Phylogenetic analysis is beneficial to plant conservation prioritization. Conservation does not only deal with species but also their evolutionary potential. A phylogenetic tree is usually reconstructed by using the alignment of DNA sequences. However, with the availability of megatrees, subsetting with a list of species of concern is possible. Here we reconstructed a list of 53 Alocasia spp. (Araceae) from Indonesia and adjacent regions using available megatrees and publicly available DNA sequences in the GenBank. The result showed placed and unplaced Alocasia spp. on the terminal nodes of reconstructed phylogenetic trees. The unplaced species show that publicly available DNA sequences are not yet available, therefore should be prioritized for sequencing. The placed species in the phylogeny could be used for conservation prioritization of these Alocasia spp. Keywords: Alocasia, Indonesia, Megatree, Phylogeny, Plant conservation
{"title":"Reconstructing Phylogenies of Alocasia spp. (Araceae) Distributed in Indonesia for Conservation Prioritization","authors":"N. Asih, I. Erlinawati, Arief Priyadi","doi":"10.11594/jtls.12.03.04","DOIUrl":"https://doi.org/10.11594/jtls.12.03.04","url":null,"abstract":"Phylogenetic analysis is beneficial to plant conservation prioritization. Conservation does not only deal with species but also their evolutionary potential. A phylogenetic tree is usually reconstructed by using the alignment of DNA sequences. However, with the availability of megatrees, subsetting with a list of species of concern is possible. Here we reconstructed a list of 53 Alocasia spp. (Araceae) from Indonesia and adjacent regions using available megatrees and publicly available DNA sequences in the GenBank. The result showed placed and unplaced Alocasia spp. on the terminal nodes of reconstructed phylogenetic trees. The unplaced species show that publicly available DNA sequences are not yet available, therefore should be prioritized for sequencing. The placed species in the phylogeny could be used for conservation prioritization of these Alocasia spp. Keywords: Alocasia, Indonesia, Megatree, Phylogeny, Plant conservation","PeriodicalId":17638,"journal":{"name":"Journal of Tropical Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43554482","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}
H. Okotie, T. Anjuwon, O. Adepoju, I. Okolo, Gilead Forcardos, D. James
Ethulia conyzoides is a plant traditionally used in managing diabetes in Nigeria. Unfortunately, its antidiabetic potential has not been scientifically examined. The research investigated the phytochemical constituents, in vitro antioxidant, and antidiabetic efficacies of E. conyzoides leaves extract. Seventy percent methanol extraction of E. conyzoides leaves was done to obtain its crude extract. It then was partitioned with n-hexane and ethyl acetate to obtain three fractions (n-hexane, ethylacetate and residual aqueous). Then, they were subjected to various phytochemistry investigations: 1,1-diphenyl 2-picryl hydrazyl (DPPH) radical scavenging activity assay and in vivo antidiabetic effects in mice. The fasting blood glucose (FBG) levels, weight change, feed and fluid intakes were determined using standard procedures. Phyto-profiles tests for the extract and its fractions revealed the presence of phenolics, tannins, cardiac glycosides, saponins and alkaloids. The result showed that the residual aqueous fraction had the nearest inhibitory concentration (IC50) of 0.011µg/ml to the standard ascorbic acid with 0.010µg/ml compared with other extract and fractions. There was a substantial (p < 0.05) rise in fluid and feed intakes and serum levels of FBG in the type 2 diabetic mice. Treatment of the mice using 100 mg/kg b.w. residual aqueous fraction for 21 days significantly (p < 0.05) reduced the fluid intake, feed intake and FBG and statistically (p < 0.05) improved the body weight. This study revealed that the residual aqueous fraction of E. conyzoides has antioxidant and antidiabetic activities against induced type 2 diabetic mice. Keywords: Antioxidant, Ethulia conyzoides, Fasting blood glucose, Phytochemical, Type 2 diabetes
