Md. Jibran Alam | University of Chittagong (original) (raw)
Papers by Md. Jibran Alam
Microbiology Insights, 2016
The pathogenic bacterium Helicobacter pylori is a causative agent of gastric diseases in Banglade... more The pathogenic bacterium Helicobacter pylori is a causative agent of gastric diseases in Bangladesh as well as throughout the world. This study aimed at analyzing the prevalence of H. pylori infection among dyspeptic patients in Chittagong, the second most populous city of Bangladesh, using 16S rRNA-based H. pylori-specific Polymerase Chain Reaction and Campylobacter-like organism test. We found that 67% of the population under study was positive for H. pylori infection. Gastric ulcer and duodenal ulcer disease showed statistically significant association with H. pylori infection; however, no association of H. pylori infection was observed in terms of age and gender. This study would play a crucial role in managing H. pylori-induced gastric diseases by understanding the current trend of H. pylori infection in the Chittagong region of Bangladesh.
Scientific Reports, 2021
Inorganic arsenic (iAs) exposure has been reported to have an impact on cardiovascular diseases (... more Inorganic arsenic (iAs) exposure has been reported to have an impact on cardiovascular diseases (CVD). However, there is not much known about the cardiac tissue injury of CVD patients in relation to iAs exposure and potential role of single nucleotide polymorphisms (SNPs) of genes related to iAs metabolism, oxidative stress, endothelial dysfunction and inflammation which may play important roles in such CVD cases. In this dual center cross-sectional study, based on the exclusion and inclusion criteria, we have recruited 50 patients out of 270, who came from known arsenic-affected and- unaffected areas of mainly Chittagong, Dhaka and Rajshahi divisions of Bangladesh and underwent open-heart surgery at the selected centers during July 2017 to June 2018. We found that the patients from arsenic affected areas contained significantly higher average iAs concentrations in their urine (6.72 ± 0.54 ppb, P = 0.028), nail (529.29 ± 38.76 ppb, P
Scientific Reports, 2021
Inorganic arsenic (iAs) exposure has been reported to have an impact on cardiovascular diseases (... more Inorganic arsenic (iAs) exposure has been reported to have an impact on cardiovascular diseases (CVD). However, there is not much known about the cardiac tissue injury of CVD patients in relation to iAs exposure and potential role of single nucleotide polymorphisms (SNPs) of genes related to iAs metabolism, oxidative stress, endothelial dysfunction and inflammation which may play important roles in such CVD cases. In this dual center cross-sectional study, based on the exclusion and inclusion criteria, we have recruited 50 patients out of 270, who came from known arsenic-affected and- unaffected areas of mainly Chittagong, Dhaka and Rajshahi divisions of Bangladesh and underwent open-heart surgery at the selected centers during July 2017 to June 2018. We found that the patients from arsenic affected areas contained significantly higher average iAs concentrations in their urine (6.72 ± 0.54 ppb, P = 0.028), nail (529.29 ± 38.76 ppb, P < 0.05) and cardiac tissue (4.83 ± 0.50 ppb, P < 0.05) samples. Patients’ age, sex, BMI, hypertension and diabetes status adjusted analysis showed that patients from arsenic-affected areas had significantly higher iAs concentration in cardiac tissue (2.854, 95%CI 1.017–8.012, P = 0.046) reflecting higher cardiac tissue injury among them (1.831, 95%CI 1.032–3.249, P = 0.039), which in turn allowed the analysis to assume that the iAs exposure have played a vital role in patients’ disease condition. Adjusted analysis showed significant association between urinary iAs concentration with AA (P = 0.012) and AG (P = 0.034) genotypes and cardiac iAs concentration with AA (P = 0.017) genotype of AS3MT rs10748835. The AG genotype of AS3MT rs10748835 (13.333 95%CI 1.280–138.845, P = 0.013), AA genotype of NOS3 rs3918181 (25.333 95%CI 2.065–310.757, P = 0.002), GG genotype of ICAM1 rs281432 (12.000 95%CI 1.325–108.674, P = 0.010) and AA genotype of SOD2 rs2758331 (13.333 95%CI 1.280–138.845, P = 0.013) were found significantly associated with CVD patients from arsenic-affected areas. Again, adjusted analysis showed significant association of AA genotype of AS3MT rs10748835 with CVD patients from arsenic affected areas. In comparison to the reference genotypes of the selected SNPs, AA of AS3MT 10748835, AG of NOS3 rs3918181 and AC of rs3918188, GG of ICAM1 rs281432, TT of VCAM1 rs3176867, AA of SOD2 rs2758331 and GT of APOE rs405509 significantly increased odds of cardiac tissue injury of CVD patients from arsenic affected areas. The results showed that the selected SNPs played a susceptibility role towards cardiac tissue iAs concentration and injury among CVD patients from iAs affected areas.
Toxicology Reports, Dec 19, 2020
Millions of people around the world are chronically exposed to Arsenic (As) through food and drin... more Millions of people around the world are chronically exposed to Arsenic (As) through food and drinking water. Studies revealed that Arsenic is genotoxic and causes damage to DNA. In this study, we evaluated Corchorus olitorius and Butea monosperma for their alleviative properties against Arsenic induced genotoxicity in vivo using Wistar Rat model. Arsenic exposed rats were given C. olitorius leaf powder and B. monosperma flower powder as supplementation with normal food. Methylation status of p53 promoter was measured using Methylation Sensitive Restriction Endonuclease PCR (MSRE-PCR) assay and mitochondrial DNA (mtDNA) copy number as well as occurrence of a common deletion in mtDNA in liver and kidney tissue was determined through quantitative realtime PCR (qPCR). Arsenic exposed rats after supplementation showed relatively less severe effects of toxicity evident by significantly higher amount of (p<0.05) mtDNA copy number and reduced occurrence of deletion containing mtDNA as well as lower levels of methylation in p53 gene promoter. Histopathological analysis revealed less severe histopathological changes of liver and kidney and normal liver and kidney function parameters in supplemented rats. So, the protective properties of B. monosperma and C. olitorius against Arsenic toxicity is evident in molecular level.
