Pub Date : 2020-07-31DOI: 10.54987/jobimb.v8i1.506
Abdalla A. M. Ali, Atef Mohammed Ebraheem, A. Mohammed
Bacterial isolate MAK4 was isolated from brown algae collected from the coastal area of the Red sea, Hurghada, Egypt and confirmed for alginate lyase production by halo formation around the colonies after flooding with cetylpyridinium chloride or Gram’s iodine. Isolate MAK4 was identified according to morphological, biochemical and phylogenetic identification through 16s rRNA. The bacterial isolate was tentatively identified as Martelella sp. strain MAK4. It is aerobic, mesophilic, Gram–ve, non-spore forming nonmotile, rod-shaped organism and produces catalase and oxidase. PCR was performed for alginate lyase gene using two pairs of degenerate primers. The alginate lyase enzyme was isolated and purified from the culture medium by ammonium sulfate precipitation, Sephadex G-100 and DEAE-Cellulose chromatography. The isolated enzyme has a specific activity of 62.9 u/mg, 6.15 purification folds and has a molecular weight of 35 kDa. The alginate lyase enzyme showed highest activity at 37 °C and at pH 7. The enzyme was stable over the pH range 6 to 9 and retained 80% of its activity after incubation at 40 °C for 90 min. The enzyme was active in the absence of metal ions, but the activity was enhanced by the addition of NaCl, KCl and Ca2+. The activity was lost with the addition of EDTA. The enzyme activity was strongly decreased in the presence of Cu2+, Zn2+, Co2+, Hg2+ and Mn2+. This novel bifunctional alginate lyase has the potential to be used in the eradication of resistant bacterial biofilm in clinical samples and production of alginate oligosaccharides in industry.
{"title":"Purification, Characterization and Sequencing of Alginate Lyase from Martelella sp. strain MAK4","authors":"Abdalla A. M. Ali, Atef Mohammed Ebraheem, A. Mohammed","doi":"10.54987/jobimb.v8i1.506","DOIUrl":"https://doi.org/10.54987/jobimb.v8i1.506","url":null,"abstract":"Bacterial isolate MAK4 was isolated from brown algae collected from the coastal area of the Red sea, Hurghada, Egypt and confirmed for alginate lyase production by halo formation around the colonies after flooding with cetylpyridinium chloride or Gram’s iodine. Isolate MAK4 was identified according to morphological, biochemical and phylogenetic identification through 16s rRNA. The bacterial isolate was tentatively identified as Martelella sp. strain MAK4. It is aerobic, mesophilic, Gram–ve, non-spore forming nonmotile, rod-shaped organism and produces catalase and oxidase. PCR was performed for alginate lyase gene using two pairs of degenerate primers. The alginate lyase enzyme was isolated and purified from the culture medium by ammonium sulfate precipitation, Sephadex G-100 and DEAE-Cellulose chromatography. The isolated enzyme has a specific activity of 62.9 u/mg, 6.15 purification folds and has a molecular weight of 35 kDa. The alginate lyase enzyme showed highest activity at 37 °C and at pH 7. The enzyme was stable over the pH range 6 to 9 and retained 80% of its activity after incubation at 40 °C for 90 min. The enzyme was active in the absence of metal ions, but the activity was enhanced by the addition of NaCl, KCl and Ca2+. The activity was lost with the addition of EDTA. The enzyme activity was strongly decreased in the presence of Cu2+, Zn2+, Co2+, Hg2+ and Mn2+. This novel bifunctional alginate lyase has the potential to be used in the eradication of resistant bacterial biofilm in clinical samples and production of alginate oligosaccharides in industry.","PeriodicalId":15132,"journal":{"name":"Journal of Biochemistry, Microbiology and Biotechnology","volume":"418 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78108889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-07-31DOI: 10.54987/jobimb.v8i1.505
A. Alhassan, A. Babandi, G. Uba, H. Yakasai
Microbial heavy metals reduction has an important role in the biological system and in environmental metals recycling to remove its toxic effects in soil and wastewater. A molybdenum-reducing bacterium with the potential to reduce toxic hexavalent molybdenum to colloidal molybdenum blue (Mo-blue) was isolated from agricultural land in Northwest-Nigeria. The Gram’s stain and microscopic examination reveal that the isolate is a Gram-negative, however, phylogenetic analysis of the 16S rRNA identifies the isolate as Pseudomonas sp. Molybdenum reduction in this bacterium is optimally supported by glucose at 1.0% (w/v). The optimum phosphate and molybdate concentrations supporting molybdate reduction were between 3.5 and 7.5 mM for phosphate and 100 mM molybdate. Molybdate reduction is optimum at 37 ᵒC and pH between 6.5 and 7.5. The capacity of this isolate to reduce toxic molybdenum to a less toxic form is novel and makes the bacterium an important instrument for bioremediation of this pollutant.
