Gene Selection Using Parallel Lion Optimization Method in Microarray Data for Cancer Classification

In the field of bioinformatics research, a large volume of genetic data has been generated. Availability of higher throughput devices at lower cost has contributed to this generation of huge volumetric data. Handling such numerous data has become extremely challenging for selecting the relevant disease-causing gene. The development of microarray technology provides higher chances of cancer diagnosis, by enabling to measure the expression level of multiple genes at the same stretch. Selecting the relevant gene by using classifiers for investigation of gene expression data is a complicated process. Proper identification of gene from the gene expression datasets plays a vital role in improving the accuracy of classification. In this article, identification of the highly relevant gene from the gene expression data for cancer treatment is discussed in detail. By using modified meta-heuristic approach, known as 'parallel lion optimization' (PLOA) for selecting genes from microarray data that can classify various cancer sub-types with more accuracy. The experimental results depict that PLOA outperforms than LOA and other well-known approaches, considering the five benchmark cancer gene expression dataset. It returns 99% classification accuracy for the dataset namely Prostate, Lung, Leukemia and Central Nervous system (CNS) for top 200 genes. Prostate and Lymphoma dataset PLOA is 99.19% and 99.93% respectively. On evaluating the result with other algorithm, the higher level of accuracy in gene selection is achieved by the proposed algorithm.

A simple and rapid method for the quantitation of secreted hepatitis B virions in cell culture models

Cell culture models for hepatitis B virus (HBV) remain the mainstay for screening and testing the efficacy of anti-hepatitis B virus agents. Gradient-based ultracentrifugation followed by Southern Blotting is used for hepatitis B virion estimation in cell culture; this method has several limitations. We report the development of an assay using a commercially available HBsAg-ELISA plate for immunocapture followed by real-time PCR for quantification of hepatitis B virions in cell cultures. This assay is rapid, highly sensitive (50 copies/reaction) and highly specific for virion-associated DNA. In addition, the assay requires only 20 μL of supernatant, allowing scaling down of transfections.

Ameliorative effect of silibinin against N-nitrosodimethylamine-induced hepatic fibrosis in rats

The protective effect of silibinin (SBN) against hepatic fibrosis induced by repeated intermittent administration of N-nitrosodimethylamine (DMN) was investigated in rats. Oral administration of SBN recovered body and liver weight loss and reversed the elevation of serum AST, ALT and ALP accompanied by their fall in the liver tissue in DMN-induced fibrotic rats. Severe oxidative stress induced in fibrotic rats was evidenced by two to three fold elevation in MDA and protein carbonyl levels associated with a fall in the activities of SOD and CAT in repeated DMN treatment and this adversity was protected by SBN post-treatment. Further, the fall in the activities of ATPases and increase in the levels of hydroxyproline and collagen observed in the liver tissue of DMN treated rats was prevented and reversed back toward normalcy by SBN post-treatment. Recovery of rat liver tissue against DMN-induced hepatocellular necrosis, inflammatory changes and hepatic fibrosis by SBN treatment is also confirmed by both H & E and Masson's trichrome stained histopathological evaluation of liver tissue. In conclusion, SBN exhibit hepatoprotective, antioxidant, free radical scavenging, membrane stabilizing and anti-fibrotic activity against DMN-induced hepatic fibrosis suggesting that it may be useful as a therapeutic agent toward amelioration of hepatic fibrosis.

Influence of N-acetylcysteine against dimethylnitrosamine induced hepatotoxicity in rats

This study evaluates the hepatoprotective and antioxidant properties of N-acetylcysteine (NAC) on dimethylnitrosamine (DMN) induced hepatotoxicity in male Wistar albino rats. A single intraperitoneal dose of DMN (5 mg/kg b.w.) caused a significant increase in the levels of the serum marker enzymes (aspartate transaminase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), lactate dehydrogenase (LDH), glutamyl transpeptidase (γ-GT)) and a subsequent decrease in AST, ALT, ALP and increase in LDH and γ-GT in the liver tissue indicating hepatocellular damage. Elevation in the status of lipid peroxidation, fall in the activities of the enzymic (superoxide dismutase, catalase) and non-enzymic antioxidants (vitamin C, vitamin E) in the liver tissue further confirms oxidative stress and hepatocellular damage induced on DMN administration. Oral administration of NAC (50 mg/kg b.w.) for 7 days significantly prevented the above alterations in the status of the marker enzymes of hepatotoxicity and antioxidant parameters and restored them towards normalcy, which was further substantiated by the histopathological studies of the liver tissue. These results suggest that NAC offers hepatoprotection by ameliorating DMN-induced oxidative stress and hepatotoxicity and this protective effect was attributed to its antioxidant and free radical scavenging properties.

