Pub Date : 2023-11-13DOI: 10.35118/apjmbb.2023.031.4.02
Evie Khoo, Roseliza Roslee, Zunita Zakaria, Nur Indah Ahmad
Salmonella enterica subsp. enterica serovar Brancaster is a chicken-associated serovar that is increasingly reported in the Asian region, including Malaysia. The shortfall of conventional serovar identification for nomenclature alone is insufficient for studying the genetic and clonal relationships of Salmonella of the same serovar. Whereas DNA sequence-based typing method is useful to study the genetic diversity and relatedness of the highly diverse Salmonella. In this study, the genetic diversity, phenotypic antimicrobial resistance (AMR) profiles, and detection of selected AMR genes from ten representative Salmonella Brancaster isolates from chicken cloacal swabs and raw chicken meat were carried out. Based on multilocus sequence typing (MLST), all Salmonella Brancaster belonged to sequence type ST2133. Further analysis of the MLST sequencing data using concatenated nucleotide sequences of the seven housekeeping genes divided them into nine clusters, revealed heterogeneity and genetic diversity among the isolates. All isolates were multidrug-resistant (MDR), which confers resistance to three or more classes of antibiotics. Seven Salmonella Brancaster isolates exhibited phenotypic ACSSuT-type MDR profile, and two of them were also resistant towards ciprofloxacin. Salmonella Brancaster in the present study possessed at least one and up to six resistance genes, with the most prevalent being the ampicillin (blaTEM), tetracycline (tetA), chloramphenicol (floR), gentamicin (ant(3”)-Ia), streptomycin (strA), and sulfonamides (sul-2). Chickens are common reservoir for serovar Brancaster and the emergence, persistence, and dissemination of MDR Salmonella Brancaster possessed a public health risk. The authorities need to strengthen salmonellosis control management programme in poultry farms, abattoirs, and processing facilities.
{"title":"Genetic diversity of multidrug resistant Salmonella enterica subsp. enterica serovar Brancaster isolated from chicken in Malaysia","authors":"Evie Khoo, Roseliza Roslee, Zunita Zakaria, Nur Indah Ahmad","doi":"10.35118/apjmbb.2023.031.4.02","DOIUrl":"https://doi.org/10.35118/apjmbb.2023.031.4.02","url":null,"abstract":"Salmonella enterica subsp. enterica serovar Brancaster is a chicken-associated serovar that is increasingly reported in the Asian region, including Malaysia. The shortfall of conventional serovar identification for nomenclature alone is insufficient for studying the genetic and clonal relationships of Salmonella of the same serovar. Whereas DNA sequence-based typing method is useful to study the genetic diversity and relatedness of the highly diverse Salmonella. In this study, the genetic diversity, phenotypic antimicrobial resistance (AMR) profiles, and detection of selected AMR genes from ten representative Salmonella Brancaster isolates from chicken cloacal swabs and raw chicken meat were carried out. Based on multilocus sequence typing (MLST), all Salmonella Brancaster belonged to sequence type ST2133. Further analysis of the MLST sequencing data using concatenated nucleotide sequences of the seven housekeeping genes divided them into nine clusters, revealed heterogeneity and genetic diversity among the isolates. All isolates were multidrug-resistant (MDR), which confers resistance to three or more classes of antibiotics. Seven Salmonella Brancaster isolates exhibited phenotypic ACSSuT-type MDR profile, and two of them were also resistant towards ciprofloxacin. Salmonella Brancaster in the present study possessed at least one and up to six resistance genes, with the most prevalent being the ampicillin (blaTEM), tetracycline (tetA), chloramphenicol (floR), gentamicin (ant(3”)-Ia), streptomycin (strA), and sulfonamides (sul-2). Chickens are common reservoir for serovar Brancaster and the emergence, persistence, and dissemination of MDR Salmonella Brancaster possessed a public health risk. The authorities need to strengthen salmonellosis control management programme in poultry farms, abattoirs, and processing facilities.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"35 7","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136346853","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 : 2023-10-22DOI: 10.35118/apjmbb.2023.031.4.01
Reema Mohammed Abed, Laith Ahmed Yaaqoob
This study evaluated the serum concentrations of IL-41 and the detection of specific single nucleotide polymorphisms (SNPs) (rs1600485907, rs762398841, and rs575275512) within the IL-41 gene in female subjects diagnosed with systemic lupus erythematosus (SLE). The study sample comprised 124 female patients who had been diagnosed with SLE, with an equivalent number of healthy control volunteers. The levels of serum were determined using the application of an enzyme-linked immunosorbent assay (ELISA) technology, while SNPs were determined by conventional polymerase chain reaction (PCR), and subsequent Sanger sequencing. The results revealed that the mean age of the healthy control group was 31.64 years, whereas the mean age of the group diagnosed with SLE was 33.66 years. The findings of the present investigation indicate that the individuals under examination demonstrated an average disease duration of 9.0 years, whereas the average SLEDAI-2k score for those diagnosed with SLE was 11.0. The concentrations of ESR, CRP, urea, creatinine, C3, and C4 in individuals diagnosed with SLE showed a statistically significant elevation in comparison to the control cohort. The analysis of patients’ anti-nuclear antibodies (ANA) revealed that 89% of individuals have ANA, whereas 95.61% display anti-dsDNA. Significantly elevated levels of serum IL-41 were seen in patients diagnosed with SLE in comparison to healthy controls. A receiver operating