{"title":"Phytochemical Constituents, Antioxidant and Antidiabetic Efficacies of the Crude Extract and Fractions of Ethulia conyzoides Leaves","authors":"H. Okotie, T. Anjuwon, O. Adepoju, I. Okolo, Gilead Forcardos, D. James","doi":"10.11594/jtls.12.03.05","DOIUrl":"https://doi.org/10.11594/jtls.12.03.05","url":null,"abstract":"Ethulia conyzoides is a plant traditionally used in managing diabetes in Nigeria. Unfortunately, its antidiabetic potential has not been scientifically examined. The research investigated the phytochemical constituents, in vitro antioxidant, and antidiabetic efficacies of E. conyzoides leaves extract. Seventy percent methanol extraction of E. conyzoides leaves was done to obtain its crude extract. It then was partitioned with n-hexane and ethyl acetate to obtain three fractions (n-hexane, ethylacetate and residual aqueous). Then, they were subjected to various phytochemistry investigations: 1,1-diphenyl 2-picryl hydrazyl (DPPH) radical scavenging activity assay and in vivo antidiabetic effects in mice. The fasting blood glucose (FBG) levels, weight change, feed and fluid intakes were determined using standard procedures. Phyto-profiles tests for the extract and its fractions revealed the presence of phenolics, tannins, cardiac glycosides, saponins and alkaloids. The result showed that the residual aqueous fraction had the nearest inhibitory concentration (IC50) of 0.011µg/ml to the standard ascorbic acid with 0.010µg/ml compared with other extract and fractions. There was a substantial (p < 0.05) rise in fluid and feed intakes and serum levels of FBG in the type 2 diabetic mice. Treatment of the mice using 100 mg/kg b.w. residual aqueous fraction for 21 days significantly (p < 0.05) reduced the fluid intake, feed intake and FBG and statistically (p < 0.05) improved the body weight. This study revealed that the residual aqueous fraction of E. conyzoides has antioxidant and antidiabetic activities against induced type 2 diabetic mice. Keywords: Antioxidant, Ethulia conyzoides, Fasting blood glucose, Phytochemical, Type 2 diabetes","PeriodicalId":17638,"journal":{"name":"Journal of Tropical Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47027879","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}
In Indonesia, the vaccine for SARS-CoV-2 is still being developed. ORF3a protein of SARS-CoV-2 could be a potential peptide for the vaccine, therapeutic antibodies, and diagnostic kit development. We used the computational approach in designing some potential epitopes against the ORF3a protein of the virus. The reference sequences of ORF3a SARS-CoV-2 were retrieved from GISAID. Our previous study found 203 non-synonymous mutations from 3,751 samples in Indonesia. We categorized and compared the variation in this protein with reference sequences. To predict B cell epitopes, we used Immune Epitope Database (IEDB) and VaxiJen v.2.0 as analysis resources. We found two epitopes, 177SPISEHDY184 and 74SKGVHFVCNLLLLFVTVYSHLLLVAAG100, that indicate antigen. Our study showed these predicted peptides could be used as a reference for the SARS-CoV-2 vaccine, therapeutic antibodies, and diagnostic development. This approach needs further studies to understand the functionality of the predicted proteins against SARSCoV-2 that circulated, especially in Indonesia. Keywords: Bioinformatics, Epitope, Mapping, ORF3a, SARS-CoV-2
{"title":"Epitope mapping of ORF3a Protein SARS-CoV-2 in Indonesia through computational study","authors":"Hartiyowidi Yuliawuri, J. Christian","doi":"10.11594/jtls.12.03.08","DOIUrl":"https://doi.org/10.11594/jtls.12.03.08","url":null,"abstract":"In Indonesia, the vaccine for SARS-CoV-2 is still being developed. ORF3a protein of SARS-CoV-2 could be a potential peptide for the vaccine, therapeutic antibodies, and diagnostic kit development. We used the computational approach in designing some potential epitopes against the ORF3a protein of the virus. The reference sequences of ORF3a SARS-CoV-2 were retrieved from GISAID. Our previous study found 203 non-synonymous mutations from 3,751 samples in Indonesia. We categorized and compared the variation in this protein with reference sequences. To predict B cell epitopes, we used Immune Epitope Database (IEDB) and VaxiJen v.2.0 as analysis resources. We found two epitopes, 177SPISEHDY184 and 74SKGVHFVCNLLLLFVTVYSHLLLVAAG100, that indicate antigen. Our study showed these predicted peptides could be used as a reference for the SARS-CoV-2 vaccine, therapeutic antibodies, and diagnostic development. This approach needs further studies to understand the functionality of the predicted proteins against SARSCoV-2 that circulated, especially in Indonesia. Keywords: Bioinformatics, Epitope, Mapping, ORF3a, SARS-CoV-2","PeriodicalId":17638,"journal":{"name":"Journal of Tropical Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41902473","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}
Silvi Ikawati, T. Himawan, A. Abdi, Hagus Sarno, Alvan Fajarudin
