Biojournal of Science & Technology

Number 2, 2015

11
A multi-objective evolutionary approach to reconstruct gene regulatory network using recurrent neural network model

Authors: Sumon Ahmed, Md. Nurul Ahad Tawhid, Kazi Sakib, Md. Mustafizur Rahman

Abstract

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Number of views: 631

With the advent of various data assaying techniques, gene expression time series data have become a useful resource to investigate the complex interactions occurring amongst the transcription factors and genes. While a number of methodologies have been developed to describe Gene Regulatory Network (GRN), the presence of high noise in gene expression data have made the estimation of non-linear interactions among the genes an ill-posed one. In this work, a multi-objective evolutionary strategy has been proposed to efficiently reconstruct the skeletal structure of the biomolecular network using the Recurrent Neural Network (RNN) formalism. Moreover, this work presents a second criterion for model evaluation to exploit the sparse and scale free nature of GRN. This evaluation criterion systematically adapts the max-min in-degrees to effectively narrow down the search space, which reduces the computation time significantly and improves the model accuracy. The two well-known performance measures applied to the experimental studies on synthetic network with expression data having different noise-levels. The experimental results clearly demonstrate the suitability of the proposed method in capturing gene interactions correctly with high precision even with noisy time-series data. The experiments carried out on analyzing well-known real expression data set of the SOS DNA repair system in Escherichia coli show a significant improvement in reconstructing the network of key regulatory genes.

13
Identification of the positively selected genes governing host-pathogen arm race in Vibrio sp. through comparative genomics approach

Authors: Atai Rabby, Sajib Chakraborty*, Atiqur Rahman, Shamma Shakila Rahman, Shahjalal Soad, Kaniz Fatima Chanda, Rajib Chakravorty.

Abstract

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Number of views: 600

Bacterial evolution is due to the adaptive nature of the core bacterial genomes that plays critical role in diversification, fitness and adaptation of the species to different environment and host. Since Vibrio cholerae represents an appropriate model organism for studying the interplay of environment and host driven factors shaping the microbial genome structure and function, the current study aims to identify genes that are under these strong forces in V. cholerae. Here, we employed a comparative genomics approach to identify genes that are under positive selection in ten strains of Vibrio sp. including four pathogenic V. cholerae strains. From the available genome sequence data, a total of 422 orthologous genes were identified by reciprocal BLAST best-hit method, recombination breakpoint frequency analysis and tree comparison method. These 422 genes, representing the core genome of Vibrio sp., constituted the dataset to be analyzed for evolutionary selections. The analysis of natural selection, based on Maximum Likelihood method on synonymous and non-synonymous substitution rate, confirms the hypothesis that the bacterial core genomes are mostly under purifying selection with a few positively selected regions. However, our finding also reveals that positively selected sites in the Vibrio genome occur in a wide range of different genes encompassing diverse functional pathways including cell surface proteins (e.g. outer membrane-specific lipoprotein transporter/assembly proteins etc.), cell motility proteins (e.g. flagellar motor switch proteins, flagellar hook and assembly proteins), nutrient acquisition (e.g. amino acid, carbohydrate and phosphate ABC transporters), DNA repair and transcription related proteins. Interestingly, these positively selected gene products are directly involved with host-pathogen interactions and fitness in gastrointestinal environment. Therefore, the collective evidences of these positively selected genes spanning several pathways raise the possibility of their involvement in evolutionary arms races with other bacteria, phages, and/or the host immune system. This finding points to the natural selections which is the responsible factor for the diversification of Vibrio genus.

Number 1, 2014

6
D4476, a cell-permeant inhibitor of CK1, potentiates the action of Bromodeoxyuridine in inducing senescence in HeLa cells

Authors: Sattya Narayan Talukdar, Dai Ayusawa, Md. Rasel Al Mahmud, Mohammad Nazir Hossain

Abstract

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Number of views: 562

To elucidate the mechanism of bromodeoxyuridine (BrdU) induced cellular senescence, we treated HeLa cells with D4476, a potent and specific inhibitor of casein kinase 1(CK1). We found that D4476 (10µM) treatment could arrest cell growth at G1 stage and induced cellular senescence when treated together with BrdU (10µM). However neither D4476 nor BrdU can induce cellular senescence alone, at a concentration of 10µM. These results suggest that the targets of CK1 may be involved in maintaining normal cellular process and their inactivation potentiates BrdU to induce senescence like phenomena.

