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In recent years, an explosion has occurred in the acquisition of biological data through the use of so-called ‘omics’ techniques. Whilst many different omics technologies are now featured in the literature, the most frequently used omics are genomics, transcriptomics, proteomics and metabolomics. A transcriptome is the complete set and quantity of all RNA molecules produced by the genome at any given time for a particular developmental stage or physiological state in a cell, a population of cells, or an organism. Transcriptomics is regarded as a highthroughput technology concerned with determining how the transcriptome changes with respect to various factors at a certain time point and at a given biological state. The study of the transcriptome is essential for understanding the functional elements of the genome and revealing the molecular constituents of cells. Nowadays, transcriptomics have come to the forefront of international scientific attention due to the rapid development of RNA-sequencing (RNA-Seq) methods. The key aim of transcriptomics is precise, comprehensive characterization of the transcriptome; the annotation of all species of transcript, including mRNAs, non-coding RNAs, such as small RNAs, the determination of the transcriptional structure of genes, and the quantification of differential expression levels of each transcript under different conditions. Generally, the goal of transcriptome analysis is to identify genes differentially expressed among different conditions, leading to a new understanding of the genes or pathways associated with the conditions. This chapter provides fundamental information into the promising technology of transcriptomics.

The main aim of the study is to assess expression levels of CDH1, FHIT, PTEN, and TTPAL genes in tumors and peripheral bloods of colorectal cancer patients in staged I-IV.Gene expression analysis of related genes were performed for tumor tissues and peripheral blood samples of 51 colorectal cancer patients and colon tissues and blood samples of 5 healthy individuals. The real-time-PCR reaction method was used for the analysis.Alteration of mRNA levels of related genes in tumor tissues of colorectal cancer cases was determined compared to control tissues. GAPDH and TBP were used for the normalization. While the mRNA levels of CDH1 decreased, the mRNA level of the FHIT and TTPAL genes increased in the tumor tissues. There was no PTEN gene expression difference in tumor tissues (total). The mRNA levels of the CDH1 and PTEN genes were increased while the mRNA levels of FHIT and TTPAL genes decreased in the blood (total). T he mRNA levels of the CDH1 gene decreased at each stage (I-IV) in the tumor tissues and increased at each stage (I-IV) in the blood. T he PTEN gene mRNA levels at each stage were controversial. The mRNA levels of the FHIT gene increased at stage I-II-III, decreased at stage IV in the tissues and decreased at each stage (I-IV) in the blood. The mRNA levels of TTPAL gene increased at each stage (I-IV) in the tissues and decreased at each stage (I-IV) in the blood.

Background/aim: The aim of the study is to assess expression levels of CPEB4, APC, TRIP13, EIF2S3, EIF4A1, IFNg, PIK3CA and CTNNB1 genes in tumors and peripheral bloods of colorectal cancer patients in stages I–IV.\ud \ud Materials and methods: The mRNA levels of the genes were determined in tumor tissues and peripheral blood samples of 45 colorectal cancer patients and colon tissues and peripheral blood samples of 5 healthy individuals. Real-time polymerase chain reaction method was used for the analysis.\ud \ud Results: The mRNA level of the CPEB4 gene was significantly downregulated in colorectal tumor tissues and was upregulated in the peripheral blood of colorectal cancer patients relative to the controls (P < 0.05). APC mRNA level was significantly downregulated in tissues and upregulated in the peripheral blood (P < 0.05). TRIP13 mRNA level was upregulated in peripheral blood and also significantly upregulated in colorectal tumor tissues (P < 0.05). EIF2S3 mRNA level was upregulated in tissues and also significantly upregulated in peripheral blood (P < 0.05). PIK3CA mRNA level was downregulated in tissues and upregulated in peripheral blood. EIF4A1 mRNA level was downregulated in tissues and significantly upregulated in peripheral blood (P < 0.05). CTNNB1 mRNA level was downregulated in tissues and upregulated in peripheral blood. IFNg mRNA level was upregulated in both colorectal cancer tumor tissues and peripheral blood.\ud \ud Conclusion: TRIP13 and CPEB4 mRNA up regulation in the peripheral blood of patients with colorectal cancer may be a potential target for early stage diagnosis. In addition to this evaluation, although there is not much study on EIF2S3 and EIF4A1 mRNA changes in cases with colorectal cancer, upregulation in peripheral blood draws attention in our study. These data will shed light on the new comprehensive studies.