Chittagong University Journal of Biological Sciences, 2020
Uropathogenic Escherichia coli are the common cause of Urinary Tract Infection affecting 150 mill... more Uropathogenic Escherichia coli are the common cause of Urinary Tract Infection affecting 150 million people each year worldwide. In this study, we investigated the prevalence of UPEC genetic regions coding for various virulence factors. The targeted genetic determinants were those coding for pili associated with pyelonephritis (pap), hemolysin (hly) , cytotoxic necrotizing factor (cnf) and aerobactin (aer). We collected 180 urine samples of UTI patients from the Chittagong region of Bangladesh and isolated UPEC. Among the studied strains the prevalence of pap, hly, cnf and aer genes were 21, 25.2, 24.3 and 7.0%, respectively. This rapid assessment of the bacterial pathogenicity may contribute to a better medical approach for the patients with urinary tract infections.
Chittagong University Journal of Biological Sciences, 2020
The uropathogenic Escherichia coli (UPEC) are causative agents of urinary tract infection (UTI) t... more The uropathogenic Escherichia coli (UPEC) are causative agents of urinary tract infection (UTI) throughout the world. This study aimed at analyzing the prevalence of UTI among different age and gender in Chittagong, the second most populous city of Bangladesh. We performed a PCR based UPEC detection method by using 16S rRNA and phylotyping by multiplex PCR. We found E. coli in 83.43% of UTI samples in this study. Among these, 42% of UPEC belongs to B2 phylogroup along with A, B1, C, D, E and F. Moreover, there was a significant association of UPEC infection with age and gender. To be more specific, 45.03% of males and 54.97% of females UTI patients were infected with UPEC. Therefore, we believe that this study would play a crucial role in detecting and managing UPEC induced UTI by understanding the prevalence of UPEC and their phylotype in the Chittagong region of Bangladesh.
BMRC Bulletin, Jul 2019
Background: Exposure to inorganic arsenic (iAs) through drinking water is currently a serious thr... more Background: Exposure to inorganic arsenic (iAs) through drinking water is currently a serious threat to public health of millions of people worldwide including Bangladesh. Some recent studies have shown that telomere dysfunction is emerging as an important factor in the pathogenesis of different cardiovascular diseases. Arsenic plays significant role on telomere dysfunction by altering the expression of telomere-related genes.
Objective: The study was aimed to investigate the effects of arsenic on hTERT mRNA levels and their combined role in increasing CVD susceptibility.
Methods: In this cross sectional study, total of 50 CVD patients who underwent open heart surgery were recruited. Urine, nail and cardiac tissue samples were collected and analysed for As. Blood samples were quantified for hTERT expression analysis using real-time polymerase chain reaction.
Results: The hTERT mRNA expression was found approximately 10 fold higher in the As-exposed patients than the As-unexposed patients (p<0.01). A strong positive correlation (p<0.01, r>0.3) was found between the hTERT mRNA levels and As contents in the cardiac tissue, nail and urine samples of the study subjects. The significant increase (approx. 4 fold) in the hTERT mRNA expression was found in the patients with coronary artery disease (CAD) than the non-CAD patients.
Conclusions: The results of the study suggest that arsenic exposure increases hTERT mRNA expression which may in turn modify As-induced cardiovascular outcomes. The findings of this study will help to look deep into the association of As exposure in cardiovascular disease pathogenesis to open a new window in the diagnosis and treatment procedure of CVD.
Aims: Helicobacter pylori is a causative agent of gastroduodenal diseases in Bangladesh as well a... more Aims: Helicobacter pylori is a causative agent of gastroduodenal diseases in Bangladesh as well as throughout the world. This study aimed to determine the H. pylori cagA, vacA and iceA virulent genotypes by PCR directly in gastric biopsies from dyspeptic patients of Chittagong, Bangladesh and evaluating the association of these genotypes with clinical manifestations. Methodology and results: CLO (Campylobacter-Like Organism) test and Hp16s PCR (16S rRNA based H. pylori specific PCR) was performed to confirm H. pylori infection. Among 111 patients, H. pylori infection was found in 60 patients by CLO test, while Hp16s PCR revealed that 54 patients were H. pylori positive. PCR amplification of the H. pylori virulence genes was successful in 35 gastric biopsies amongst the 54 Hp16s PCR positive biopsies. The positive rates for the cagA, vacAs1, vacAs2, vacAm1, vacAm2, iceA1, iceA2 genes were 34.3%, 71.4%, 8.6%, 62.9%, 28.6%, 20% and 11.4%, respectively. The allelic variant vacAs1m1 had a predominant percentage with 51.4%, followed by vacAs1m2, vacAs2m2 and vacAs1m1m2 with 14.3%, 5.7% and 2.9%, respectively. Among the subtypes of vacAs1, only s1a was detected in 54.3% of biopsies while none of the cases showed the s1b and s1c genotypes. However, there was no statistically significant association (P>0.05) observed between the virulent genotypes and clinical conditions. Conclusion, significance and impact of study: We found that cagA, vacAs1m1 and iceA1 were the most frequent H. pylori genotypes in severe clinical outcomes of the infection. The data in this study would provide a basis for understanding the diverse virulence pattern of this bacterium in Bangladeshi dyspeptic patients.
