plots had a relatively higher rate of soil loss, with an average of 0.678, 0.757 and 0.493ton/ha/year. Whereas, the NBM is one of the highest rate of soil loss from 0.842 ton/ha/year to maximum 16.466 ton/ha/year. The NBM plot was located at bare the land; hence the magnitude of C factor(C=0.15) was the highest one.

Keywords: USLE model, GIS, Guthrie Corridor Expressway (GCE), Malaysia

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Authors: Nicholas Jobe

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English Language Learners (ELLs) often struggle in a classroom setting, too embarrassed at their skill level to write or speak in front of peers and too lacking in confidence to practice. Storytelling is an age-old method of teaching that allows learners to remember important details while listening or sharing a narrative. In the modern world, digital storytelling through the use of technological tools such as podcasts and videos allow students to safely interact with each other to build skills in a fun and engaging way that also works as a confidence booster. Specifically using a constructionist approach to learning, digital storytelling allows ELL students to grow and build new and prior knowledge by creating stories via these technological means. Research herein suggests, through the use of case studies and mixed methodologies, that digital storytelling mainly yields positive results for effective learning in an ELL classroom setting.

Keywords: digital storytelling, ELL, narrative, podcast

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Authors: Ankan Roy, Niharika, Samir Kumar Patra

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Anomalous nexus of complex topological assemblies and spatiotemporal epigenetic choreography at chromosomal territory may forms the most sophisticated regulatory layer of gene expression in cancer. Colon cancer is one of the leading malignant neoplasms of the lower gastrointestinal tract worldwide. There is still a paucity of information about the complex molecular mechanisms of colonic cancerogenesis. Bioinformatics prediction and analysis helps to identify essential genes and significant pathways for monitoring and conquering this deadly disease. The present study investigates and explores potential hub genes as biomarkers and effective therapeutic targets for colon cancer treatment. Colon cancer patient sample containing gene expression profile datasets, such as GSE44076, GSE20916, and GSE37364 were downloaded from Gene Expression Omnibus (GEO) database and thoroughly screened using the GEO2R tool and Funrich software to find out common 2 differentially expressed genes (DEGs). Other approaches, including Gene Ontology (GO) and KEGG pathway analysis, Protein-Protein Interaction (PPI) network construction and hub gene investigation, Overall Survival (OS) analysis, gene correlation analysis, methylation pattern analysis, and hub gene-Transcription factors regulatory network construction, were performed and validated using various bioinformatics tool. Initially, we identified 166 DEGs, including 68 up-regulated and 98 down-regulated genes. Up-regulated genes are mainly associated with the Cytokine-cytokine receptor interaction, IL17 signaling pathway, ECM-receptor interaction, Focal adhesion and PI3K-Akt pathway. Downregulated genes are enriched in metabolic pathways, retinol metabolism, Steroid hormone biosynthesis, and bile secretion. From the protein-protein interaction network, thirty hub genes with high connectivity are selected using the MCODE and cytoHubba plugin. Survival analysis, expression validation, correlation analysis, and methylation pattern analysis were further verified using TCGA data. Finally, we predicted COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as potential master regulators in colonic cancerogenesis. Moreover, our experimental data highlights that disruption of lipid raft and RAS/MAPK signaling cascade affects this gene hub at mRNA level. We identified COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as determinant hub genes in colon cancer progression. They can be considered as biomarkers for diagnosis and promising therapeutic targets in colon cancer treatment. Additionally, our experimental data advertise that signaling pathway act as connecting link between membrane hub and gene hub.

Keywords: hub genes, colon cancer, DNA methylation, epigenetic engineering, bioinformatic predictions

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Authors: O. Abiodun Adeyinka, B. Adeyemo Adesesan

