Pub Date : 2022-03-31DOI: 10.26740/jrba.v4n1.p42-50
F. Fatimah, Risky Lailatul Ayu Fadilah, Annida Izzatul Millah, T. Nurhariyati, B. Irawan, Ni’matuzahroh Ni’matuzahroh, M. Affandi, Afifa Rini Nur Izza Zuhri, Eva Watamtin Widhiya, S. Salsabila, Zakia Asrifah Ramly
Most of the plant-associated bacteria can synthesize active biological components of phytohormones such as auxin. This study aimed to examine the potency of 61 endophytic bacteria isolates from the mangroves at Kutang Beach, Lamongan in producing IAA hormone and to identify types of isolates effecting the concentration of IAA, morphological characteristics of isolates, as well as endophytic bacterial species that have the most potential to produce IAA hormone. Screening of endophytic bacteria isolates was performed using the colorimetric method and the production of IAA was carried out using the spectrophotometric method. IAA production by endophytic bacteria was analyzed descriptively and statistically. One-Way ANOVA was employed to determine the effect of the isolate type on the concentration of IAA. The most potential isolates to produce IAA hormone are identified by 16s rRNA gene marker. The screening results showed that 12 isolates of endophytic bacteria have the potential to produce IAA hormones (2.0-9.3 ppm), coded with LMG 7, 15, 31, 32, 43, 53, 54, 55, 56, 57, 62, and 63. The results of the One-Way ANOVA test suggested that the type of isolates did not affect the concentration of IAA produced by endophytic bacteria. The twelve isolates had different morphological characters and those were Gram-positive bacilli with cell sizes ranging from 1.5 µm - 3 µm. The highest concentration of IAA was produced by LMG 15 (9.3 ppm). LMG 15 was identified as Bacillus cereus strain LMG 15, having 99.33% similarity to Bacillus cereus strain IAM 12605.
{"title":"Ability Test of IAA (Indole-3-Acetic Acid) Hormone-Producing Endophytic Bacteria from Lamongan Mangrove","authors":"F. Fatimah, Risky Lailatul Ayu Fadilah, Annida Izzatul Millah, T. Nurhariyati, B. Irawan, Ni’matuzahroh Ni’matuzahroh, M. Affandi, Afifa Rini Nur Izza Zuhri, Eva Watamtin Widhiya, S. Salsabila, Zakia Asrifah Ramly","doi":"10.26740/jrba.v4n1.p42-50","DOIUrl":"https://doi.org/10.26740/jrba.v4n1.p42-50","url":null,"abstract":"Most of the plant-associated bacteria can synthesize active biological components of phytohormones such as auxin. This study aimed to examine the potency of 61 endophytic bacteria isolates from the mangroves at Kutang Beach, Lamongan in producing IAA hormone and to identify types of isolates effecting the concentration of IAA, morphological characteristics of isolates, as well as endophytic bacterial species that have the most potential to produce IAA hormone. Screening of endophytic bacteria isolates was performed using the colorimetric method and the production of IAA was carried out using the spectrophotometric method. IAA production by endophytic bacteria was analyzed descriptively and statistically. One-Way ANOVA was employed to determine the effect of the isolate type on the concentration of IAA. The most potential isolates to produce IAA hormone are identified by 16s rRNA gene marker. The screening results showed that 12 isolates of endophytic bacteria have the potential to produce IAA hormones (2.0-9.3 ppm), coded with LMG 7, 15, 31, 32, 43, 53, 54, 55, 56, 57, 62, and 63. The results of the One-Way ANOVA test suggested that the type of isolates did not affect the concentration of IAA produced by endophytic bacteria. The twelve isolates had different morphological characters and those were Gram-positive bacilli with cell sizes ranging from 1.5 µm - 3 µm. The highest concentration of IAA was produced by LMG 15 (9.3 ppm). LMG 15 was identified as Bacillus cereus strain LMG 15, having 99.33% similarity to Bacillus cereus strain IAM 12605.","PeriodicalId":17741,"journal":{"name":"Jurnal Riset Biologi dan Aplikasinya","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89756959","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 : 2022-03-31DOI: 10.26740/jrba.v4n1.p26-33
F. Fatimah, Annida Izzatul Millah, Risky Lailatul Ayu Fadilah, S. Salsabila, Zakia Asrifah Ramly, Tipuk Sugiarti, T. Nurhariyati, Ni’matuzahroh Ni’matuzahroh, M. Affandi
Endophytic bacteria are microorganisms that live in plant tissues and some of them contribute to nitrogen fixation for plants. This study aimed to isolate and identify endophytic bacteria from mangroves of Kutang Beach, Lamongan, which potentially as nitrogen fixing bacteria. Bacterial Isolates were used as candidates for biofertilizers. Leaves samples were taken from 10 sampling points. Bacterial isolation was initiated by sterilizing the surface of the leaves sample and grinding it aseptically. Isolation was carried out with a pour plate method on Nutrient Agar medium. Screening for endophytic bacteria's potential as N-fixing agent was carried out by growing the bacterial isolates on a semi-solid Nitrogen Free Bromothymol Blue (NFB) medium. The isolates that produced a positive reaction with a change in the color of the medium to blue were then subjected to macroscopic (shape, color, elevation, and the edge of the colony) and