Elvina Clarie Dullah, Nur Syahadatain Abdul Razak, Clarence M. Ongkudon
In plasmid DNA (pDNA) production from Gram-negative bacteria, endotoxin has been known as the major contaminant. The separation becomes difficult due to its ability to form a stable complex with pDNA apart from sharing common properties like surface charge, molecular size, temperature, and pH stability. This study focused on the analysis of the zeta potential values of endotoxin, the theoretical number of cations bound per molecule of endotoxin as well as the binding tendency of cations towards endotoxin in the presence of pDNA. These analyses were conducted under various experimental conditions such as types of divalent metal cation, cation concentration, pH and incubation time. The analysis of zeta potential at different cation concentrations and pH values showed that Mg2+ had the most significant effect on endotoxin surface charge. The zeta potential of endotoxin was reduced by a magnitude of 43.55 mV, from −43.53 mV to 0.02 mV in the presence of 2.0 M Mg2+, and a magnitude of 44.12 mV, from −43.53 mV to 0.59 mV at the lowest pH level. However, in the analysis of the theoretical number of cations bound per molecule of endotoxin, Zn2+ showed the highest number (0.6) compared to Ca2+ (0.12) and Mg2+ (0.05). The tendency of Zn2+ to preferentially bind with endotoxins forming a larger aggregated structure was also evident in the DNA gel electrophoresis and transmission electron microscopic analysis. The manuscript highlights the significance of cations in the binding and aggregation of endotoxins, which ultimately improves the recovery of pDNA and affects its subsequent downstream processing.
{"title":"The Effects of Magnesium, Zinc and Calcium Ions on Endotoxin-Plasmid DNA Interaction at Various Cation Concentrations, pH Values and Incubation Times","authors":"Elvina Clarie Dullah, Nur Syahadatain Abdul Razak, Clarence M. Ongkudon","doi":"10.51200/bijb.v3i.4719","DOIUrl":"https://doi.org/10.51200/bijb.v3i.4719","url":null,"abstract":"In plasmid DNA (pDNA) production from Gram-negative bacteria, endotoxin has been known as the major contaminant. The separation becomes difficult due to its ability to form a stable complex with pDNA apart from sharing common properties like surface charge, molecular size, temperature, and pH stability. This study focused on the analysis of the zeta potential values of endotoxin, the theoretical number of cations bound per molecule of endotoxin as well as the binding tendency of cations towards endotoxin in the presence of pDNA. These analyses were conducted under various experimental conditions such as types of divalent metal cation, cation concentration, pH and incubation time. The analysis of zeta potential at different cation concentrations and pH values showed that Mg2+ had the most significant effect on endotoxin surface charge. The zeta potential of endotoxin was reduced by a magnitude of 43.55 mV, from −43.53 mV to 0.02 mV in the presence of 2.0 M Mg2+, and a magnitude of 44.12 mV, from −43.53 mV to 0.59 mV at the lowest pH level. However, in the analysis of the theoretical number of cations bound per molecule of endotoxin, Zn2+ showed the highest number (0.6) compared to Ca2+ (0.12) and Mg2+ (0.05). The tendency of Zn2+ to preferentially bind with endotoxins forming a larger aggregated structure was also evident in the DNA gel electrophoresis and transmission electron microscopic analysis. The manuscript highlights the significance of cations in the binding and aggregation of endotoxins, which ultimately improves the recovery of pDNA and affects its subsequent downstream processing.","PeriodicalId":9042,"journal":{"name":"Borneo International Journal of Biotechnology (BIJB)","volume":"68 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138945650","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}
Nurul Hazwani Abd Hilmi, Valeritta Lodin, Melissa Sharmah Gilbert Jesuet
The properties of polyurethane (PU) film are greatly influenced not only by the raw materials but also by the compatibility of polyol and isocyanate. This paper aimed to evaluate the effect of the isocyanate index (NCO/OH ratio) on the biodegradability properties of Eucalyptus pellita PU film. E. pellita wood polyol and polymeric methylene diphenyl diisocyanate (pMDI) were mixed at different NCO/OH ratios (1.8 – 3.0). The PU film was produced through the one-shot method. The effect of the NCO/OH ratio on the biodegradability properties of PU film was evaluated. The rate of biodegradation of PU film by soil burial test decreases proportionally to the NCO/OH ratio. The biodegradation rate is the highest (14.02%) when the NCO/OH ratio is the lowest (1.8). The results of water solubility showed that PU films with low NCO/OH ratios are easily soluble in water. The band associated with the ester compound was detected at nearly 1,060 cm−1. Based on the findings of this study, increasing the NCO/OH ratio made the PU film from E. pellita less degradable. Therefore, lowering the NCO/OH ratio is an ideal option to produce films with better biodegradability.
