CpG methylation of the FHIT, FANCF, cyclin-D2, BRCA2 and RUNX3 genes in Granulosa cell tumors (GCTs) of ovarian origin

BACKGROUND: Granulosa cell tumors (GCTs) are relatively rare and are subtypes of the sex-cord stromal neoplasms. Methylation induced silencing in the promoters of genes such as tumor suppressor genes, DNA repair genes and pro-apoptotic genes is recognised as a critical factor in cancer development. METHODS: We examined the role of promoter hypermethylation, an epigenetic alteration that is associated with the silencing tumor suppressor genes in human cancer, by studying 5 gene promoters in 25 GCTs cases by methylation specific PCR and RT-PCR. In addition, the compatible tissues (normal tissues distant from lesion) from three non-astrocytoma patients were also included as the control. RESULTS: Frequencies of methylation in GCTs were 7/25 (28 % for FHIT), 6/25 (24% for FNACF), 3/25 (12% for Cyclin D2), 1/25 (4% for BRCA2) and 14/25 (56%) in RUNX3 genes. Correlation of promoter methylation with clinical characteristics and other genetic changes revealed that overall promoter methylation was higher in more advanced stage of the disease. Promoter methylation was associated with gene silencing in GCT cell lines. Treatment with methylation or histone deacetylation-inhibiting agents resulted in profound reactivation of gene expression. CONCLUSIONS: These results may have implications in better understanding the underlying epigenetic mechanisms in GCT development, provide prognostic indicators, and identify important gene targets for treatment

Databases and QSAR for Cancer Research

In this review, we take a survey of bioinformatics databases and quantitative structure-activity relationship studies reported in published literature. Databases from the most general to special cancer-related ones have been included. Most commonly used methods of structure-based analysis of molecules have been reviewed, along with some case studies where they have been used in cancer research. This article is expected to be of use for general bioinformatics researchers interested in cancer and will also provide an update to those who have been actively pursuing this field of research

Hepatitis B Virus Gene Mutations in Liver Diseases: A Report from New Delhi

The study was designed to characterize the surface, core promoter, precore/core region sequences for the presence of mutations in hepatitis B virus (HBV) associated with different liver diseases.567 HBV associated patients with different liver diseases were enrolled in this study. All samples were analyzed for HBV surface, core promoter, precore/core region mutations and genotypes using PCR and direct sequencing.HBV genotype D (72.8%) was the predominant type followed by genotype A (27.2%). The serum viral load of HBV was highest in HBsAg carriers group and lowest in patients with hepatocellular carcinoma. 17.9% patients with cirrhosis and 24.6% hepatocellular carcinoma cases were ADV-resistant with rtA181T/V mutations in the S-gene. A1896T was found more frequently in fulminant hepatic failure compared to acute viral hepatitis patients (p = 0.038). T1753V mutation was significantly higher in patients with cirrhosis of liver (34.6%) than in chronic hepatitis (18.9%) and hepatocellular carcinoma patients (21.2%; p = 0.001). T1762/A1764 mutation was observed in all the groups. C1914G core gene mutation was associated with the hepatocellular carcinoma (32.2%) compared to other groups. HBV genotype D predominated in comparison to genotype A. An increased frequency of precore mutation and BCP double mutations amongst the population studied was also observed.Mutations such as T1762/A1764, T1753V and C1914G were usually associated with advanced forms of liver disease and had an increased risk of HCC. The nucleotide variability in the basal core promoter and precore regions possibly plays a role in the progression of HBV disease. Prospective studies on the sequence variations of the preC/C region of the HBV genome and the molecular mechanisms in relation to progression of liver disease would aid in better understanding of the biological significance of HBV strains in India

Neural Network Approaches for Computation of Soil Thermal Conductivity

The effective thermal conductivity (ETC) of soil is an essential parameter for the design and unhindered operation of underground energy transportation and storage systems. Various experimental, empirical, semi-empirical, mathematical, and numerical methods have been tried in the past, but lack either accuracy or are computationally cumbersome. The recent developments in computer science provided a new computational approach, the neural networks, which are easy to implement, faster, versatile, and reasonably accurate. In this study, we present three classes of neural networks based on different network constructions, learning and computational strategies to predict the ETC of the soil. A total of 384 data points are collected from literature, and the three networks, Artificial neural network (ANN), group method of data handling (GMDH) and gene expression programming (GEP), are constructed and trained. The best accuracy of each network is measured with the coefficient of determination (R2) and found to be 91.6, 83.2 and 80.5 for ANN, GMDH and GEP, respectively. Furthermore, two sands with 80% and 99% quartz content are measured, and the best performing network from each class of ANN, GMDH and GEP is independently validated. The GEP model provided the best estimate for 99% quartz sand and GMDH with 80%

