Additional file 3: Supplementary File 3. Structural quality reports of Mutant PLPros. The structu... more Additional file 3: Supplementary File 3. Structural quality reports of Mutant PLPros. The structural quality reports of V843F, A889V and A889V evaluated by RAMPAGE, MolProbity, ERRAT and PROVE.
Additional file 1: Supplementary File 1. Parameters for Molecular Docking. The number of Points i... more Additional file 1: Supplementary File 1. Parameters for Molecular Docking. The number of Points in Dimension, Spacing (Angstrom) and Center Grid Box values that were taken during the molecular docking of Wild type/ Mutant PLPros and GRL0617.
Additional file 2: Supplementary File 2. Effect of the Mutations in NSP1 Protein Stability, Funct... more Additional file 2: Supplementary File 2. Effect of the Mutations in NSP1 Protein Stability, Function and Structure. MUpro, PROVEAN and HOPE results for mutant L122I NSP1.
Additional file 4: Supplementary File 4. Sanger Sequencing Reads for Wild Type and Mutant SARS-Co... more Additional file 4: Supplementary File 4. Sanger Sequencing Reads for Wild Type and Mutant SARS-CoV-2 PLPro. Sequencing Reads of SARS-CoV-2 PLPro V843 coding regions for both Wild type and Mutant isolates. Around 29% samples showed G → T transversion or V843F substitution.
As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like... more As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of Mid-June 2021, over 1500 SARS-CoV-2 genomes have been sequenced across the country. From our analyses, it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%). Wave-2 samples also had a higher frequency of deletion, and transversion events. During the first wave, the GR clade was the most predominant but it was replaced by the GH clade in the latter wave. The B.1.1.25 variant showed the highest frequency in wave-1 while in case of wave-2, the B.1.351.3 variant, was the most common one. A notable presence of the delta vari...
Coronavirus disease-19 (COVID-19) caused by SARS-CoV-2 has already killed more than one million p... more Coronavirus disease-19 (COVID-19) caused by SARS-CoV-2 has already killed more than one million people worldwide. Since novel coronavirus is a new virus, mining its genome sequence is of crucial importance for drug/vaccine(s) development. Whole genome sequencing is a helpful tool in identifying genetic changes that occur in a virus when it spreads through the population. In this study, we performed complete genome sequencing of SARS-CoV-2 to unveil the genomic variation and indel, if present. We discovered thirteen (13) mutations in Orf1ab, S and N gene where seven (7) of them turned out to be novel mutations from our sequenced isolate. Besides, we found one (1) insertion and seven (7) deletions from the indel analysis among the 323 Bangladeshi isolates. However, the indel did not show any effect on proteins. Our energy minimization analysis showed both stabilizing and destabilizing impact on viral proteins depending on the mutation. Interestingly, all the variants were located in the binding site of the proteins. Furthermore, drug binding analysis revealed marked difference in interacting residues in mutants when compared to the wild type. Our analysis also suggested that eleven (11) mutations could exert damaging effects on their corresponding protein structures. irritation prompting sepsis, 22-25 intense cardiovascular injury, 26-31 cardiovascular breakdown 26,32-35 and multiorgan failure in critical patients. 36 COVID-19 has been rightly announced as a global pandemic by the World Health Organization (WHO) as it has spanned over 200 countries and territories around the world. 37-42 Coronaviruses (CoVs) are enveloped, single-stranded, (+) RNA viruses that are pathogenic to their hosts. 43-47 SARS-CoV-2 is the causative agent behind COVID-19 and is more pathogenic in contrast with previously observed SARS-CoV (2002) and Middle East respiratory syndrome coronavirus (MERS-CoV, 2013). 48-57 There is a dire need to examine the virus more comprehensively to analyze the pathogenesis, its destructiveness and development of powerful therapeutic measures. 58 CoVs belongs to the Coronaviridae family under Nidovirales order. They have been grouped into four genera that belong to a-, b-, g-, and d-coronaviruses. 59 Among them, a-and b-COVs infect vertebrates, g-coronaviruses avians, while the d-coronaviruses infect both. SARS-CoV, mouse hepatitis coronavirus (MHV), MERS-CoV, Bovine coronavirus (BCoV), bat coronavirus HKU4, and human coronavirus OC43, including SARS-CoV-2, are b-coronaviruses. 60 Zoonotic transmission is the medium of transmission for each of the three CoVs, SARS-, MERS-, and SARS-CoV-2, and they spread through close contact. The essential multiplication number (R 0) of the individual-to