characteristic (ROC) analysis was performed on a cohort of patients diagnosed with SLE to assess the diagnostic efficacy of IL-41 in discriminating between SLE patients and non-afflicted persons. The study determined that the specificity of IL-41 was 82.26%, representing the percentage of accurate negative outcomes. In contrast, the sensitivity of IL-41 was found to be 84.68%, indicating the percentage of accurate positive outcomes. The computed value for the area under the curve (AUC) was found to be 0.937. The statistical analysis revealed a significant connection between the existence of both heterozygote and homozygote mutant genotypes of IL-41 (rs1600485907) and an increased vulnerability to the formation of SLE. In conclusion, it has been shown that individuals diagnosed with SLE demonstrate heightened concentrations of IL-41in their circulating blood plasma. Furthermore, a particular genetic variation, specifically a single nucleotide polymorphism (SNP) denoted as rs1600485907 located within the IL-41 gene, has been recognized as a potential susceptibility factor for the onset of this disorder.
{"title":"Novel single nucleotide polymorphism (rs1600485907) of IL-41 gene associated with systemic lupus erythematous","authors":"Reema Mohammed Abed, Laith Ahmed Yaaqoob","doi":"10.35118/apjmbb.2023.031.4.01","DOIUrl":"https://doi.org/10.35118/apjmbb.2023.031.4.01","url":null,"abstract":"This study evaluated the serum concentrations of IL-41 and the detection of specific single nucleotide polymorphisms (SNPs) (rs1600485907, rs762398841, and rs575275512) within the IL-41 gene in female subjects diagnosed with systemic lupus erythematosus (SLE). The study sample comprised 124 female patients who had been diagnosed with SLE, with an equivalent number of healthy control volunteers. The levels of serum were determined using the application of an enzyme-linked immunosorbent assay (ELISA) technology, while SNPs were determined by conventional polymerase chain reaction (PCR), and subsequent Sanger sequencing. The results revealed that the mean age of the healthy control group was 31.64 years, whereas the mean age of the group diagnosed with SLE was 33.66 years. The findings of the present investigation indicate that the individuals under examination demonstrated an average disease duration of 9.0 years, whereas the average SLEDAI-2k score for those diagnosed with SLE was 11.0. The concentrations of ESR, CRP, urea, creatinine, C3, and C4 in individuals diagnosed with SLE showed a statistically significant elevation in comparison to the control cohort. The analysis of patients’ anti-nuclear antibodies (ANA) revealed that 89% of individuals have ANA, whereas 95.61% display anti-dsDNA. Significantly elevated levels of serum IL-41 were seen in patients diagnosed with SLE in comparison to healthy controls. A receiver operating characteristic (ROC) analysis was performed on a cohort of patients diagnosed with SLE to assess the diagnostic efficacy of IL-41 in discriminating between SLE patients and non-afflicted persons. The study determined that the specificity of IL-41 was 82.26%, representing the percentage of accurate negative outcomes. In contrast, the sensitivity of IL-41 was found to be 84.68%, indicating the percentage of accurate positive outcomes. The computed value for the area under the curve (AUC) was found to be 0.937. The statistical analysis revealed a significant connection between the existence of both heterozygote and homozygote mutant genotypes of IL-41 (rs1600485907) and an increased vulnerability to the formation of SLE. In conclusion, it has been shown that individuals diagnosed with SLE demonstrate heightened concentrations of IL-41in their circulating blood plasma. Furthermore, a particular genetic variation, specifically a single nucleotide polymorphism (SNP) denoted as rs1600485907 located within the IL-41 gene, has been recognized as a potential susceptibility factor for the onset of this disorder.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"45 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135461097","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 : 2023-10-14DOI: 10.35118/apjmbb.2023.031.3.10
Gabrielle Shiao Wei Chieng, Boon Chin Tan, Chee How Teo
Cucumis sativus is one of the most cultivated and consumed plants worldwide. To meet the demanding requirements following the rise in population, it is important to maintain and enhance the growth and development of this crop. Recent findings suggest that small open reading frames (sORFs) are associated not only with plant growth but with plant stress responses, especially in the case of drought and salt stress conditions. Hence, in this present study, we aim to determine the function and expression profile reflected in Cucumis sativus var. hardwickii PI183967 sORFs in the variety C. sativus var. sativus through transcriptomic analyses of publicly available RNA-seq datasets of var. sativus. We managed to obtain 14,799 transcribed sORF from the transcriptome datasets of var. sativus. Among these, only 689 (4.66%) transcribed sORF have translational potential. We were able to unveil the roles of transcribed sORFs associated with biological processes (reproductive process, immune response, and multicellular organism reproduction), molecular functions (transferase activity, catalytic activity, acting on a protein, hydrolase activity, and oxidoreductase activity), and cellular component (cytoplasm). KEGG pathway analysis revealed that the transcribed sORFs were significantly enriched in two of the KEGG Ontology (KO) terms, namely, plant-pathogen interaction and plant hormone signal transduction. Results from this study aid the understanding of sORF roles in Cucumis sativus and pave the way for future attempts to utilize these sORFs involved in stress responses to enhance the quality of the crop.
