Pub Date : 2024-07-10DOI: 10.4308/hjb.31.5.1030-1036
Firda Nuri Asyhari, Heni Sukma Zulfatim, Nenis Try Melani Putri, Moh Dliyauddin, Ahmad Shobrun Jamil, A. Soewondo, Muhammad Halim Natsir, Mansur Ibrahim, Sri Rahayu, M. S. Djati, M. Rifa’i
Maintaining immunoglobulin levels in the body is important to protect the body from exposure to pathogens. One effort can be made by consuming herbs containing immunomodulatory compounds, such as Cheral®, which includes a combination of herbs Phyllanthus niruri and Curcuma longa. This research aims to determine the expression of immunoglobulin M (IgM) and immunoglobulin G (IgG) following the administration of Cheral® to Wistar rats. The study was conducted in vivo, utilizing 24 healthy male Wistar rats for a 90-day treatment period. The research was divided into four treatment groups, including a control group and three dosage groups: Dose 1 (156.25 mg/kg BW), Dose 2 (312.5 mg/kg BW), and Dose 3 (468.75 mg/kg BW). IgM and IgG were isolated from the spleen and analyzed using flow cytometry. Flow cytometry data were analyzed using SPSS with a one-way ANOVA and post hoc test (p-value <0.05). The analysis showed that the relative number of IgM-producing cells in the control group was significantly higher than in the treatment groups, with a difference of 44.40%. In contrast, the relative number of IgG-producing cells in Dose 3 was significantly lower than all other treatment groups, showing a decrease of 29.21%. Overall, the expression of IgG and IgM did not differ substantially across all treatments. The lower IgG and IgM profiles compared to the control group indicate Cheral®'s ability to prevent infections and maintain the immune system of the rats throughout the treatment period.
{"title":"Expression of Immunoglobulin M (IgM) and Immunoglobulin G (IgG) in Normal Wistar Rat Post-Cheral® Administration","authors":"Firda Nuri Asyhari, Heni Sukma Zulfatim, Nenis Try Melani Putri, Moh Dliyauddin, Ahmad Shobrun Jamil, A. Soewondo, Muhammad Halim Natsir, Mansur Ibrahim, Sri Rahayu, M. S. Djati, M. Rifa’i","doi":"10.4308/hjb.31.5.1030-1036","DOIUrl":"https://doi.org/10.4308/hjb.31.5.1030-1036","url":null,"abstract":"Maintaining immunoglobulin levels in the body is important to protect the body from exposure to pathogens. One effort can be made by consuming herbs containing immunomodulatory compounds, such as Cheral®, which includes a combination of herbs Phyllanthus niruri and Curcuma longa. This research aims to determine the expression of immunoglobulin M (IgM) and immunoglobulin G (IgG) following the administration of Cheral® to Wistar rats. The study was conducted in vivo, utilizing 24 healthy male Wistar rats for a 90-day treatment period. The research was divided into four treatment groups, including a control group and three dosage groups: Dose 1 (156.25 mg/kg BW), Dose 2 (312.5 mg/kg BW), and Dose 3 (468.75 mg/kg BW). IgM and IgG were isolated from the spleen and analyzed using flow cytometry. Flow cytometry data were analyzed using SPSS with a one-way ANOVA and post hoc test (p-value <0.05). The analysis showed that the relative number of IgM-producing cells in the control group was significantly higher than in the treatment groups, with a difference of 44.40%. In contrast, the relative number of IgG-producing cells in Dose 3 was significantly lower than all other treatment groups, showing a decrease of 29.21%. Overall, the expression of IgG and IgM did not differ substantially across all treatments. The lower IgG and IgM profiles compared to the control group indicate Cheral®'s ability to prevent infections and maintain the immune system of the rats throughout the treatment period.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141660519","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 : 2024-07-05DOI: 10.4308/hjb.31.5.1019-1029