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The forensic use of handwriting depends on the analysis, comparison, and evaluation decisions made by forensic document examiners. When using biometric technology in forensic applications, it is necessary to compute Likelihood Ratio (LR) for quantifying strength of evidence under two competing hypotheses, namely the prosecution and the defense hypotheses wherein a set of assumptions and methods for a given data set will be made. It is therefore important to know how repeatable and reproducible our estimated LR is. This paper evaluated the accuracy and reproducibility of examiners' decisions. Confidence interval for the estimated LR were presented so as not get an incorrect estimate that will be used to deliver wrong judgment in the court of Law. The estimate of LR is fundamentally a Bayesian concept and we used two LR estimators, namely Logistic Regression (LoR) and Kernel Density Estimator (KDE) for this paper. The repeatability evaluation was carried out by retesting the initial experiment after an interval of six months to observe whether examiners would repeat their decisions for the estimated LR. The experimental results, which are based on handwriting dataset, show that LR has different confidence intervals which therefore implies that LR cannot be estimated with the same certainty everywhere. Though the LoR performed better than the KDE when tested using the same dataset, the two LR estimators investigated showed a consistent region in which LR value can be estimated confidently. These two findings advance our understanding of LR when used in computing the strength of evidence in handwriting using forensics.

Keywords: confidence interval, handwriting, kernel density estimator, KDE, logistic regression LoR, repeatability, reproducibility

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Authors: Yun-Chin Chung, Nileema Divate, Gen-Hung Chen, Pei-Ru Huang, Rupesh Divate

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Many environmental factors, such as glucose concentration, ethanol, temperature, osmotic pressure and pH, decrease the production rate of ethanol using yeast as a starter. Fermentation starters with high tolerance to various stresses are always demanded for brewing industry. Trehalose, a storage carbohydrate in cell wall of yeast, plays an important role in tolerance of environmental stress by preserving integrity of plasma membrane and stabilizing proteins. Furan aldehydes are toxic to yeast and the growth rate of yeast is significantly reduced if furan aldehydes were present in the fermentation medium. In yeast, aldehyde reductase is involved in the detoxification of reactive aldehydes and consequently the growth of yeast is improved. The aims of this study were to construct a genetic recombinant Saccharomyces cerevisiae or Pichia pastoris with furfural and HMF degrading and high ethanol tolerance capacities. Yeast strains were engineered by genetic recombination for overexpression of trehalose-6-phosphate synthase gene (tps1) and aldehyde reductase gene (ari1). TPS1 gene was cloned from S. cerevisiae by reverse transcription-polymerase chain reaction (RT-PCR) and then ligated with pGAPZαC vector. The constructed vector, pGAPZC-tps1, was transformed to recombinant yeasts strain with overexpression of ari1. The transformants with pGAPZC-tps1-ari1 were generated called STA (S. cerevisiae) and PTA (P. pastoris) with overexpression of tps1, ari1. PCR with tps1-specific primers and western blot with his-tag confirmed the gene insertion and protein expression of tps1 in the transformants, respectively. The neutral trehalase gene (nth1) of STA was successfully deleted and the novel strain STAΔN will be used for further study, including the measurement of trehalose concentration and ethanol, furfural tolerance assay.

Keywords: genetic recombinant, yeast, ethanol tolerance, trehalase, aldehyde reductase

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Authors: Ali Bayram, Remzi Yiğiter

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Objective: Alzheimer's disease (AD), the most common cause of dementia, is a progressive neurodegenerative disease. At present, diagnosis of AD is rather late in the disease. Therefore, we attempted to find peripheral biomarkers for the early diagnosis of AD. Herein, we conducted a study to investigate the unc-51 like autophagy activating kinase-1 (ULK1) mRNA expression levels in human peripheral blood mononuclear cells from patients with Alzheimer's disease. Method: To determine whether ULK1 gene expression are altered in AD patients, we measured their gene expression in human peripheral blood cell in 50 patients with AD and 50 age and gender matched healthy controls by quantitative real-time PCR technique. Results: We found that both ULK1 gene expression in peripheral blood cell were significantly decreased in patients with AD as compared with controls (p <0.05). Lower levels of ULK1 gene expression were significantly associated with the increased risk for AD. Conclusions: Serine/threonine-protein kinase involved in autophagy in response to starvation. Acts upstream of phosphatidylinositol 3-kinase PIK3C3 to regulate the formation of autophagophores, the precursors of autophagosomes. Part of regulatory feedback loops in autophagy: acts both as a downstream effector and negative regulator of mammalian target of rapamycin complex 1 (mTORC1) via interaction with RPTOR. Activated via phosphorylation by AMPK and also acts as a regulator of AMPK by mediating phosphorylation of AMPK subunits PRKAA1, PRKAB2, and PRKAG1, leading to negatively regulate AMPK activity. May phosphorylate ATG13/KIAA0652 and RPTOR; however such data need additional evidences. Plays a role early in neuronal differentiation and is required for granule cell axon formation. Alzheimer is the most common neurodegenerative disease. Our results provide useful information that the ULK1 gene expression is decreased in the neurodegeneration and AD patients with, indicating their possible systemic involvement in AD.