Background: In the present study, we investigated the arsenic accumulation in different parts of ... more Background: In the present study, we investigated the arsenic accumulation in different parts of rice irrigated with arsenic contaminated water. Besides, we also evaluated the protective effects of Corchorus olitorius leaves against arsenic contaminated rice induced toxicities in animal model. Methods: A pot experiment was conducted with arsenic amended irrigation water (0.0, 25.0, 50.0 and 75.0 mg/L As) to investigate the arsenic accumulation in different parts of rice. In order to evaluate the protective effects of Corchorus olitorius leaves, twenty Wistar albino rats were divided into four different groups. The control group (Group-I) was supplied with normal laboratory pellets while groups II, III, and IV received normal laboratory pellets supplemented with arsenic contaminated rice, C. olitorius leaf powder (4 %), arsenic contaminated rice plus C. olitorius leaf powder (4 %) respectively. Different haematological parameters and serum indices were analyzed to evaluate the protective effects of Corchorus olitorius leaves against arsenic intoxication. To gather more supportive evidences of Corchorus olitorius potentiality against arsenic intoxication, histopathological analysis of liver, kidney, spleen and heart tissues was also performed. Results: From the pot experiment, we have found a significant (p ≤ 0.05) increase of arsenic accumulation in different parts of rice with the increase of arsenic concentrations in irrigation water and the trend of accumulation was found as root > straw > husk > grain. Another part of the experiment revealed that supplementation of C. olitorius leaves with arsenic contaminated rice significantly (p < 0.05) restored the altered haematological parameters and other serum indices towards the normal values. Arsenic deposition pattern on different organs and histological studies on the ultrastructural changes of liver, kidneys, spleen and heart also supported the protective roles of Corchorus olitorius leaves against arsenic contaminated rice induced toxicities.
The pathogenic bacterium Helicobacter pylori is a causative agent of gastric diseases in Banglade... more The pathogenic bacterium Helicobacter pylori is a causative agent of gastric diseases in Bangladesh as well as throughout the world. This study aimed at analyzing the prevalence of H. pylori infection among dyspeptic patients in Chittagong, the second most populous city of Bangladesh, using 16S rRNA-based H. pylori-specific Polymerase Chain Reaction and Campylobacter-like organism test. We found that 67% of the population under study was positive for H. pylori infection. Gastric ulcer and duodenal ulcer disease showed statistically significant association with H. pylori infection; however, no association of H. pylori infection was observed in terms of age and gender. This study would play a crucial role in managing H. pylori-induced gastric diseases by understanding the current trend of H. pylori infection in the Chittagong region of Bangladesh.
A pot experiment was conducted with As amended irrigation water (0.0, 25.0, 50.0 and 75.0 mg/L As... more A pot experiment was conducted with As amended irrigation water (0.0, 25.0, 50.0 and 75.0 mg/L As) to investigate the As accumulation in different parts of rice. A significant (p ≤ 0.05) increase of As accumulation was found with the increase of As concentrations in irrigation water and the trend of accumulation was found as root > straw > husk> grain. The animals were fed As contaminated rice exhibited a significant (p<0.05) alterations in haematological parameters, liver marker enzymes, kidney function test along with alterations in lipid profile. Supplementation of B. monosperma with As contaminated rice significantly (p<0.05) restored these parameters towards the normal values. As deposition pattern on different organs and histological studies on the ultra structural changes of liver, kidneys, spleen and heart also supported the protective role of B. monosperma. In fine, it can be concluded that B. monosperma has significant role in protecting animals from As contaminated rice induced toxicity.
Objective: This study aims to analyze and predict the possibility of designing a vaccine that cou... more Objective: This study aims to analyze and predict the possibility of designing a vaccine that could make humans immune to krait toxin. Materials and Methods: Bungarus caeruleus or common Indian krait is a member of the venomous big four snake species. Its venom contains a neurotoxic protein alpha-delta-bungarotoxin-4 and is found to be responsible for human death 4-8 h after the snake bite. Antigenicity of this protein was determined by Hopp and Woods and Kolaskar and Tangaonkar method. We predicted major histocompatibility complex (MHC) Class I and MHC Class II binding peptides of antigenic protein from alpha-deltabungarotoxin-4, which are an important determinant for protection of host from snake bite. Fragments selected through this study revealed higher effi ciency binders. Result: Higher percentages of their atoms are directly involved in binding in comparison with larger molecules. These potential fragments, therefore can be a novel tool in the arena of cross protection to develop host specifi c antibodies in different objectives. We operated AllerHunter for predicting allergenicity based on the structural and physiochemical properties of whole alpha-delta-bungarotoin-4, and it was found to be nonallergen. The potential epitopes of alpha-delta-bungarotoxin-4 were found to be located at sequences "GENLCYTKM" and "FCSSRGKVI" and these were found to be suffi cient for eliciting the desired immune response. In this study, a hypothetical immunization is developed, which demands more validation and study. It can be emphasized that such predictive in silico study requires an in vivo experiments comprehensibly, which must be assured to validate such approaches. Hence, our goal was to identify a conformationally biased epitope sequence, which aims to provide a new paradigm to design epitope-based peptide vaccines in order to alleviate immunological infections from Krait neurotoxin. Conclusion: Computational techniques manifest the attention of Krait neurotoxin as crucial immunodiagnostic tool for fatal venom proved that most snake venoms are in poorly characterized although they are biologically important proteins with therapeutic potentialities.