{"title":"Biodegradability Properties of Polyurethane Film Made from Eucalyptus pellita Wood Polyol","authors":"Nurul Hazwani Abd Hilmi, Valeritta Lodin, Melissa Sharmah Gilbert Jesuet","doi":"10.51200/bijb.v3i.4720","DOIUrl":"https://doi.org/10.51200/bijb.v3i.4720","url":null,"abstract":"The properties of polyurethane (PU) film are greatly influenced not only by the raw materials but also by the compatibility of polyol and isocyanate. This paper aimed to evaluate the effect of the isocyanate index (NCO/OH ratio) on the biodegradability properties of Eucalyptus pellita PU film. E. pellita wood polyol and polymeric methylene diphenyl diisocyanate (pMDI) were mixed at different NCO/OH ratios (1.8 – 3.0). The PU film was produced through the one-shot method. The effect of the NCO/OH ratio on the biodegradability properties of PU film was evaluated. The rate of biodegradation of PU film by soil burial test decreases proportionally to the NCO/OH ratio. The biodegradation rate is the highest (14.02%) when the NCO/OH ratio is the lowest (1.8). The results of water solubility showed that PU films with low NCO/OH ratios are easily soluble in water. The band associated with the ester compound was detected at nearly 1,060 cm−1. Based on the findings of this study, increasing the NCO/OH ratio made the PU film from E. pellita less degradable. Therefore, lowering the NCO/OH ratio is an ideal option to produce films with better biodegradability.","PeriodicalId":9042,"journal":{"name":"Borneo International Journal of Biotechnology (BIJB)","volume":"89 21","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138945351","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}
Nur Amalina Amirullah, Nurhayati Zainal Abidin, Noorlidah Abdullah, Sivakumar Manickam
The Pleurotus pulmonarius (Fr.) Quel. (Grey Oyster mushroom) is one of the most widely consumed mushroom species worldwide, and it possesses various medicinal properties. The application of ultrasound resulted in P. pulmonarius extracts with improved bioactivities both in cellular and animal models. However, no studies have investigated the preventive effects of ultrasound extract of P. pulmonarius in animal models. In this study, Wistar-Kyoto rats were pre-treated with the ultrasound extract of P. pulmonarius at high (500 mg/kg bw) and low (200 mg/kg bw) doses for 15 days. The rats were subsequently fed with a high-fat diet (HFD) for another 15 days. Rats pre-treated with P. pulmonarius extract from a high-dose ultrasound showed lower levels of serum cholesterol (1.50 mmol/L), triglyceride (0.60 mmol/L), and LDL (0.29 mmol/L). These rats also had lower oxidative stress, with MDA levels of only 10.81 µg/mg protein. The ultrasound extract of P. pulmonarius also exhibited anti-hyperglycaemic effects, whereby rats had lower blood glucose levels. Rats pre-treated with the ultrasound extract of P. pulmonarius also had inhibited inflammatory biomarkers CREB1 (2.85 pmol/mL), NF-κB2 (0.81 ng/mL), and STAT3 (0.48 ng/mL), proving the anti-inflammatory activity of the ultrasound extract. This study is the first to show the ability of P. pulmonarius extract prepared using ultrasound to prevent developing metabolic syndrome such as hyperlipidaemia, hyperglycaemia, oxidative stress, and inflammation in rats fed with HFD.