Obesity is a complex disorder with nearly epidemic proportions in many parts of the world. Genome-wide association studies have demonstrated high heritability for obesity and body mass, with associations of certain candidate genes and their variations with respect to race, geographical location/country of origin. However, the functional mechanisms and different ethnic data of these loci are still poorly understood. In this case-control study, we investigated two single nucleotide polymorphisms, rs2815752 in the neuronal growth regulator 1 (NEGR1) gene and rs6548238 in the transmembrane protein 18 (TMEM18) gene, for association in a group of obese residents of Afyonkarahisar province (Turkey). Polymorphisms were genotyped in 172 obese subjects and 77 healthy controls. The results showed no significant differences between the obese subjects and the controls in terms of the allele and genotype frequencies of the NEGR1 gene rs2815752 and the TMEM18 gene rs6548238 polymorphisms. There were no significant associations of the rs2815752 polymorphism in obese subjects and controls with regard to anthropometric measurements and body composition parameters. However, several significant associations were found for the rs6548238 polymorphism with regard to anthropometric measurements and body composition. Consequently, there were no significant differences between the genotype and allele frequencies of NEGR1 gene rs2815752 and TMEM18 gene rs6548238 polymorphisms in the obese group and the controls. There were significant associations for the rs6548238 polymorphism, but not the rs2815752 polymorphism, with the anthropometric measurements and body composition parameters in the group of obese subjects.

Vitiligo is a disease characterized by sharply limited white macular depigmentation as a result of melanocyte loss. Disease is divided into three types according to prevalence and localization as localized, general and universal. Etiology of vitiligo is unknown, but clearly shows a complex structure. Genetic predisposition, stress, many influencing factors such as systemic diseases and physical trauma causes vitiligo. In our study, MYG1 gene rs1465073 (-119C/ G) and CTLA4 gene rs231775 (49A/G) polymorphisms were evaluated in 106 patients diagnosed with vitiligo and 97 controls. Genotyping was performed using real time PCR method. There is no statistically significant differences between patients and controls in terms of allele frequencies of MYG1 gene rs1465073 and ve CTLA4 gene rs231775 polymorphisms. Beside, there is no statistically significant differences between patients and controls in terms of genotype frequencies of CTLA4 gene rs231775 polymorphism. On contrary to this there is statistically significant differences between patients and controls in terms of genotype frequencies of MYG1 gene rs1465073 polymorphism. In conclusion, consistent with the literature data, there is a significant association between MYG1 gene rs1465073 polymorphism and vitiligo. But there is no directly association between CTLA4 gene rs231775 polymorphism and vitiligo. Journal of Advances in Internal Medicine 2016;05(01):1-5

We report on a Yq/15p translocation in a 23-year-old infertile male referred for Klinefelter Syndrome testing, who had azoospermia and bilateral small testes. Hormonal studies revealed hypergonadotropic hypogonadism. Conventional cytogenetic procedures giemsa trypsin giemsa (GTG) and high resolution banding (HRB) and molecular cytogenetic techniques Fluorescence In Situ Hybridization (FISH) performed on high-resolution lymphocyte chromosomes revealed the karyotype 46,XX, t(Y;15)(q12;p11). SRY-gene was confirmed to be present by classical Polymerase Chain Reaction (PCR) methods. His father carried de novo derivative chromosome 15 [45,X, t(Y;15)(q12;p11)] and was fertile; the karyotype of the father using G-band technique confirmed a reciprocal balanced translocation between chromosome Y and 15. In the proband, the der (15) has been inherited from the father because the mother had a normal karyotype (46,XX). In the proband, the der (15) could have produced genetic imbalance leading to unbalanced robertson translocation between chromosome Y and 15, which might have resulted in azoospermia and infertility in the proband. The paternal translocation might have lead to formation of imbalanced ova, which might be resulted infertility in the proband. Sister's karyotypes was normal (46,XX) while his brother was not analyzed.