Diabetes is a chronic metabolic disorder triggered by disturbances in carbohydrate, protein, and ... more Diabetes is a chronic metabolic disorder triggered by disturbances in carbohydrate, protein, and lipid metabolisms, where either reduced secretion or sensitivity of insulin is observed coupled with poor glucose control. Date palm fruits are one of the fruits reported to have good potential in diabetes treatment due to its presence of polyphenols exerting strong antioxidant activities. Other possible mechanisms of action include the polyphenolic compounds, which can inhibit enzymes like α-amylase and α-glucosidase. Flavonoids in dates can stimulate β-cells by increasing the number of islets and β-cells, recovering endocrine pancreatic tissues, reducing β-cell apoptosis, activating insulin receptors following the increase in insulin secretion, in addition to improving diabetes-induced complications. In this review, the in vitro, in vivo, and human study-based evidence of date palm as an anti-diabetic fruit is summarised.
American Journal of Pure and Applied Biosciences, 2019
Rapeseed oil is one of the important and cheapest vegetable oil in Bangladesh and many other coun... more Rapeseed oil is one of the important and cheapest vegetable oil in Bangladesh and many other countries. It is commonly used as cooking oil in Bangladesh particularly in rural areas and also used as other food items. This study evaluated the physiological effects of four type’s rapeseeds namely Mustard (Wild), Mustard (hybrid), Rai (Wild), Rai (hybrid) oil on six strains of bacteria in addition to studying the effects of two varieties of rapeseeds oil Mustard (Wild) and Rai (hybrid) oil on Wistar rat’s organs including liver, kidney, heart and skeletal muscles. Firstly, we examined the effects of these Rapeseeds oil on bacteria and found that these Rapeseeds oils possess antibacterial activities. Six bacterial strains such as B. subtilis, S. lutea, X. campestris, E. coli, K. Pneumonia, P. denitrificans was used to test the effect of these rapeseeds oil and observed that rapeseed oil showed inhibition against tested microorganisms in a concentration-dependent manner. Finally, the effe...
The in vitro antibacterial activity of different extracts of Cissus quadrangularis Linn (Vitaceae... more The in vitro antibacterial activity of different extracts of Cissus quadrangularis Linn (Vitaceae) against some Gram-negative and Gram-positive bacteria, were investigated. The methanol and ethyl acetate extract showed high activity against the bacteria tested.
experimental evidence suggests a causal role of serum uric acid (sUA) in hypertension development... more experimental evidence suggests a causal role of serum uric acid (sUA) in hypertension development. Currently, there are few data available on the association between sUA and hypertension; data from Bangladeshi adults are not available yet. this study evaluated the association of sUA with hypertension among Bangladeshi adults. Blood samples were obtained from 140 males and 115 females and analyzed for SUA and lipid levels. Hypertension was defined as SBP ≥ 140 mmHg and/ or DBp ≥ 90 mmHg. All participants were divided into four quartiles based on SUA concentrations. Association of sUA with hypertension was evaluated by logistic regression models. the prevalence of hypertension and prehypertension was significantly higher in male (15.4 and 47.6%, respectively) than in the female (5.6 and 33.4%, respectively) subjects (p < 0.01). Males had a higher mean level of SUA (310.7 ± 67.9 µmol/L) than in the females (255.3 ± 69.3 µmol/L) (p < 0.001). Hyperuricemia was prevalent 9.1% in males and 10.3% in females. An increasing trend for hypertension and prehypertension was found in both genders with increasing sUA levels in the quartiles (p < 0.01). SUA levels in the quartiles were positively correlated with blood pressure (p < 0.01). After adjusting for baseline covariates, SUA levels were significantly associated with hypertension (p < 0.01). Findings of this study indicate the significance of maintaining normal SUA level to prevent hypertension.