{"title":"Influence of ultrasound on Pleurotus pulmonarius (Fr.) Quél. (Grey Oyster Mushroom) – Protective Effects Against Metabolic Syndrome in Rats Fed with a High-fat Diet","authors":"Nur Amalina Amirullah, Nurhayati Zainal Abidin, Noorlidah Abdullah, Sivakumar Manickam","doi":"10.51200/bijb.v3i.4529","DOIUrl":"https://doi.org/10.51200/bijb.v3i.4529","url":null,"abstract":"The Pleurotus pulmonarius (Fr.) Quel. (Grey Oyster mushroom) is one of the most widely consumed mushroom species worldwide, and it possesses various medicinal properties. The application of ultrasound resulted in P. pulmonarius extracts with improved bioactivities both in cellular and animal models. However, no studies have investigated the preventive effects of ultrasound extract of P. pulmonarius in animal models. In this study, Wistar-Kyoto rats were pre-treated with the ultrasound extract of P. pulmonarius at high (500 mg/kg bw) and low (200 mg/kg bw) doses for 15 days. The rats were subsequently fed with a high-fat diet (HFD) for another 15 days. Rats pre-treated with P. pulmonarius extract from a high-dose ultrasound showed lower levels of serum cholesterol (1.50 mmol/L), triglyceride (0.60 mmol/L), and LDL (0.29 mmol/L). These rats also had lower oxidative stress, with MDA levels of only 10.81 µg/mg protein. The ultrasound extract of P. pulmonarius also exhibited anti-hyperglycaemic effects, whereby rats had lower blood glucose levels. Rats pre-treated with the ultrasound extract of P. pulmonarius also had inhibited inflammatory biomarkers CREB1 (2.85 pmol/mL), NF-κB2 (0.81 ng/mL), and STAT3 (0.48 ng/mL), proving the anti-inflammatory activity of the ultrasound extract. This study is the first to show the ability of P. pulmonarius extract prepared using ultrasound to prevent developing metabolic syndrome such as hyperlipidaemia, hyperglycaemia, oxidative stress, and inflammation in rats fed with HFD.","PeriodicalId":9042,"journal":{"name":"Borneo International Journal of Biotechnology (BIJB)","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139023394","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}
Nabilah Mohamad Khairi, Wilson Thau Lym Yong, J. Kulip, K. Rodrigues
Conservation of plant species plays a vital role in preventing the loss of valuable plant resources. The success of conservation depends on the correct identification and characterization of plant species. Bamboo is one of the most important plants with multiple uses that have contributed to the economy and socio-economy of many people in rural areas. It is under the subfamily of Bambusoideae that includes both woody and herbaceous bamboo. Conventionally, like other plants, bamboo has been classified dependently based on morphological characteristics. However, morphological identification leads to difficulties and misclassification of bamboo species due to their infrequent flowering behaviour and peculiar reproductive biology. Since then, molecular markers have been introduced to overcome the problems associated with bamboo taxonomy and phylogeny. This paper provides an overview of the diverse, predominantly molecular techniques used to assess and determine the genetic diversity of bamboo species.
{"title":"A GLANCE AT MOLECULAR IDENTIFICATION OF BAMBOO (Poaceae: Bambusoideae)","authors":"Nabilah Mohamad Khairi, Wilson Thau Lym Yong, J. Kulip, K. Rodrigues","doi":"10.51200/bijb.vi.2775","DOIUrl":"https://doi.org/10.51200/bijb.vi.2775","url":null,"abstract":"Conservation of plant species plays a vital role in preventing the loss of valuable plant resources. The success of conservation depends on the correct identification and characterization of plant species. Bamboo is one of the most important plants with multiple uses that have contributed to the economy and socio-economy of many people in rural areas. It is under the subfamily of Bambusoideae that includes both woody and herbaceous bamboo. Conventionally, like other plants, bamboo has been classified dependently based on morphological characteristics. However, morphological identification leads to difficulties and misclassification of bamboo species due to their infrequent flowering behaviour and peculiar reproductive biology. Since then, molecular markers have been introduced to overcome the problems associated with bamboo taxonomy and phylogeny. This paper provides an overview of the diverse, predominantly molecular techniques used to assess and determine the genetic diversity of bamboo species.","PeriodicalId":9042,"journal":{"name":"Borneo International Journal of Biotechnology (BIJB)","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79239994","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}
Stevia rebaudiana has recently gained the attention of the food industry as one of the natural sweeteners. The sweet flavour is contributed by the glycoside compounds, especially the rebaudioside A and stevioside, which are the stevia main chemical markers. The aim of the work reported here was to compare the different extraction techniques of stevia leaves using different technologies such as the high pressure and ultrasonic on the extraction of steviol glycosides. In this paper, the extraction techniques yielding the highest glycosides from the leaves of Stevia rebaudiana were determined using hot water extraction (HWE), pressurised liquid extraction (PLE) and ultrasound-assisted extraction (UAE). The steviol glycoside yields were quantified by two chemical markers, rebaudioside A and stevioside of Stevia rebaudiana using highperformance liquid chromatography (HPLC) analysis. The result showed that the HWE managed to obtain 1,110 mg of steviol glycosides. The PLE obtained 294 mg steviol glycosides and the UAE obtained 427.5 mg steviol glycosides. As a conclusion, the results suggested the most efficient technique for stevia extraction in this study was the HWE.