We report on the clinical and molecular findings of a patient who presented alopecia, epicanthus, micrognathia, retrognathia, high arched palate, hypertelorism, Chiari type I malformation, mixed-type hearing loss but with normal heartbeat Q-T interval, malformed earlobes, down-slanted palpebral fissures, downturned corners of the mouth, syndactyly, atopic eczema, and seizures. The patient was a male adult, 23 years old, with short stature (153 cm) and low weight (50.5 kg), due to severe aortic insufficiency and dilatation of the ascending aorta. Conventional cytogenetic screening did not show any chromosomal gains or losses. Molecular genetic screening was conducted for gene mutations involved in various syndromes; the mutations found included [beta-fibrinogen -455 G>A wt/wt (wt/mut), PAI-1 4G/5G (4G/4G), HPA1 a/b (a/a), MTHFR C677T wt/wt (wt/mut), ACE I/D (I/I), and Apo E E3/E4]. Many clinical and molecular genetics findings overlapped with other conditions associated with arterial tortuosity and arterial aneurysms, including the Marfan, Ehler-Danlos, Shprintzen-Goldberg, and Loeys-Dietz syndromes. Although a diagnosis of Shprintzen-Goldberg syndrome was based on clinical findings and radiographic findings indicate other syndromes, aortic root dilatation seems to be a new symptom, similar to phenotypes of connective tissue disorders. The unique grouping of clinical manifestations in this patient and the molecular genetics findings lead us to suggest that this case could be an example of a previously unrecognized syndrome.

Laparoscopic surgical techniques have been increasingly preferred to classic laparotomy by surgeons since 1987. The pneumoperitoneum is often used to facilitate the intra-abdominal field, but it carries the risk of its ischemic potential and has differences [l2]of metabolic, inflammatory, and infectious consequences, depending on the pressure set and kind of gas used. However, the mechanisms related with the cell injury observed after laparoscopy are still unknown. The aim of this study was to evaluate the effects of different pressures of CO(2) on apoptosis and p53 expression in small and large intestines and the stomach.In total, 30 Sprague-Dawley male rats were used in the study. CO(2) is insufflated into the intra-abdominal cavity through a angiocatheter cannule by an insufflator set at two different pressures of 10 and 20 mm Hg during 60 minutes. In the control group, the cannule was inserted into the intra-abdominal cavity without any other surgical procedure and no gas was insufflated. After 60 minutes, the rats were sacrificed and a laparotomy was performed. The small and large intestines and stomach were excised. The samples were histologically processed and an immunohistochemical analysis was performed.The results of the study revealed that the number of apoptotic cells in intra-abdominal organs we studied increased in proportion to the CO(2) pressure level. However, the p53 expression was detected only in the stomach.Our study showed that the number of apoptotic cells rises in parallel to the increase in intra-abdominal pressure following the CO(2) pneumoperitoneum in rat large and small intestine and stomach. Although the apoptosis was activated by the p53 pathway in the stomach, it was not so in the large and small intestine.

Epigenetic modifications, particularly DNA methylation in selected gene promoters is a pivotal role in the development of colorectal cancer. DNA methylation is considered as one of the most important epigenetic mechanisms and it is catalyzed by DNA methyltransferases (DNMTs). DNMT1 abundance has been frequently seen in colorectal cancers but the reasons are not well understood. We investigated to the effect of chemotherapeutics used in treatment of colorectal cancer on expression of DNMT1 and this effect is achieved over which signalling pathway. In this study, GSK3β; IWP2 for β-catenin) and chemotherapeutics (oxaliplatin, fluorouracil, irinotecan) were detected by WST1. DNMT1 expression level was determinated by real-time PCR; and protein levels of GSK3β, pGSK3β(Ser9), Akt1, pAkt1(Ser473), β-catenin, pβ-catenin(Ser675) and DNMT1 by western blot. Our results indicated taht Akt1 increased the protein level of DNMT1 expression with coordinate transcriptional change via β-catenin pathway. Fluorouracil and irinotecan decreased DNMT1 expression at both transcriptional and translational levels but not oxaliplatin. Oxaliplatin increased DNMT1 expression at mRNA and protein levels. This effect is achieved by specific phosphorylation of β-catenin protein. The results revealed that use of some chemotherapeutic, particularly oxaliplatin, with spesific inhibitors (such as β-catenin inhibitor) in combination led to a reduced DNMT1 expression. Our findings may offer a new approach for determining the molecular effects of β-catenin signal pathway on DNMT1. This may allow us to identify new molecular targets for the treatment of colorectal cancers. However, the results revealed that some chemotherapeutics may contribute the aberration of DNA methylation. Citation Format: NURAY VAROL, SUNA ARIKAN TERZİ, ZAFER SOYLEMEZ, HANDAN YILDIZ, MUJGAN OZDEMİR, MUSTAFA SOLAK. Does chemotherapeutics contribute to DNMT1 expression level in colorectal cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5386. doi:10.1158/1538-7445.AM2017-5386