Keywords: Alzheimer’s sisease, ULK1, mRNA expression, RT-PCR

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Authors: Jae Woong Sull, Sun Ha Jee

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High-density lipoprotein (HDL) cholesterol levels are associated with decreased risk of coronary artery disease. Several genome-wide association studies (GWAS) for HDL cholesterol levels have implicated cholesterol ester transfer protein (CETP) as possibly causal. We tested for the association between single nucleotide polymorphisms (SNPs) in CETP gene and HDL cholesterol levels in Korean population. Subjects were selected from the Korean Metabolic Syndrome Research Initiative study in the Bundang-Gu area. A total of 2,304 individuals from Bundang-Gu were recruited in 2008. Other subjects were selected from the Severance Hospital (N=4,294). SNP rs6499861 in the CETP gene was associated with mean HDL cholesterol levels (effect per allele -2.044 mg/dL, p=7.23×10-7). Subjects with the CG/GG genotype had a 1.46 -fold (range 1.24–1.72-fold) higher risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. When analyzed by gender, the association of CETP was stronger in women than in men. When analyzed by physical activity behavior, the association with CETP was much stronger in male subjects with low physical activity (OR=1.54, 95% CI: 1.23-1.92, P=0.0001) than in male subjects with high physical activity. This study clearly demonstrates that genetic variants in CETP influence HDL cholesterol levels in Korean adults.

Keywords: CETP, HDL cholesterol, physical activity, polymorphisms

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Authors: Dipanshu Sur, Ratnabali Chakravorty

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Background: Polycystic ovary syndrome (PCOS) is the most common metabolic abnormality such as changes in lipid profile, diabetes, hypertension and metabolic syndrome occurring in young women of reproductive age. Low vitamin D levels were found to be associated with the development of obesity and insulin resistance in women with PCOS. Variants on vitamin D receptor (VDR) gene have also been related to metabolic comorbidities in general population. Aim: The aim of this case-control study was to investigate whether the VDR gene polymorphisms are associated with susceptibility to PCOS. Methods: Women with PCOS and a control group, all aged 16-40 years, were enrolled. Genotyping of VDR Fok-I (rs2228570), VDR Apa-I (rs7975232) as well as GC (rs2282679), DHCR7 (rs12785878) SNPs between groups were determined by using direct sequencing. Serum 25-hydroxyvitamin D [25(OH)] levels were measured by ELISA. Results: Mean serum 25(OH)D in the PCOS and control samples were 19.08±7 and 23.27±6.03 (p=0.048) which were significantly lower in PCOS patients compared with controls. CC genotype of the VDR Apa-I SNP was same frequent in PCOS (25.6%) and controls (25.6%) (OR: 0.9995; 95%CI: 0.528 to 1.8921; p= 0.9987). The CC genotype was also significantly associated with both lower E2 (p=0.031) and Androstenedione levels (p=0.062). We observed a significant association of GC polymorphism with 25(OH)D levels. PCOS women carrying the GG genotype (in GC genes) had significantly higher risk for vitamin D deficiency than women carrying the TT genotype. Conclusions: In conclusion, data from this study indicate that vitamin D levels are lower, and vitamin D deficiency more frequent, in PCOS than in controls. The present findings suggest that the Apa-I, Fok-I polymorphism of the VDR gene is associated with PCOS and seems to modulate ovarian steroid secretion. Further studies are needed to better clarify the biological mechanisms by which the polymorphism influences PCOS risk.