黄瓜是世界上栽培和消费最多的植物之一。为了满足人口增长的需求，保持和提高这种作物的生长和发展是很重要的。最近的研究表明，小开放阅读框(sorf)不仅与植物生长有关，而且与植物的胁迫反应有关，特别是在干旱和盐胁迫条件下。因此，本研究旨在通过公开的sativus var. hardwickii PI183967 sORFs转录组学分析，确定sativus var. hardwickii PI183967 sORFs在sativus var. sativus中的功能和表达谱。我们成功地从sativus变种的转录组数据集中获得了14,799个转录的sORF。其中，只有689个(4.66%)转录的sORF具有翻译潜力。我们能够揭示转录的sorf与生物过程(生殖过程、免疫反应和多细胞生物繁殖)、分子功能(转移酶活性、催化活性、作用于蛋白质、水解酶活性和氧化还原酶活性)和细胞成分(细胞质)相关的作用。KEGG通路分析显示，转录的sorf在KEGG本体(KO)的两个术语，即植物-病原体相互作用和植物激素信号转导中显著富集。本研究的结果有助于理解sORF在黄瓜中的作用，并为今后利用这些sORF参与胁迫应答以提高作物品质铺平道路。
{"title":"In silico expression profiling and function prediction of transcribed small open reading frames from Cucumis sativus var. hardwickii PI183967 in C. sativus var. sativus","authors":"Gabrielle Shiao Wei Chieng, Boon Chin Tan, Chee How Teo","doi":"10.35118/apjmbb.2023.031.3.10","DOIUrl":"https://doi.org/10.35118/apjmbb.2023.031.3.10","url":null,"abstract":"Cucumis sativus is one of the most cultivated and consumed plants worldwide. To meet the demanding requirements following the rise in population, it is important to maintain and enhance the growth and development of this crop. Recent findings suggest that small open reading frames (sORFs) are associated not only with plant growth but with plant stress responses, especially in the case of drought and salt stress conditions. Hence, in this present study, we aim to determine the function and expression profile reflected in Cucumis sativus var. hardwickii PI183967 sORFs in the variety C. sativus var. sativus through transcriptomic analyses of publicly available RNA-seq datasets of var. sativus. We managed to obtain 14,799 transcribed sORF from the transcriptome datasets of var. sativus. Among these, only 689 (4.66%) transcribed sORF have translational potential. We were able to unveil the roles of transcribed sORFs associated with biological processes (reproductive process, immune response, and multicellular organism reproduction), molecular functions (transferase activity, catalytic activity, acting on a protein, hydrolase activity, and oxidoreductase activity), and cellular component (cytoplasm). KEGG pathway analysis revealed that the transcribed sORFs were significantly enriched in two of the KEGG Ontology (KO) terms, namely, plant-pathogen interaction and plant hormone signal transduction. Results from this study aid the understanding of sORF roles in Cucumis sativus and pave the way for future attempts to utilize these sORFs involved in stress responses to enhance the quality of the crop.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135803362","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 : 2023-09-16DOI: 10.35118/apjmbb.2023.031.3.08
Jesreen Tega, Cha Thye San, Malinna Jusoh
Microalgal oils and lipids are the potential sources of sustainable industrial products for pharmaceuticals, nutraceuticals, and cosmeceuticals. However, the production cost of microalgal-based products is still expensive and hinders their marketability. Therefore, research has been focusing on increasing microalgae's oil and lipids content to be economically reasonable. Nutrient stresses were often used to enhance oils and lipids production in microalgae. In this study, the microalga Chlorella vulgaris was exposed to nitrogen starvation for 21 days to examine the effect of nitrogen removal on cell density, total oil content, fatty acids composition, and the expression of two triacylglycerols (TAG) biosynthetic genes, glycerol-3-phosphate acyltransferase (GPAT) and diacylglycerol acyltransferase (DGAT). The results showed that the C. vulgaris cells grew extremely slowly (p<0.05) under nitrogen starvation conditions. However, despite the growth outcome, the nitrogen starvation increased (p<0.05) total oil contents on days 3, 11 and 14 relatives to control. Nitrogen starvation also stimulated (p<0.05) the production of saturated fatty acids (SFA). The primary fatty acids detected were C16:0, C18:0, C18:1, C18:2, C18:3 and C20:0. The effect of nitrogen starvation on the expression of TAG biosynthetic genes, GPAT and DGAT genes were enumerated using real-time PCR. Both GPAT and DGAT were downregulated in this study. Interestingly, the buildup of C18:2 and C18:3 was positively linked with GPAT expression, demonstrating that GPAT affected the synthesis of polyunsaturated fatty acids (PUFA) in nitrogen-starved circumstances. This suggests that the GPAT gene may be altered to increase PUFA in microalgae, notably C18:2 and C18:3.