Saint Louis encephalitis virus, a member of the flaviviridae subgroup, is a culex mosquito-borne ... more Saint Louis encephalitis virus, a member of the flaviviridae subgroup, is a culex mosquito-borne pathogen. Despite severe epidemic outbreaks on several occasions, not much progress has been made with regard to an epitope-based vaccine designed for Saint Louis encephalitis virus. The envelope proteins were collected from a protein database and analyzed with an in silico tool to identify the most immunogenic protein. The protein was then verified through several parameters to predict the T-cell and B-cell epitopes. Both T-cell and B-cell immunity were assessed to determine that the protein can induce humoral as well as cell-mediated immunity. The peptide sequence from 330-336 amino acids and the sequence REYCYEATL from the position 57 were found as the most potential B-cell and T-cell epitopes, respectively. Furthermore, as an RNA virus, one important thing was to establish the epitope as a conserved one; this was also done by in silico tools, showing 63.51% conservancy. The epitope was further tested for binding against the HLA molecule by computational docking techniques to verify the binding cleft epitope interaction. However, this is a preliminary study of designing an epitope-based peptide vaccine against Saint Louis encephalitis virus; the results awaits validation by in vitro and in vivo experiments.
Background: Australian Box Jellyfish (C. fleckeri) has the most rapid acting venom known to in th... more Background: Australian Box Jellyfish (C. fleckeri) has the most rapid acting venom known to in the arena of toxicological research and is capable enough of killing a person in less than 5 minutes inflicting painful, debilitating and potentially life-threatening stings in humans. It has been understood that C. fleckeri venom proteins CfTX-1, 2 and HSP70-1 contain cardiotoxic, neurotoxic and highly dermatonecrotic components that can cause itchy bumpy rash and cardiac arrest. Subjects and Methods: As there is no effective drug available, novel approaches regarding epitope prediction for vaccine development were performed in this study. Peptide fragments as nonamers of these antigenic venom proteins were analyzed by using computational tools that would elicit humoral and cell mediated immunity, were focused for attempting vaccine design. By ranking the peptides according to their proteasomal cleavage sites, TAP scores and IC50<250 nM, the predictions were scrutinized. Furthermore, the epitope sequences were examined by in silico docking simulation with different specific HLA receptors. Results: Interestingly, to our knowledge, this is the maiden hypothetical immunization that predicts the promiscuous epitopes with potential contributions to the tailored design of improved safe and effective vaccines against antigenic venom proteins of C. fleckeri which would be effective especially for the Australian population. Conclusion: Although the computational approaches executed here are based on concrete confidence which demands more validation and in vivo experiments to validate such in silico approach.
Potato virus Y (PVY) is one of the most prevalent and important viruses that affect potatoes. The... more Potato virus Y (PVY) is one of the most prevalent and important viruses that affect potatoes. The virus can be acquired from the infected plant within seconds, and transmitted to a healthy plant just as fast. PVY can also be transmitted mechanically by machinery, tools, and damaging plants while walking through the field. Its strains can interact with other potato viruses such as Potato virus A (PVA) and Potato virus X (PVX) to result in heavier losses. As PVY is a non-persistent virus so the use of insecticides to control spread is generally not effective. The best strategy to control PVY is to use seed potatoes certified to have low virus content. Analysis showed that peptide fragments of this antigenic coat protein of Potato Y virus contain 203 amino acids which point out 195 nonamers. These nonamers can be focused for designing a sero-diagnostic tool to detect PVY infection. By analyzing antigenecity, hydrophilicity, solvent accessibility and exposed surface area, we found the location potential epitopes at the sequences 181-MPRYGLVRN-189, 41-THTVPRIKAI-50 and 94-YEAVQLAYDIGETEM-108, and may be sufficient for eliciting immune response and targeting for virus detection. Apart from these, the high affinity TAP transporter peptide regions were found which were predicted by using cascade Support Vector Machine (SVM) and Position Specific Scoring Matrices (PSSM). These high efficiency binding fragments are found to tightly bind to the HLA receptors by in silico molecular docking and therefore, be used in cross protection and to develop host specific antibodies. We Predicted MHC class-I and class-II binding peptides of antigen protein from Potato Y virus which can be important determinant in sero-diagnostic issue. Besides, we operated AllerHunter for predicting allergenicity and it predicted Potato Y virus as non allergen protein with significant scores based on the structural and physicochemical properties of whole protein. Although the computational predictions made here are based on concrete confidence hence we have developed a hypothetical immunization based detection tool which demands more validation and in vivo experiments to validate such in silico approaches.
Bovine collagen alpha-1 is a naturally occurring extracellular matrix protein found in tendons an... more Bovine collagen alpha-1 is a naturally occurring extracellular matrix protein found in tendons and other connective tissues. It plays a vital role in cell growth, differentiation, attachment, and migration. Recent findings have established that collagen alpha-1 is involved in osteogenesis imperfecta phenotype in cattle but deep information about other members of this large family is not available so far. So with a view to finding a new edge and attempt to figure out a correlation among the well attributed Bovine alpha-1 collagen sequences are executed and analyzed. To do so, comparative analysis among the 28 members of collagen family has been carried out using Computational tools. Consequently, based on the physico-chemical, secondary structural, functional and phylogenetic classifications, we have selected collagen 12, 14 and 20 as targets for pathological conditions. These proteins belong to the FACIT family and significantly showed low glycine and proline content, high instability and aliphatic index. Moreover, FACIT family collagens contain multiple triple helical domains and being members of the FACIT family, bovine collagen 12, 14, 20 do not form fibrils by themselves but they are associated to collagen 1 associated fibrils. These collagen molecules might be crucial candidates to detect and understand the process of matrix remodeling in diseases especially in the arena of cellular compartments.
