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Genomics data introduce a substantial computational burden as well as data privacy and ownership issues. Data sets generated by high-throughput sequencing platforms require immense amounts of computational resources to align to reference genomes and to call and annotate genomic variants. This problem is even more pronounced if reanalysis is needed for new versions of reference genomes, which may impose high loads to existing computational infrastructures. Additionally, after the compute-intensive analyses are completed, the results are either kept in centralized repositories with access control, or distributed among stakeholders using standard file transfer protocols. This imposes two main problems: (1) Centralized servers become gatekeepers of the data, essentially acting as an unnecessary mediator between the actual data owners and data users; and (2) servers may create single points of failure both in terms of service availability and data privacy. Therefore, there is a need for secure and decentralized platforms for data distribution with user-level data governance. A new technology, blockchain, may help ameliorate some of these problems. In broad terms, the blockchain technology enables decentralized, immutable, incorruptible public ledgers. In this Perspective, we aim to introduce current developments toward using blockchain to address several problems in omics, and to provide an outlook of possible future implications of the blockchain technology to life sciences., (© 2018 Ozercan et al.; Published by Cold Spring Harbor Laboratory Press.)

Objective: Colon adenocarcinomas are the most common malignancy of the gastrointestinal tract. Many factors are described in the prognosis. Herein we aimed to determine the relationship between signal transducer and activator of transcription 3(STAT3), B-cell lymphoma-extra large (Bcl-xL) and matrix metalloproteinase-2 (MMP-2) expression in colon adenocarcinomas and their relationship with prognostic factors., Material and Method: A total of 45 colon adenocarcinomas (15 well, 15 moderately, 15 poorly differentiated) and 15 normal colon mucosa samples were selected randomly. The STAT3, Bcl-xL and MMP-2 immunohistochemicals were applied to the samples., Results: There was a significant difference between the normal mucosa and carcinoma group regarding the STAT3 staining diffuseness and intensity (p < 0.05), but not for Bcl-xL (p > 0.05). The intensity of MMP-2 significantly differed between the normal mucosa and the carcinoma group (p < 0.05). The diffuseness of STAT3 and the intensity of MMP2 showed a significant association with the degree of differentiation (p < 0.05). The intensity and diffuseness of BcL-xL did not show a relationship with the degree of differentiation (p > 0.05). Evaluation of the diffuseness and intensity of the three markers with lymph node metastasis and tumor size revealed that only MMP2 diffuseness had a negative correlation with tumor size (r= -0.318)., Conclusion: We observed that Bcl-xL does not have a role in the diagnosis of colon adenocarcinomas or the detection of the degree of differentiation, a prognostic factor, but such a relationship was observed for STAT3 and MMP-2.

The objective of the present study was to investigate the potential association between the presence of BK virus (BKV) DNA and mRNA and renal cell carcinoma and bladder transitional cell carcinoma. The formalin-fixed and paraffin-embedded tissue samples were obtained from 50 cancer patients with renal cell carcinoma, 40 cancer patients with bladder transitional cell carcinoma, 45 control patients with the benign renal pathology, and from another 25 control patients with benign bladder pathology. The samples were subjected to nested PCR for detection of BKV DNA and real-time reverse transcription PCR (real-time RT-PCR) for determining mRNA levels of BKV. The results of the nested PCR indicated that 23 (14.3%) of 160 samples were positive for BKV DNA. The relationship between the cancer and the presence of BKV DNA was significant (P < 0.05). The BKV DNA positivity was significantly associated with the histological diagnosis of renal cell carcinoma (P = 0.03), but not with that of bladder transitional cell carcinoma. The results of real-time RT-PCR showed that the mRNA of BKV VP1 was present in 69.5% of the BKV DNA positive samples. The levels of BKV mRNA were significantly higher in the renal cell cancer samples than in the control samples (P < 0.05). The results of the present study confirm the association between BKV and renal cell cancer. The findings also indicated that the presence of BKV DNA resulted in a fivefold increase in the risk of development of renal cell carcinoma., (Copyright © 2013 Wiley Periodicals, Inc.)