{"title":"Effects of nitrogen starvation on TAG biosynthesis genes expression in Chlorella vulgaris","authors":"Jesreen Tega, Cha Thye San, Malinna Jusoh","doi":"10.35118/apjmbb.2023.031.3.08","DOIUrl":"https://doi.org/10.35118/apjmbb.2023.031.3.08","url":null,"abstract":"Microalgal oils and lipids are the potential sources of sustainable industrial products for pharmaceuticals, nutraceuticals, and cosmeceuticals. However, the production cost of microalgal-based products is still expensive and hinders their marketability. Therefore, research has been focusing on increasing microalgae's oil and lipids content to be economically reasonable. Nutrient stresses were often used to enhance oils and lipids production in microalgae. In this study, the microalga Chlorella vulgaris was exposed to nitrogen starvation for 21 days to examine the effect of nitrogen removal on cell density, total oil content, fatty acids composition, and the expression of two triacylglycerols (TAG) biosynthetic genes, glycerol-3-phosphate acyltransferase (GPAT) and diacylglycerol acyltransferase (DGAT). The results showed that the C. vulgaris cells grew extremely slowly (p<0.05) under nitrogen starvation conditions. However, despite the growth outcome, the nitrogen starvation increased (p<0.05) total oil contents on days 3, 11 and 14 relatives to control. Nitrogen starvation also stimulated (p<0.05) the production of saturated fatty acids (SFA). The primary fatty acids detected were C16:0, C18:0, C18:1, C18:2, C18:3 and C20:0. The effect of nitrogen starvation on the expression of TAG biosynthetic genes, GPAT and DGAT genes were enumerated using real-time PCR. Both GPAT and DGAT were downregulated in this study. Interestingly, the buildup of C18:2 and C18:3 was positively linked with GPAT expression, demonstrating that GPAT affected the synthesis of polyunsaturated fatty acids (PUFA) in nitrogen-starved circumstances. This suggests that the GPAT gene may be altered to increase PUFA in microalgae, notably C18:2 and C18:3.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135307262","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}
Chronic periodontitis is oral inflammatory gum disease which affects the tissues that support the teeth. It is caused by formation of bacterial plaque consisting of bacterial species that produces various virulence factors. Oral bacterial species from the periodontitis patients include species of Fusobacterium, Porphyromonas, Prevotella, Tannerella, etc. In the present study, we isolated the Klebsiella pneumoniae strain 9A from the pockets of patients suffering from chronic periodontitis. The strain was isolated on enriched tryptic soya media containing 10 mM fumarate and identified based on Gram staining, 16S rRNA gene sequencing, biochemical tests and ability to reduce fumarate. Our study is the first report of anaerobic fumarate reduction capabilities of Klebsiella spp. isolated from chronic periodontitis patients, which may help in growth and survival of species in periodontal pockets leading to progression of the disease. In addition, experimental evidence is provided through reduction, growth, and inhibitor assays for the presence of fumarate reductase (Frd) activities. Furthermore, we detected a 400 bp frdA gene fragment in Klebsiella pneumoniae strain 9A using degenerate PCR. This fragment show similarity to fumarate reductases flavoprotein subunit (FrdA). Our findings suggest that the FrdA subunit is responsible for anaerobic fumarate respiration in Klebsiella spp. to be important in the survival of bacteria in oxygen-deprived environments in humans such as periodontal pockets, thus contributing to its pathogenicity.