Alternative storage pest control that is more environmentally friendly than the use of synthetic chemical pesticides is to use botanical pesticides from plant essential oils, including clove (Syzygium aromaticum) which contains the main compounds eugenol and trans-caryophyllene. To study the various mechanisms of action of essential oils as botanical insecticides could use in silico approach through molecular docking. This study aims to predict the dominant binding mode(s) of a ligand with a protein of a known three-dimensional structure through docking. Then tested its fumigant activity on Tribolium castaneum. The docking results showed that the trans-caryophyllene and eugenol compounds had a more stable bond strength in the acetylcholinesterase enzyme T. castaneum than the control compound linalool. In addition, there is a synergy between eugenol and trans-caryophyllene when the two compounds interact with acetylcholinesterase. These results can be used as prediction material that trans-caryophyllene and eugenol have potential as protein acetylcholinesterase inhibitors of T. castaneum. After being tested in the laboratory, clove oil which contains two main compounds namely eugenol and trans-caryophylene has the potential to control T. castaneum with an LC50 value of 5,227 μL/L air. Keywords: Botanical insecticide, Caryophyllene, Docking, Eugenol, Fumigant,Syzygium aromaticum
{"title":"In Silico Study of Eugenol and trans-Caryophyllene also Clove Oil Fumigant Toxicity on Tribolium castaneum","authors":"Silvi Ikawati, T. Himawan, A. Abdi, Hagus Sarno, Alvan Fajarudin","doi":"10.11594/jtls.12.03.07","DOIUrl":"https://doi.org/10.11594/jtls.12.03.07","url":null,"abstract":"Alternative storage pest control that is more environmentally friendly than the use of synthetic chemical pesticides is to use botanical pesticides from plant essential oils, including clove (Syzygium aromaticum) which contains the main compounds eugenol and trans-caryophyllene. To study the various mechanisms of action of essential oils as botanical insecticides could use in silico approach through molecular docking. This study aims to predict the dominant binding mode(s) of a ligand with a protein of a known three-dimensional structure through docking. Then tested its fumigant activity on Tribolium castaneum. The docking results showed that the trans-caryophyllene and eugenol compounds had a more stable bond strength in the acetylcholinesterase enzyme T. castaneum than the control compound linalool. In addition, there is a synergy between eugenol and trans-caryophyllene when the two compounds interact with acetylcholinesterase. These results can be used as prediction material that trans-caryophyllene and eugenol have potential as protein acetylcholinesterase inhibitors of T. castaneum. After being tested in the laboratory, clove oil which contains two main compounds namely eugenol and trans-caryophylene has the potential to control T. castaneum with an LC50 value of 5,227 μL/L air. Keywords: Botanical insecticide, Caryophyllene, Docking, Eugenol, Fumigant,Syzygium aromaticum","PeriodicalId":17638,"journal":{"name":"Journal of Tropical Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48553217","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}
Brown Planthopper is one of the economically important rice pests that cause several crop failures in Asian countries. Unfortunately, Brown Planthopper could migrate to neighboring countries to generate interpopulation breeding, thus further increasing the gene flow and spreading insecticide resistance. This research aimed to understand the genetic differentiation of Brown Planthopper among all Asian populations. This study used two COI sequences from Malang, Indonesia, and 25 sequences from GenBank to analyze the genetic structure with phylogenetic tree and haplotype network. The uncorrected pairwise distance result showed that the Brown Planthopper population in Asia has a relatively low genetic distance. We also found that the Brown Planthopper population was clustered based on the geographical region of South Asia, East Asia-Mainland South East Asia, and Indonesia. Thus, we concluded that the migration of Brown Planthopper was limited to East Asia and Mainland South East Asia only. Further studies are needed to confirm the migration route of Brown Planthopper in South Asia and Southeast AsiaKeywords: BPH, Genetic differentiation, Haplotype network, Phylogenetic