We aimed to examine the protective effects of resveratrol against homocysteine induced oxidative stress, apoptosis and cognitive impairment. Rats were randomly divided into three groups. Control group received standard rat food; homocysteine group (Hcy group) received daily methionine at a dose of 1g/kg-body weight dissolved in drinking water for thirty days; third group (Hcy+Res group) received same amount of methionine plus 20mg/kg/day resveratrol intraperitoneally for thirty days. Cognitive performances of the animals were tested by Morris water maze test. Then all animals were sacrificed to study lipid peroxidation (LPO), DNA fragmentation and p53 mRNA expression in the rat brain. The aortas of the sacrificed rats were processed for histopathological examination. Apoptosis in the aortas was assessed by TUNEL staining. Resveratrol significantly decreased serum levels of homocysteine, reversed Hcy induced LPO increase, decreased DNA fragmentation and p53 mRNA expression in the rat brains, and improved homocysteine induced impairment of long term spatial memory. Resveratrol could inhibit homocysteine induced apoptosis and histopathological deterioration in the rat aortic sections. In conclusion, resveratrol is effective in preventing homocysteine induced vascular and neural defects. In hyperhomocysteinemic rat model, our findings consequently warrant in future studies to reveal the true improvement mechanism of resveratrol., (Copyright © 2012 Elsevier B.V. All rights reserved.)

The underlying molecular mechanism of carcinogenesis in oral squamous cell carcinoma (OSCC) is poorly understood and appears to be controlled on many genetic, environmental, and hormonal factors. Obestatin and ghrelin, two recently discovered hormones, are co-expressed in endocrine cells. The purpose of this investigation was to examine the immunohistochemical features of OSCCs in relation to the tissue concentration of ghrelin and obestatin. The association between OSCC and Epstein Barr Virus (EBV) status was also explored. The expression of ghrelin and obestatin was examined by immunohistochemistry and immunoassay in oral biopsy specimens: 10 benign squamous epithelial cell samples, 10 microinvasive squamous cell carcinomas, and seven well-differentiated and seven poorly differentiated OSCCs. The presence of EBV was evaluated in these samples using immunohistochemistry. The concentrations of ghrelin and obestatin in tissue homogenates were measured by RIA and ELISA, respectively. Squamous cell carcinomas and benign tissue samples were positive for anti-EBV antibody, and obestatin and ghrelin were shown to be co-expressed in all stratified squamous epithelium samples. Expression of ghrelin and obestatin was decreased or absent in OSCCs in relation to the invasiveness of the carcinoma; ghrelin and obestatin levels in cancerous tissue homogenates were lower than in benign tissue homogenates. These results indicate that the concentrations and distribution of immunoreactive obestatin and ghrelin might be helpful in distinguishing OSCC from benign tumors. Maintaining normal levels of these hormones might be required for regulation of normal cell division. However, detailed studies will be required for better understanding of the complex mechanism of carcinogenesis relating to OSCCs.

The aim of this study was to examine the effects of ovulation induction agents on the ovarian surface epithelium in rats. Sixty adult females were randomly divided into six groups, each containing 10 rats. In four of these groups ovulation induction was applied with six cycles of clomiphene citrate, human menopausal gonadotrophin (HMG), recombinant FSH (rFSH) or human chorionic gonadotrophin (HCG), respectively, followed by unilateral oophorectomy, and another six cycles of the same treatment. After a total of 12 cycles of ovulation induction, the remaining ovary was taken out and the alterations in ovarian surface epithelium were examined. No malignancies were observed on the ovarian surface epithelium of the rats that were given clomiphene citrate, rFSH or HMG as ovulation induction agents, while identification rates of histopathological parameters constituting epithelial dysplasia were found to be significant (P < 0.05). There was no significant dysplasia in the epithelium of the group which was given HCG only, relative to control groups. The findings suggest that the ovulation induction agents except for HCG bring about dysplasia in the ovarian surface epithelium. It is not clear whether these dysplasias are precursory lesions of ovarian malignancies.

Ghrelin and obestatin are a single gene products and are a multiple functional peptides that regulates energy homeostasis, and food intake. In the present work, we studied the secretion of ghrelin and its co-secreted peptide obestatin in 44 patients with ischemic heart disease with that of 27 healthy matched controls. Here we first conducted using an immunohistochemistry assay to screen whether human salivary glands have any obestatin immunoreactivity. Then, serum and saliva obestatin and acylated ghrelin levels were determined by using Radioimmunoassay. Our immunohistochemical analysis demonstrated that obestatin was localized in the striated and excretory duct of human salivary gland. We also report for the first time that obestatin, like ghrelin, is present in human salivary gland and saliva. No evidence of the role of obestatin or ghrelin saliva levels in the context of ischemic heart disease was found. Salivary ghrelin and obestatin levels are correlated in controls with the blood levels. Determination of salivary values could represent a non-invasive alternative to serum ones that can be useful in clinical practice.