microscopic observations (Gram stain and bacterial cell measurements). The isolates showed the fastest change in the color of the medium were identified by the molecular marker of the 16S rRNA gene. The data obtained were analyzed descriptively. As many as 20 isolates were obtained from the mangroves of Kutang Lamongan Beach, and ten isolates of twenty potentially as nitrogen-fixing bacteria. The ten nitrogen-fixing bacteria isolates had varying macroscopic characteristics. The microscopic characteristics showed that eight isolates had Gram-positive bacilli, and two isolates were Gram-negative with varying bacterial sizes. Based on the 16S rRNA gene sequence, the most potential of nitrogen-fixing bacteria was LMG II-14 isolate and identified as Paenibacillus alvei LMG II-14 with 99.36% similarity to Paenibacillus alvei strain DSM 29 based on the NCBI database. The ten nitrogen fixing isolates that have been obtained can later be used as candidates for biofertilizer composition, especially Paenibacillus alvei LMG II-14.
{"title":"Isolation and Potency Test of Endophytic Bacteria as Nitrogen Fixer from Mangrove Plant in Lamongan","authors":"F. Fatimah, Annida Izzatul Millah, Risky Lailatul Ayu Fadilah, S. Salsabila, Zakia Asrifah Ramly, Tipuk Sugiarti, T. Nurhariyati, Ni’matuzahroh Ni’matuzahroh, M. Affandi","doi":"10.26740/jrba.v4n1.p26-33","DOIUrl":"https://doi.org/10.26740/jrba.v4n1.p26-33","url":null,"abstract":"Endophytic bacteria are microorganisms that live in plant tissues and some of them contribute to nitrogen fixation for plants. This study aimed to isolate and identify endophytic bacteria from mangroves of Kutang Beach, Lamongan, which potentially as nitrogen fixing bacteria. Bacterial Isolates were used as candidates for biofertilizers. Leaves samples were taken from 10 sampling points. Bacterial isolation was initiated by sterilizing the surface of the leaves sample and grinding it aseptically. Isolation was carried out with a pour plate method on Nutrient Agar medium. Screening for endophytic bacteria's potential as N-fixing agent was carried out by growing the bacterial isolates on a semi-solid Nitrogen Free Bromothymol Blue (NFB) medium. The isolates that produced a positive reaction with a change in the color of the medium to blue were then subjected to macroscopic (shape, color, elevation, and the edge of the colony) and microscopic observations (Gram stain and bacterial cell measurements). The isolates showed the fastest change in the color of the medium were identified by the molecular marker of the 16S rRNA gene. The data obtained were analyzed descriptively. As many as 20 isolates were obtained from the mangroves of Kutang Lamongan Beach, and ten isolates of twenty potentially as nitrogen-fixing bacteria. The ten nitrogen-fixing bacteria isolates had varying macroscopic characteristics. The microscopic characteristics showed that eight isolates had Gram-positive bacilli, and two isolates were Gram-negative with varying bacterial sizes. Based on the 16S rRNA gene sequence, the most potential of nitrogen-fixing bacteria was LMG II-14 isolate and identified as Paenibacillus alvei LMG II-14 with 99.36% similarity to Paenibacillus alvei strain DSM 29 based on the NCBI database. The ten nitrogen fixing isolates that have been obtained can later be used as candidates for biofertilizer composition, especially Paenibacillus alvei LMG II-14.","PeriodicalId":17741,"journal":{"name":"Jurnal Riset Biologi dan Aplikasinya","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75163555","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 : 2022-03-31DOI: 10.26740/jrba.v4n1.p34-41
A. Prasetya, Lusiawati Dewi, Risya Pramana Situmorang
Tempeh (tempe) has been known to have antibacterial properties due to the presence of glycoprotein compounds, antimicrobial peptides, and flavonoids produced by the fungus Rhizopus spp. during the fermentation process. The addition of garlic powder is expected to increase the antibacterial activity of tempeh against contaminant bacteria. This research aimed to analyze the antibacterial activity, water content, and organoleptic properties (taste, aroma, and color) of tempeh with garlic powder supplementation. Garlic powder was added to the tempeh fermentation process with various concentrations of 0.15, 0.25, 0.50, and 0.75%. Antibacterial activity, water content, and qualitative organoleptic tests were analyzed using paper disk diffusion, gravimetric, and questionnaire methods. The results showed that the addition of garlic powder in all treatments for Bacillus sp had shown an inhibitory activity with moderate strength with an inhibitory power of 0.15; 0.25; 0.50; and 0.75% respectively 8±1.71; 10±1.71; 7±0.96; 9±0.58. Meanwhile, Escherichia coli showed no inhibitory activity. The addition of garlic powder at a concentration of 0.25% reduced the water content to 58.25±0.03. In addition, the addition of garlic powder was not able to affect the color but was able to influence the aroma and taste of tempeh. Garlic powder was able to inhibit Bacillus sp with the best concentration of 0.25%; the addition of garlic powder can reduce the water content and affect the aroma and taste of tempeh.