{"title":"Genetic Differentiation of Brown Planthopper Nilaparvata lugens (Stål) Populations in Asia","authors":"B. Yanuwiadi, Rahmat Grahadi","doi":"10.11594/jtls.12.02.15","DOIUrl":"https://doi.org/10.11594/jtls.12.02.15","url":null,"abstract":"Brown Planthopper is one of the economically important rice pests that cause several crop failures in Asian countries. Unfortunately, Brown Planthopper could migrate to neighboring countries to generate interpopulation breeding, thus further increasing the gene flow and spreading insecticide resistance. This research aimed to understand the genetic differentiation of Brown Planthopper among all Asian populations. This study used two COI sequences from Malang, Indonesia, and 25 sequences from GenBank to analyze the genetic structure with phylogenetic tree and haplotype network. The uncorrected pairwise distance result showed that the Brown Planthopper population in Asia has a relatively low genetic distance. We also found that the Brown Planthopper population was clustered based on the geographical region of South Asia, East Asia-Mainland South East Asia, and Indonesia. Thus, we concluded that the migration of Brown Planthopper was limited to East Asia and Mainland South East Asia only. Further studies are needed to confirm the migration route of Brown Planthopper in South Asia and Southeast AsiaKeywords: BPH, Genetic differentiation, Haplotype network, Phylogenetic","PeriodicalId":17638,"journal":{"name":"Journal of Tropical Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44901287","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}
Orthosiphon stamineus is one of the most prominent medicinal herbs widely grown in Southeast Asia. Propagation of O. stamineus using tissue culture technique helps to rapidly produce samples for research purposes, increase the production of secondary metabolites and is considered as one of the strategies in plant genetic improvement. Despite vast information on O. stamineus pharmacological properties, the protein profile of this species is currently underexplored. In the present study, proteins expressed in embryogenic callus developed from O. stamineus leaves in Murashige and Skoog medium supplemented with 1-naphthaleneacetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D) were identified via Liquid chromatography- tandem mass spectrometry (LC-MS/MS). The presence of embryogenic callus was confirmed with microscope observation and Evan Blue assay. Using this proteomic approach, we identified peptides that represent 22 proteins localized to different cell compartments and involved in various biological and metabolic functions in plants. This finding is useful to improve our understanding of protein functions, thus their future applications could be further explored. Keywords: Embryogenic, Callus, Herb, Orthosiphon stamineus, Proteins
{"title":"Protein Profiling of Orthosiphon stamineus Embryogenic Callus using Liquid Chromatography Coupled with Tandem-Mass Spectrometry (LC-MS/MS)","authors":"D. Mamat, Z. Rahmat, Tsun-Thai Chai, F. Manan","doi":"10.11594/jtls.12.02.01","DOIUrl":"https://doi.org/10.11594/jtls.12.02.01","url":null,"abstract":"Orthosiphon stamineus is one of the most prominent medicinal herbs widely grown in Southeast Asia. Propagation of O. stamineus using tissue culture technique helps to rapidly produce samples for research purposes, increase the production of secondary metabolites and is considered as one of the strategies in plant genetic improvement. Despite vast information on O. stamineus pharmacological properties, the protein profile of this species is currently underexplored. In the present study, proteins expressed in embryogenic callus developed from O. stamineus leaves in Murashige and Skoog medium supplemented with 1-naphthaleneacetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D) were identified via Liquid chromatography- tandem mass spectrometry (LC-MS/MS). The presence of embryogenic callus was confirmed with microscope observation and Evan Blue assay. Using this proteomic approach, we identified peptides that represent 22 proteins localized to different cell compartments and involved in various biological and metabolic functions in plants. This finding is useful to improve our understanding of protein functions, thus their future applications could be further explored. Keywords: Embryogenic, Callus, Herb, Orthosiphon stamineus, Proteins","PeriodicalId":17638,"journal":{"name":"Journal of Tropical Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46387544","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}