{"title":"Isolation and Characterization of Molybdenum-reducing Pseudomonas sp. from Agricultural Land in Northwest-Nigeria","authors":"A. Alhassan, A. Babandi, G. Uba, H. Yakasai","doi":"10.54987/jobimb.v8i1.505","DOIUrl":"https://doi.org/10.54987/jobimb.v8i1.505","url":null,"abstract":"Microbial heavy metals reduction has an important role in the biological system and in environmental metals recycling to remove its toxic effects in soil and wastewater. A molybdenum-reducing bacterium with the potential to reduce toxic hexavalent molybdenum to colloidal molybdenum blue (Mo-blue) was isolated from agricultural land in Northwest-Nigeria. The Gram’s stain and microscopic examination reveal that the isolate is a Gram-negative, however, phylogenetic analysis of the 16S rRNA identifies the isolate as Pseudomonas sp. Molybdenum reduction in this bacterium is optimally supported by glucose at 1.0% (w/v). The optimum phosphate and molybdate concentrations supporting molybdate reduction were between 3.5 and 7.5 mM for phosphate and 100 mM molybdate. Molybdate reduction is optimum at 37 ᵒC and pH between 6.5 and 7.5. The capacity of this isolate to reduce toxic molybdenum to a less toxic form is novel and makes the bacterium an important instrument for bioremediation of this pollutant.","PeriodicalId":15132,"journal":{"name":"Journal of Biochemistry, Microbiology and Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89604906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-07-31DOI: 10.54987/jobimb.v8i1.502
Alhassan Ahmad Siddan, S. Abubakar, A. Gadanya, F. U. Maigari, AbdulRazaq Sani Yahaya, M. Yarima
Proximate, minerals, vitamins, amino acids composition and phytochemicals of Moringa oleifera and Arachis hypogaea were investigated. The parameters evaluated were moisture contents; ash contents; crude protein; crude lipids; crude fiber; carbohydrates; mineral ions; vitamins; amino acids and phytochemicals. The results obtained showed that, all the proximate parameters, vitamins; A, C and E, all the phytochemical parameters and minerals; sodium and potassium are significantly different (p<0.05) while no significant different at p<0.05 was found in the amount of magnesium, potassium, iron, calcium and copper in M. oleifera and A. hypogaea. High caloric value was found in A. hypogaea while high amount of vitamin A and C were found in M. oleifera. Also, phytochemicals such as flavonoids and steroids were found in A. hypogaea at high amount. Eighteen amino acids were detected in both the M. oleifera and A. hypogaea. Glutamic acid, aspartic acid, leucine, arginine, valine, proline were present at high concentration in both the two samples.