Background Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiologic agent of c... more Background Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiologic agent of coronavirus disease 2019 (COVID-19), is rapidly acquiring new mutations. Analysis of these mutations is necessary for gaining knowledge regarding different aspects of therapeutic development. Previously, we have reported a Sanger method-based genome sequence of a viral isolate named SARS-CoV-2 NIB-1, circulating in Bangladesh. The genome has four novel non-synonymous mutations in V121D, V843F, A889V, and G1691C positions. Results Using different computational tools, we have found V121D substitution has the potential to destabilize the non-structural protein-1 (NSP-1). NSP-1 inactivates the type-1 interferon-induced antiviral system. Hence, this mutant could be a basis of attenuated vaccines against SARS-CoV-2. V843F, A889V, and G1691C are all located in nonstructural protein-3 (NSP-3). G1691C can decrease the flexibility of the protein. V843F and A889V might change the binding pattern and...
Diabetes is a chronic metabolic disorder triggered by disturbances in carbohydrate, protein, and ... more Diabetes is a chronic metabolic disorder triggered by disturbances in carbohydrate, protein, and lipid metabolisms, where either reduced secretion or sensitivity of insulin is observed coupled with poor glucose control. Date palm fruits are one of the fruits reported to have good potential in diabetes treatment due to its presence of polyphenols exerting strong antioxidant activities. Other possible mechanisms of action include the polyphenolic compounds, which can inhibit enzymes like α-amylase and α-glucosidase. Flavonoids in dates can stimulate β-cells by increasing the number of islets and β-cells, recovering endocrine pancreatic tissues, reducing β-cell apoptosis, activating insulin receptors following the increase in insulin secretion, in addition to improving diabetes-induced complications. In this review, the in vitro, in vivo, and human study-based evidence of date palm as an anti-diabetic fruit is summarised.
American Journal of Pure and Applied Biosciences, 2019
Rapeseed oil is one of the important and cheapest vegetable oil in Bangladesh and many other coun... more Rapeseed oil is one of the important and cheapest vegetable oil in Bangladesh and many other countries. It is commonly used as cooking oil in Bangladesh particularly in rural areas and also used as other food items. This study evaluated the physiological effects of four type’s rapeseeds namely Mustard (Wild), Mustard (hybrid), Rai (Wild), Rai (hybrid) oil on six strains of bacteria in addition to studying the effects of two varieties of rapeseeds oil Mustard (Wild) and Rai (hybrid) oil on Wistar rat’s organs including liver, kidney, heart and skeletal muscles. Firstly, we examined the effects of these Rapeseeds oil on bacteria and found that these Rapeseeds oils possess antibacterial activities. Six bacterial strains such as B. subtilis, S. lutea, X. campestris, E. coli, K. Pneumonia, P. denitrificans was used to test the effect of these rapeseeds oil and observed that rapeseed oil showed inhibition against tested microorganisms in a concentration-dependent manner. Finally, the effects of oil obtained from these two varieties were investigated after feeding rats for 8 weeks. Male Wistar rats were divided into three groups, each group contains 4 rats. Group A was considered as control diet group, while Group B was mustard (Wild) oil group and Group C was Rai (hybrid) oil group. Group A was containing 0.6 gram oil plus 14.4gm diet. We found that rats of both experimental groups exhibit weight loss, reduction of food efficiency ratio and increase cardiac and hepatic enzymes including CK-MB, ALP, SGPT and SGOT compared to the rats fed controlled diet. Furthermore, we also found that the body weight loss, food efficiency ratio markedly decreased and tested enzymes increased in rats fed Mustard (Wild) oil compared to rat fed Rai (hybrid) oil.