Pitaya belongs to the family Cactaceae and the genus Hylocereus. It is essential todevelop tissue culture protocols according to the appropriate variety to spread pitayacommercial production and ensure healthy sapling production. This study aimed todetermine the best plant growth regulators (PGRs) in the micropropagation process,and their effects on different pitaya cultivars were evaluated. Shoots of different pitayacultivars were cultured in Murashige and Skoog (MS) basal medium supplementedwith Indole-3-butyric (IBA), 6-benzyl amino purine (BAP), and gibberellic acid(GA3). The highest micropropagation coefficient was determined in Physical Graffitivariety cultured in MS medium supplemented with 2 mg/L BAP. The general evaluation based on the variety determined that the best micropropagation was in the RoyalRed variety. In in vitro rooting studies, the best rooting variety was Royal Red(54.47%), followed by Siam Red (50.33%), Physical Graffiti (47.75%), and SeoulKitchen (44.82%). It was determined that the Royal Red variety is grown in R2 (MSmedium supplemented with 1 mg/l IBA) medium gave the best results in all criteriaof shoot length (4.28 cm), root length (6.45 cm), and root formation on the face(74.48%). It was envisioned that these differences between the micropropagation,growth, and rooting of the cultivars used in the studies resulted from the cultivar characteristics.Keywords: Pitaya, In vitro, Micropropagation, Royal Red, Seoul Kitchen, Siam Red,Physical Graffiti
{"title":"Effect of Different Plant Growth Regulators on Micropropagation of Some Pitaya Varieties","authors":"Taner Bozkurt, S. Inan, Ijlal Dundar, Selda Kozak","doi":"10.11594/jtls.12.02.04","DOIUrl":"https://doi.org/10.11594/jtls.12.02.04","url":null,"abstract":"Pitaya belongs to the family Cactaceae and the genus Hylocereus. It is essential todevelop tissue culture protocols according to the appropriate variety to spread pitayacommercial production and ensure healthy sapling production. This study aimed todetermine the best plant growth regulators (PGRs) in the micropropagation process,and their effects on different pitaya cultivars were evaluated. Shoots of different pitayacultivars were cultured in Murashige and Skoog (MS) basal medium supplementedwith Indole-3-butyric (IBA), 6-benzyl amino purine (BAP), and gibberellic acid(GA3). The highest micropropagation coefficient was determined in Physical Graffitivariety cultured in MS medium supplemented with 2 mg/L BAP. The general evaluation based on the variety determined that the best micropropagation was in the RoyalRed variety. In in vitro rooting studies, the best rooting variety was Royal Red(54.47%), followed by Siam Red (50.33%), Physical Graffiti (47.75%), and SeoulKitchen (44.82%). It was determined that the Royal Red variety is grown in R2 (MSmedium supplemented with 1 mg/l IBA) medium gave the best results in all criteriaof shoot length (4.28 cm), root length (6.45 cm), and root formation on the face(74.48%). It was envisioned that these differences between the micropropagation,growth, and rooting of the cultivars used in the studies resulted from the cultivar characteristics.Keywords: Pitaya, In vitro, Micropropagation, Royal Red, Seoul Kitchen, Siam Red,Physical Graffiti","PeriodicalId":17638,"journal":{"name":"Journal of Tropical Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49360992","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}
The intensive use of antibiotics in aquaculture results in the proliferation of antibiotic. In this study, antibiotic resistant bacteria from six different aquaculture sources (pond of Fisheries Research Institute (FRI), and rivers of Kukup, Pulai, Pendas Laut, Sungai Melayu and Kong Kong) were isolated. These isolates were tested for antibiotic resistance against seven antibiotics via the disc diffusion method. Finally, phenotypic and genotypic identification via 16S rRNA sequencing and phylogenetic analysis were carried out. The results show that 58 out of 118 bacterial isolates are resistant to multiple antibiotics. The highest isolate resistance was observed towards rifampicin (89.66%), followed by ampicillin (79.31%) and sulfafurazole (67.24%). The isolates with multiple antibiotic resistant (MAR) index values with more than 20% were subjected to 16S rRNA gene sequencing. The majority of the bacterial strains exhibit multiple antibiotic resistance, indicating that they were isolated from highly contaminated sources based on the tested water qualities profiles, which showed the high level of turbidity and total dissolved solid (TDS) in most sampling sites with the high number of MAR bacteria obtained.Keywords: Antibiotic resistance, Multiple antibiotic resistance, Aquaculture sources,MAR index value, 16S rRNA gene sequencing
