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This study applied a subtractive genomics approach to identify a potential drug target in the Porphyromonas gingivalis strain (ATCC BAA-308/W83). The aim was to characterize the whole proteome and hypothetical proteins (HPs) through structural, functional, and pathway predictions. The proteome was systematically reduced to identify essential proteins (EPs), non-homologous proteins (NHPs), and non-paralogous proteins (NPPs) while excluding those that were similar to the human proteome. Out of 1,836 proteins, the cluster database at high identity with tolerance algorithm identified 36 sequences as paralogous, having 80% identity. The resulting 1,827 proteins were compared to the human proteome using BLASTp (e-value 10−3), resulting in 1,427 NHPs. These were then aligned with the DEG database using BLASTp (e-value of 10−5), identifying 396 NHPs essential for pathogen survival. CELLO predicted the sub-cellular localization, and KEGG Automated Annotation Server identified potential metabolic pathways using a BLASTp similarity search of NHPs and EPs against the infrequently updated KEGG database. A total of 79 HPs essential for P. gingivalis were selected, and their molecular weights were determined. HPs were screened for metabolic pathway prediction, and the 3D structures of the proposed HPs were determined using homology modeling, and validation was performed. Only one HP (putative arginine deiminase) was qualified and found to be involved in the arginine and proline metabolic pathway.

Color contrast pertains to graphics and the field of design. Visual objects can be described nicely with the best contrast combinations used in their representation. Color contrast suggestion is usually done with color theory, which defines two colors exactly opposite or adjacent in color hue are good contrast with each other. Herein, this paper presents a Color Contrast Recommendation System (CCRS) as an innovative solution based on Artificial Neural Networks (ANN). The main aim of the paper is to facilitate different users to find suitable contrast for any base color. We used a simple neural network model with two hidden layers for a regression task. The proposed model suggests three contrast layers for the base color given by the user. We prepare a data set of 420 color combinations for training our Neural Network model that looks appealing together and enhances the visuals. The proposed color contrast recommendation application based on Neural Networks represents a significant advancement in leveraging AI technology to streamline the design process, improve accessibility, and enhance user experiences across digital platforms.

Soil exists mainly in unsaturated conditions. Therefore, accurate prediction of the soil shear strength for unsaturated conditions also becomes equally important for the geotechnical design of earth structures. This study primarily investigates the effect of the moisture content of unsaturated soil on its shear strength. The strength characteristics of silica sands with different grain sizes were studied using the modified triaxial apparatus and analytical methods. For this purpose, four series of triaxial compression tests on silica sands were performed by varying the moisture content of the test sample at compaction and shearing as optimum or residual moisture content. The test results showed that the test sample sheared at optimum and residual moisture content exhibited higher shear strength when the sample was initially compacted at residual and optimum moisture content, respectively. The moisture content at compaction and the soil grain size considerably influence the shear strength of unsaturated sandy soils. Furthermore, the analytical method used in this study for unsaturated soil shear strength prediction does not account for the effect of initial moisture content in predicting unsaturated soil shear strength.

The main difference between Islamic and conventional banking is that Islamic banking works on profit and loss while conventional banking work is interest based. The aim of this research study is to measure and compare the financial performance of Islamic and conventional banking in Pakistan during 2006 to 2015. This study is to examine and to evaluate the performance of 5 Islamic banks (Meezan Islamic Bank, Bank Islami Limited, Al Baraka Islamic Bank, Dubai Islamic Bank Limited and Burj Bank Limited) and 5 conventional banks (Muslim Commercial Bank Limited, United Bank Limited, Askari Bank Limited, Allied Bank Limited, Habib Bank Limited) in terms of profitability, liquidity, risk, capital and efficiency. We used quantitative and qualitative data for comparison of Islamic and conventional banks. Collection of data consists on both primary as well as secondary sources. Primary data has been gathered from interviews and Secondary data has been gathered from the balance sheets and income statements of the sampled banks for the period of 2006 to 2015.Financial ratios such as profitability ratios, liquidity ratios, solvency ratios, capital ratios and efficiency ratios are used for measure of the financial performance of both banking sector. The results indicate that Islamic banks are less profitable, more liquid, less risky and less efficient. There is no significant difference in terms of capital between Islamic and conventional banks.