Inotropic and chronotropic effects of methanol extract of Aquilaria agallocha on rabbit heart

Aquilaria agallocha Roxb. (Thymelaeceae) heartwood is used in cardiac failure; however, its cardiotonic properties are poorly understood at a pharmacological level. This study investigated methanol extract of A. agallochafor presence of glycosides and its effects on force of contraction, heart rate and coronary flow on rabbit isolated heart. Furthermore, contribution of β1-adrenoceptors and/or L-type Ca2+ channels in A. agallocha-induced cardiac effects was explored. A. agallocha extract, digoxin, verapamil and metoprolol were administered in a retrograde manner. Force of contraction and heart rate were recorded with a force transducer attached to the heart. Coronary flow was measured from collected effluent. The extract induced a significant increase in force of contraction (p<0.001), decrease in heart rate (p<0.05) and coronary flow (p<0.001). Metoprolol (p<0.01) and verapamil (p<0.01) significantly inhibited the plant extract-induced effects. Thus, A. agallocha exhibited cardiotonic effects, most likely via cardiac glycosides, involving ?1-adrenoceptors and L-type Ca2+ channels

Iono- and chronotropic effects of aqueous extract of berberis lycium royle root bark and berberine on in situ frog-heart preparation

Berberis lycium Royle is used in folk medicines for treating various ailments however it has not been investigated in cardiac problems at pharmacological level. Here, iono- and chronotropic effects of B. lycium root bark’s aqueous extract and berberine were studied on frog-heart. Present data showed that aqueous extracts of B. lycium and berberine exhibited dose-dependent negative chronotropic and ionotropic effects and at higher doses both caused a heart block. Berberine also displayed a positive ionotropic effect but at very low doses. Diltiazem did not antagonize positive ionotropic effect of berberine indicating that this activity is independent of L-type calcium channels, while propranolol antagonized the positive ionotropic effect, suggesting involvement of β1 - adrenoceptors. It is concluded that ionotropic and chronotropic effects exerted by aqueous extract of B. lycium may be due to berberine while its negative ionotropic actions and heart block may attribute to other active principle(s) present in the extract.Colegio de Farmacéuticos de la Provincia de Buenos Aire

Association of mutation and expression of the brother of the regulator of imprinted sites (BORIS) gene with breast cancer progression

INTRODUCTION: The BORIS, 11 zinc-finger transcription factors, is a member of the cancer-testis antigen (CTA) family. It is mapped to chromosome number 20q13.2 and this region is genetically linked to the early onset of breast cancer. The current study analyzed the correlation between BORIS mutations and the expression of the protein in breast cancer cases. MATERIALS AND METHODS: A population-based study including a total of 155 breast cancer tissue samples and an equal number of normal adjacent tissues from Indian female breast cancer patients was carried out. Mutations of the BORIS gene were detected by polymerase chain reaction-single standard confirmation polymorphisms (PCR-SSCP) and automated DNA sequencing and by immunohistochemistry for BORIS protein expression were performed. The observed findings were correlated with several clinicopathological parameters to find out the clinical relevance of associations. RESULTS: Of all the cases 16.12% (25/155) showed mutations in the BORIS gene. The observed mutations present on codon 329 are missense, leading to Val\u3e Ile (G\u3eA) change on exon 5 of the BORIS gene. A significant association was observed between mutations of the BORIS gene and some clinicopathological features like nodal status (p = 0.013), estrogen receptor (ER) expression (p = 0.008), progesterone receptor (PR) expression (p = 0.039), clinical stage (p = 0.010) and menopausal status (p = 0.023). The protein expression analysis showed 20.64% (32/155) samples showing low or no expression (+), 34.19% (53/155) with moderate expression (++), and 45.17% (70/155) showing high expression (+++) of BORIS protein. A significant association was observed between the expression of BORIS protein and clinicopathological features like clinical stage (p = 0.013), nodal status (p = 0.049), ER expression (p = 0.039), and PR expression (p = 0.027). When mutation and protein expression were correlated in combination with clinicopathological parameters a significant association was observed in the category of high (+++) level of BORIS protein expression (p = 0.017). CONCLUSION: The BORIS mutations and high protein expression occur frequently in carcinoma of the breast suggesting their association with the onset and progression of breast carcinoma. Further, the BORIS has the potential to be used as a biomarker

