Mohammad Al-Forkan, Fahmida Binta Wali, Laila Khaleda, Md. Jibran Alam, Rahee Hasan Chowdhury, Amit Datta, Md. Zillur Rahman, Nazmul Hosain, Mohammad Fazle Maruf, Muhammad Abdul Quaium Chowdhury, N. K. M. Mirazul Hasan, Injamamul Ismail Shawon, Rubhana Raqib
11(1); Springer Nature Publishing Group, UK; Scientific Reports; page: 6263; March 2021

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 

A Datta, MJ Alam, L Khaleda, M Al-Forkan
Toxicology Reports, 8 (30-37); Elsevier Scientific Publishers, Ireland; page: 30-37; December 2020

Abstract: 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

L Khaleda, B Rudra, II Shawon, MJ Alam, A Datta, M Al-Forkan
The Chittagong University Journal of Biological Sciences 9 (1 & 2), 39-48, 2020; University of Chittagong, Bangladesh; page: 39-48; November 2020

Abstract: 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.

L Khaleda, B Rudra, II Shawon, MJ Alam, M Al-Forkan
The Chittagong University Journal of Biological Sciences 9 (1 & 2), 29-38, 2020; University of Chittagong, Bangladesh; page: 29-38; November 2020

Abstract: 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.

L Khaleda, M Al-Forkan, FB Wali, MJ Alam, A Datta, II Shawon, N Hosain, ...
Bangladesh Medical Research Council Bulletin 45 (1), 3-10, 2019; Bangladesh Medical Research Council, Bangladesh; page: 3-10; June 2019

Abstract: 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

AM Habib, MJ Alam, B Rudra, MA Quader, M Al-forkan
Malaysian Journal of Microbiology 13 (1), 33-40, 2017; Malaysian Society for Microbiology, Malaysia; page: 33-40; March 2017

Abstract: 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.

AM Habib, J Alam, B Rudra, A Quader, M Al-Forkan
Microbiology insights 9, MBI. S39858, 2016; SAGE Publishing, United Kingdom; page: 47-50; November 2016

Abstract: 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.

SMI Hosen, D Das, R Kobi, MJ Alam, B Rudra, MA Bakar, S Islam, ...
BMC Pharmacology and Toxicology 17 (1), 46, 2016; BioMed Central Ltd., United Kingdom; October 2016

Abstract: 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. Conclusion: Arsenic accumulation in different parts of rice increased dose-dependently. Hence, for irrigation purpose arsenic contaminated water cannot be used. Furthermore, arsenic contaminated rice induced several toxicities in animal model, most of which could be minimized with the food supplementation of Corchorus olitorius leaves. Therefore, Corchorus olitorius can be used as a potential food supplement to the affected people of arsenic prone zone to ensure the food security.

SMI Hosen, R Kobi, D Das, DUS Chowdhury, MJ Alam, B Rudra, ...
Canadian Journal of Pure and Applied Sciences 10 (2), 3873-3881, 2016; SENRA Academic Publishers, British Columbia, Canada; page: 3873-3881; June 2016

Abstract: 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

KUM Ashraf, P Barua, A Saha, N Muhammad, J Ferdoush, D Das, ...
Journal of Young Pharmacists 6 (2), 35-43, 2014; EManuscript Services; page: 35-43; May 2014

Abstract: 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 hours after the snake bite. Antigenecity of this protein was determined by Hopp & Woods and Kolaskar & Tangaonkar method. We predicted MHC class I and MHC class II binding peptides of antigenic protein from alpha-delta-bungarotoxin-4 which are important determinant for protection of host from snake bite. Fragments selected through this study revealed higher efficiency binders. As a 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 specific 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 non-allergen. The potential epitopes of alpha-delta-bungarotoxin-4 were found to be located at sequences “GENLCYTKM” and “FCSSRGKVI” and these were found to be sufficient 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. So 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.

MJ Alam, KUM Ashraf
Toxicology international 20 (3), 235, 2013; The Society of Toxicology, India; page: 235-253; December 2013

Abstract: 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

A Hasan, M Hossain, J Alam
Bioinformatics and Biology insights 7, BBI. S13402, 2013; SAGE Publishing, United Kingdom; page: 347-355; November 2013

Abstract: 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.

MJ Alam, KUM Ashraf, SD Gupta, MAK Emon
Int. J. Comput. Bioinfo. Silic. Model 2, 186-198, 2013; AIZEON Publishers, India; page: 186-198; August 2013

Abstract: Potato virus Y (PVY) is one of the most prevalent and important viruses that affect potatoes. The virus can beacquired from the infected plant within seconds, and transmitted to a healthy plant just as fast. PVY can also betransmitted mechanically by machinery, tools, and damaging plants while walking through the field. Its strainscan interact with other potato viruses such as Potato virus A (PVA) and Potato virus X (PVX) to result in heavierlosses. As PVY is a non-persistent virus so the use of insecticides to control spread is generally not effective. Thebest strategy to control PVY is to use seed potatoes certified to have low virus content. Analysis showed thatpeptide fragments of this antigenic coat protein of Potato Y virus contain 203 amino acids which point out 195nonamers. These nonamers can be focused for designing a sero-diagnostic tool to detect PVY infection. Byanalyzing antigenecity, hydrophilicity, solvent accessibility and exposed surface area, we found the locationpotential 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, thehigh affinity TAP transporter peptide regions were found which were predicted by using cascade Support VectorMachine (SVM) and Position Specific Scoring Matrices (PSSM). These high efficiency binding fragments are foundto tightly bind to the HLA receptors by in silico molecular docking and therefore, be used in cross protection andto develop host specific antibodies. We Predicted MHC class-I and class-II binding peptides of antigen proteinfrom Potato Y virus which can be important determinant in sero-diagnostic issue. Besides, we operatedAllerHunter for predicting allergenicity and it predicted Potato Y virus as non allergen protein with significantscores based on the structural and physicochemical properties of whole protein. Although the computationalpredictions made here are based on concrete confidence hence we have developed a hypothetical immunizationbased detection tool which demands more validation and in vivo experiments to validate such in silico approaches.

A Saha, MJ Alam, KUM Ashraf, A Mannan
Bioinformation 9 (1), 42-48, 2013; Biomedical Informatics, India; page: 42-48; January 2013

Abstract: 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.

MJ Alam, M Rahman, HR Bhuiyan, S Islam, L Khaleda and M Al-Forkan
Annual Plant Tissue Culture & Biotechnology Conference 2015; Bangladesh Association for Plant Tissue Culture and Biotechnology (BAPTC&B); page: 11; November 2015

Annual Plant Tissue Culture & Biotechnology Conference 2015, 13-14 November 2015, Hotel Sea Palace, Cox's Bazar, Bangladesh.