{"title":"Determination of Nutrients and Anti-Nutrients Contents of Moringa oleifera and Arachis hypogaea","authors":"Alhassan Ahmad Siddan, S. Abubakar, A. Gadanya, F. U. Maigari, AbdulRazaq Sani Yahaya, M. Yarima","doi":"10.54987/jobimb.v8i1.502","DOIUrl":"https://doi.org/10.54987/jobimb.v8i1.502","url":null,"abstract":"Proximate, minerals, vitamins, amino acids composition and phytochemicals of Moringa oleifera and Arachis hypogaea were investigated. The parameters evaluated were moisture contents; ash contents; crude protein; crude lipids; crude fiber; carbohydrates; mineral ions; vitamins; amino acids and phytochemicals. The results obtained showed that, all the proximate parameters, vitamins; A, C and E, all the phytochemical parameters and minerals; sodium and potassium are significantly different (p<0.05) while no significant different at p<0.05 was found in the amount of magnesium, potassium, iron, calcium and copper in M. oleifera and A. hypogaea. High caloric value was found in A. hypogaea while high amount of vitamin A and C were found in M. oleifera. Also, phytochemicals such as flavonoids and steroids were found in A. hypogaea at high amount. Eighteen amino acids were detected in both the M. oleifera and A. hypogaea. Glutamic acid, aspartic acid, leucine, arginine, valine, proline were present at high concentration in both the two samples.","PeriodicalId":15132,"journal":{"name":"Journal of Biochemistry, Microbiology and Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80800572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-07-31DOI: 10.54987/jobimb.v8i1.503
G. Uba, H. Yakasai, Abdussamad Abubakar
Synthetic chemicals are extremely harmful, particularly those man-made ones. Models are used to describe the behavior of microorganisms under different physical or chemical conditions such as temperature, pH, and water activity. Phenol is one of the potentially hazardous synthetic industrial contaminants capable of causing deteriorating effects in humans. In this paper, for the first time we present different kinetics models such as Von Bertalanffy, Baranyi-Roberts, modified Schnute, modified Richards, modified Gompertz, modified Logistics and the most recent Huang were used to get values for the above kinetic constants or parameters from simultaneous biodegradation of phenol from industrial effluents using immobilized Pseudomonas putida. All the curves present the best models with highest adjusted R2 value with the lowest RMSE and AICc value. The Accuracy and Bias Factors values were close to unity (1.0). Nearly all of the models best fit the curves indicating that Pseudomonas putida growth on phenol can be described mathematically the modelling parameters obtained can be utilized for predicting bioremediation of phenols in batch culture and perhaps in the future will be valuable in modelling growth eon industrial effluent containing phenol.
{"title":"Mathematical Modeling of The Biodegradation of Phenol from Industrial Effluents Using Immobilized Pseudomonas putida","authors":"G. Uba, H. Yakasai, Abdussamad Abubakar","doi":"10.54987/jobimb.v8i1.503","DOIUrl":"https://doi.org/10.54987/jobimb.v8i1.503","url":null,"abstract":"Synthetic chemicals are extremely harmful, particularly those man-made ones. Models are used to describe the behavior of microorganisms under different physical or chemical conditions such as temperature, pH, and water activity. Phenol is one of the potentially hazardous synthetic industrial contaminants capable of causing deteriorating effects in humans. In this paper, for the first time we present different kinetics models such as Von Bertalanffy, Baranyi-Roberts, modified Schnute, modified Richards, modified Gompertz, modified Logistics and the most recent Huang were used to get values for the above kinetic constants or parameters from simultaneous biodegradation of phenol from industrial effluents using immobilized Pseudomonas putida. All the curves present the best models with highest adjusted R2 value with the lowest RMSE and AICc value. The Accuracy and Bias Factors values were close to unity (1.0). Nearly all of the models best fit the curves indicating that Pseudomonas putida growth on phenol can be described mathematically the modelling parameters obtained can be utilized for predicting bioremediation of phenols in batch culture and perhaps in the future will be valuable in modelling growth eon industrial effluent containing phenol.","PeriodicalId":15132,"journal":{"name":"Journal of Biochemistry, Microbiology and Biotechnology","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74264405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-07-31DOI: 10.54987/jobimb.v8i1.501
Sulaiman Mohammed, Mohammed Jibrin Ndejiko, M. M. Usman, Y. Kaya, F. Huyop
Starch-branching enzymes (SBE) serves as the only enzyme generating glucan branches in green plants and consequently plays a significant role on the resulting starch final structure. Research on rice (Oryza sativa) SBE1 (OsSBE1) structural biology remain untapped. Therefore, there is a necessity for research on the enzyme molecular structure which could lead to the protein function annotation, starch production and energy booster drug design. Analysis of OsSBE1 secondary structure, domains and their interactions, enzyme 3D structure prediction and validation based on C-score were carried out. The OsSBE1 primary sequence was retrieved from GenBank and its secondary structure was predicted to be; α-helix (27.68%), extended strand (22.78%) and higher random coil (949.54%). Enzyme domains were found to be carbohydrate-binding module (CBM) 48 (isoamylase N-terminal domain), α-amylase catalytic domain and α-amylase C-terminal all-beta domain with active sites important amino acids asparagine and glutamic acid. From the five 3D models generated, model 3 displayed best prediction. The Ramachandran refinement has 97.3 amino acids residues in favoured region and 0.4 C-score. This bioinformatics study has elucidated on the OsSBE1 molecular model and first to report on its domain interaction.