7
Association of Maternal Hypothyroidism with Preeclampsia in Bangladeshi population

Authors: Md. Bayejid Hosen, Hasan Al Banna, Yearul Kabir and M Zakir Hossain Hawlader

Abstract

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Number of views: 629

Preeclampsia (PE) is a leading cause of perinatal morbidity and mortality. Our aim of the study was to evaluate the association of hypothyroidism with preeclampsia during pregnancy and after delivery. The study comprises a total of 52 subjects including PE women (n=27) and uncomplicated pregnant women (n=25) matched by age. The serum hormone levels were estimated by ELISA methods. The demographic data and hormone levels were analyzed using unpaired t test and pearson two tailed analysis was used for correlation. Over all, significantly decreased concentrations of total triiodothyronine (T3) and thyroxine (T4) were observed in the preeclamptic group (p<0.001; p<0.01, respectively) compared with the normal pregnant group while the thyroid stimulating hormone (TSH) level was significantly (p<0.001) high. On the other hand, significant differences in T3 (p<0.05) and T4 (p<0.001) levels were found during pregnancy and after delivery among PE patients while TSH level non-significantly (p>0.05) increased. There were negative correlations of TSH with T3 (r=-0.16; p>0.05) and T4 (r=-0.11; p>0.05) observed though these were not statistically significant. Our findings suggested that hypothyroidism is associated with preeclampsia, and after delivery thyroid function become more deteriorated. Therefore, identification of thyroid abnormalities and appropriate measures might affect the occurrence and severity of the morbidity and mortality associated with preeclampsia.

8
In silico miRNA Target Identification within the Human Peroxisome Proliferator -Activated Receptor Gamma (PPARG) Gene

Authors: Sudip Paul, M.S., Kazi Saiful Islam, Md. Yeashin Gazi, Sohel Ahmed

Abstract

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Number of views: 600

MicroRNAs (miRNAs), an abundant class of 21-25 nucleotides long non-coding RNAs, regulate eukaryotic gene expression and therefore implicated in a wide range of biological processes. The miRNA- related genetic alterations are possibly more implicated in human diseases than currently appreciated. miRNA target prediction using bioinformatics tools is often the first line approach in studying gene regulation. Such predictions will help in setting search priorities for experimental validation of gene controlling mechanisms. But finding a functional miRNA target in the human genome yet remains a challenging task. In the present study, miRNA target sites within the complete sequences (5′ UTR, CDS and 3′ UTR) of human PPARG gene were investigated using miRwalk database. We found 26, 52 and 85 different miRNA target sites within the 5′ UTR, CDS and 3′ UTR regions of the gene, respectively. This computational approach will subsequently allow better in vitro confirmation of the miRNA regulatory networks in cellular systems.

10
Plasma cholesterol modulate functions of neutrophils in streptozotocin-induced type 1 diabetic rats

Authors: AHM Nurun Nabi, Mahfuzur Rahman and Laila N Islam

Abstract

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Number of views: 618

Objectives: Our previous study demonstrated neutrophil dysfunction in streptozotocin (STZ)-induced diabetic rats. This study was aimed to investigate the biochemical indices such as plasma levels of cholesterol, triglycerides, creatinine, urea, alanine transaminase and aspatate transaminase in diabetic and control rats and thus, investigate their relationship with the previously studied neutrophil functions. Methods: Diabetes was induced in Long Evans rats by an intraperitoneal injection of citrate buffer dissolved streptozotocin (STZ). Age matched control rats were injected with citrate buffer only. Neutrophils were isolated from blood using standard dextran sedimentation followed by Ficoll-Hypaque centrifugation; morphological changes in neutrophils, their ability to reduce nitroblue tetrazolium (NBT) dye and phagocytic activity from both the groups of rats were evaluated formerly. Biochemical indices were measured by standard colorimetric methods. Results: The average levels of glucose, triglycerides, cholesterol, creatinine, urea in the plasma of diabetic and control rats were 302.6 ± 87.5 vs 100.7 ± 11.5 mg/dL, 174.9 ± 18.6 vs 82.2 ± 10.2 mg/dL; 250.8 ± 22.3 vs 165.2 ± 24.1 mg/dL; 0.94 ± 0.19 vs 0.81 ± 0.05 mg/dL; 77.1 ± 9.7 vs 26.8 v 5.8 mg/dL, respectively. The mean values of aspartate transaminase (AST) and alanine transaminase (ALT) in diabetic and control rats were 141.4 ± 28.0 vs 61.6 ± 18.6 IU/L and 61.4 ± 13.6 vs 48.5 ± 6.0 IU/L, respectively. Biochemical parameters measured in diabetic rats varied significantly (p < 0.001) compared to those of control rats. Plasma indices such as triglycerides, cholesterol, creatinine, urea, AST and ALT had no relation with the functions of neutrophils. However, multidimensional scaling found a close relation between plasma cholesterol and phagocytic activity of neutrophils from diabetic rats. Ability to reduce NBT dye was closely related to the morphology of the activated neutrophils. On the other hand, levels of plasma glucose were distantly related to the functions of neutrophils. Conclusion: Thus, important liver and kidney functions indices, lipid profile parameters were significantly altered in diabetic rats and plasma cholesterol modulated the phagocytic activity of neutrophils.