{"title":"Antibacterial Activity of Garlic Added to Tempeh against Bacillus sp. and Escherichia coli","authors":"A. Prasetya, Lusiawati Dewi, Risya Pramana Situmorang","doi":"10.26740/jrba.v4n1.p34-41","DOIUrl":"https://doi.org/10.26740/jrba.v4n1.p34-41","url":null,"abstract":"Tempeh (tempe) has been known to have antibacterial properties due to the presence of glycoprotein compounds, antimicrobial peptides, and flavonoids produced by the fungus Rhizopus spp. during the fermentation process. The addition of garlic powder is expected to increase the antibacterial activity of tempeh against contaminant bacteria. This research aimed to analyze the antibacterial activity, water content, and organoleptic properties (taste, aroma, and color) of tempeh with garlic powder supplementation. Garlic powder was added to the tempeh fermentation process with various concentrations of 0.15, 0.25, 0.50, and 0.75%. Antibacterial activity, water content, and qualitative organoleptic tests were analyzed using paper disk diffusion, gravimetric, and questionnaire methods. The results showed that the addition of garlic powder in all treatments for Bacillus sp had shown an inhibitory activity with moderate strength with an inhibitory power of 0.15; 0.25; 0.50; and 0.75% respectively 8±1.71; 10±1.71; 7±0.96; 9±0.58. Meanwhile, Escherichia coli showed no inhibitory activity. The addition of garlic powder at a concentration of 0.25% reduced the water content to 58.25±0.03. In addition, the addition of garlic powder was not able to affect the color but was able to influence the aroma and taste of tempeh. Garlic powder was able to inhibit Bacillus sp with the best concentration of 0.25%; the addition of garlic powder can reduce the water content and affect the aroma and taste of tempeh.","PeriodicalId":17741,"journal":{"name":"Jurnal Riset Biologi dan Aplikasinya","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79648235","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 : 2022-03-31DOI: 10.26740/jrba.v4n1.p19-25
Anggiresti Kinasih, Alim El Hakim, Dyah Ayu Puspita Arum, Aulia Noor Ramadhani, E. Semiarti
Infection and deaths cases by SARS-CoV-2 still increase and have not decreased significantly. Main protease (Mpro) is playing an important role in the replication of SARS-CoV-2 life cycle and causes of rapid transmission. Natural compounds are potential to be antiviral candidates with high bioavailability and low cytotoxicity. Orchids of Dendrobium genus have high diversity in Indonesia. Dendrobium has been used as traditional Chinese medicine and contains a group of secondary metabolites with antiviral activity. This study aimed to determine the potential of secondary metabolites of Dendrobium orchids as antiviral candidates against Mpro SARS-CoV-2 with in silico molecular docking. Secondary metabolites obtained from the KNApSAck and PubChem act as ligands. N3 inhibitors as native ligands were obtained from the RCSB. Mpro SARS-CoV-2 (6LU7) as a target macromolecule. Molecular docking was carried out using the online Covid-19 Docking Server using AutoDock Vina device. The most negative binding affinity value for each ligand compared to the native ligand binding affinity. Visualization with Discovery Studio software has been used to observe the protein amino acid residues contact for each ligand. The binding affinity of the native ligand inhibitor N3 is -7.5 kcal/mol. Based on the results of Mpro docking, three phytochemicals from Dendrobium spp., i.e., dendrocandin B, denthyrsinone, and denthyrsinol compounds have binding affinities of -7.7 kcal/mol, -7.9 kcal/mol, and -8.1 kcal/mol, respectively. It can be concluded that in Dendrobium orchid, denthyrsinol has the highest chance of binding so it has the potential to inhibit the Mpro SARS-CoV-2 activity.