Muhammad Indra Maulana, S. Pakpahan, Andy Darmawan, Yanti Ariyanti
The Calotes genus presents a challenge due to the complexity of its species. However, research on the cryptic species complex within the Indonesian Calotes genus is still lacking. This study aims to determine the extent of genetic relationships and assess the potential existence of a species complex within the Indonesian genus Calotes (Daudin, 1802) (Squamata, Agamidae) using the partial Cytochrome c Oxidase Subunit 1 (COI) gene sequence as a molecular marker. Samples of the Indonesian Calotes genus in this study were collected from South Lampung (Lampung), Bogor (West Java), and Langkat (North Sumatra). By aligning 582 bp sequence similarities with reference sequences in GenBank, we confirmed that seven out of eight samples analyzed belonged to Calotes vultuosus, while one sample was identified as Calotes versicolor. The identity values ranged from 96 to 100%. The C. vultuosus samples in this study displayed lower genetic distances, ranging from 0 to 3%, with the reference C. vultuosus sequence from Indonesia compared to the reference sequence from India, which ranged from 6 to 9%. Phylogenetic tree reconstruction, utilizing both maximum likelihood with IQ-Tree and Bayesian Inference with BEAST methods, further supports these findings. It reveals distinct groupings between C. vultuosus samples from Indonesia and India. These results suggest the potential occurrence of a species complex within the Indonesian genus Calotes. Furthermore, the inclusion of eight COI gene sequences from two Calotes species in the GenBank database has the potential to confirm the existence of previously undocumented species in Indonesia.
Calotes 属因其物种的复杂性而成为一项挑战。然而，印尼菖蒲属中的隐性物种群研究仍然缺乏。本研究旨在利用部分细胞色素 c 氧化酶亚基 1（COI）基因序列作为分子标记，确定印尼 Calotes 属（Daudin，1802 年）（有鳞目，蟾蜍科）的遗传关系范围，并评估该属可能存在的物种复合体。本研究中的印尼菖蒲属样本采集自南楠榜（楠榜）、茂物（西爪哇）和兰卡（北苏门答腊）。通过与 GenBank 中的参考序列进行 582 bp 序列相似性比对，我们确认分析的 8 个样本中有 7 个属于 Calotes vultuosus，1 个样本被鉴定为 Calotes versicolor。同一性值从 96%到 100%不等。与来自印度的 C. vultuosus 参考序列相比，本研究中的 C. vultuosus 样本与来自印度尼西亚的 C. vultuosus 参考序列的遗传距离较低，从 0% 到 3% 不等，而来自印度的 C. vultuosus 参考序列的遗传距离则从 6% 到 9% 不等。利用最大似然法（IQ-Tree）和贝叶斯推理法（BEAST）重建的系统发生树进一步证实了这些发现。它揭示了来自印度尼西亚和印度的 C. vultuosus 样本之间不同的分组。这些结果表明，在印度尼西亚的 Calotes 属中可能存在一个物种复合体。此外，GenBank 数据库中包含了来自两个 Calotes 物种的八个 COI 基因序列，这有可能证实印度尼西亚存在以前未记录的物种。
{"title":"Genetic Relationship and the Putative Occurrence of A Species Complex Within the Indonesian Calotes (Daudin, 1802) (Squamata, Agamidae) Genus Based on COI Gene Sequences","authors":"Muhammad Indra Maulana, S. Pakpahan, Andy Darmawan, Yanti Ariyanti","doi":"10.4308/hjb.31.5.1019-1029","DOIUrl":"https://doi.org/10.4308/hjb.31.5.1019-1029","url":null,"abstract":"The Calotes genus presents a challenge due to the complexity of its species. However, research on the cryptic species complex within the Indonesian Calotes genus is still lacking. This study aims to determine the extent of genetic relationships and assess the potential existence of a species complex within the Indonesian genus Calotes (Daudin, 1802) (Squamata, Agamidae) using the partial Cytochrome c Oxidase Subunit 1 (COI) gene sequence as a molecular marker. Samples of the Indonesian Calotes genus in this study were collected from South