{"title":"Molecular Modelling of Oryza sativa Starch-branching Enzyme 1","authors":"Sulaiman Mohammed, Mohammed Jibrin Ndejiko, M. M. Usman, Y. Kaya, F. Huyop","doi":"10.54987/jobimb.v8i1.501","DOIUrl":"https://doi.org/10.54987/jobimb.v8i1.501","url":null,"abstract":"Starch-branching enzymes (SBE) serves as the only enzyme generating glucan branches in green plants and consequently plays a significant role on the resulting starch final structure. Research on rice (Oryza sativa) SBE1 (OsSBE1) structural biology remain untapped. Therefore, there is a necessity for research on the enzyme molecular structure which could lead to the protein function annotation, starch production and energy booster drug design. Analysis of OsSBE1 secondary structure, domains and their interactions, enzyme 3D structure prediction and validation based on C-score were carried out. The OsSBE1 primary sequence was retrieved from GenBank and its secondary structure was predicted to be; α-helix (27.68%), extended strand (22.78%) and higher random coil (949.54%). Enzyme domains were found to be carbohydrate-binding module (CBM) 48 (isoamylase N-terminal domain), α-amylase catalytic domain and α-amylase C-terminal all-beta domain with active sites important amino acids asparagine and glutamic acid. From the five 3D models generated, model 3 displayed best prediction. The Ramachandran refinement has 97.3 amino acids residues in favoured region and 0.4 C-score. This bioinformatics study has elucidated on the OsSBE1 molecular model and first to report on its domain interaction.","PeriodicalId":15132,"journal":{"name":"Journal of Biochemistry, Microbiology and Biotechnology","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81055958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-07-31DOI: 10.54987/jobimb.v8i1.500
Xuan-Yi Sim, Waqas Ahmad, Yan-Fen Lee, Ying-Hui Teh, V. Murugaiyah, B. Ibrahim, P. Greimel, L. Gam
Diabetic is known to be the main non-commutable public health concern. In this study, we evaluated the relationship between diet, body weight and accumulation of adipose tissue in healthy, diabetic and prediabetic rats. Physiologically, adipose tissue plays a central role in lipid and glucose metabolisms. Therefore, accumulation of adipose tissue in diabetic and prediabetic may lead to others non-commutable diseases. The rats in control, diabetic and prediabetic groups were fed with normal and high fat diets for 6 consecutive weeks, while the rats in 4 sub-groups of diabetic and prediabetic groups also received metformin, a common drug to control diabetes. The results indicated that in diabetic rats, a small increase of food calories by high fat diet caused a significant gained in body weight and a significant increase in adipose tissue accumulation with or without metformin treatment, however in prediabetic rats, rats with metformin treatment shown to be beneficial in maintaining body weight and adipose accumulation. The data of the study imply that balance diet at high calories should be practiced by patients as high fat diet with similar calories can caused a significant health deterioration to the patients in term of body weight gained and adipose tissue accumulation.