{"title":"SEPARATION OF STEVIOL GLYCOSIDES FROM Stevia rebaudiana USING DIFFERENT AQUEOUS EXTRACTION TECHNIQUES","authors":"Chong Saw Peng, M. Akil, Norellia Bahari","doi":"10.51200/bijb.vi.1240","DOIUrl":"https://doi.org/10.51200/bijb.vi.1240","url":null,"abstract":"Stevia rebaudiana has recently gained the attention of the food industry as one of the natural sweeteners. The sweet flavour is contributed by the glycoside compounds, especially the rebaudioside A and stevioside, which are the stevia main chemical markers. The aim of the work reported here was to compare the different extraction techniques of stevia leaves using different technologies such as the high pressure and ultrasonic on the extraction of steviol glycosides. In this paper, the extraction techniques yielding the highest glycosides from the leaves of Stevia rebaudiana were determined using hot water extraction (HWE), pressurised liquid extraction (PLE) and ultrasound-assisted extraction (UAE). The steviol glycoside yields were quantified by two chemical markers, rebaudioside A and stevioside of Stevia rebaudiana using highperformance liquid chromatography (HPLC) analysis. The result showed that the HWE managed to obtain 1,110 mg of steviol glycosides. The PLE obtained 294 mg steviol glycosides and the UAE obtained 427.5 mg steviol glycosides. As a conclusion, the results suggested the most efficient technique for stevia extraction in this study was the HWE.","PeriodicalId":9042,"journal":{"name":"Borneo International Journal of Biotechnology (BIJB)","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83188443","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}
Eugene M Obeng, Chan Yi Wei, Siti Nurul Nadzirah Adam, Clarence M. Ongkudon
Cellulases have been vital for the saccharification of lignocellulosic biomass into reduced sugars to produce biofuels and other essential biochemicals. However, the sugar yields achievable for canonical cellulases (i.e. endoglucanases, exoglucanases and β-glucosidases) have not been convincing in support of the highly acclaimed prospects and end-uses heralded. The persistent pursuit of the biochemical industry to obtain high quantities of useful chemicals from lignocellulosic biomass has resulted in the supplementation of cellulose-degrading enzymes with other biologicalcomplementation. Also, chemical additives (e.g. salts, surfactants and chelating agents) have been employed to enhance the stability and improve the binding and overall functionality of cellulases to increase product titre. Herein, we report the roadmap of cellulase-additive supplementations and the associated yield performances.
{"title":"ADDITIVES FOR CELLULASE ENHANCEMENT","authors":"Eugene M Obeng, Chan Yi Wei, Siti Nurul Nadzirah Adam, Clarence M. Ongkudon","doi":"10.51200/bijb.vi.1174","DOIUrl":"https://doi.org/10.51200/bijb.vi.1174","url":null,"abstract":"Cellulases have been vital for the saccharification of lignocellulosic biomass into reduced sugars to produce biofuels and other essential biochemicals. However, the sugar yields achievable for canonical cellulases (i.e. endoglucanases, exoglucanases and β-glucosidases) have not been convincing in support of the highly acclaimed prospects and end-uses heralded. The persistent pursuit of the biochemical industry to obtain high quantities of useful chemicals from lignocellulosic biomass has resulted in the supplementation of cellulose-degrading enzymes with other biologicalcomplementation. Also, chemical additives (e.g. salts, surfactants and chelating agents) have been employed to enhance the stability and improve the binding and overall functionality of cellulases to increase product titre. Herein, we report the roadmap of cellulase-additive supplementations and the associated yield performances.","PeriodicalId":9042,"journal":{"name":"Borneo International Journal of Biotechnology (BIJB)","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81788500","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}
Gilbert Ringgit, S. Siddiquee, S. Saallah, Mohammad Tamrin Mohamad Lal
In this work, an electrochemical method for detection of trace amount of aluminium (Al3+), a heavy metal ion, based on a bare gold electrode (AuE) was developed. Current responses of the AuE under various type of electrolytes, redox indicators, pH, scan rate and accumulation time were investigated using cyclic voltammetry (CV) method to obtain the optimum conditions for Al3+ detection. The sensing properties of the AuE towards the target ion with different concentrations were investigated using differential pulse voltammetry (DPV) method. From the CV results, the optimalconditions for the detection of Al3+ were Tris-HCl buffer (0.1 M, pH 2) supported by 5 mM Prussian blue with scan rate and accumulation time respectively of 100 mVs−1 and 15 s. Under the optimum conditions, the DPV method was detected with different concentrations of aluminium ion ranging from 0.2 to 1.0 ppm resulted in a good linear regression r² = 0.9806. This result suggests that the optimisation of the basic parameters in electrochemical detection using AuE is crucial before further modification of the Au-electrode to improve the sensitivity and selectivity especially for the low concentration of ion detection. The developed method has a great potential for rapid detection of heavy metal ion (Al3+) in drinking water samples.