{"title":"In Silico Study of Secondary Metabolites in Dendrobium spp. as SARS-CoV-2 Antivirus on Main Protease (Mpro)","authors":"Anggiresti Kinasih, Alim El Hakim, Dyah Ayu Puspita Arum, Aulia Noor Ramadhani, E. Semiarti","doi":"10.26740/jrba.v4n1.p19-25","DOIUrl":"https://doi.org/10.26740/jrba.v4n1.p19-25","url":null,"abstract":"Infection and deaths cases by SARS-CoV-2 still increase and have not decreased significantly. Main protease (Mpro) is playing an important role in the replication of SARS-CoV-2 life cycle and causes of rapid transmission. Natural compounds are potential to be antiviral candidates with high bioavailability and low cytotoxicity. Orchids of Dendrobium genus have high diversity in Indonesia. Dendrobium has been used as traditional Chinese medicine and contains a group of secondary metabolites with antiviral activity. This study aimed to determine the potential of secondary metabolites of Dendrobium orchids as antiviral candidates against Mpro SARS-CoV-2 with in silico molecular docking. Secondary metabolites obtained from the KNApSAck and PubChem act as ligands. N3 inhibitors as native ligands were obtained from the RCSB. Mpro SARS-CoV-2 (6LU7) as a target macromolecule. Molecular docking was carried out using the online Covid-19 Docking Server using AutoDock Vina device. The most negative binding affinity value for each ligand compared to the native ligand binding affinity. Visualization with Discovery Studio software has been used to observe the protein amino acid residues contact for each ligand. The binding affinity of the native ligand inhibitor N3 is -7.5 kcal/mol. Based on the results of Mpro docking, three phytochemicals from Dendrobium spp., i.e., dendrocandin B, denthyrsinone, and denthyrsinol compounds have binding affinities of -7.7 kcal/mol, -7.9 kcal/mol, and -8.1 kcal/mol, respectively. It can be concluded that in Dendrobium orchid, denthyrsinol has the highest chance of binding so it has the potential to inhibit the Mpro SARS-CoV-2 activity.","PeriodicalId":17741,"journal":{"name":"Jurnal Riset Biologi dan Aplikasinya","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90854366","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 : 2021-11-11DOI: 10.26740/JRBA.V3N2.P73-79
A. Santoso, P. Purnomo
Tobacco (Nicotiana tabacum L.) is a plant used as a mixture of cigarettes, and recreational media especially for men. This study aimed to identify variations, and determine the relationship between tobacco cultivars in Central Java and Yogyakarta based on macromorphological and micromorphological characters. Sampling locations are determined by surveying locations in both regions. Tobacco samples found include 5 cultivars in Central Java namely 'Mantili', 'Uler Magetan', 'Garut', ‘Gober Boyolali’, 'Manila', and 3 cultivars in Yogyakarta namely 'Siluk', 'Java', and 'Virginia'. Characterization with 23 qualitative macromorphological characters including leaves, and stems, with 9 qualitative and quantitative micromorphological characters including trichome and stomata. Descriptive data analysis is done to obtain the typical character of each cultivar, followed by numerical analysis including scoring characters processed with MVSP (Multi Variate Statistical Package), clustering with UPGMA (Unweighted Pair Group Method with Averages), and calculation of similarity coefficients with Simple matching formula. The results showed variations in the macromorphological characters including the shape of the leaf lamina, the base of the leaf, the absence of leaf stalks, and type of leaf venation. Tobacco has anisositic stomata, and varies in terms of length, width, and density of stomata. Tobacco trichomes are glandular. The result dendrograms form two clusters (A and B) with the similarity index of each cluster above 0.80. Cultivars with close relationships such as 'Siluk'-'Java', and far relationship like 'Java'-'Manila'.