The purpose of this study was to investigate the influence of intravitreally injected different doses of melatonin on retinal morphology. The right eyes of 35 male albino guinea pigs were used. The animals were classified randomly into five groups in equal numbers. First group was used as control and received intravitreal injection of placebo. Groups 2, 3, 4 and 5 received intravitreally injections of melatonin at 50, 100, 150 and 200microg/body weight (BW) each, respectively. The animals were sacrificed 15 days after the injections. The eyes were enucleated and processed for light microscopic evaluation. Intravitreal injection of melatonin at doses ranging from 50 to 150microg did not induce morphological changes, although a higher thickness of the inner plexiform layer (IPL) was found in Group 5 compared to other groups (p < 0.05). The mean retinal ganglion cell (RGC) counts were found to be lower in Group 5 compared to other groups (p < 0.05). Our findings indicate that intravitreal injection of melatonin at doses ranging from 50 to 150microg/BW does not induce morphological changes. The dose of 200microg/BW produced significant damage including retinal ganglion cell loss and formation of retinal edema.

Purpose: The aim of this study was investigate the role of aprotinin on retinal lipid peroxidation and histopathological changes during ischemia/reperfusion (I/R) of guinea pigs., Methods: Three groups of seven pigmented guinea pigs each were formed: a control (group 1), ischemia/saline (group 2) and ischemia/aprotinin (group 3). One eye of each animal was selected for histopathological evaluation and the other for biochemical assay. Bilateral pressure-induced retinal ischemia was instigated for 90 min and was followed by 24 hours of reperfusion. Animals in the ischemia/aprotinin and ischemia/saline groups received either 20,000 KIU/kg of aprotinin or saline, repeated four times at 6-hour intervals, with the first dose administered 5 min prior to the ischemic insult. The animals were killed at 24 hours of reperfusion. Retinal malondialdehyde (MDA) levels and the thickness of the inner plexiform layers were measured., Results: The level of MDA in group 1 was significantly (p<0.001) lower than the other groups. The mean MDA level in group 2 was significantly (p<0.01) higher than in group 3. The inner plexiform layer in group 1 was significantly (p<0.001) thinner than in the other groups. The mean thickness of the inner plexiform layer in group 2 was significantly (p<0.01) higher than in group 3., Conclusions: These data indicate that intraperitoneally administrated aprotinin has a protective effect against I/R injury in the retina of guinea pig as evidenced by reduced retinal MDA level and retinal thickness.

Functional irregularities due to damage after ischaemia-reperfusion vary depending upon the organs affected. High energy phosphates such as ATP and ADP are destroyed after ischaemia-reperfusion damage. Subsequently, protons and inorganic phosphates accumulate within the cells and the proton pumps such as adenosine triphosphatase (ATPase), which maintain intracellular ion balance are damaged. In the present study, malondialdehyde (MDA), a product of lipid peroxidation, was measured as an indicator of tissue damage. Additionally, we measured sodium-potassium-ATPase levels and determined the interactions between MDA and Na+-K+ ATPase levels. A total of 31 female guinea pigs were divided into four groups: sham operated guinea pigs (group 1), ischaemia-reperfusion (group 2), ischaemia-reperfusion + superoxide dismutase (SOD) (group 3), ischaemia-reperfusion + allopurinol (group 4). Following reperfusion, the livers of guinea pigs in each group were removed for histopathological examination and the levels of MDA and Na+-K+ ATPase were determined in homogenized tissue samples. There was a statistically significant (p < 0.05) reduction in tissue MDA levels in group 2 when compared with group 1. The level of tissue MDA in groups 3 and 4 was significantly lower than tissue MDA levels of group 2. However, there was a statistically significant (p < 0.05) reduction in tissue Na+-K+ ATPase levels of group 2 when compared with group 1. Similarly, the level of tissue Na+-K+ ATPase in groups 3 and 4 was significantly higher than the tissue Na+-K+ ATPase levels of group 2. The results of the histopathologic examination also revealed the beneficial effects of the use of SOD and allopurinol in preventing liver damage in cases of ischaemia-reperfusion. Although the levels of MDA and Na+-K+ ATP ase in group 2 were not equal to the level in group 1, antioxidant therapy significantly improved the tendency to reverse the effects of ischaemia-reperfusion and to protect the liver from damage due to ischaemia-reperfusion., (Copyright 2001 John Wiley & Sons, Ltd.)