{"title":"OPTIMISATION OF AN ELECTROCHEMICAL SENSOR BASED ON BARE GOLD ELECTRODE FOR DETECTION OF ALUMINIUM ION","authors":"Gilbert Ringgit, S. Siddiquee, S. Saallah, Mohammad Tamrin Mohamad Lal","doi":"10.51200/bijb.vi.2203","DOIUrl":"https://doi.org/10.51200/bijb.vi.2203","url":null,"abstract":"In this work, an electrochemical method for detection of trace amount of aluminium (Al3+), a heavy metal ion, based on a bare gold electrode (AuE) was developed. Current responses of the AuE under various type of electrolytes, redox indicators, pH, scan rate and accumulation time were investigated using cyclic voltammetry (CV) method to obtain the optimum conditions for Al3+ detection. The sensing properties of the AuE towards the target ion with different concentrations were investigated using differential pulse voltammetry (DPV) method. From the CV results, the optimalconditions for the detection of Al3+ were Tris-HCl buffer (0.1 M, pH 2) supported by 5 mM Prussian blue with scan rate and accumulation time respectively of 100 mVs−1 and 15 s. Under the optimum conditions, the DPV method was detected with different concentrations of aluminium ion ranging from 0.2 to 1.0 ppm resulted in a good linear regression r² = 0.9806. This result suggests that the optimisation of the basic parameters in electrochemical detection using AuE is crucial before further modification of the Au-electrode to improve the sensitivity and selectivity especially for the low concentration of ion detection. The developed method has a great potential for rapid detection of heavy metal ion (Al3+) in drinking water samples.","PeriodicalId":9042,"journal":{"name":"Borneo International Journal of Biotechnology (BIJB)","volume":"105 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74340768","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}
C. Budiman, Carlmond Goh Kah Wun, Lee Ping Chin, Rafida Razali, Thean Chor Leow
FK506-binding protein35 of Plasmodium knowlesi (Pk-FKBP35) is a member of peptidyl prolyl cis-trans isomerase (PPIase) and is considered as a promising avenue of antimalarial drug target development. This protein is organized into the N-terminal domain responsible for PPIase catalytic activity followed and the tetratricopeptide repeat domain for its dimerization. The protease-coupling and protease-free assays are known to be the common methods for investigating the catalytic properties of PPIase. Earlier, the protease-coupling assay was used to confirm the catalytic activity of Pk-FKBP35 in accelerating cis-trans isomerization of the peptide substrate. This report is aimed to re-assess the catalytic and substrate specificity of Pk-FKBP35 using an alternative method of a protease-free assay. The result indicated that while Pk-FKBP35 theoretically contained many possible cleavage sites of chymotrypsin, experimentally, the catalytic domain was relatively stable from chymotrypsin. Furthermore, under protease-free assay, Pk-FKBP35 also demonstrated remarkable PPIase catalytic activity with kcat/KM of 4.5 + 0.13 × 105 M−1 s−1, while the kcat/KM of active site mutant of D55A is 0.81 + 0.05 × 105 M−1 s−1. These values were considered comparable to kcat/KM obtained from the protease-coupling assay. Interestingly, the substrate specificities of Pk-FKBP35 obtained from both methods are also similar, with the preference of Pk-FKBP35 towards Xaa at P1 position was Leu>Phe>Lys>Trp>Val>Ile>His>Asp>Ala>Gln>Glu. Altogether, we proposed that protease-free and protease-coupling assays arereliable for Pk-FKBP35.