{"title":"Prevalence of Antibiotic Resistance Bacteria in Aquaculture Sources in Johor, Malaysia Prevalence of Antibiotic Resistance","authors":"K. Yern, N. Zain, M. Jaafar, M. Sani, M. Suhaimin","doi":"10.11594/jtls.12.02.07","DOIUrl":"https://doi.org/10.11594/jtls.12.02.07","url":null,"abstract":"The intensive use of antibiotics in aquaculture results in the proliferation of antibiotic. In this study, antibiotic resistant bacteria from six different aquaculture sources (pond of Fisheries Research Institute (FRI), and rivers of Kukup, Pulai, Pendas Laut, Sungai Melayu and Kong Kong) were isolated. These isolates were tested for antibiotic resistance against seven antibiotics via the disc diffusion method. Finally, phenotypic and genotypic identification via 16S rRNA sequencing and phylogenetic analysis were carried out. The results show that 58 out of 118 bacterial isolates are resistant to multiple antibiotics. The highest isolate resistance was observed towards rifampicin (89.66%), followed by ampicillin (79.31%) and sulfafurazole (67.24%). The isolates with multiple antibiotic resistant (MAR) index values with more than 20% were subjected to 16S rRNA gene sequencing. The majority of the bacterial strains exhibit multiple antibiotic resistance, indicating that they were isolated from highly contaminated sources based on the tested water qualities profiles, which showed the high level of turbidity and total dissolved solid (TDS) in most sampling sites with the high number of MAR bacteria obtained.Keywords: Antibiotic resistance, Multiple antibiotic resistance, Aquaculture sources,MAR index value, 16S rRNA gene sequencing","PeriodicalId":17638,"journal":{"name":"Journal of Tropical Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42300881","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}
Sefatullah Zakary, Hamida Mashal, Abdul Osmani, Habeebat Oyewus, F. Huyop, Muzhgan Nasim
Halogenated organic compounds are found as waste in the biosphere and can causenumerous dilemmas because of their toxicity and persistence in the environment. Theyplay a major role in the quality of life of both, human beings and other living organisms. Degradation of these compounds by microorganisms is significant to reduce recalcitrant and cost. Thus, in the current study, an in-silico approach was used for homology modelling and docking assessment of a newly identified DehLt4, type IIdehalogenase to predict its ability to degrade selected haloalkanoic acids and haloacetates. The study aimed to establish the catalytic tendencies of the enzyme to optimallydegrade the selected halogenated haloacids. The refined modelled structure of DehLt4using GROMACS 5.1.2 software revealed satisfactory scores of ERRAT (94.73%),Verify3D (90.83%) and PROCHECK (99.05 %) assessments. Active site predictionby blind docking and multiple sequence alignment indicated the catalytic triads forDehLt4 were Asp9-Lys149-Asn175. Both L-2-chloropropionic acid (L-2-CP) and trichloroacetate (TCA) docked with DehLt4 exhibited binding energy of -3.9 kcal/mol.However, the binding energy for D-2-chloropropionic acid (D-2-CP) and monochloroacetate (MCA) was -3.8 kcal/mol and -3.1 kcal/mol, respectively. Thus, the findingsof the study successfully identified the catalytic important residues of DehLt4 for possible pollutant degradation. The in-silico study as such has a good potential for characterization of newly identified dehalogenases based on basic molecular structure andfunctions analysis.Keywords: Dehalogenase, Haloacid dehalogenase, Mesorhizobium loti strain TONO,Protein structure
{"title":"In Silico Molecular Characterization of a Putative Haloacid Dehalogenase Type II from Genomic of Mesorhizobium loti Strain TONO","authors":"Sefatullah Zakary, Hamida Mashal, Abdul Osmani, Habeebat Oyewus, F. Huyop, Muzhgan Nasim","doi":"10.11594/jtls.12.02.10","DOIUrl":"https://doi.org/10.11594/jtls.12.02.10","url":null,"abstract":"Halogenated organic compounds are found as waste in the biosphere and can causenumerous dilemmas because of their toxicity and persistence in the environment. Theyplay a major role in the quality of life of both, human beings and other living organisms. Degradation of these compounds by microorganisms is significant to reduce recalcitrant and cost. Thus, in the current study, an in-silico approach was used for homology modelling and docking assessment of a newly identified DehLt4, type IIdehalogenase to predict its ability to degrade selected haloalkanoic acids and haloacetates. The study aimed to establish the catalytic tendencies of the enzyme to optimallydegrade the selected halogenated haloacids. The refined modelled structure of DehLt4using GROMACS 5.1.2 software revealed satisfactory scores of ERRAT (94.73%),Verify3D (90.83%) and PROCHECK (99.05 %) assessments. Active site predictionby blind docking and multiple sequence alignment indicated the catalytic triads forDehLt4 were Asp9-Lys149-Asn175. Both L-2-chloropropionic acid (L-2-CP) and trichloroacetate (TCA) docked with DehLt4 exhibited binding energy of -3.9 kcal/mol.However, the binding energy for D-2-chloropropionic acid (D-2-CP) and monochloroacetate (MCA) was -3.8 kcal/mol and -3.1 kcal/mol, respectively. Thus, the findingsof the study successfully identified the catalytic important residues of DehLt4 for possible pollutant degradation. The in-silico study as such has a good potential for characterization of newly identified dehalogenases based on basic molecular structure andfunctions analysis.Keywords: Dehalogenase, Haloacid dehalogenase, Mesorhizobium loti strain TONO,Protein structure","PeriodicalId":17638,"journal":{"name":"Journal of Tropical Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45072364","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}