Developing local guidelines for management of sepsis in adults: sepsis guidelines for Pakistan (SGP)

Background: The purpose of developing ‘Sepsis Guidelines for Pakistan’ (SGP) is to provide clinicians practicing in local hospitals with a framework to aid timely recognition and management of adult patients in sepsis by adopting evidence-based recommendations of Surviving Sepsis Campaign (SSC) tailored to available resources. These recommendations are not meant to replace the SSC Guidelines. Methodology: SGP is an initiative of Pakistan Society of Critical Care Medicine (PSCCM). Four key decision points to be addressed in the guidelines were identified by a thirteen member multidisciplinary committee i.e., grading the hospitals in the country, recognition of sepsis and associated organ dysfunction, essential interventions to manage sepsis, and general measures for provision of a comprehensive care to patients in sepsis according to the level of education and training of healthcare providers and facilities and resources available in different levels of hospitals. The draft was presented at the 3rd Sepsis Symposium held on 13th September, 2014 in Karachi. The final document was approved by a panel of experts from across the country, representatives of relevant societies and Global Sepsis Alliance (GSA). Recommendations: Hospitals are divided into basic, intermediate and tertiary depending on the availability of diagnostic facilities and training of the medical personnel. Modified definitions of sepsis, severe sepsis, and septic shock are used given the lack of facilities to diagnose sepsis according to international definitionsand criteria in Pakistan. Essential interventions include fluid resuscitation, vasopressors to support the circulation, maintaining oxygen saturation ≥ 90% with oxygen, non-invasive ventilation or mechanical ventilation with lung protective strategies, prompt administration of antibiotics as recommended by the Medical Microbiology & Infectious Diseases Society of Pakistan (MMIDSP) and early source control. It is recommended to avoid starvation, keep an upper blood glucose ≤180 mg/dL, use daily pharmacoprophylaxis against venous thromboembolism (VTE), use stress ulcer prophylaxis, target haemoglobin of 7-9 g/dl in the absence of ischaemic heart disease, avoid sodium bicarbonate therapy as long as pH \u3e 7.20, avoid fresh frozen plasma in the absence of bleeding, transfuse platelets if indicated, not use intravenous immunoglobulins and avoid neuromuscular blocking agents (NMBAs) in the absence of ARDS, target specific titration endpoints when continuous or intermittent sedation is required in mechanically ventilated patients and use continuous renal replacement therapy (CRRT) to facilitate management of fluid balance in hemodynamically unstable septic patients in tertiary care centers. In addition a comprehensive, meticulous and multidisciplinary general care is required to improve outcome of sepsis by reinforcing hand hygiene and other infection control measures, adequate monitoring and documentation tailored to the available resources. Goals of care and prognosis should be discussed with patients and families early and either shifting the patient to a hospital with better facilities or limiting or withdrawing therapy in case of poor prognosis should be considered

FOXO3 gene hypermethylation and its marked downregulation in breast cancer cases: A study on female patients

BackgroundFOXO3, a member of the FOX transcription factor family, is frequently described as being deregulated in cancer. Additionally, notable role of FOXO3 can be easily recognized in the process of ageing and survival. Even though various studies have been done to acknowledge the tumour-suppressive or oncogenic role of FOXO3 in cancer, still there exist a lack of understanding in terms of cancer prognosis and treatment. Therefore, to provide better insight, our study aims to evaluate the role and function of FOXO3 in breast cancer in Indian female patients. We examined the FOXO3 expression levels in breast cancer samples by analyzing mRNA and protein expression along with its clinicopathological parameters.ResultsA total of 127 cases of breast cancer with equal normal cases (n=127) were assessed with methylation (MS-PCR), Immunohistochemistry (IHC), mRNA expression using Real-time PCR was analysed and 66.14% cases at mRNA level were found to be downregulated, while 81.10% of cases had little or very little protein expression. Our data state, the promoter hypermethylation of the FOXO3 gene and the downregulated protein expression are significantly correlated (p=0.0004). Additionally, we found a significant correlation between the level of FOXO3 mRNA with ER (p=0.04) and status of lymph node (p=0.01) along with this.ConclusionData suggests the prognostic significance and the tumour-suppressive role of FOXO3 in breast cancer cases studied in India. However, there is a need for the extended research targeting FOXO3 to measure its clinical potential and develop well-defined therapeutic strategies