{"title":"Characterization of fumarate reduction by Klebsiella pneumoniae isolated from patients with chronic periodontitis","authors":"Geetika Sharma, Nancy Garg, Shamimul Hasan, Daad Saffarini, Sheetal Shirodkar","doi":"10.35118/apjmbb.2023.031.3.07","DOIUrl":"https://doi.org/10.35118/apjmbb.2023.031.3.07","url":null,"abstract":"Chronic periodontitis is oral inflammatory gum disease which affects the tissues that support the teeth. It is caused by formation of bacterial plaque consisting of bacterial species that produces various virulence factors. Oral bacterial species from the periodontitis patients include species of Fusobacterium, Porphyromonas, Prevotella, Tannerella, etc. In the present study, we isolated the Klebsiella pneumoniae strain 9A from the pockets of patients suffering from chronic periodontitis. The strain was isolated on enriched tryptic soya media containing 10 mM fumarate and identified based on Gram staining, 16S rRNA gene sequencing, biochemical tests and ability to reduce fumarate. Our study is the first report of anaerobic fumarate reduction capabilities of Klebsiella spp. isolated from chronic periodontitis patients, which may help in growth and survival of species in periodontal pockets leading to progression of the disease. In addition, experimental evidence is provided through reduction, growth, and inhibitor assays for the presence of fumarate reductase (Frd) activities. Furthermore, we detected a 400 bp frdA gene fragment in Klebsiella pneumoniae strain 9A using degenerate PCR. This fragment show similarity to fumarate reductases flavoprotein subunit (FrdA). Our findings suggest that the FrdA subunit is responsible for anaerobic fumarate respiration in Klebsiella spp. to be important in the survival of bacteria in oxygen-deprived environments in humans such as periodontal pockets, thus contributing to its pathogenicity.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135306443","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}
Over the past few decades, traditional medicinal products have grown in popularity. It is estimated that 80% of patients worldwide use them for basic health treatment. Due to its extraordinary bioactive properties, propolis is a bee product commonly utilised in alternative medicines. Propolis is a complicated mixture of substances, procured by bees from diverse vegetations and mix them with beeswax and bee saliva enzymes. Propolis bioactivities have been examined and reported in the treatments of numerous chronic diseases. Given the differences in pharmacological activity and compound markup of propolis, huge variation exists due to numerous hive localities. This study intends to define and explore the bioactive qualities of propolis in Malaysia. Information on the antibacterial, antioxidant, anti-inflammatory, and other bioactivity properties from studies conducted on Malaysian propolis have been consolidated in this review. This research would result in an enhanced understanding of the safe consumption of Malaysian propolis and may spur the development of novel and more affordable treatments for various infections.
{"title":"Review of bioactive components property of Malaysian propolis: A review","authors":"Khor Goot Heah, Eleena Mohd Yusof, Sharvitha Dhamotharan, Ikmal Hisham Ismail","doi":"10.35118/apjmbb.2023.031.3.09","DOIUrl":"https://doi.org/10.35118/apjmbb.2023.031.3.09","url":null,"abstract":"Over the past few decades, traditional medicinal products have grown in popularity. It is estimated that 80% of patients worldwide use them for basic health treatment. Due to its extraordinary bioactive properties, propolis is a bee product commonly utilised in alternative medicines. Propolis is a complicated mixture of substances, procured by bees from diverse vegetations and mix them with beeswax and bee saliva enzymes. Propolis bioactivities have been examined and reported in the treatments of numerous chronic diseases. Given the differences in pharmacological activity and compound markup of propolis, huge variation exists due to numerous hive localities. This study intends to define and explore the bioactive qualities of propolis in Malaysia. Information on the antibacterial, antioxidant, anti-inflammatory, and other bioactivity properties from studies conducted on Malaysian propolis have been consolidated in this review. This research would result in an enhanced understanding of the safe consumption of Malaysian propolis and may spur the development of novel and more affordable treatments for various infections.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"234 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135306439","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 : 2023-09-02DOI: 10.35118/apjmbb.2023.031.3.06
Irma Rohmawati, B. K. Adji, Dea Putri Andeska, E. Suyono
Arthrospira platensis mass culture contamination is a recurring concern. Salinity alteration appears to be a promising approach, given that A. platensis can withstand various salinities. In addition, biopesticide is also expected to eliminate the bacteria. Therefore, it is critical to investigate the effects of salinity and biopesticide on the growth, nutritional value, and bacterial diversity of A. platensis mass culture. A completely randomized design was used, with five salinity treatment levels: 5 ppt (S5B), 10 ppt (S10B), 15 ppt (S15B), 20 ppt (S20B), and 25 ppt (S25B), with 0.5 ml/L of biopesticide Azadirachta indica applied on days 2 and 4. The growth rate was calculated using daily density and biomass, and on day 7, carbohydrates, proteins, lipids, and pigments were determined. Furthermore, the contamination test and bacterial diversity were determined using Total Plate Count and Next-Generation Sequencing, respectively. The results showed that the S15B had the fastest growth rate and the largest carbohydrate content. However, S5B produced the best results in terms of protein, chlorophyll, and phycocyanin content, while S25B produced the most carotene and lipids. Proteobacteria were the most abundant in all NGS samples. The number of OTU treatments obtained for A (NCD7), B (NCD0), and C (S15BD7) were 646, 636, and 286, respectively. Moreover, C (S15BD7) was the most effective treatment to reduce bacterial diversity contamination, in which several bacterial diversity, including Acidobacteriota, Chloroflexi, Gemmatimonadota, Myxococcota, and Desulfobacterota, were eliminated completely. As a result of the salinity adjustment and the use of biopesticides, the mass culture of A. platensis was able to grow more quickly and contain more nutrients while having less bacterial diversity.