E. Tenriawaru, S. Suharjono, T. Ardyati, E. Zubaidah
Sago is one of commodities in South Sulawesi. The extraction process of sago flour produces waste water that still contains organic matter and smells sour. So, it has the potential as a pollutant. The sour odor produced allows the presence of acid-producing bacteria that can be used for waste treatment. The objective of this research is to explore the bacterial community structure in sago pith and sago waste water through high-throughput sequencing technology and its potential uses as organic acids producer. Samples were obtained from a traditional sago factory in Palopo City, South Sulawesi, Indonesia. The acidity degree, total dissolve solid, and temperature were measured in the sago pool at the sampling area, while the nutrient contents were analyzed by titration method in Testing Laboratory of Food Quality and Food Safety, Brawijaya University. Bacterial cells in the sago waste water were acquired through a multilevel filtering process on filter paper with pore nitrocellulose membrane sizes of 0.45 and 0.20 µm. Total DNA trapped in the nitrocellulose membrane with pore size of 0.20 µm was isolated using FastDNA Spin Kit (MPBIO) and the V3-V4 regions of 16S rDNA (341f-806r) were amplified. Amplicons were analyzed by Miseq of Illumina and further analyzed by Muscle v.3.8.31, QIIME v.1.7.0, and R v.2.15.3. The result shows that nutrient content in sago pith is higher than in sago waste water. Both samples are dominated by Phylum Proteobacteria and share 189 common bacterial species. The dominant bacteria that can produce organic acid in sago pith are Dysgonomonas sp., Propionispira sp., and Lactobacillus pentosus. While, Lactobacillus mali and Gluconobacter frateurii are the dominant organic acid-producer bacteria in sago waste water. Keywords: Bacterial community structure, Next generating sequencing, Sago pith, Sago wastewater
{"title":"Bacterial Community Structure in Sago Pith and Sago Waste Water and Its Potential Uses as Organic Acids Producer","authors":"E. Tenriawaru, S. Suharjono, T. Ardyati, E. Zubaidah","doi":"10.11594/jtls.12.02.03","DOIUrl":"https://doi.org/10.11594/jtls.12.02.03","url":null,"abstract":"Sago is one of commodities in South Sulawesi. The extraction process of sago flour produces waste water that still contains organic matter and smells sour. So, it has the potential as a pollutant. The sour odor produced allows the presence of acid-producing bacteria that can be used for waste treatment. The objective of this research is to explore the bacterial community structure in sago pith and sago waste water through high-throughput sequencing technology and its potential uses as organic acids producer. Samples were obtained from a traditional sago factory in Palopo City, South Sulawesi, Indonesia. The acidity degree, total dissolve solid, and temperature were measured in the sago pool at the sampling area, while the nutrient contents were analyzed by titration method in Testing Laboratory of Food Quality and Food Safety, Brawijaya University. Bacterial cells in the sago waste water were acquired through a multilevel filtering process on filter paper with pore nitrocellulose membrane sizes of 0.45 and 0.20 µm. Total DNA trapped in the nitrocellulose membrane with pore size of 0.20 µm was isolated using FastDNA Spin Kit (MPBIO) and the V3-V4 regions of 16S rDNA (341f-806r) were amplified. Amplicons were analyzed by Miseq of Illumina and further analyzed by Muscle v.3.8.31, QIIME v.1.7.0, and R v.2.15.3. The result shows that nutrient content in sago pith is higher than in sago waste water. Both samples are dominated by Phylum Proteobacteria and share 189 common bacterial species. The dominant bacteria that can produce organic acid in sago pith are Dysgonomonas sp., Propionispira sp., and Lactobacillus pentosus. While, Lactobacillus mali and Gluconobacter frateurii are the dominant organic acid-producer bacteria in sago waste water. Keywords: Bacterial community structure, Next generating sequencing, Sago pith, Sago wastewater","PeriodicalId":17638,"journal":{"name":"Journal of Tropical Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43115804","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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