Microbiology Insights, 2016
The pathogenic bacterium Helicobacter pylori is a causative agent of gastric diseases in Banglade... more The pathogenic bacterium Helicobacter pylori is a causative agent of gastric diseases in Bangladesh as well as throughout the world. This study aimed at analyzing the prevalence of H. pylori infection among dyspeptic patients in Chittagong, the second most populous city of Bangladesh, using 16S rRNA-based H. pylori-specific Polymerase Chain Reaction and Campylobacter-like organism test. We found that 67% of the population under study was positive for H. pylori infection. Gastric ulcer and duodenal ulcer disease showed statistically significant association with H. pylori infection; however, no association of H. pylori infection was observed in terms of age and gender. This study would play a crucial role in managing H. pylori-induced gastric diseases by understanding the current trend of H. pylori infection in the Chittagong region of Bangladesh.
Scientific Reports, 2021
Inorganic arsenic (iAs) exposure has been reported to have an impact on cardiovascular diseases (... more Inorganic arsenic (iAs) exposure has been reported to have an impact on cardiovascular diseases (CVD). However, there is not much known about the cardiac tissue injury of CVD patients in relation to iAs exposure and potential role of single nucleotide polymorphisms (SNPs) of genes related to iAs metabolism, oxidative stress, endothelial dysfunction and inflammation which may play important roles in such CVD cases. In this dual center cross-sectional study, based on the exclusion and inclusion criteria, we have recruited 50 patients out of 270, who came from known arsenic-affected and- unaffected areas of mainly Chittagong, Dhaka and Rajshahi divisions of Bangladesh and underwent open-heart surgery at the selected centers during July 2017 to June 2018. We found that the patients from arsenic affected areas contained significantly higher average iAs concentrations in their urine (6.72 ± 0.54 ppb, P = 0.028), nail (529.29 ± 38.76 ppb, P
Scientific Reports, 2021
Inorganic arsenic (iAs) exposure has been reported to have an impact on cardiovascular diseases (... more Inorganic arsenic (iAs) exposure has been reported to have an impact on cardiovascular diseases (CVD). However, there is not much known about the cardiac tissue injury of CVD patients in relation to iAs exposure and potential role of single nucleotide polymorphisms (SNPs) of genes related to iAs metabolism, oxidative stress, endothelial dysfunction and inflammation which may play important roles in such CVD cases. In this dual center cross-sectional study, based on the exclusion and inclusion criteria, we have recruited 50 patients out of 270, who came from known arsenic-affected and- unaffected areas of mainly Chittagong, Dhaka and Rajshahi divisions of Bangladesh and underwent open-heart surgery at the selected centers during July 2017 to June 2018. We found that the patients from arsenic affected areas contained significantly higher average iAs concentrations in their urine (6.72 ± 0.54 ppb, P = 0.028), nail (529.29 ± 38.76 ppb, P < 0.05) and cardiac tissue (4.83 ± 0.50 ppb, P < 0.05) samples. Patients’ age, sex, BMI, hypertension and diabetes status adjusted analysis showed that patients from arsenic-affected areas had significantly higher iAs concentration in cardiac tissue (2.854, 95%CI 1.017–8.012, P = 0.046) reflecting higher cardiac tissue injury among them (1.831, 95%CI 1.032–3.249, P = 0.039), which in turn allowed the analysis to assume that the iAs exposure have played a vital role in patients’ disease condition. Adjusted analysis showed significant association between urinary iAs concentration with AA (P = 0.012) and AG (P = 0.034) genotypes and cardiac iAs concentration with AA (P = 0.017) genotype of AS3MT rs10748835. The AG genotype of AS3MT rs10748835 (13.333 95%CI 1.280–138.845, P = 0.013), AA genotype of NOS3 rs3918181 (25.333 95%CI 2.065–310.757, P = 0.002), GG genotype of ICAM1 rs281432 (12.000 95%CI 1.325–108.674, P = 0.010) and AA genotype of SOD2 rs2758331 (13.333 95%CI 1.280–138.845, P = 0.013) were found significantly associated with CVD patients from arsenic-affected areas. Again, adjusted analysis showed significant association of AA genotype of AS3MT rs10748835 with CVD patients from arsenic affected areas. In comparison to the reference genotypes of the selected SNPs, AA of AS3MT 10748835, AG of NOS3 rs3918181 and AC of rs3918188, GG of ICAM1 rs281432, TT of VCAM1 rs3176867, AA of SOD2 rs2758331 and GT of APOE rs405509 significantly increased odds of cardiac tissue injury of CVD patients from arsenic affected areas. The results showed that the selected SNPs played a susceptibility role towards cardiac tissue iAs concentration and injury among CVD patients from iAs affected areas.
Toxicology Reports, Dec 19, 2020
Millions of people around the world are chronically exposed to Arsenic (As) through food and drin... more Millions of people around the world are chronically exposed to Arsenic (As) through food and drinking water. Studies revealed that Arsenic is genotoxic and causes damage to DNA. In this study, we evaluated Corchorus olitorius and Butea monosperma for their alleviative properties against Arsenic induced genotoxicity in vivo using Wistar Rat model. Arsenic exposed rats were given C. olitorius leaf powder and B. monosperma flower powder as supplementation with normal food. Methylation status of p53 promoter was measured using Methylation Sensitive Restriction Endonuclease PCR (MSRE-PCR) assay and mitochondrial DNA (mtDNA) copy number as well as occurrence of a common deletion in mtDNA in liver and kidney tissue was determined through quantitative realtime PCR (qPCR). Arsenic exposed rats after supplementation showed relatively less severe effects of toxicity evident by significantly higher amount of (p<0.05) mtDNA copy number and reduced occurrence of deletion containing mtDNA as well as lower levels of methylation in p53 gene promoter. Histopathological analysis revealed less severe histopathological changes of liver and kidney and normal liver and kidney function parameters in supplemented rats. So, the protective properties of B. monosperma and C. olitorius against Arsenic toxicity is evident in molecular level.