Keywords: vitamin D receptor, polymorphism, vitamin D, polycystic ovary syndrome

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Authors: Micheale Yifter Weldemichael, Hailay Mehari Gebremedhn, Teklehaimanot Hailesslasie

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The advancement of target-specific genome editing tools, including clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein9 (Cas9), mega-nucleases, base editing (BE), prime editing (PE), transcription activator-like endonucleases (TALENs), and zinc-finger nucleases (ZFNs), have paved the way for a modern era of gene editing. CRISPR/Cas9, as a versatile, simple, cost-effective and robust system for genome editing, has dominated the genome manipulation field over the last few years. The application of CRISPR/Cas9 in sorghum improvement is particularly vital in the context of ecological, environmental and agricultural challenges, as well as global climate change. In this context, gene editing using CRISPR/Cas9 can improve nutritional value, yield, resistance to pests and disease and tolerance to different abiotic stress. Moreover, CRISPR/Cas9 can potentially perform complex editing to reshape already available elite varieties and new genetic variations. However, existing research is targeted at improving even further the effectiveness of the CRISPR/Cas9 genome editing techniques to fruitfully edit endogenous sorghum genes. These findings suggest that genome editing is a feasible and successful venture in sorghum. Newer improvements and developments of CRISPR/Cas9 techniques have further qualified researchers to modify extra genes in sorghum with improved efficiency. The fruitful application and development of CRISPR techniques for genome editing in sorghum will not only help in gene discovery, creating new, improved traits in sorghum regulating gene expression sorghum functional genomics, but also in making site-specific integration events.

Keywords: CRISPR/Cas9, genome editing, quality, sorghum, stress, yield

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Authors: Abdullah M. Alzahrani

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Our physiopathological assumption is that u-PA, t-PA, and PAI-1 are released by calcified aortic valves and play a role in the calcification of these valves. Sixty-five calcified aortic valves were collected from patients suffering from aortic stenosis. Each valve was incubated for 24 hours in culture medium. The supernatants were used to measure u-PA, t-PA, and PAI-1 concentrations; the valve calcification was evaluated using biphotonic absorptiometry. Aortic stenosis valves expressed normal plasminogen activators concentrations and overexpressed PAI-1 (u-PA, t-PA, and PAI-1 mean concentrations were, resp., 1.69 ng/mL ± 0.80, 2.76 ng/mL ± 1.33, and 53.27 ng/mL ± 36.39). There was no correlation between u-PA and PAI-1 (r = 0.3) but t-PA and PAI-1 were strongly correlated with each other (r = 0.6). Over expression of PAI-1 was proportional to the calcium content of theAS valves. Our results demonstrate a consistent increase of PAI-1 proportional to the calcification. The over expression of PAI-1 may be useful as a predictive indicator in patients with aortic stenosis.

Keywords: aortic valve, PAI-1, tPA gene, uPA gene

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Authors: Omneya M. Helmy, Mona T. Kashef

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Aminoglycosides are used in treating a wide range of infections caused by both Gram-negative and Gram positive bacteria. The presence of 16S rRNA methyl transferases (16S-RMTase) is among the newly discovered resistance mechanisms that confer high resistance to clinically useful aminoglycosides. Cephalosporins are the most commonly used antimicrobials in Egypt; therefore, this study was conducted to determine the isolation frequency of 16S rRNA methyl transferases among third generation cephalosporin-resistant clinical isolates in Egypt. One hundred and twenty three cephalosporin resistant Gram-negative clinical isolates were screened for aminoglycoside resistance by the Kirby Bauer disk diffusion method and tested for possible production of 16S-RMTase. PCR testing and sequencing were used to confirm the presence of 16S-RMTase and the associated antimicrobial resistance determinants, as well as the genetic region surrounding the armA gene. Out of 123 isolates, 66 (53.66%) were resistant to at least one aminoglycoside antibiotic. Only one Escherichia coli isolate (E9ECMO) which was totally resistant to all tested aminoglycosides, was confirmed to have the armA gene in association with blaTEM-1, blaCTX-M-15, blaCTX-M-14 and aac(6)-Ib genes. The armA gene was found to be carried on a large A/C plasmid. Genetic mapping of the armA surrounding region revealed, for the first time, the association of armA with aac(6)-Ib on the same transposon. In Conclusion, the isolation frequency of 16S-RMTase was low among the tested cephalosporin-resistant clinical samples. However, a novel composite transposon has been detected conferring high-level aminoglycosides resistance.