Additional file 3: Supplementary File 3. Structural quality reports of Mutant PLPros. The structu... more Additional file 3: Supplementary File 3. Structural quality reports of Mutant PLPros. The structural quality reports of V843F, A889V and A889V evaluated by RAMPAGE, MolProbity, ERRAT and PROVE.
Additional file 1: Supplementary File 1. Parameters for Molecular Docking. The number of Points i... more Additional file 1: Supplementary File 1. Parameters for Molecular Docking. The number of Points in Dimension, Spacing (Angstrom) and Center Grid Box values that were taken during the molecular docking of Wild type/ Mutant PLPros and GRL0617.
Additional file 2: Supplementary File 2. Effect of the Mutations in NSP1 Protein Stability, Funct... more Additional file 2: Supplementary File 2. Effect of the Mutations in NSP1 Protein Stability, Function and Structure. MUpro, PROVEAN and HOPE results for mutant L122I NSP1.
Additional file 4: Supplementary File 4. Sanger Sequencing Reads for Wild Type and Mutant SARS-Co... more Additional file 4: Supplementary File 4. Sanger Sequencing Reads for Wild Type and Mutant SARS-CoV-2 PLPro. Sequencing Reads of SARS-CoV-2 PLPro V843 coding regions for both Wild type and Mutant isolates. Around 29% samples showed G → T transversion or V843F substitution.
As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like... more As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of Mid-June 2021, over 1500 SARS-CoV-2 genomes have been sequenced across the country. From our analyses, it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%). Wave-2 samples also had a higher frequency of deletion, and transversion events. During the first wave, the GR clade was the most predominant but it was replaced by the GH clade in the latter wave. The B.1.1.25 variant showed the highest frequency in wave-1 while in case of wave-2, the B.1.351.3 variant, was the most common one. A notable presence of the delta vari...
Coronavirus disease-19 (COVID-19) caused by SARS-CoV-2 has already killed more than one million p... more Coronavirus disease-19 (COVID-19) caused by SARS-CoV-2 has already killed more than one million people worldwide. Since novel coronavirus is a new virus, mining its genome sequence is of crucial importance for drug/vaccine(s) development. Whole genome sequencing is a helpful tool in identifying genetic changes that occur in a virus when it spreads through the population. In this study, we performed complete genome sequencing of SARS-CoV-2 to unveil the genomic variation and indel, if present. We discovered thirteen (13) mutations in Orf1ab, S and N gene where seven (7) of them turned out to be novel mutations from our sequenced isolate. Besides, we found one (1) insertion and seven (7) deletions from the indel analysis among the 323 Bangladeshi isolates. However, the indel did not show any effect on proteins. Our energy minimization analysis showed both stabilizing and destabilizing impact on viral proteins depending on the mutation. Interestingly, all the variants were located in the binding site of the proteins. Furthermore, drug binding analysis revealed marked difference in interacting residues in mutants when compared to the wild type. Our analysis also suggested that eleven (11) mutations could exert damaging effects on their corresponding protein structures. irritation prompting sepsis, 22-25 intense cardiovascular injury, 26-31 cardiovascular breakdown 26,32-35 and multiorgan failure in critical patients. 36 COVID-19 has been rightly announced as a global pandemic by the World Health Organization (WHO) as it has spanned over 200 countries and territories around the world. 37-42 Coronaviruses (CoVs) are enveloped, single-stranded, (+) RNA viruses that are pathogenic to their hosts. 43-47 SARS-CoV-2 is the causative agent behind COVID-19 and is more pathogenic in contrast with previously observed SARS-CoV (2002) and Middle East respiratory syndrome coronavirus (MERS-CoV, 2013). 48-57 There is a dire need to examine the virus more comprehensively to analyze the pathogenesis, its destructiveness and development of powerful therapeutic measures. 58 CoVs belongs to the Coronaviridae family under Nidovirales order. They have been grouped into four genera that belong to a-, b-, g-, and d-coronaviruses. 59 Among them, a-and b-COVs infect vertebrates, g-coronaviruses avians, while the d-coronaviruses infect both. SARS-CoV, mouse hepatitis coronavirus (MHV), MERS-CoV, Bovine coronavirus (BCoV), bat coronavirus HKU4, and human coronavirus OC43, including SARS-CoV-2, are b-coronaviruses. 60 Zoonotic transmission is the medium of transmission for each of the three CoVs, SARS-, MERS-, and SARS-CoV-2, and they spread through close contact. The essential multiplication number (R 0) of the individual-to