Chittagong University Journal of Biological Sciences, 2020
Uropathogenic Escherichia coli are the common cause of Urinary Tract Infection affecting 150 mill... more Uropathogenic Escherichia coli are the common cause of Urinary Tract Infection affecting 150 million people each year worldwide. In this study, we investigated the prevalence of UPEC genetic regions coding for various virulence factors. The targeted genetic determinants were those coding for pili associated with pyelonephritis (pap), hemolysin (hly) , cytotoxic necrotizing factor (cnf) and aerobactin (aer). We collected 180 urine samples of UTI patients from the Chittagong region of Bangladesh and isolated UPEC. Among the studied strains the prevalence of pap, hly, cnf and aer genes were 21, 25.2, 24.3 and 7.0%, respectively. This rapid assessment of the bacterial pathogenicity may contribute to a better medical approach for the patients with urinary tract infections.
Chittagong University Journal of Biological Sciences, 2020
The uropathogenic Escherichia coli (UPEC) are causative agents of urinary tract infection (UTI) t... more The uropathogenic Escherichia coli (UPEC) are causative agents of urinary tract infection (UTI) throughout the world. This study aimed at analyzing the prevalence of UTI among different age and gender in Chittagong, the second most populous city of Bangladesh. We performed a PCR based UPEC detection method by using 16S rRNA and phylotyping by multiplex PCR. We found E. coli in 83.43% of UTI samples in this study. Among these, 42% of UPEC belongs to B2 phylogroup along with A, B1, C, D, E and F. Moreover, there was a significant association of UPEC infection with age and gender. To be more specific, 45.03% of males and 54.97% of females UTI patients were infected with UPEC. Therefore, we believe that this study would play a crucial role in detecting and managing UPEC induced UTI by understanding the prevalence of UPEC and their phylotype in the Chittagong region of Bangladesh.
BMRC Bulletin, Jul 2019
Background: Exposure to inorganic arsenic (iAs) through drinking water is currently a serious thr... more Background: Exposure to inorganic arsenic (iAs) through drinking water is currently a serious threat to public health of millions of people worldwide including Bangladesh. Some recent studies have shown that telomere dysfunction is emerging as an important factor in the pathogenesis of different cardiovascular diseases. Arsenic plays significant role on telomere dysfunction by altering the expression of telomere-related genes.
Objective: The study was aimed to investigate the effects of arsenic on hTERT mRNA levels and their combined role in increasing CVD susceptibility.
Methods: In this cross sectional study, total of 50 CVD patients who underwent open heart surgery were recruited. Urine, nail and cardiac tissue samples were collected and analysed for As. Blood samples were quantified for hTERT expression analysis using real-time polymerase chain reaction.
Results: The hTERT mRNA expression was found approximately 10 fold higher in the As-exposed patients than the As-unexposed patients (p<0.01). A strong positive correlation (p<0.01, r>0.3) was found between the hTERT mRNA levels and As contents in the cardiac tissue, nail and urine samples of the study subjects. The significant increase (approx. 4 fold) in the hTERT mRNA expression was found in the patients with coronary artery disease (CAD) than the non-CAD patients.
Conclusions: The results of the study suggest that arsenic exposure increases hTERT mRNA expression which may in turn modify As-induced cardiovascular outcomes. The findings of this study will help to look deep into the association of As exposure in cardiovascular disease pathogenesis to open a new window in the diagnosis and treatment procedure of CVD.
Aims: Helicobacter pylori is a causative agent of gastroduodenal diseases in Bangladesh as well a... more Aims: Helicobacter pylori is a causative agent of gastroduodenal diseases in Bangladesh as well as throughout the world. This study aimed to determine the H. pylori cagA, vacA and iceA virulent genotypes by PCR directly in gastric biopsies from dyspeptic patients of Chittagong, Bangladesh and evaluating the association of these genotypes with clinical manifestations. Methodology and results: CLO (Campylobacter-Like Organism) test and Hp16s PCR (16S rRNA based H. pylori specific PCR) was performed to confirm H. pylori infection. Among 111 patients, H. pylori infection was found in 60 patients by CLO test, while Hp16s PCR revealed that 54 patients were H. pylori positive. PCR amplification of the H. pylori virulence genes was successful in 35 gastric biopsies amongst the 54 Hp16s PCR positive biopsies. The positive rates for the cagA, vacAs1, vacAs2, vacAm1, vacAm2, iceA1, iceA2 genes were 34.3%, 71.4%, 8.6%, 62.9%, 28.6%, 20% and 11.4%, respectively. The allelic variant vacAs1m1 had a predominant percentage with 51.4%, followed by vacAs1m2, vacAs2m2 and vacAs1m1m2 with 14.3%, 5.7% and 2.9%, respectively. Among the subtypes of vacAs1, only s1a was detected in 54.3% of biopsies while none of the cases showed the s1b and s1c genotypes. However, there was no statistically significant association (P>0.05) observed between the virulent genotypes and clinical conditions. Conclusion, significance and impact of study: We found that cagA, vacAs1m1 and iceA1 were the most frequent H. pylori genotypes in severe clinical outcomes of the infection. The data in this study would provide a basis for understanding the diverse virulence pattern of this bacterium in Bangladeshi dyspeptic patients.