{"title":"Weight Gain and Adipose Tissue Accumulation in Diabetic and Prediabetic Rats Fed with Palm Olein enriched High Fat Diet","authors":"Xuan-Yi Sim, Waqas Ahmad, Yan-Fen Lee, Ying-Hui Teh, V. Murugaiyah, B. Ibrahim, P. Greimel, L. Gam","doi":"10.54987/jobimb.v8i1.500","DOIUrl":"https://doi.org/10.54987/jobimb.v8i1.500","url":null,"abstract":"Diabetic is known to be the main non-commutable public health concern. In this study, we evaluated the relationship between diet, body weight and accumulation of adipose tissue in healthy, diabetic and prediabetic rats. Physiologically, adipose tissue plays a central role in lipid and glucose metabolisms. Therefore, accumulation of adipose tissue in diabetic and prediabetic may lead to others non-commutable diseases. The rats in control, diabetic and prediabetic groups were fed with normal and high fat diets for 6 consecutive weeks, while the rats in 4 sub-groups of diabetic and prediabetic groups also received metformin, a common drug to control diabetes. The results indicated that in diabetic rats, a small increase of food calories by high fat diet caused a significant gained in body weight and a significant increase in adipose tissue accumulation with or without metformin treatment, however in prediabetic rats, rats with metformin treatment shown to be beneficial in maintaining body weight and adipose accumulation. The data of the study imply that balance diet at high calories should be practiced by patients as high fat diet with similar calories can caused a significant health deterioration to the patients in term of body weight gained and adipose tissue accumulation.","PeriodicalId":15132,"journal":{"name":"Journal of Biochemistry, Microbiology and Biotechnology","volume":"2012 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73780727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-12-26DOI: 10.54987/jobimb.v7i2.476
Wan Nur Fadhilah Shamsudin, S. Loo, Y. Ho, N. Abdullah, W. Saad, K. Wan
Three lactic acid bacteria (LAB) isolates which demonstrated probiotic properties were obtained from chicken intestine. The isolates demonstrated good tolerance to acidic pH 3, 0.3% bile salts and strong adhesion to Caco-2 cells. These isolates also showed antagonistic activity against pathogenic E. coli (078:K80), Salmonella enterica serovar Typhimurium, C. perfringens (Type A), Salmonella enterica serovar Enteritidis, E. faecium (FM3), E. faecalis (E227). All three isolates had high inhibition zone (> 6 mm) against E. coli 078:K80 and Salmonella enterica serovar Typhimurium and were susceptible to antibiotics gentamicin, kanamycin, streptomycin, tetracycline, erythromycin, clindamycin, chloramphenicol and ampicillin. These isolates were identified by using 16S rRNA sequencing technique and as two L. salivarius and one L. reuteri with accession number MH375403, MH375402 and MH375404, respectively.