Keywords: aminoglcosides, armA gene, β lactmases, 16S rRNA methyl transferases

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Authors: S. MacDougall-Davis, S. Wysling, R. Willmore

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Background: The application of good non-technical skills, also known as crew resource management (CRM), is central to the delivery of safe, effective healthcare. The authors have been running remote trauma courses for over 10 years, primarily focussing on developing participants’ CRM in time-critical, high-stress clinical situations. The course has undergone an iterative process over the past 10 years. We employ a number of experiential learning techniques for improving CRM, including small group workshops, military command tasks, high fidelity simulations with reflective debriefs, and a ‘flipped classroom’, where participants are asked to create their own simulations and assess and debrief their colleagues’ CRM. We created a randomised simulation study to assess the impact of our course on UK medical students’ CRM, both at an individual and a teams level. Methods: Sixteen students took part. Four clinical scenarios were devised, designed to be of similar urgency and complexity. Professional moulage effects and experienced clinical actors were used to increase fidelity and to further simulate high-stress environments. Participants were block randomised into teams of 4; each team was randomly assigned to one pre-course simulation. They then underwent our 5 day remote trauma CRM course. Post-course, students were re-randomised into four new teams; each was randomly assigned to a post-course simulation. All simulations were videoed. The footage was reviewed by two independent CRM-trained assessors, who were blinded to the before/after the status of the simulations. Assessors used the internationally validated team emergency assessment measure (TEAM) to evaluate key areas of team performance, as well as a global outcome rating. Prior to the study, assessors had scored two unrelated scenarios using the same assessment tool, demonstrating 89% concordance. Participants also completed pre- and post-course questionnaires. Likert scales were used to rate individuals’ perceived NTS ability and their confidence to work in a team in time-critical, high-stress situations. Results: Following participation in the course, a significant improvement in CRM was observed in all areas of team performance. Furthermore, the global outcome rating for team performance was markedly improved (40-70%; mean 55%), thus demonstrating an impact at Level 4 of Kirkpatrick’s hierarchy. At an individual level, participants’ self-perceived CRM improved markedly after the course (35-70% absolute improvement; mean 55%), as did their confidence to work in a team in high-stress situations. Conclusion: Our study demonstrates that with a short, cost-effective course, using easily reproducible teaching sessions, it is possible to significantly improve participants’ CRM skills, both at an individual and, perhaps more importantly, at a teams level. The successful functioning of multi-disciplinary teams is vital in a healthcare setting, particularly in high-stress, time-critical situations. Good CRM is of paramount importance in these scenarios. The authors believe that these concepts should be introduced from the earliest stages of medical education, thus promoting a culture of effective CRM and embedding an early appreciation of the importance of these skills in enabling safe and effective healthcare.

Keywords: crew resource management, non-technical skills, training, simulation

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Authors: Subzar Ahmad Bhat, Saraswati Setia, V. K.Sehgal

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During the past earthquakes, open ground storey buildings have performed poorly due to the soft storey defect. Indian Standard IS 1893:2002 allows analysis of open ground storey buildings without considering infill stiffness but with a multiplication factor 2.5 in compensation for the stiffness discontinuity. Therefore, the aim of this paper is to check the applicability of the multiplication factor of 2.5 and study behaviour of the structure after the application of the multiplication factor. For this purpose, study is performed on models considering infill stiffness using SAP 2000 (Version 14) by linear static analysis and response spectrum analysis. Total seven models are analysed and designed for the range of multiplication factor ranging from 1.25 to 2.5. The value of multiplication factor equal to 2.5 has been found on the higher side, resulting in increased dimension and percentage of reinforcement without significant enhancement beyond a certain multiplication factor. When the building with OGS is designed for values of MF higher than 1.25 considering infill stiffness soft storey effect shifts from ground storey to first storey. For the analysis of the OGS structure best way to analysis the structure is to analyse it as the frame with stiffness and strength of the infill taken into account. The provision of infill walls in the upper storeys enhances the performance of the structure in terms of displacement and storey drift controls.