Background: In the present study, we investigated the arsenic accumulation in different parts of ... more Background: In the present study, we investigated the arsenic accumulation in different parts of rice irrigated with arsenic contaminated water. Besides, we also evaluated the protective effects of Corchorus olitorius leaves against arsenic contaminated rice induced toxicities in animal model. Methods: A pot experiment was conducted with arsenic amended irrigation water (0.0, 25.0, 50.0 and 75.0 mg/L As) to investigate the arsenic accumulation in different parts of rice. In order to evaluate the protective effects of Corchorus olitorius leaves, twenty Wistar albino rats were divided into four different groups. The control group (Group-I) was supplied with normal laboratory pellets while groups II, III, and IV received normal laboratory pellets supplemented with arsenic contaminated rice, C. olitorius leaf powder (4 %), arsenic contaminated rice plus C. olitorius leaf powder (4 %) respectively. Different haematological parameters and serum indices were analyzed to evaluate the protective effects of Corchorus olitorius leaves against arsenic intoxication. To gather more supportive evidences of Corchorus olitorius potentiality against arsenic intoxication, histopathological analysis of liver, kidney, spleen and heart tissues was also performed. Results: From the pot experiment, we have found a significant (p ≤ 0.05) increase of arsenic accumulation in different parts of rice with the increase of arsenic concentrations in irrigation water and the trend of accumulation was found as root > straw > husk > grain. Another part of the experiment revealed that supplementation of C. olitorius leaves with arsenic contaminated rice significantly (p < 0.05) restored the altered haematological parameters and other serum indices towards the normal values. Arsenic deposition pattern on different organs and histological studies on the ultrastructural changes of liver, kidneys, spleen and heart also supported the protective roles of Corchorus olitorius leaves against arsenic contaminated rice induced toxicities.
The pathogenic bacterium Helicobacter pylori is a causative agent of gastric diseases in Banglade... more The pathogenic bacterium Helicobacter pylori is a causative agent of gastric diseases in Bangladesh as well as throughout the world. This study aimed at analyzing the prevalence of H. pylori infection among dyspeptic patients in Chittagong, the second most populous city of Bangladesh, using 16S rRNA-based H. pylori-specific Polymerase Chain Reaction and Campylobacter-like organism test. We found that 67% of the population under study was positive for H. pylori infection. Gastric ulcer and duodenal ulcer disease showed statistically significant association with H. pylori infection; however, no association of H. pylori infection was observed in terms of age and gender. This study would play a crucial role in managing H. pylori-induced gastric diseases by understanding the current trend of H. pylori infection in the Chittagong region of Bangladesh.
A pot experiment was conducted with As amended irrigation water (0.0, 25.0, 50.0 and 75.0 mg/L As... more A pot experiment was conducted with As amended irrigation water (0.0, 25.0, 50.0 and 75.0 mg/L As) to investigate the As accumulation in different parts of rice. A significant (p ≤ 0.05) increase of As accumulation was found with the increase of As concentrations in irrigation water and the trend of accumulation was found as root > straw > husk> grain. The animals were fed As contaminated rice exhibited a significant (p<0.05) alterations in haematological parameters, liver marker enzymes, kidney function test along with alterations in lipid profile. Supplementation of B. monosperma with As contaminated rice significantly (p<0.05) restored these parameters towards the normal values. As deposition pattern on different organs and histological studies on the ultra structural changes of liver, kidneys, spleen and heart also supported the protective role of B. monosperma. In fine, it can be concluded that B. monosperma has significant role in protecting animals from As contaminated rice induced toxicity.
Objective: This study aims to analyze and predict the possibility of designing a vaccine that cou... more Objective: This study aims to analyze and predict the possibility of designing a vaccine that could make humans immune to krait toxin. Materials and Methods: Bungarus caeruleus or common Indian krait is a member of the venomous big four snake species. Its venom contains a neurotoxic protein alpha-delta-bungarotoxin-4 and is found to be responsible for human death 4-8 h after the snake bite. Antigenicity of this protein was determined by Hopp and Woods and Kolaskar and Tangaonkar method. We predicted major histocompatibility complex (MHC) Class I and MHC Class II binding peptides of antigenic protein from alpha-deltabungarotoxin-4, which are an important determinant for protection of host from snake bite. Fragments selected through this study revealed higher effi ciency binders. Result: Higher percentages of their atoms are directly involved in binding in comparison with larger molecules. These potential fragments, therefore can be a novel tool in the arena of cross protection to develop host specifi c antibodies in different objectives. We operated AllerHunter for predicting allergenicity based on the structural and physiochemical properties of whole alpha-delta-bungarotoin-4, and it was found to be nonallergen. The potential epitopes of alpha-delta-bungarotoxin-4 were found to be located at sequences "GENLCYTKM" and "FCSSRGKVI" and these were found to be suffi cient for eliciting the desired immune response. In this study, a hypothetical immunization is developed, which demands more validation and study. It can be emphasized that such predictive in silico study requires an in vivo experiments comprehensibly, which must be assured to validate such approaches. Hence, our goal was to identify a conformationally biased epitope sequence, which aims to provide a new paradigm to design epitope-based peptide vaccines in order to alleviate immunological infections from Krait neurotoxin. Conclusion: Computational techniques manifest the attention of Krait neurotoxin as crucial immunodiagnostic tool for fatal venom proved that most snake venoms are in poorly characterized although they are biologically important proteins with therapeutic potentialities.