Based on the learning organization theory the main purpose of this research is to discuss how demographics variables affect the learning organization disciplines perception in faculty members of higher education institutes (HEIs) of Pakistan. This study explores that how demographic variables affect the learning organization disciplines perception at the HEIs level. We use the demographic variables and learning organization model in higher education institutions of Pakistan. In doing so, we used a survey instrument to collect data from 253 faculty members of HEIs in Pakistan. In addition, 15 in-depth interviews were conducted with the same respondents. Study findings revealed that there is a low application of the learning organization disciplines in HEIs in Pakistan. Further study also explains that demographic variables generated a variance of 2.7% in learning organization culture. Further, this study suggested some substantial implications for universities and regulatory bodies of HEIs.

Abstract Background Hepatitis C virus (HCV) causes liver fibrosis that may lead to liver cirrhosis or hepatocellular carcinoma (HCC), and may partially depend on infecting viral genotype. HCV genotype 3a is being more common in Asian population, especially Pakistan; the detail mechanism of infection still needs to be explored. In this study, we investigated and compared the gene expression profile between initial fibrosis stage and cirrhotic 3a genotype patients. Methods Gene expression profiling of human liver tissues was performed containing more than 22000 known genes. Using Oparray protocol, preparation and hybridization of slides was carried out and followed by scanning with GeneTAC integrator 4.0 software. Normalization of the data was obtained using MIDAS software and Significant Microarray Analysis (SAM) was performed to obtain differentially expressed candidate genes. Results Out of 22000 genes studied, 219 differentially regulated genes found with P ≤ 0.05 between both groups; 107 among those were up-regulated and 112 were down-regulated. These genes were classified into 31 categories according to their biological functions. The main categories included: apoptosis, immune response, cell signaling, kinase activity, lipid metabolism, protein metabolism, protein modulation, metabolism, vision, cell structure, cytoskeleton, nervous system, protein metabolism, protein modulation, signal transduction, transcriptional regulation and transport activity. Conclusion This is the first study on gene expression profiling in patients associated with genotype 3a using microarray analysis. These findings represent a broad portrait of genomic changes in early HCV associated fibrosis and cirrhosis. We hope that identified genes in this study will help in future to act as prognostic and diagnostic markers to differentiate fibrotic patients from cirrhotic ones.

Abstract Background Hepatitis C virus (HCV) is one of the major health concerns globally, with genotype 3a as the most prevalent in Pakistan. Lack of efficient HCV genotype 3a small animal models as well as genomic replicons has hampered the complete understanding of its life cycle, pathogenesis and therapeutic options. In this study we aimed to develop a persistent HCV genotype 3a infectious cell culture model. Methods We inoculated Huh-7 cells with HCV genotype 3a serum. Cells and media supernatant were collected at different time periods up to 40th day post infection. Culture media supernatant was also collected to find out its ability to infect naive Huh-7 cells. Results HCV replication was confirmed at both RNA and protein level through Real Time RCR and western blot using HCV core as marker. In order to validate the persistence of our model for HCV genotype 3a replication we inhibited the HCV replication through core specific siRNAs. The HCV RNA was detected intracellularly from the day one post infection up till 40th day, while HCV core protein was detected from the second day up to 40th day consistently. In culture media supernatant HCV RNA was also actively detected conferring its ability to infect the naive Huh-7 cells. Furthermore, core specific siRNA showed significant inhibition at 24th hour post transfection both at RNA and protein level with progressive increase in the expression of core gene after 3rd day. It clearly depicts that the Huh-7 successfully retained the HCV replication after degradation of siRNA. Conclusion Finally, we report that our persistent infection cell culture model consistently replicate HCV genotype 3a for more than 1 month.

Abstract Background and Aims Erythropoietin (EPO) is a glycoprotein hormone which is required to regulate the production of red blood cells. Deficiency of EPO is known to cause anemia in chronically infected renal patients and they require regular blood transfusion. Availability of recombinant EPO has eliminated the need for blood transfusion and now it is extensively used for the treatment of anemia. Glycosylation of erythropoietin is essential for its secretion, stability, protein conformation and biological activity. However, maintenance of human like glycosylation pattern during manufacturing of EPO is a major challenge in biotechnology. Currently, Chinese hamster ovary (CHO) cell line is used for the commercial production of erythropoietin but this cell line does not maintain glycosylation resembling human system. With the trend to eliminate non-human constituent from biopharmaceutical products, as a preliminary approach, we have investigated the potential of human hepatoma cell line (Huh-7) to produce recombinant EPO. Materials and methods Initially, the secretory signal and Kozak sequences was added before the EPO mature protein sequence using overlap extension PCR technique. PCR-amplified cDNA fragments of EPO was inserted into mammalian expression vector under the control of the cytomegalovirus (CMV) promoter and transiently expressed in CHO and Huh-7 cell lines. After RT-PCR analysis, ELISA and Western blotting was performed to verify the immunochemical properties of secreted EPO. Results Addition of secretory signal and Kozak sequence facilitated the extra-cellular secretion and enhanced the expression of EPO protein. Significant expression (P < 0.05) of EPO was observed in the medium from Huh-7 cell line. Conclusion Huh-7 cell line has a great potential to produce glycosylated EPO, suggesting the use of this cell line to produce glycoproteins of the therapeutic importance resembling to the natural human system.