Keywords: open ground storey, multiplication factor, IS 1893:2002 provisions, static analysis, response spectrum analysis, infill stiffness, equivalent strut

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Authors: İsmail İnce, Mustafa Fener, Sair Kahraman

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The uniaxial compressive strength (UCS) of rocks is an important input parameter for the design of rock engineering project. Compressive strength can be determined in the laboratory using the uniaxial compressive strength (UCS) test. Although the test is relatively simple, the method is time consuming and expensive. Therefore many researchers have tried to assess the uniaxial compressive strength values of rocks via relatively simple and indirect tests (e.g. point load strength test, Schmidt Hammer hardness rebound test, P-wave velocity test, etc.). Pyroclastic rocks are widely exposed in the various regions of the world. Cappadocia region located in the Central Anatolia is one of the most spectacular cite of these regions. It is important to determine the mechanical behaviour of the pyroclastic rocks due to their ease of carving, heat insulation properties and building some civil engineering constructions in them. The purpose of this study is to estimate a widely varying uniaxial strength of pyroclastic rocks from Cappadocia region by means of point load strength, porosity, dry density and saturated density tests utilizing gene expression programming.

Keywords: pyroclastic rocks, uniaxial compressive strength, gene expression programming (GEP, Cappadocia region

Procedia PDF Downloads 305

Authors: X. Cervantes-López, C. Arriaga-Canon, L. Contreras Espinosa

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The goal of this study is to validate the overexpression of the lncRNA GATA3-AS1 associated with resistance to neoadjuvant chemotherapy of female patients with locally advanced mammary adenocarcinoma of luminal B subtype This study involved a cohort of one hundred thirty-seven samples for which total RNA was isolated from formalin fixed paraffin embedded (FFPE) tissue. Samples were cut using a Microtome Hyrax M25 Zeiss and RNA was isolated using the RNeasy FFPE kit and a deparaffinization solution, the next step consisted in the analysis of RNA concentration and quality, then 18 µg of RNA was treated with DNase I, and cDNA was synthesized from 50 ng total RNA, finally real-time PCR was performed with SYBR Green/ROX qPCR Master Mix in order to determined relative gene expression using RPS28 as a housekeeping gene to normalize in a fold calculation ΔCt. As a result, we validated by real-time PCR that the overexpression of the lncRNA GATA3-AS1 is associated with resistance to neoadjuvant chemotherapy in locally advanced breast cancer patients of luminal B subtype.

Keywords: breast cancer, biomarkers, genomics, neoadjuvant chemotherapy, lncRNAS

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Authors: Mandeep Singh Azad.Dibyendu Chakraborty, Vikas Vohra

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Introduction: Poonch is one of the remotest districts of the Jammu and Kashmir (UT) and situated on international borders. This native poultry population in these areas is quite hardy and thrives well in adverse climatic conditions. Till date, no local breed from this area (Jammu Province) has been characterized thus present study was undertaken with the main objectives of molecular characterization of ChB6 gene in local native chicken of Poonch region located at international borders between India and Pakistan. The chicken B-cell marker (ChB6) gene has been proposed as a candidate gene in regulating B-cell development. Material and Method: RNA was isolated by Blood RNA Purification Kit (HiPura) and Trizol method from whole blood samples. Positive PCR products with size 1110 bp were selected for further purification, sequencing and analysis. The amplified PCR product was sequenced by Sangers dideoxy chain termination method. The obtained sequence of ChB6 gene of Poonchi chicken were compared by MEGAX software. BioEdit software was used to construct phylogenic tree, and Neighbor Joining method was used to infer evolutionary history. In order to compute evolutionary distance Maximum Composite Likelihood method was used. Results: The positively amplified samples of ChB6 genes were then subjected to Sanger sequencing with “Primer Walking. The sequences were then analyzed using MEGA X and BioEdit software. The sequence results were compared with other reported sequence from different breed of chicken and with other species obtained from the NCBI (National Center for Biotechnology Information). ClustalW method using MEGA X software was used for multiple sequence alignment. The sequence results of ChB6 gene of Poonchi chicken was compared with Centrocercus urophasianus, G. gallus mRNA for B6.1 protein, G. gallus mRNA for B6.2, G. gallus mRNA for B6.3, Gallus gallus B6.1, Halichoeres bivittatus, Miniopterus fuliginosus Ferringtonia patagonica, Tympanuchus phasianellus. The genetic distances were 0.2720, 0.0000, 0.0245, 0.0212, 0.0147, 1.6461, 2.2394, 2.0070 and 0.2363 for ChB6 gene of Poonchi chicken sequence with other sequences in the present study respectively. Sequencing results showed variations between different species. It was observed that AT content were higher then GC content for ChB6 gene. The lower AT content suggests less thermostable. It was observed that there was no sequence difference within the Poonchi population for ChB6 gene. The high homology within chicken population indicates the conservation of ChB6 gene. The maximum difference was observed with Miniopterus fuliginosus (Eastern bent-wing bat) followed by Ferringtonia patagonica and Halichoeres bivittatus. Conclusion: Genetic variation is the essential component for genetic improvement. The results of immune related gene Chb6 shows between population genetic variability. Therefore, further association studies of this gene with some prevalent diseases in large population would be helpful to identify disease resistant/ susceptible genotypes in the indigenous chicken population.