Saint Louis encephalitis virus, a member of the flaviviridae subgroup, is a culex mosquito-borne ... more Saint Louis encephalitis virus, a member of the flaviviridae subgroup, is a culex mosquito-borne pathogen. Despite severe epidemic outbreaks on several occasions, not much progress has been made with regard to an epitope-based vaccine designed for Saint Louis encephalitis virus. The envelope proteins were collected from a protein database and analyzed with an in silico tool to identify the most immunogenic protein. The protein was then verified through several parameters to predict the T-cell and B-cell epitopes. Both T-cell and B-cell immunity were assessed to determine that the protein can induce humoral as well as cell-mediated immunity. The peptide sequence from 330-336 amino acids and the sequence REYCYEATL from the position 57 were found as the most potential B-cell and T-cell epitopes, respectively. Furthermore, as an RNA virus, one important thing was to establish the epitope as a conserved one; this was also done by in silico tools, showing 63.51% conservancy. The epitope was further tested for binding against the HLA molecule by computational docking techniques to verify the binding cleft epitope interaction. However, this is a preliminary study of designing an epitope-based peptide vaccine against Saint Louis encephalitis virus; the results awaits validation by in vitro and in vivo experiments.
Background: Australian Box Jellyfish (C. fleckeri) has the most rapid acting venom known to in th... more Background: Australian Box Jellyfish (C. fleckeri) has the most rapid acting venom known to in the arena of toxicological research and is capable enough of killing a person in less than 5 minutes inflicting painful, debilitating and potentially life-threatening stings in humans. It has been understood that C. fleckeri venom proteins CfTX-1, 2 and HSP70-1 contain cardiotoxic, neurotoxic and highly dermatonecrotic components that can cause itchy bumpy rash and cardiac arrest. Subjects and Methods: As there is no effective drug available, novel approaches regarding epitope prediction for vaccine development were performed in this study. Peptide fragments as nonamers of these antigenic venom proteins were analyzed by using computational tools that would elicit humoral and cell mediated immunity, were focused for attempting vaccine design. By ranking the peptides according to their proteasomal cleavage sites, TAP scores and IC50<250 nM, the predictions were scrutinized. Furthermore, the epitope sequences were examined by in silico docking simulation with different specific HLA receptors. Results: Interestingly, to our knowledge, this is the maiden hypothetical immunization that predicts the promiscuous epitopes with potential contributions to the tailored design of improved safe and effective vaccines against antigenic venom proteins of C. fleckeri which would be effective especially for the Australian population. Conclusion: Although the computational approaches executed here are based on concrete confidence which demands more validation and in vivo experiments to validate such in silico approach.
Potato virus Y (PVY) is one of the most prevalent and important viruses that affect potatoes. The... more Potato virus Y (PVY) is one of the most prevalent and important viruses that affect potatoes. The virus can be acquired from the infected plant within seconds, and transmitted to a healthy plant just as fast. PVY can also be transmitted mechanically by machinery, tools, and damaging plants while walking through the field. Its strains can interact with other potato viruses such as Potato virus A (PVA) and Potato virus X (PVX) to result in heavier losses. As PVY is a non-persistent virus so the use of insecticides to control spread is generally not effective. The best strategy to control PVY is to use seed potatoes certified to have low virus content. Analysis showed that peptide fragments of this antigenic coat protein of Potato Y virus contain 203 amino acids which point out 195 nonamers. These nonamers can be focused for designing a sero-diagnostic tool to detect PVY infection. By analyzing antigenecity, hydrophilicity, solvent accessibility and exposed surface area, we found the location potential epitopes at the sequences 181-MPRYGLVRN-189, 41-THTVPRIKAI-50 and 94-YEAVQLAYDIGETEM-108, and may be sufficient for eliciting immune response and targeting for virus detection. Apart from these, the high affinity TAP transporter peptide regions were found which were predicted by using cascade Support Vector Machine (SVM) and Position Specific Scoring Matrices (PSSM). These high efficiency binding fragments are found to tightly bind to the HLA receptors by in silico molecular docking and therefore, be used in cross protection and to develop host specific antibodies. We Predicted MHC class-I and class-II binding peptides of antigen protein from Potato Y virus which can be important determinant in sero-diagnostic issue. Besides, we operated AllerHunter for predicting allergenicity and it predicted Potato Y virus as non allergen protein with significant scores based on the structural and physicochemical properties of whole protein. Although the computational predictions made here are based on concrete confidence hence we have developed a hypothetical immunization based detection tool which demands more validation and in vivo experiments to validate such in silico approaches.
Bovine collagen alpha-1 is a naturally occurring extracellular matrix protein found in tendons an... more Bovine collagen alpha-1 is a naturally occurring extracellular matrix protein found in tendons and other connective tissues. It plays a vital role in cell growth, differentiation, attachment, and migration. Recent findings have established that collagen alpha-1 is involved in osteogenesis imperfecta phenotype in cattle but deep information about other members of this large family is not available so far. So with a view to finding a new edge and attempt to figure out a correlation among the well attributed Bovine alpha-1 collagen sequences are executed and analyzed. To do so, comparative analysis among the 28 members of collagen family has been carried out using Computational tools. Consequently, based on the physico-chemical, secondary structural, functional and phylogenetic classifications, we have selected collagen 12, 14 and 20 as targets for pathological conditions. These proteins belong to the FACIT family and significantly showed low glycine and proline content, high instability and aliphatic index. Moreover, FACIT family collagens contain multiple triple helical domains and being members of the FACIT family, bovine collagen 12, 14, 20 do not form fibrils by themselves but they are associated to collagen 1 associated fibrils. These collagen molecules might be crucial candidates to detect and understand the process of matrix remodeling in diseases especially in the arena of cellular compartments.