烟草(Nicotiana tabacum L.)是一种混合香烟的植物，也是男性的娱乐媒介。本研究旨在基于大形态和微形态特征，鉴定中爪哇和日惹地区烟草品种间的变异和关系。抽样地点由两个地区的调查地点确定。发现的烟草样品包括中爪哇的5个品种，即“Mantili”、“Uler Magetan”、“Garut”、“Gober Boyolali”和“Manila”，以及日惹的3个品种，即“Siluk”、“Java”和“Virginia”。鉴定了叶、茎等23个定性大形态性状和毛状体、气孔等9个定性定量小形态性状。通过描述性数据分析获得各品种的典型性状，然后进行数值分析，包括用MVSP (Multi - Variate Statistical Package)对性状进行评分，用UPGMA (Unweighted Pair Group Method with average)进行聚类，用简单匹配公式计算相似系数。结果表明，在叶面形状、叶基、叶柄缺失、叶脉类型等宏观形态学特征上存在差异。烟草具有各向异性气孔，气孔的长度、宽度和密度各不相同。烟草毛状体是腺状的。结果树状图形成A、B两类，每类相似度均在0.80以上。亲缘关系较近的品种，如‘Siluk’-‘Java’，亲缘关系较远的品种，如‘Java’-‘Manila’。
{"title":"Variation and Phenetic Relationship of Tobacco (Nicotiana tabacum L.) In Central Java and Yogyakarta Based on Morphological Characters","authors":"A. Santoso, P. Purnomo","doi":"10.26740/JRBA.V3N2.P73-79","DOIUrl":"https://doi.org/10.26740/JRBA.V3N2.P73-79","url":null,"abstract":"Tobacco (Nicotiana tabacum L.) is a plant used as a mixture of cigarettes, and recreational media especially for men. This study aimed to identify variations, and determine the relationship between tobacco cultivars in Central Java and Yogyakarta based on macromorphological and micromorphological characters. Sampling locations are determined by surveying locations in both regions. Tobacco samples found include 5 cultivars in Central Java namely 'Mantili', 'Uler Magetan', 'Garut', ‘Gober Boyolali’, 'Manila', and 3 cultivars in Yogyakarta namely 'Siluk', 'Java', and 'Virginia'. Characterization with 23 qualitative macromorphological characters including leaves, and stems, with 9 qualitative and quantitative micromorphological characters including trichome and stomata. Descriptive data analysis is done to obtain the typical character of each cultivar, followed by numerical analysis including scoring characters processed with MVSP (Multi Variate Statistical Package), clustering with UPGMA (Unweighted Pair Group Method with Averages), and calculation of similarity coefficients with Simple matching formula. The results showed variations in the macromorphological characters including the shape of the leaf lamina, the base of the leaf, the absence of leaf stalks, and type of leaf venation. Tobacco has anisositic stomata, and varies in terms of length, width, and density of stomata. Tobacco trichomes are glandular. The result dendrograms form two clusters (A and B) with the similarity index of each cluster above 0.80. Cultivars with close relationships such as 'Siluk'-'Java', and far relationship like 'Java'-'Manila'.","PeriodicalId":17741,"journal":{"name":"Jurnal Riset Biologi dan Aplikasinya","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83431194","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 : 2021-11-11DOI: 10.26740/jrba.v3n2.p68-72
S. Zulaikha, M. A. D. Susanto
Selorejo Waterfall is a natural tourist area that is directly adjacent to the Sigogor Mountain Nature Reserve and has a beautiful and natural environment. This makes the Selorejo Waterfall area has a good environment for the sustainability of various species of butterflies. This research aimed to find out the diversity and abundance of butterflies in the Selorejo Waterfall area. This research was conducted using the Visual Day Flaying method by following the trail in the Selorejo Waterfall area. This study found 26 species belongs 4 families with 109 individuals in total. The value of the species diversity index at the location of H'= 2.81 moderate category. The diversity of butterflies in the Selorejo Waterfall area was influenced by the availability of host plants and feed as well as abiotic factors.
{"title":"Diversity of Lepidoptera: Rhopalocera at Selorejo Waterfall Area, Ponorogo District, East Java, Indonesia","authors":"S. Zulaikha, M. A. D. Susanto","doi":"10.26740/jrba.v3n2.p68-72","DOIUrl":"https://doi.org/10.26740/jrba.v3n2.p68-72","url":null,"abstract":"Selorejo Waterfall is a natural tourist area that is directly adjacent to the Sigogor Mountain Nature Reserve and has a beautiful and natural environment. This makes the Selorejo Waterfall area has a good environment for the sustainability of various species of butterflies. This research aimed to find out the diversity and abundance of butterflies in the Selorejo Waterfall area. This research was conducted using the Visual Day Flaying method by following the trail in the Selorejo Waterfall area. This study found 26 species belongs 4 families with 109 individuals in total. The value of the species diversity index at the location of H'= 2.81 moderate category. The diversity of butterflies in the Selorejo Waterfall area was influenced by the availability of host plants and feed as well as abiotic factors.","PeriodicalId":17741,"journal":{"name":"Jurnal Riset Biologi dan Aplikasinya","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87311960","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 : 2021-11-11DOI: 10.26740/jrba.v3n2.p63-67
A. Rohman, Ragil Satriyo Gumilang
Sanderling (Calidris alba) is a type of shorebird that migrates from the northern hemisphere to the southern hemisphere. Indonesia is a migration route for East Asia-Australasia. The southern coastal area of the Jember Regency, one of the wetlands, especially in East Java, has become an air route and a stopover for shorebirds every year. The research objective was to determine the population of Sanderling (Calidris alba) on the southern coast of Puger and Getem, Jember Regency. Method of collecting encounter rates. Bird watching is carried out in the morning at 06.00-08.00 and in the afternoon at 15.30-17.30. Data recording includes species, number of birds, and other supporting data. Identification using the book by Mac Kinnon et al. (2010) and Bhushan, B., et al. (1993). Tools used for binocular observation, monocular, camera, and GPS. Data analysis used the density index for individual bird species using the formula method (Alikodra, 1990). The results of the study were a total of 445 individuals. Data analysis of Muara Sungai population density was the location with the four other survey locations' highest number.