Keywords: ChB6, sequencing, ClustalW, genetic distance, poonchi chicken, SNP

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Authors: Jodie Stevenson, Lisa-Marie Emerson, Abigail Millings

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Mindfulness has been conceptualized as a dispositional trait, which is different across individuals. Previous research has independently identified both adult attachment orientations and emotion regulation abilities as correlates of dispositional mindfulness. Research has also presented a two-factor model of the relationship between these three constructs. The present study aimed to further develop this model and investigated theses relationships in a sample of 186 participants. Participants completed the Five Factor Mindfulness Questionnaire Short Form (FFMQ-SF), the Experiences in Close Relationships Scale for global attachment (ECR), the Emotion Regulation Questionnaire (ERC), and the Adult Disorganized Attachment scale (ADA). Exploratory factor analysis revealed a 3-factor solution accounting for 59% of the variance across scores on these measures. The first factor accounted for 32% of the variance and loaded highly on attachment and mindfulness subscales. The second factor accounted for 15% of the variance with strong loadings on emotion regulation subscales. The third factor accounted for 12% of the variance with strong loadings on disorganized attachment, and the mindfulness observes subscale. The results further confirm the relationship between attachment, mindfulness, and emotion regulation along with the unique addition of disorganized attachment. The extracted factors will then be used to predict well-being outcomes for an undergraduate student population.

Keywords: adult attachment, emotion regulation, mindfulness, well-being

Procedia PDF Downloads 355

Authors: Mahmoud M. Zakaria, Omnia F. Elmoursi, Mahmoud M. Gabr, Camelia A. AbdelMalak, Mohamed A. Ghoneim

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Many protocols were publicized for differentiation of human mesenchymal stem cells (MSCS) into insulin-producing cells (IPCs) in order to excrete insulin hormone ingoing to treat diabetes disease. Our aim is to evaluate relative gene expression for each independent protocol. Human bone marrow cells were derived from three volunteers that suffer diabetes disease. After expansion of mesenchymal stem cells, differentiation of these cells was done by three different protocols (the one-step protocol was used conophylline protein, the two steps protocol was depending on trichostatin-A, and the three-step protocol was started by beta-mercaptoethanol). Evaluation of gene expression was carried out by real-time PCR: Pancreatic endocrine genes, transcription factors, glucose transporter, precursor markers, pancreatic enzymes, proteolytic cleavage, extracellular matrix and cell surface protein. Quantitation of insulin secretion was detected by immunofluorescence technique in 24-well plate. Most of the genes studied were up-regulated in the in vitro differentiated cells, and also insulin production was observed in the three independent protocols. There were some slight increases in expression of endocrine mRNA of two-step protocol and its insulin production. So, the two-step protocol was showed a more efficient in expressing of pancreatic endocrine genes and its insulin production than the other two protocols.