{"title":"Probiotic Properties of Lactobacillus Isolates from Chicken Intestines","authors":"Wan Nur Fadhilah Shamsudin, S. Loo, Y. Ho, N. Abdullah, W. Saad, K. Wan","doi":"10.54987/jobimb.v7i2.476","DOIUrl":"https://doi.org/10.54987/jobimb.v7i2.476","url":null,"abstract":"Three lactic acid bacteria (LAB) isolates which demonstrated probiotic properties were obtained from chicken intestine. The isolates demonstrated good tolerance to acidic pH 3, 0.3% bile salts and strong adhesion to Caco-2 cells. These isolates also showed antagonistic activity against pathogenic E. coli (078:K80), Salmonella enterica serovar Typhimurium, C. perfringens (Type A), Salmonella enterica serovar Enteritidis, E. faecium (FM3), E. faecalis (E227). All three isolates had high inhibition zone (> 6 mm) against E. coli 078:K80 and Salmonella enterica serovar Typhimurium and were susceptible to antibiotics gentamicin, kanamycin, streptomycin, tetracycline, erythromycin, clindamycin, chloramphenicol and ampicillin. These isolates were identified by using 16S rRNA sequencing technique and as two L. salivarius and one L. reuteri with accession number MH375403, MH375402 and MH375404, respectively.","PeriodicalId":15132,"journal":{"name":"Journal of Biochemistry, Microbiology and Biotechnology","volume":"238 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75845105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-12-26DOI: 10.54987/jobimb.v7i2.477
N. N. Razali, Hwu Ting Tzer, H. King, M. Kennerson, Karuppiah Thilakavathy
Hypophosphataemic Rickets (HR) is a rare bone disorder characterised by chronic hypophosphataemia caused by defective phosphate reabsorption in the renal tubules. Variants in phosphate-regulating endopeptidase homolog, X-linked (PHEX), fibroblast growth factor-23 (FGF23) and dentin matrix protein-1 (DMP1) genes contribute to X-linked dominant, autosomal dominant and autosomal recessive forms of HR, respectively. In this study, four Malaysian patients’ DNA samples were subjected to polymerase chain reaction and Sanger sequencing to identify the types and locations of the variants. Then, in silico study was conducted based on the variants found to predict the effects of amino acid substitution on protein functions using SIFT and PolyPhen-2 software and RNAfold was used to construct the mRNA secondary structure. Mutational analyses had revealed two variants in PHEX; c.10G>C (E4Q), c.1970A>G (Y657C), one mutation in FGF23; c.716C>T (T239M) and three variants on DMP1; c.309A>T (S69C), c.1322C>T (S406S), c.1334G>A (E410E). The variants in these Malay patients were previously reported in different ethnic HR patients. Protein prediction programs suggested that the PHEX Y657C and DMP1 S69C variants may affect protein function. All variants were predicted to alter the secondary mRNA structure. These findings suggest that these missense and silent variants may lead to changes in protein function and mRNA secondary structure that are associated with the manifestation of HR phenotype.
{"title":"Predicting the Impact of PHEX, FGF23 and DMP1 Gene Variants Found in Malaysian Malay Patients with Hypophosphataemic Rickets Through In Silico Analysis of Protein Function and mRNA Secondary Structure","authors":"N. N. Razali, Hwu Ting Tzer, H. King, M. Kennerson, Karuppiah Thilakavathy","doi":"10.54987/jobimb.v7i2.477","DOIUrl":"https://doi.org/10.54987/jobimb.v7i2.477","url":null,"abstract":"Hypophosphataemic Rickets (HR) is a rare bone disorder characterised by chronic hypophosphataemia caused by defective phosphate reabsorption in the renal tubules. Variants in phosphate-regulating endopeptidase homolog, X-linked (PHEX), fibroblast growth factor-23 (FGF23) and dentin matrix protein-1 (DMP1) genes contribute to X-linked dominant, autosomal dominant and autosomal recessive forms of HR, respectively. In this study, four Malaysian patients’ DNA samples were subjected to polymerase chain reaction and Sanger sequencing to identify the types and locations of the variants. Then, in silico study was conducted based on the variants found to predict the effects of amino acid substitution on protein functions using SIFT and PolyPhen-2 software and RNAfold was used to construct the mRNA secondary structure. Mutational analyses had revealed two variants in PHEX; c.10G>C (E4Q), c.1970A>G (Y657C), one mutation in FGF23; c.716C>T (T239M) and three variants on DMP1; c.309A>T (S69C), c.1322C>T (S406S), c.1334G>A (E410E). The variants in these Malay patients were previously reported in different ethnic HR patients. Protein prediction programs suggested that the PHEX Y657C and DMP1 S69C variants may affect protein function. All variants were predicted to alter the secondary mRNA structure. These findings suggest that these missense and silent variants may lead to changes in protein function and mRNA secondary structure that are associated with the manifestation of HR phenotype.","PeriodicalId":15132,"journal":{"name":"Journal of Biochemistry, Microbiology and Biotechnology","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88896470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-12-26DOI: 10.54987/jobimb.v7i2.478