鹬(学名Calidris alba)是一种从北半球迁徙到南半球的滨鸟。印度尼西亚是东亚-澳大拉西亚移民的必经之地。Jember Regency的南部沿海地区是其中一个湿地，特别是在东爪哇，每年都成为一条空中航线和岸鸟的中途停留地。研究目的是确定在Jember reggency的Puger和Getem南部海岸的Sanderling (Calidris alba)的种群数量。收集相遇率的方法。观鸟时间为上午6时至8时，下午15时至17时30分。数据记录包括鸟类的种类、数量和其他支持数据。Mac Kinnon et al.(2010)和Bhushan, B.， et al.(1993)使用这本书进行识别。用于双目观察、单眼、相机和GPS的工具。数据分析采用公式法计算鸟类个体密度指数(Alikodra, 1990)。这项研究的结果是445个人。数据分析Muara Sungai的人口密度是其他四个调查点人口密度最高的地点。
{"title":"The population of Sanderling (Calidris alba) in 2020 Migration on the South Coast of Puger, Getem, Jember","authors":"A. Rohman, Ragil Satriyo Gumilang","doi":"10.26740/jrba.v3n2.p63-67","DOIUrl":"https://doi.org/10.26740/jrba.v3n2.p63-67","url":null,"abstract":"Sanderling (Calidris alba) is a type of shorebird that migrates from the northern hemisphere to the southern hemisphere. Indonesia is a migration route for East Asia-Australasia. The southern coastal area of the Jember Regency, one of the wetlands, especially in East Java, has become an air route and a stopover for shorebirds every year. The research objective was to determine the population of Sanderling (Calidris alba) on the southern coast of Puger and Getem, Jember Regency. Method of collecting encounter rates. Bird watching is carried out in the morning at 06.00-08.00 and in the afternoon at 15.30-17.30. Data recording includes species, number of birds, and other supporting data. Identification using the book by Mac Kinnon et al. (2010) and Bhushan, B., et al. (1993). Tools used for binocular observation, monocular, camera, and GPS. Data analysis used the density index for individual bird species using the formula method (Alikodra, 1990). The results of the study were a total of 445 individuals. Data analysis of Muara Sungai population density was the location with the four other survey locations' highest number.","PeriodicalId":17741,"journal":{"name":"Jurnal Riset Biologi dan Aplikasinya","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86647095","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 : 2021-11-11DOI: 10.26740/jrba.v3n2.p45-53
N. Anggraini, D. Listyorini
COVID-19 is a pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The first case was found in the city of Wuhan, Hubei province, China. The first case in Indonesia was reported in March 2020 and currently there are 0.5 million cases with a death rate of 3.1%. This rapid increase in cases is thought to due to presence of the mutant strain S-D614G, which causes a faster rate of infection and spread. The purpose of this study was to determine the presence of S-D614G mutations in Indonesian samples in order to find the origin of COVID-19 which was spread in Indonesia based on the Spike gene sequences and the RdRp genes from 25 countries, and one control sequence China/Wuhan-Hu-1 obtained from the NCBI and GISAID databases. Mutation analysis was carried out through multiple alignments using BioEdit software. Phylogenetic tree reconstruction using MEGA6 software with the Neighbor Joining method. This study found mutation of S-D614G in one Indonesian sample, namely the Indonesian/SBY9 sample along with 23 samples from Europe, America, and Africa. The phylogenetic tree reconstruction confirmed these findings; the mutated samples were closely related to samples from these continents, while the non-mutated Indonesian samples were closely related to sample from East Asia. These findings indicate that the origin of the SARS-CoV-2 virus in Indonesia possibly came from the East Asia cluster and the European-American cluster.