{"title":"REASSESSMENT OF THE CATALYTIC ACTIVITY AND SUBSTRATE SPECIFICITY OF FKBP35 FROM Plasmodium knowlesi USING PROTEASE-FREE ASSAY","authors":"C. Budiman, Carlmond Goh Kah Wun, Lee Ping Chin, Rafida Razali, Thean Chor Leow","doi":"10.51200/bijb.vi.2602","DOIUrl":"https://doi.org/10.51200/bijb.vi.2602","url":null,"abstract":"FK506-binding protein35 of Plasmodium knowlesi (Pk-FKBP35) is a member of peptidyl prolyl cis-trans isomerase (PPIase) and is considered as a promising avenue of antimalarial drug target development. This protein is organized into the N-terminal domain responsible for PPIase catalytic activity followed and the tetratricopeptide repeat domain for its dimerization. The protease-coupling and protease-free assays are known to be the common methods for investigating the catalytic properties of PPIase. Earlier, the protease-coupling assay was used to confirm the catalytic activity of Pk-FKBP35 in accelerating cis-trans isomerization of the peptide substrate. This report is aimed to re-assess the catalytic and substrate specificity of Pk-FKBP35 using an alternative method of a protease-free assay. The result indicated that while Pk-FKBP35 theoretically contained many possible cleavage sites of chymotrypsin, experimentally, the catalytic domain was relatively stable from chymotrypsin. Furthermore, under protease-free assay, Pk-FKBP35 also demonstrated remarkable PPIase catalytic activity with kcat/KM of 4.5 + 0.13 × 105 M−1 s−1, while the kcat/KM of active site mutant of D55A is 0.81 + 0.05 × 105 M−1 s−1. These values were considered comparable to kcat/KM obtained from the protease-coupling assay. Interestingly, the substrate specificities of Pk-FKBP35 obtained from both methods are also similar, with the preference of Pk-FKBP35 towards Xaa at P1 position was Leu>Phe>Lys>Trp>Val>Ile>His>Asp>Ala>Gln>Glu. Altogether, we proposed that protease-free and protease-coupling assays arereliable for Pk-FKBP35.","PeriodicalId":9042,"journal":{"name":"Borneo International Journal of Biotechnology (BIJB)","volume":"69 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83328980","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}
A. Simon, V. Subbiah, Chee Fong Tyng, Noor Hydayaty Md Yusuf
Rice is the most important staple crop in Malaysia and is cultivated all over the country, including the state of Sabah. The uniqueness of rice cultivation in Sabah lies in the type of rice itself, deriving mainly from local or non-commercial cultivars but with distinctive characteristics including long grains, aromatic properties, and drought tolerance. However, despite having these important agricultural traits, information on the genetic diversity of Sabah rice remains limited. Hence, the purpose of this study was to determine the genetic polymorphisms of Sabah rice using random amplification of polymorphic DNA (RAPD) markers. A total of 101 alleles were profiled, from which 94% were identified as polymorphic. Phylogenetic analysis grouped the rice samples into three clusters, with two clusters classifying the ability of rice to grow under different planting conditions, suitable for growth irrigate and upland condition. The first cluster was dominated by cultivars that could survive in wet (irrigated) areas, while the other featured those that were found in dry (upland) areas. Furthermore, two alleles, OPA-05-B2 and OPA-01-B11, were found to be unique to cultivars within the upland cluster and were thus proposed to be involved in dry environmental adaptation. The results of the present study provide an insight into the genetic relationships and diversity of Sabah rice.