Abstract Background Hepatitis C virus (HCV) Core protein regulates multiple signaling pathways and alters cellular genes expression responsible for HCV induced pathogenesis leading to hepatocellular carcinoma (HCC). Prevalence of HCV genotype 3a associated HCC is higher in Pakistan as compare to the rest of world; however the molecular mechanism behind this is still unclear. This study has been designed to evaluate the effect of HCV core 3a on apoptosis and cell proliferation which are involved in HCC Methodology We examined the in vitro effect of HCV Core protein of genotype 3a and 1a on cellular genes involved in apoptosis by Real time PCR in liver cell line (Huh-7). We analyzed the effect of HCV core of genotype 1a and 3a on cell proliferation by MTT assay and on phosphrylation of Akt by western blotting in Huh-7 cells. Results The HCV 3a Core down regulates the gene expression of Caspases (3, 8, 9 and 10), Cyto C and p53 which are involved in apoptosis. Moreover, HCV 3a Core gene showed stronger effect in regulating protein level of p-Akt as compared to HCV 1a Core accompanied by enhanced cell proliferation in Huh-7 cell line. Conclusion From the current study it has been concluded that reduced expression of cellular genes involved in apoptosis, increased p-Akt (cell survival gene) and enhanced cell proliferation in response to HCV 3a core confirms anti apoptotic effect of HCV 3a Core gene in Huh-7 that may lead to HCC.

Abstract Background and Aims HCV infection may lead to hepatic fibrosis. In this study, we tried to determine whether there is any correlation of HCV genotypes and viral load to the clinical parameters such as ALT, AST, ALP, bilirubin, Hb level, patient's age and gender; and then correlated this association with disease progression in liver biopsy samples. Methods In cross-sectional and observational study, 6048 serum HCV RNA positive patients were chosen. The study consists of 53 months from March 2006 to September 2010. Patients were divided into three cohorts to validate our data. Statistical analysis and correlation of lab parameters with viral factors was determined by using SPSS version 16. Results The most prevalent genotype was 3 (70.9%) followed by 1 (13.3%) and 4 (7.4%), collectively. During Univariate analysis, in all cohorts; serum bilirubin, ALP, ALT and AAR showed significant correlation with genotypes, however multivariate analysis showed that all genotypes except 4a have no association with host biochemical markers. Disease progression was also independent of all genotypes. Serum ALP, ALT, bilirubin and viremea levels were significantly elevated in patients with genotype 4a. Viral load showed negative association with serum bilirubin (r = -0.112, P = 0.000) and ALP levels (r = -0.098, P = 0.000). We observed positive correlation of ALP and bilirubin levels, while negative associations of viral load with HCV liver disease progression. Conclusion Disease progression seems independent of the genotypes. Relationship between ALP and bilirubin with viral load may be an attractive marker to guess disease progression in patients with hepatitis C.

Abstract Eukaryotic chromatin is a combination of DNA and histone proteins. It is established fact that epigenetic mechanisms are associated with DNA and histones. Initial studies emphasize on core histones association with DNA, however later studies prove the importance of linker histone H1 epigenetic. There are many types of linker histone H1 found in mammals. These subtypes are cell specific and their amount in different types of cells varies as the cell functions. Many types of post-translational modifications which occur on different residues in each subtype of linker histone H1 induce conformational changes and allow the different subtypes of linker histone H1 to interact with chromatin at different stages during cell cycle which results in the regulation of transcription and gene expression. Proposed O-glycosylation of linker histone H1 promotes condensation of chromatin while phosphorylation of linker histone H1 is known to activate transcription and gene regulation by decondensation of chromatin. Interplay between phosphorylation and O-β-GlcNAc modification on Ser and Thr residues in each subtype of linker histone H1 in Homo sapiens during cell cycle may result in diverse functional regulation of proteins. This in silico study describes the potential phosphorylation, o-glycosylation and their possible interplay sites on conserved Ser/Thr residues in various subtypes of linker histone H1 in Homo sapiens.