COVID-19是由严重急性呼吸综合征冠状病毒2 (SARS-CoV-2)病毒引起的大流行疾病。首例病例是在中国湖北省武汉市发现的。印度尼西亚于2020年3月报告了第一例病例，目前有50万例病例，死亡率为3.1%。病例的迅速增加被认为是由于突变株S-D614G的存在，它导致更快的感染和传播速度。本研究的目的是利用来自25个国家的Spike基因序列和RdRp基因，以及NCBI和GISAID数据库中获得的一个对照序列China/武汉- hu -1，确定印度尼西亚样本中是否存在S-D614G突变，以寻找在印度尼西亚传播的COVID-19的起源。突变分析采用BioEdit软件进行多重比对。采用MEGA6软件进行系统发育树重建，采用Neighbor Joining法。本研究在印度尼西亚的1个样本(即印度尼西亚/SBY9样本)以及来自欧洲、美洲和非洲的23个样本中发现S-D614G突变。系统发育树重建证实了这些发现;突变样本与来自这些大陆的样本密切相关，而未突变的印度尼西亚样本与来自东亚的样本密切相关。这些发现表明，印度尼西亚SARS-CoV-2病毒的起源可能来自东亚聚集性和欧美聚集性。
{"title":"S-D614G Mutation Reveals the Euro-America and East-Asia Origin SARS-CoV-2 Virus Spread in Indonesia","authors":"N. Anggraini, D. Listyorini","doi":"10.26740/jrba.v3n2.p45-53","DOIUrl":"https://doi.org/10.26740/jrba.v3n2.p45-53","url":null,"abstract":"COVID-19 is a pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The first case was found in the city of Wuhan, Hubei province, China. The first case in Indonesia was reported in March 2020 and currently there are 0.5 million cases with a death rate of 3.1%. This rapid increase in cases is thought to due to presence of the mutant strain S-D614G, which causes a faster rate of infection and spread. The purpose of this study was to determine the presence of S-D614G mutations in Indonesian samples in order to find the origin of COVID-19 which was spread in Indonesia based on the Spike gene sequences and the RdRp genes from 25 countries, and one control sequence China/Wuhan-Hu-1 obtained from the NCBI and GISAID databases. Mutation analysis was carried out through multiple alignments using BioEdit software. Phylogenetic tree reconstruction using MEGA6 software with the Neighbor Joining method. This study found mutation of S-D614G in one Indonesian sample, namely the Indonesian/SBY9 sample along with 23 samples from Europe, America, and Africa. The phylogenetic tree reconstruction confirmed these findings; the mutated samples were closely related to samples from these continents, while the non-mutated Indonesian samples were closely related to sample from East Asia. These findings indicate that the origin of the SARS-CoV-2 virus in Indonesia possibly came from the East Asia cluster and the European-American cluster.","PeriodicalId":17741,"journal":{"name":"Jurnal Riset Biologi dan Aplikasinya","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89574524","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 : 2021-03-31DOI: 10.26740/JRBA.V3N1.P38-44
Fikriani Choirun Nita, Ardana I Kade Karisma Gita, Listyorini Dwi
SARS-CoV-2 is a virus that has caused COVID-19 pandemic. This virus is a new variant of the SARS-CoV virus and also closely related to MERS-CoV, which caused similar acute respiratory infections. All these viruses recognize target cells by binding to the Receptor Binding Domain (RBD) on Spike protein with receptors. This study aimed to determine the SARS-CoV-2, MERS-CoV, and SARS-CoV genome structure, Spike protein sequence differences, and variations of RBD’s Receptor Binding Motif (RBM). This research was using data mining approach. Genome sequences were downloaded from NCBI, except for Indonesian samples were downloaded from GISAID. Genomic structures, Spike sequence, and RBD structure were analyzed using Bioedit, followed by protein modelling using SwissModel and PyMol applications. The result showed that the SARS-CoV-2, MERS-CoV, and SARS-CoV genome shared the same genes yet in different numbers and length. SARS-CoV-2 Spike protein sequence was quite similar to SARS-CoV Spike protein, but very different to the Spike protein of MERS-CoV. There were variations of RBD’s RBM structure due to the mutations occurred among these viruses. It is suggested that these differences may increase the affinity between SARS-CoV-2 Spike protein to its hACE2 receptor which caused SARS-CoV-2 becomes more infective and spread wider than SARS-CoV and MERS-CoV, in turn. This result expected to be basic information for the development of SARS-CoV-2 introduction inhibition agent and spreading prevention.