W. Loke, H. Saud
Overuse of antibiotics was contributed to the increasing of bacterial infection resistance against antibiotics and caused a serious issue to the public health. Anti-quorum sensing is a new alternative ways or treatments to fight bacterial pathogenicity. Traditional Chinese herbs were screened of their anti-quorum sensing activities. Six selected traditional Chinese herbs were screened for a simple anti-quorum sensing activity by using Chromobacterium violaceum as the biomonitor. Two out of these herbs were found to be able to exhibit anti-quorum sensing properties; Lycium barbarum and Zingiber officinale. Extraction from Lycium barbarum has stronger anti-quorum sensing activity than Zingiber officinale. Colonies of biomonitor C. violaceum treated with Lycium barbarum almost fully loss its purple pigment. The loss and lack of purple colour from the colonies of C. violaceum indicated that quorum sensing activity was inhibited by the herb’s extracted. It is believed that this herb contains rich source of compounds to fight or control pathogenic bacteria and potentially a new therapeutic way to reduce the development of antibiotic resistanc
{"title":"Screening of Anti-Quorum Sensing Activity from Selected Chinese Herbs Against Chromobacterium violaceum","authors":"W. Loke, H. Saud","doi":"10.54987/jobimb.v7i2.478","DOIUrl":"https://doi.org/10.54987/jobimb.v7i2.478","url":null,"abstract":"Overuse of antibiotics was contributed to the increasing of bacterial infection resistance against antibiotics and caused a serious issue to the public health. Anti-quorum sensing is a new alternative ways or treatments to fight bacterial pathogenicity. Traditional Chinese herbs were screened of their anti-quorum sensing activities. Six selected traditional Chinese herbs were screened for a simple anti-quorum sensing activity by using Chromobacterium violaceum as the biomonitor. Two out of these herbs were found to be able to exhibit anti-quorum sensing properties; Lycium barbarum and Zingiber officinale. Extraction from Lycium barbarum has stronger anti-quorum sensing activity than Zingiber officinale. Colonies of biomonitor C. violaceum treated with Lycium barbarum almost fully loss its purple pigment. The loss and lack of purple colour from the colonies of C. violaceum indicated that quorum sensing activity was inhibited by the herb’s extracted. It is believed that this herb contains rich source of compounds to fight or control pathogenic bacteria and potentially a new therapeutic way to reduce the development of antibiotic resistanc","PeriodicalId":15132,"journal":{"name":"Journal of Biochemistry, Microbiology and Biotechnology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88676889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-12-26DOI: 10.54987/jobimb.v7i2.480
M. K. Sabullah, K. Subramaniam, A. A. Basirun, A. M. Umar
Rapid industrial development has caused many hazardous toxicants, especially heavy metals, to be released directly or indirectly into the environment which resulted in the polluted environment, mainly the water bodies. There are numerous Malaysian rivers that are largely polluted by heavy metals which can cause negative impact on health of public as well as the environment. Hence, a rapid and simple biomonitoring method will aid in notifying government agencies as well the public to such threat. Accordingly, acetylcholinesterase (AChE) inhibition has been widely used as a biomarker for heavy metals detection. In this study, the potential of AChE from Osteochilus hasselti brain as an alternative biosensor for heavy metals detection is measured. We discovered that out of seven heavy metals tested at the final concentration of 5 mg/L, only Hg2+, Ag2+, and Cu2+ exerted more than 50% significant inhibition (p<0.05) based on ANOVA analysis. The As5+ and Cd2+ exhibited inhibition by lowering the activity of AChE to less than 50%, displaying no significant difference (ð‘ƒð‘ƒ > 0.05) compared to each other. Meanwhile, the Cr6+ and Pb2+ showed no notable inhibitory effect on the activity of AChE. The results exhibited that AChE of O. hasselti has the capability to be used as a biosensor for the detection of metal ions.
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