{"title":"Effect of salinity and biopesticide on Arthrospira platensis mass culture growth, metabolites, and bacterial diversity","authors":"Irma Rohmawati, B. K. Adji, Dea Putri Andeska, E. Suyono","doi":"10.35118/apjmbb.2023.031.3.06","DOIUrl":"https://doi.org/10.35118/apjmbb.2023.031.3.06","url":null,"abstract":"Arthrospira platensis mass culture contamination is a recurring concern. Salinity alteration appears to be a promising approach, given that A. platensis can withstand various salinities. In addition, biopesticide is also expected to eliminate the bacteria. Therefore, it is critical to investigate the effects of salinity and biopesticide on the growth, nutritional value, and bacterial diversity of A. platensis mass culture. A completely randomized design was used, with five salinity treatment levels: 5 ppt (S5B), 10 ppt (S10B), 15 ppt (S15B), 20 ppt (S20B), and 25 ppt (S25B), with 0.5 ml/L of biopesticide Azadirachta indica applied on days 2 and 4. The growth rate was calculated using daily density and biomass, and on day 7, carbohydrates, proteins, lipids, and pigments were determined. Furthermore, the contamination test and bacterial diversity were determined using Total Plate Count and Next-Generation Sequencing, respectively. The results showed that the S15B had the fastest growth rate and the largest carbohydrate content. However, S5B produced the best results in terms of protein, chlorophyll, and phycocyanin content, while S25B produced the most carotene and lipids. Proteobacteria were the most abundant in all NGS samples. The number of OTU treatments obtained for A (NCD7), B (NCD0), and C (S15BD7) were 646, 636, and 286, respectively. Moreover, C (S15BD7) was the most effective treatment to reduce bacterial diversity contamination, in which several bacterial diversity, including Acidobacteriota, Chloroflexi, Gemmatimonadota, Myxococcota, and Desulfobacterota, were eliminated completely. As a result of the salinity adjustment and the use of biopesticides, the mass culture of A. platensis was able to grow more quickly and contain more nutrients while having less bacterial diversity.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74709653","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 : 2023-09-02DOI: 10.35118/apjmbb.2023.031.3.05
D. Ayuningrum, D. Novitasari, A. Sabdaningsih, O. Jati
The enzyme is a catalyst that serves as an accelerator in a biochemical process. A hydrolytic enzyme is among the existing enzymes useful for environmental organic waste degradation. This research aimed to (1) investigate the ability of bacteria isolated from Litopenaeus vannamei pond sediment to produce proteolytic and lipolytic enzymes, (2) identify the isolates with 16S rRNA gene amplification, and (3) construct a phylogenetic tree according to the 16S rRNA genes. The preliminary proteolytic assay consisted of a skim milk agar medium and the lipolytic assay consisted of a Tween 20/80 medium or so-called precipitation test. Among 28 bacterial isolates, 4 of them showed potential for proteolytic activity and 6 of them showed lipolytic activity as well. Further, the amplification of 16S rRNA gene showed that 5 out of the 28 isolates were closely related to Bacillus infantis SA 3.2 (IM8), Marinobacter koreensis SB 1.1 (IM6), Vibrio algynolyticus SA 4.2 (IM6), Streptomyces euryhalinus SB 1.2 (IM6), and Cytobacillus kochii SC 3.4 (IM6). Amongst the most active isolate, one of the was included in Actinobacteria phylum. Many Bacilli strains shows enzymatic activity such as amylase, protease and lypase. The genus Marinobacter also found to be able to produce hydrolytic enzyme such as amylase and protease. Furthermore, the genus Vibrio such as V. algynoliticus produce several enzymes i.e., gelatinase, lecithinase, caseinase, amylase and lipase. In summary, the bacteria from L. vannamei pond sediment exhibit a potential as proteolytic and lipolytic enzyme producers.