Diabetes is a chronic metabolic disorder triggered by disturbances in carbohydrate, protein, and ... more Diabetes is a chronic metabolic disorder triggered by disturbances in carbohydrate, protein, and lipid metabolisms, where either reduced secretion or sensitivity of insulin is observed coupled with poor glucose control. Date palm fruits are one of the fruits reported to have good potential in diabetes treatment due to its presence of polyphenols exerting strong antioxidant activities. Other possible mechanisms of action include the polyphenolic compounds, which can inhibit enzymes like α-amylase and α-glucosidase. Flavonoids in dates can stimulate β-cells by increasing the number of islets and β-cells, recovering endocrine pancreatic tissues, reducing β-cell apoptosis, activating insulin receptors following the increase in insulin secretion, in addition to improving diabetes-induced complications. In this review, the in vitro, in vivo, and human study-based evidence of date palm as an anti-diabetic fruit is summarised.
American Journal of Pure and Applied Biosciences, 2019
Rapeseed oil is one of the important and cheapest vegetable oil in Bangladesh and many other coun... more Rapeseed oil is one of the important and cheapest vegetable oil in Bangladesh and many other countries. It is commonly used as cooking oil in Bangladesh particularly in rural areas and also used as other food items. This study evaluated the physiological effects of four type’s rapeseeds namely Mustard (Wild), Mustard (hybrid), Rai (Wild), Rai (hybrid) oil on six strains of bacteria in addition to studying the effects of two varieties of rapeseeds oil Mustard (Wild) and Rai (hybrid) oil on Wistar rat’s organs including liver, kidney, heart and skeletal muscles. Firstly, we examined the effects of these Rapeseeds oil on bacteria and found that these Rapeseeds oils possess antibacterial activities. Six bacterial strains such as B. subtilis, S. lutea, X. campestris, E. coli, K. Pneumonia, P. denitrificans was used to test the effect of these rapeseeds oil and observed that rapeseed oil showed inhibition against tested microorganisms in a concentration-dependent manner. Finally, the effe...
The in vitro antibacterial activity of different extracts of Cissus quadrangularis Linn (Vitaceae... more The in vitro antibacterial activity of different extracts of Cissus quadrangularis Linn (Vitaceae) against some Gram-negative and Gram-positive bacteria, were investigated. The methanol and ethyl acetate extract showed high activity against the bacteria tested.
experimental evidence suggests a causal role of serum uric acid (sUA) in hypertension development... more experimental evidence suggests a causal role of serum uric acid (sUA) in hypertension development. Currently, there are few data available on the association between sUA and hypertension; data from Bangladeshi adults are not available yet. this study evaluated the association of sUA with hypertension among Bangladeshi adults. Blood samples were obtained from 140 males and 115 females and analyzed for SUA and lipid levels. Hypertension was defined as SBP ≥ 140 mmHg and/ or DBp ≥ 90 mmHg. All participants were divided into four quartiles based on SUA concentrations. Association of sUA with hypertension was evaluated by logistic regression models. the prevalence of hypertension and prehypertension was significantly higher in male (15.4 and 47.6%, respectively) than in the female (5.6 and 33.4%, respectively) subjects (p < 0.01). Males had a higher mean level of SUA (310.7 ± 67.9 µmol/L) than in the females (255.3 ± 69.3 µmol/L) (p < 0.001). Hyperuricemia was prevalent 9.1% in males and 10.3% in females. An increasing trend for hypertension and prehypertension was found in both genders with increasing sUA levels in the quartiles (p < 0.01). SUA levels in the quartiles were positively correlated with blood pressure (p < 0.01). After adjusting for baseline covariates, SUA levels were significantly associated with hypertension (p < 0.01). Findings of this study indicate the significance of maintaining normal SUA level to prevent hypertension.