Plasminogen Activator Inhibitor-1 (PAI-1) 4G/5G Allele Polymorphisms and NIDDM(Non-Insulin Dependent Diabetes Mellitus) Risk Factor for Early Onset Myocardial Infarction Cardiovascular diseases are major causes of mortality and morbidity in diabetic populations and are frequently present even at the time of diagnosis.

The aim of the study was to investigate relationship between polymorphisms in genes that are clinical and environmental features and the risk of myocardial infarction (MI) in Afyonkarahisar subjects living in Turkey. Prevalence of the several genes polymorphisms, ≤45 (42.04 ± 3.3) and ≥46 (57.19 ± 7.5) years were studied in individuals with MI and without MI (40.30 ± 9.01) individuals were studied. We tested 140 with MI individuals for factor V (FV) Leiden, FV H1299R, Prothrombin G20210A, factor XIII (FXIII) V34L, β-fibrinogen b-455G/A, plasminogen activator inhibitor-1 (PAI-1)-675 4G/5G, human platelet antigens 1 (HPA-1) a/b, apolipoprotein B (ApoB) R3500Q, apolipoprotein E (ApoE), E2, E3, and E4, angiotensin-converting enzyme (ACE) D/I, 5,10 methylenetetrahydrofolate reductase (MTHFR) 677C/T, and MTHFR 1298A/C polymorphisms using a ViennaLab CVD strip assay. This study results were compared without MI control groups. According to the our results, prothrombin, factor XIII and MTHFRC677T deletions were the most frequent genetic variants in risk groups of hyperlipidemic patients (value of odds ratio sequentially [OR] = 4.5, p = 0.05, [OR] = 2.16, p = 0.04 and [OR] = 2.8, p = 0.09). MTHFRA1298C and PAI-1 deletions were most frequent genetic variants in risk groups for MI in patients with diabetes mellitus (value of odds ratio sequentially [OR] = 3.79, p = 0.06 and [OR] = 5 × 10(8), p = 0.000). ACE deletions were positively associated with family history of cardiovascular events (OR = 3.62, p = 0.03). We found a strong relationship between genetic variants and risk factors. Significant associations between genetic variants predicting cardiovascular events and common risk factors (hyperlipidemia, smoking, diabetes mellitus and family history) patients were found.

During laparoscopic surgery, gases such as carbon dioxide (CO(2)), helium, or normal air are insufflated into the intra-abdominal cavity so the surgeon can obtain a clear surgical field; however, this insufflation technique may cause injury to the intra-abdominal organs. This study was undertaken to evaluate the effects of different pressures of CO(2) on the apoptotic index in the peritoneum during laparoscopic surgery. A total of 30 Sprague-Dawley male rats were used in the study. CO(2) was insufflated into the intra-abdominal cavity via an angiocatheter cannula by an insufflator at pressures of 10 and 20 mm Hg over 60 min. In the control group, the cannula was inserted into the intra-abdominal cavity, but no gas was insufflated. After 60 min, the rats were killed; peritoneum was harvested from the abdominal wall and was cultured in the cell culture laboratory. Apoptotic and living cells were detected immunohistochemically, and the apoptotic index was calculated and statistically analyzed. The data collected revealed that the apoptotic index increases in proportion to the level of CO(2) pressure. CO(2) pneumoperitoneum is a very useful technique. Gas pressure must be carefully set during the operation, however, or injured mesothelial cells may cause serious malfunction.