{"title":"Preliminary molecular identification of proteolytic and\u0000lipolytic-enzyme producing bacteria isolated from sediment of Litopenaeus vannamei pond","authors":"D. Ayuningrum, D. Novitasari, A. Sabdaningsih, O. Jati","doi":"10.35118/apjmbb.2023.031.3.05","DOIUrl":"https://doi.org/10.35118/apjmbb.2023.031.3.05","url":null,"abstract":"The enzyme is a catalyst that serves as an accelerator in a biochemical process. A hydrolytic enzyme is among the existing enzymes useful for environmental organic waste degradation. This research aimed to (1) investigate the ability of bacteria isolated from Litopenaeus vannamei pond sediment to produce proteolytic and lipolytic enzymes, (2) identify the isolates with 16S rRNA gene amplification, and (3) construct a phylogenetic tree according to the 16S rRNA genes. The preliminary proteolytic assay consisted of a skim milk agar medium and the lipolytic assay consisted of a Tween 20/80 medium or so-called precipitation test. Among 28 bacterial isolates, 4 of them showed potential for proteolytic activity and 6 of them showed lipolytic activity as well. Further, the amplification of 16S rRNA gene showed that 5 out of the 28 isolates were closely related to Bacillus infantis SA 3.2 (IM8), Marinobacter koreensis SB 1.1 (IM6), Vibrio algynolyticus SA 4.2 (IM6), Streptomyces euryhalinus SB 1.2 (IM6), and Cytobacillus kochii SC 3.4 (IM6). Amongst the most active isolate, one of the was included in Actinobacteria phylum. Many Bacilli strains shows enzymatic activity such as amylase, protease and lypase. The genus Marinobacter also found to be able to produce hydrolytic enzyme such as amylase and protease. Furthermore, the genus Vibrio such as V. algynoliticus produce several enzymes i.e., gelatinase, lecithinase, caseinase, amylase and lipase. In summary, the bacteria from L. vannamei pond sediment exhibit a potential as proteolytic and lipolytic enzyme producers.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"57 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76693678","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 : 2023-08-27DOI: 10.35118/apjmbb.2023.031.3.03
A. M. Suhaimi, Rabiatul Adawiah Zainal Abidin, Fairuz Fatini Mohd Yusof, Abdullah Munir Roslan, A. Sipat, K. Yusoff
Bacillus coagulans ST-6 is a thermophile isolated from a local hot spring in Malaysia. It expresses xylanase activity and has potential industrial applications. In silico structure prediction and modeling of a 210 amino acid sequence (XYNBC) translated from 872 bp Bacillus coagulans ST-6 xylanase gene was performed. The predicted molecular weight of the translated amino acid sequence is 20 kDa with theoretical isoelectric point value at 9.10 predicting that the xylanase belongs to the GH11 xylanase family. The protein is predicted to be hydrophilic with Grand average of hydropathicity (GRAVY) value of -0.6555 and possibly has better interaction with water. Predicted motif for XYNBC was revealed to be from Glycosyl hydrolases family 11(IPR00137) with signature motif 1 and 2 and only one known activity, xylanase. A three-dimensional (3D) model was constructed using PDB ID 2DCZ|A (http://www.rcsb. org) as the template as it has the highest similarity with XYNBC protein sequence. The 2DCZ|A xylanase sequence is from Bacillus Subtilis family-11 and is 185 amino acid long. The predicted 3D model consists of eleven beta sheets and one alpha helix. The stereochemical quality of protein structure revealed by Ramachandran Plot showed acceptable model with 99.4% residues fall in the most favored regions. Ten residues were predicted to be involved in active sites where residues Tyr7, Val15 and Asn16 are located at beta sheet while Asp118, Gly119, Thr120 are located at the loop. The catalytic residues E78 and E172 common to other G1H1 xylanases were also revealed.