Background Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiologic agent of c... more Background Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiologic agent of coronavirus disease 2019 (COVID-19), is rapidly acquiring new mutations. Analysis of these mutations is necessary for gaining knowledge regarding different aspects of therapeutic development. Previously, we have reported a Sanger method-based genome sequence of a viral isolate named SARS-CoV-2 NIB-1, circulating in Bangladesh. The genome has four novel non-synonymous mutations in V121D, V843F, A889V, and G1691C positions. Results Using different computational tools, we have found V121D substitution has the potential to destabilize the non-structural protein-1 (NSP-1). NSP-1 inactivates the type-1 interferon-induced antiviral system. Hence, this mutant could be a basis of attenuated vaccines against SARS-CoV-2. V843F, A889V, and G1691C are all located in nonstructural protein-3 (NSP-3). G1691C can decrease the flexibility of the protein. V843F and A889V might change the binding pattern and...
Diabetes is a chronic metabolic disorder triggered by disturbances in carbohydrate, protein, and ... more Diabetes is a chronic metabolic disorder triggered by disturbances in carbohydrate, protein, and lipid metabolisms, where either reduced secretion or sensitivity of insulin is observed coupled with poor glucose control. Date palm fruits are one of the fruits reported to have good potential in diabetes treatment due to its presence of polyphenols exerting strong antioxidant activities. Other possible mechanisms of action include the polyphenolic compounds, which can inhibit enzymes like α-amylase and α-glucosidase. Flavonoids in dates can stimulate β-cells by increasing the number of islets and β-cells, recovering endocrine pancreatic tissues, reducing β-cell apoptosis, activating insulin receptors following the increase in insulin secretion, in addition to improving diabetes-induced complications. In this review, the in vitro, in vivo, and human study-based evidence of date palm as an anti-diabetic fruit is summarised.
American Journal of Pure and Applied Biosciences, 2019
Rapeseed oil is one of the important and cheapest vegetable oil in Bangladesh and many other coun... more Rapeseed oil is one of the important and cheapest vegetable oil in Bangladesh and many other countries. It is commonly used as cooking oil in Bangladesh particularly in rural areas and also used as other food items. This study evaluated the physiological effects of four type’s rapeseeds namely Mustard (Wild), Mustard (hybrid), Rai (Wild), Rai (hybrid) oil on six strains of bacteria in addition to studying the effects of two varieties of rapeseeds oil Mustard (Wild) and Rai (hybrid) oil on Wistar rat’s organs including liver, kidney, heart and skeletal muscles. Firstly, we examined the effects of these Rapeseeds oil on bacteria and found that these Rapeseeds oils possess antibacterial activities. Six bacterial strains such as B. subtilis, S. lutea, X. campestris, E. coli, K. Pneumonia, P. denitrificans was used to test the effect of these rapeseeds oil and observed that rapeseed oil showed inhibition against tested microorganisms in a concentration-dependent manner. Finally, the effects of oil obtained from these two varieties were investigated after feeding rats for 8 weeks. Male Wistar rats were divided into three groups, each group contains 4 rats. Group A was considered as control diet group, while Group B was mustard (Wild) oil group and Group C was Rai (hybrid) oil group. Group A was containing 0.6 gram oil plus 14.4gm diet. We found that rats of both experimental groups exhibit weight loss, reduction of food efficiency ratio and increase cardiac and hepatic enzymes including CK-MB, ALP, SGPT and SGOT compared to the rats fed controlled diet. Furthermore, we also found that the body weight loss, food efficiency ratio markedly decreased and tested enzymes increased in rats fed Mustard (Wild) oil compared to rat fed Rai (hybrid) oil.
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