{"title":"GENETIC DIVERSITY OF SABAH RICE CULTIVARS USING RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS","authors":"A. Simon, V. Subbiah, Chee Fong Tyng, Noor Hydayaty Md Yusuf","doi":"10.51200/bijb.vi.1991","DOIUrl":"https://doi.org/10.51200/bijb.vi.1991","url":null,"abstract":"Rice is the most important staple crop in Malaysia and is cultivated all over the country, including the state of Sabah. The uniqueness of rice cultivation in Sabah lies in the type of rice itself, deriving mainly from local or non-commercial cultivars but with distinctive characteristics including long grains, aromatic properties, and drought tolerance. However, despite having these important agricultural traits, information on the genetic diversity of Sabah rice remains limited. Hence, the purpose of this study was to determine the genetic polymorphisms of Sabah rice using random amplification of polymorphic DNA (RAPD) markers. A total of 101 alleles were profiled, from which 94% were identified as polymorphic. Phylogenetic analysis grouped the rice samples into three clusters, with two clusters classifying the ability of rice to grow under different planting conditions, suitable for growth irrigate and upland condition. The first cluster was dominated by cultivars that could survive in wet (irrigated) areas, while the other featured those that were found in dry (upland) areas. Furthermore, two alleles, OPA-05-B2 and OPA-01-B11, were found to be unique to cultivars within the upland cluster and were thus proposed to be involved in dry environmental adaptation. The results of the present study provide an insight into the genetic relationships and diversity of Sabah rice.","PeriodicalId":9042,"journal":{"name":"Borneo International Journal of Biotechnology (BIJB)","volume":"49 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74265727","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}
Rajeena Sugumaran, Pamela David Jocksing, N. A. Yusof
Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) are contributors to infection cases among the Asian population. S. aureus is found in the mucous lining of noses and is mainly non-pathogenic while E. coli, mostly harmless bacteria, are found in the intestine. Pathogenic strains of both bacteria have adverse effects on the elderly and younger age group of the population. Samples were collected from recreational parks around Kota Kinabalu as they are hotspots frequently visited by families with both age groups. The bacterial samples were isolated and cultured on selective media such as Baird-Parker agar (BPA), Brain Heart Infusion (BHI) agar, MacConkey agar and Eosin-Methylene Blue (EMB) agar. Morphological characteristics of bacterial growth were observed, where S. aureus had black-shiny growth in BPAand E. coli had a metallic-green sheen in EMB agar. The suspected bacteria samples were then stained and viewed under a light microscope. S. aureus was identified as gram-positive, stained violet with a circular shape and clustered appearance. E. coli was identified as gram-negative, stained red, rod-shaped with 2 – 3 bacterial alignment. Antibiotic resistance test resulted in S. aureus and E. coli samples did not display 100% resistance among 4 antibiotics tested (ampicillin, penicillin, tetracycline and chloramphenicol). Most of the bacteria samples were a minimum inhibitory of 0.1 mg/mL of antibiotic concentration. These results provide a foundation for further research on identifying bacterial strains using molecular methods. The findings can then be used to disseminate information to the public to create awareness of potential disease outbreaks in the city.
{"title":"IDENTIFICATION AND OCCURRENCE OF ANTIBIOTIC RESISTANCE OF Staphylococcus aureus AND Escherichia coli ISOLATED FROM RECREATIONAL PARKS AROUND KOTA KINABALU, SABAH","authors":"Rajeena Sugumaran, Pamela David Jocksing, N. A. Yusof","doi":"10.51200/bijb.vi.1975","DOIUrl":"https://doi.org/10.51200/bijb.vi.1975","url":null,"abstract":"Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) are contributors to infection cases among the Asian population. S. aureus is found in the mucous lining of noses and is mainly non-pathogenic while E. coli, mostly harmless bacteria, are found in the intestine. Pathogenic strains of both bacteria have adverse effects on the elderly and younger age group of the population. Samples were collected from recreational parks around Kota Kinabalu as they are hotspots frequently visited by families with both age groups. The bacterial samples were isolated and cultured on selective media such as Baird-Parker agar (BPA), Brain Heart Infusion (BHI) agar, MacConkey agar and Eosin-Methylene Blue (EMB) agar. Morphological characteristics of bacterial growth were observed, where S. aureus had black-shiny growth in BPAand E. coli had a metallic-green sheen in EMB agar. The suspected bacteria samples were then stained and viewed under a light microscope. S. aureus was identified as gram-positive, stained violet with a circular shape and clustered appearance. E. coli was identified as gram-negative, stained red, rod-shaped with 2 – 3 bacterial alignment. Antibiotic resistance test resulted in S. aureus and E. coli samples did not display 100% resistance among 4 antibiotics tested (ampicillin, penicillin, tetracycline and chloramphenicol). Most of the bacteria samples were a minimum inhibitory of 0.1 mg/mL of antibiotic concentration. These results provide a foundation for further research on identifying bacterial strains using molecular methods. The findings can then be used to disseminate information to the public to create awareness of potential disease outbreaks in the city.","PeriodicalId":9042,"journal":{"name":"Borneo International Journal of Biotechnology (BIJB)","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79782305","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}
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