Hepatitis B viral DNA is methylated in liver tissues

The mechanisms that regulate hepatitis B virus (HBV) replication within the liver are poorly understood. Given that methylation of CpG islands regulates gene expression in human tissues, we sought to identify CpG islands in HBV-DNA and to determine if they are methylated in human tissues. In silico analysis demonstrated three CpG islands in HBV genotype A sequences, two of which were of particular interest because of their proximity to the HBV surface gene start codon (island 1) and to the enhancer 1/X gene promoter region (island 2). Human sera with intact virions that were largely unmethylated were used to transfect HepG2 cells and HBV-DNA became partially methylated at both islands 1 and 2 by day 6 following exposure of HepG2 to virus. Examination of three additional human sera and 10 liver tissues showed no methylation in sera but tissues showed methylation of island 1 in six of 10 cases and of island 2 in five of 10 cases. The cell line Hep3B, with integrated HBV, showed complete methylation of island 1 but no methylation of island 2. In conclusion, HBV-DNA can be methylated in human tissues and methylation may play an important role in regulation of HBV gene expression.

Protective effect of picroliv against hydrazine-induced hyperlipidemia and hepatic steatosis in rats

The protective effect of picroliv (PIC) obtained from Picrorhiza kurroa (family: Scrophulariaceae) against hydrazine (Hz)-induced hyperlipidemia was evaluated in rats. Hz administration (50 mg/kg, i.p.) caused an increase in triglyceride (TG), cholesterol (CHO), free fatty acids (FFA), and total lipids (TL) in both the plasma and liver tissue of rats accompanied by a fall in phospholipids (PL) in the liver tissue 24 h after its administration, indicating its hyperlipidemic property. The above abnormality was prevented by simultaneous treatment of PIC (50 mg/kg, p.o.) with Hz. Hz treatment also caused an increase in the mobility of TG and TL from adipose tissue, and these results indicate that Hz administration could cause hepatic steatosis by nonhepatocellular factors (such as mobilization of depot fats). This effect was also prevented by simultaneous treatment of PIC with Hz. PIC-alone treatment, however, did not produce any change in the status of all the lipid parameters evaluated in plasma, liver, and adipose tissues. These results indicate that increased mobilization of depot fats from adipose tissue may contribute to the development of hepatic steatosis in addition to decreased lipoprotein secretion, increased hepatic TG biosynthesis, and increased hepatic uptake of FFA. These have been reported as the mechanism responsible for the development of Hz-induced hepatic steatosis. PIC prevents Hz-induced hyperlipidemia, hepatic steatosis, and mobilization of lipids from depot fats, but the mechanism behind the protective effect of PIC remains to be elucidated.

Significance of the hepatitis C virus (HCV) core antigen as an alternative plasma marker of active HCV infection

PURPOSE

To evaluate the role of core antigen (Ortho trak-C assay) as a marker of active HCV infection in comparison to HCV RNA as detected by reverse transcription polymerase chain reaction (RT-PCR).

METHODS

This evaluation was carried out during January 2000 to December 2003 in HCV infected individuals who were treatment naomicronve or were on anti-viral therapy. Additionally, sequential plasma samples from patients on clinical follow-up were included in this study. A total of 167 samples from 61 patients were tested by trak-C and RT-PCR. HCV RNA detection was achieved by a RT-PCR. Trak-C assay results were also compared in a limited proportion of these samples with known HCV viral load and genotype.

RESULTS

Of 167 samples tested, 56.9% were RNA positive and 43.1% were RNA negative while 50.3% were trak-C positive and 49.7% were trak-C negative, yielding a sensitivity of 85.3% and a specificity of 95.8% for the trak-C assay (Kappa co-efficient = 0.8). The concentration of HCVcAg and HCV RNA showed significant correlation (n=38, r=0.334, P =0.04). The trak-C assay detected the most prevalent HCV genotypes in India without significant difference (P =0.335). The difference between mean absorbance values of HCV RNA positive samples compared to HCV RNA negative samples in the trak-C assay was highly significant (P < 0.000). Qualitative results of trak-C assay and RT-PCR were comparable in 93% of follow-up samples.

CONCLUSIONS

Trak-C assay can be recommended for confirmation of HCV infection and follow-up in laboratories with resource-poor facilities.