Keywords: mesenchymal stem cells, insulin producing cells, conophylline protein, trichostatin-A, beta-mercaptoethanol, gene expression, immunofluorescence technique

Procedia PDF Downloads 192

Authors: A. Ferasat, S. Rostampour Yasouri

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Seasonal flu is a highly contagious infection caused by influenza viruses. These viruses undergo genetic changes that result in new epidemics across the globe. Medical attention is crucial in severe cases, particularly for the elderly, frail, and those with chronic illnesses, as their immune systems are often weaker. The purpose of this study was to detect new subtypes of the influenza A virus rapidly using a specific RT-PCR method based on the HA gene (hemagglutinin). In the winter and spring of 2022_2023, 120 embryonated egg samples were cultured, suspected of seasonal influenza. RNA synthesis, followed by cDNA synthesis, was performed. Finally, the PCR technique was applied using a pair of specific primers designed based on the HA gene. The PCR product was identified after purification, and the nucleotide sequence of purified PCR products was compared with the sequences in the gene bank. The results showed a high similarity between the sequence of the positive samples isolated from the patients and the sequence of the new strains isolated in recent years. This RT-PCR technique is entirely specific in this study, enabling the detection and multiplication of influenza and its subspecies from clinical samples. The RT-PCR technique based on the HA gene, along with sequencing, is a fast, specific, and sensitive diagnostic method for those infected with influenza viruses and its new subtypes. Rapid molecular diagnosis of influenza is essential for suspected people to control and prevent the spread of the disease to others. It also prevents the occurrence of secondary (sometimes fatal) pneumonia that results from influenza and pathogenic bacteria. The critical role of rapid diagnosis of new strains of influenza is to prepare a drug vaccine against the latest viruses that did not exist in the community last year and are entirely new viruses.

Keywords: influenza, molecular diagnosis, patients, RT-PCR technique

Procedia PDF Downloads 38

Authors: Seyed Abolhassan Naeini, Azam Kouhpeyma

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Reduction of water level at which a slope is submerged with it is called drawdown. Draw down can took place rapidly or slowly and in both situations, it can affect slope stability. Using coupled analysis (seepage and stability analysis) causes more accurate results. In this study, the stability of homogeneous embankment is investigated numerically. Slope safety factor changes due to changes in three factors of height, slope and drawdown rate have been investigated and compared. It was found that with increasing height and slope, the safety factor decreases, and with increasing the discharge rate, the safety factor increases.

Keywords: drawdown, slope stability, coupled seepage and stability analysis

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Authors: R. Fardid, R. Coppes

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Introduction: In mediastinal radiotherapy and to a lesser extend also in total-body irradiation (TBI) radiation exposure may lead to development of cardiac diseases. Radiation-induced heart disease is dose-dependent and it is characterized by a loss of cardiac function, associated with progressive heart cells degeneration. We aimed to determine the in-vivo radiation effects on fibronectin, ColaA1, ColaA2, galectin and TGFb1 gene expression levels in left ventricle heart tissues of rats after irradiation. Material and method: Four non-treatment adult Wistar rats as control group (group A) were selected. In group B, 4 adult Wistar rats irradiated to 20 Gy single dose of 150 Mev proton beam locally in heart only. In heart plus lung irradiate group (group C) 4 adult rats was irradiated by 50% of lung laterally plus heart radiation that mentioned in before group. At 8 weeks after radiation animals sacrificed and left ventricle heart dropped in liquid nitrogen for RNA extraction by Absolutely RNA® Miniprep Kit (Stratagen, Cat no. 400800). cDNA was synthesized using M-MLV reverse transcriptase (Life Technologies, Cat no. 28025-013). We used Bio-Rad machine (Bio Rad iQ5 Real Time PCR) for QPCR testing by relative standard curve method. Results: We found that gene expression of fibronectin in group C significantly increased compared to control group, but it was not showed significant change in group B compared to group A. The levels of gene expressions of Cola1 and Cola2 in mRNA did not show any significant changes between normal and radiation groups. Changes of expression of galectin target significantly increased only in group C compared to group A. TGFb1 expressions in group C more than group B showed significant enhancement compared to group A. Conclusion: In summary we can say that 20 Gy of proton exposure of heart tissue may lead to detectable damages in heart cells and may distribute function of them as a component of heart tissue structure in molecular level.

Keywords: gene expression, heart damage, proton irradiation, radiotherapy

Procedia PDF Downloads 462