凝结芽孢杆菌ST-6是一种从马来西亚当地温泉分离出来的嗜热菌。它表达木聚糖酶活性，具有潜在的工业应用价值。对从872 bp的凝固芽孢杆菌ST-6木聚糖酶基因中翻译的210个氨基酸序列(XYNBC)进行了硅结构预测和建模。预测翻译氨基酸序列的分子量为20 kDa，理论等电点值为9.10，预测该木聚糖酶属于GH11木聚糖酶家族。预测该蛋白具有亲水性，亲水性(GRAVY)的大平均值为-0.6555，可能与水有较好的相互作用。预测的XYNBC基序来自糖基水解酶家族11(IPR00137)，其特征基序为1和2，只有一个已知的活性，即木聚糖酶。使用PDB ID 2DCZ|A (http://www.rcsb)构建三维(3D)模型。org)作为模板，因为它与XYNBC蛋白序列相似性最高。2DCZ|A木聚糖酶序列来自枯草芽孢杆菌家族11，全长185个氨基酸。预测的3D模型由11个β层和一个α螺旋组成。Ramachandran图显示的蛋白质结构立体化学质量符合可接受的模型，99.4%的残基落在最有利的区域。预计有10个残基参与活性位点，其中残基Tyr7、Val15和Asn16位于β片上，而残基Asp118、Gly119、Thr120位于环上。同时还发现了其他G1H1木聚糖酶共有的催化残基E78和E172。
{"title":"In silico analysis of xylanase in Bacillus coagulans ST-6","authors":"A. M. Suhaimi, Rabiatul Adawiah Zainal Abidin, Fairuz Fatini Mohd Yusof, Abdullah Munir Roslan, A. Sipat, K. Yusoff","doi":"10.35118/apjmbb.2023.031.3.03","DOIUrl":"https://doi.org/10.35118/apjmbb.2023.031.3.03","url":null,"abstract":"Bacillus coagulans ST-6 is a thermophile isolated from a local hot spring in Malaysia. It expresses xylanase activity and has potential industrial applications. In silico structure prediction and modeling of a 210 amino acid sequence (XYNBC) translated from 872 bp Bacillus coagulans ST-6 xylanase gene was performed. The predicted molecular weight of the translated amino acid sequence is 20 kDa with theoretical isoelectric point value at 9.10 predicting that the xylanase belongs to the GH11 xylanase family. The protein is predicted to be hydrophilic with Grand average of hydropathicity (GRAVY) value of -0.6555 and possibly has better interaction with water. Predicted motif for XYNBC was revealed to be from Glycosyl hydrolases family 11(IPR00137) with signature motif 1 and 2 and only one known activity, xylanase. A three-dimensional (3D) model was constructed using PDB ID 2DCZ|A (http://www.rcsb. org) as the template as it has the highest similarity with XYNBC protein sequence. The 2DCZ|A xylanase sequence is from Bacillus Subtilis family-11 and is 185 amino acid long. The predicted 3D model consists of eleven beta sheets and one alpha helix. The stereochemical quality of protein structure revealed by Ramachandran Plot showed acceptable model with 99.4% residues fall in the most favored regions. Ten residues were predicted to be involved in active sites where residues Tyr7, Val15 and Asn16 are located at beta sheet while Asp118, Gly119, Thr120 are located at the loop. The catalytic residues E78 and E172 common to other G1H1 xylanases were also revealed.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"97 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81512488","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 : 2023-08-27DOI: 10.35118/apjmbb.2023.031.3.04
Lim Yee Thing, Lejaniya Abdul Kalam Saleena, Crystale Lim Siew Ying, R. Koh, Pui Liew Phing
Eggplant, also known as Solanum aethiopicum (S. aethiopicum), is a highly favoured vegetable globally and belongs to the Solanaceae family. Various research studies have provided evidence of African eggplant's biological properties, such as antioxidant potential, anti-inflammatory, anti-cancer, anti-diabetic, liver-protective, and renal-protective effects. Therefore, our investigation focused on examining the impact of S. aethiopicum on the cytotoxicity of HeLa cells, which are derived from human cervical cancer. Fruits were freeze-dried or oven-dried before being subjected to aqueous infusion or hot aqueous extraction. Hot aqueous extracted (oven-dried) samples contained the highest concentration of total phenol and flavonoids. After that, HeLa cells were treated with hot aqueous extracts. After a 24-hour incubation period, the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) test was conducted. According to the cytotoxicity analysis, neither oven-dried nor freeze-dried induced significant inhibitory effects towards HeLa cell proliferation. These findings suggest that both extracts demonstrated weak cytotoxic effects on cervical cancer cells.
{"title":"Phytochemical and cytotoxic properties of Solanum aethiopicum fruit extracts against HeLa human cervical cancer cell line","authors":"Lim Yee Thing, Lejaniya Abdul Kalam Saleena, Crystale Lim Siew Ying, R. Koh, Pui Liew Phing","doi":"10.35118/apjmbb.2023.031.3.04","DOIUrl":"https://doi.org/10.35118/apjmbb.2023.031.3.04","url":null,"abstract":"Eggplant, also known as Solanum aethiopicum (S. aethiopicum), is a highly favoured vegetable globally and belongs to the Solanaceae family. Various research studies have provided evidence of African eggplant's biological properties, such as antioxidant potential, anti-inflammatory, anti-cancer, anti-diabetic, liver-protective, and renal-protective effects. Therefore, our investigation focused on examining the impact of S. aethiopicum on the cytotoxicity of HeLa cells, which are derived from human cervical cancer. Fruits were freeze-dried or oven-dried before being subjected to aqueous infusion or hot aqueous extraction. Hot aqueous extracted (oven-dried) samples contained the highest concentration of total phenol and flavonoids. After that, HeLa cells were treated with hot aqueous extracts. After a 24-hour incubation period, the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) test was conducted. According to the cytotoxicity analysis, neither oven-dried nor freeze-dried induced significant inhibitory effects towards HeLa cell proliferation. These findings suggest that both extracts demonstrated weak cytotoxic effects on cervical cancer cells.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"67 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79959834","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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