{"title":"The Comparison of SARS-CoV-2, SARS-CoV, and MERS-CoV Genome and Spike Protein Variations","authors":"Fikriani Choirun Nita, Ardana I Kade Karisma Gita, Listyorini Dwi","doi":"10.26740/JRBA.V3N1.P38-44","DOIUrl":"https://doi.org/10.26740/JRBA.V3N1.P38-44","url":null,"abstract":"SARS-CoV-2 is a virus that has caused COVID-19 pandemic. This virus is a new variant of the SARS-CoV virus and also closely related to MERS-CoV, which caused similar acute respiratory infections. All these viruses recognize target cells by binding to the Receptor Binding Domain (RBD) on Spike protein with receptors. This study aimed to determine the SARS-CoV-2, MERS-CoV, and SARS-CoV genome structure, Spike protein sequence differences, and variations of RBD’s Receptor Binding Motif (RBM). This research was using data mining approach. Genome sequences were downloaded from NCBI, except for Indonesian samples were downloaded from GISAID. Genomic structures, Spike sequence, and RBD structure were analyzed using Bioedit, followed by protein modelling using SwissModel and PyMol applications. The result showed that the SARS-CoV-2, MERS-CoV, and SARS-CoV genome shared the same genes yet in different numbers and length. SARS-CoV-2 Spike protein sequence was quite similar to SARS-CoV Spike protein, but very different to the Spike protein of MERS-CoV. There were variations of RBD’s RBM structure due to the mutations occurred among these viruses. It is suggested that these differences may increase the affinity between SARS-CoV-2 Spike protein to its hACE2 receptor which caused SARS-CoV-2 becomes more infective and spread wider than SARS-CoV and MERS-CoV, in turn. This result expected to be basic information for the development of SARS-CoV-2 introduction inhibition agent and spreading prevention.","PeriodicalId":17741,"journal":{"name":"Jurnal Riset Biologi dan Aplikasinya","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82210432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-09-30DOI: 10.26740/jrba.v1n2.p71-79
Sandra Rafika Devi, Luhur Septiadi, Muhammad Prayogi Erfanda, Berry Fakhry Hanifa, Dinda Tinalanisari Firizki, Qoyin Nadhori
Amfibi (Ordo Anura) merupakan bagian dari komponen ekosistem yang memiliki peranan sangat penting. Penelitian ini bertujuan untuk menganalisis struktur komunitas Ordo Anura di Lokasi Wisata Bedengan daerah Kabupaten Malang. Metode yang digunakan adalah Visual Encounter Survey (VES) yang dikombinasikan dengan purposive sampling melalui jalur akuatik yang dibagi menjadi 2 zona yaitu 300×5 meter di bagian atas jembatan dan 300×5 meter di bagian bawah jembatan. Penelitian dilakukan sebelum musim penghujan, penghujan awal, dan penghujan, pada bulan Oktober-Desember 2018. Data yang diperoleh dianalisis dengan menggunakan indeks keanekaragaman Shannon-Wiener, kepadatan dan kepadatan relatif. Hasil penelitian menunjukkan bahwaempat famili yang berhasil diidentifikasi yang meliputi Famili Ranidae, Bufonidae, Microhylidae, dan Megophrydae. Perhitungan indeks keanekaragaman di Bedengan menunjukkan nilai yang rendah yakni sebesar 0,96. Kepadatan dan kepadatan relatif mengalami kenaikan dimulai dari sebelum penghujan, penghujan awal dan pada saat musim penghujan, akan tetapi keanekaragaman mengalami fluktuasi.
{"title":"Struktur Komunitas Ordo Anura di Lokasi Wisata Bedengan Desa Selorejo Kecamatan Dau Kabupaten Malang","authors":"Sandra Rafika Devi, Luhur Septiadi, Muhammad Prayogi Erfanda, Berry Fakhry Hanifa, Dinda Tinalanisari Firizki, Qoyin Nadhori","doi":"10.26740/jrba.v1n2.p71-79","DOIUrl":"https://doi.org/10.26740/jrba.v1n2.p71-79","url":null,"abstract":"Amfibi (Ordo Anura) merupakan bagian dari komponen ekosistem yang memiliki peranan sangat penting. Penelitian ini bertujuan untuk menganalisis struktur komunitas Ordo Anura di Lokasi Wisata Bedengan daerah Kabupaten Malang. Metode yang digunakan adalah Visual Encounter Survey (VES) yang dikombinasikan dengan purposive sampling melalui jalur akuatik yang dibagi menjadi 2 zona yaitu 300×5 meter di bagian atas jembatan dan 300×5 meter di bagian bawah jembatan. Penelitian dilakukan sebelum musim penghujan, penghujan awal, dan penghujan, pada bulan Oktober-Desember 2018. Data yang diperoleh dianalisis dengan menggunakan indeks keanekaragaman Shannon-Wiener, kepadatan dan kepadatan relatif. Hasil penelitian menunjukkan bahwaempat famili yang berhasil diidentifikasi yang meliputi Famili Ranidae, Bufonidae, Microhylidae, dan Megophrydae. Perhitungan indeks keanekaragaman di Bedengan menunjukkan nilai yang rendah yakni sebesar 0,96. Kepadatan dan kepadatan relatif mengalami kenaikan dimulai dari sebelum penghujan, penghujan awal dan pada saat musim penghujan, akan tetapi keanekaragaman mengalami fluktuasi.","PeriodicalId":17741,"journal":{"name":"Jurnal Riset Biologi dan Aplikasinya","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86061575","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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