Lampung (Lampung), Bogor (West Java), and Langkat (North Sumatra). By aligning 582 bp sequence similarities with reference sequences in GenBank, we confirmed that seven out of eight samples analyzed belonged to Calotes vultuosus, while one sample was identified as Calotes versicolor. The identity values ranged from 96 to 100%. The C. vultuosus samples in this study displayed lower genetic distances, ranging from 0 to 3%, with the reference C. vultuosus sequence from Indonesia compared to the reference sequence from India, which ranged from 6 to 9%. Phylogenetic tree reconstruction, utilizing both maximum likelihood with IQ-Tree and Bayesian Inference with BEAST methods, further supports these findings. It reveals distinct groupings between C. vultuosus samples from Indonesia and India. These results suggest the potential occurrence of a species complex within the Indonesian genus Calotes. Furthermore, the inclusion of eight COI gene sequences from two Calotes species in the GenBank database has the potential to confirm the existence of previously undocumented species in Indonesia.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141673699","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 : 2024-07-03DOI: 10.4308/hjb.31.5.1007-1018
E. Giri-rachman, Marselina Irasonia Tan, Novia Syari Intan, Putri Ayu Fajar, Gladys Emmanuella, Putri Wojciechowska, R. Hertadi, Debbie Soefie
Hepatitis B virus (HBV) remains an important healthcare challenge, leading to liver diseases like cirrhosis and cancer. In response, we created a prophylactic and therapeutic HBV vaccine by integrating HBcAg and HBsAg from HBV genotype B into Norovirus (NoV) GII.2 P domain (PdomGII.2-HBV) for enhanced intranasal delivery. This vaccine also aimed to simultaneously prevent NoV infection, which causes gastroenteritis. Since the selected HBV epitopes have undergone extensive research and are tailored to the Indonesian population, this study focused on identifying NoV epitopes and assessing T cell epitopes coverage of the PdomGII.2-HBV for the Indonesian population. Following that, we expressed the PdomGII.2-HBV protein using Escherichia coli BL21(DE3) and employed a gentle solubilization technique for protein purification. Our in-silico analysis identified two B cell epitopes, along with 15 CD4+T cell epitopes and 35 CD8+T cell epitopes within the GII.2 P domain. These T cell epitopes cover 100% of the Javanese-Sundanese population's HLA allele variations, which constituted the largest demographic group in Indonesia. Subsequently, we successfully purified the presumed PdomGII.2-HBV protein, revealing a molecular weight of 39.5 kDa. Following the successful expression and purification of the presumed PdomGII.2-HBV protein, it is evident that this vaccine design has significant potential, warranting further study.
乙型肝炎病毒（HBV）仍是一项重要的医疗挑战，可导致肝硬化和癌症等肝脏疾病。为此，我们将乙型肝炎病毒（HBV）基因型中的 HBcAg 和 HBsAg 整合到诺罗病毒（NoV）GII.2 P 结构域（PdomGII.2-HBV）中，创建了一种预防性和治疗性乙型肝炎病毒疫苗（PdomGII.2-HBV），以增强鼻内给药效果。该疫苗还旨在同时预防导致肠胃炎的诺罗病毒感染。由于所选的 HBV 表位经过广泛研究并适合印尼人群，因此本研究侧重于确定印尼人群的 NoV 表位并评估 PdomGII.2-HBV 的 T 细胞表位覆盖率。随后，我们使用大肠杆菌 BL21(DE3)表达了 PdomGII.2-HBV 蛋白，并采用温和溶解技术进行蛋白纯化。我们的内部分析确定了 GII.2 P 结构域中的两个 B 细胞表位、15 个 CD4+T 细胞表位和 35 个 CD8+T 细胞表位。这些 T 细胞表位覆盖了爪哇-巽他人群 100% 的 HLA 等位基因变异，而爪哇-巽他人群是印尼最大的人口群体。随后，我们成功纯化了假定的 PdomGII.2-HBV 蛋白，发现其分子量为 39.5 kDa。在成功表达和纯化推测的 PdomGII.2-HBV 蛋白后，这种疫苗设计显然具有巨大的潜力，值得进一步研究。
{"title":"In Silico Study, Design, and Expression of an Intranasal Dual Chimeric Vaccine for Indonesian-Based Norovirus GII-2 and Hepatitis B","authors":"E. Giri-rachman, Marselina Irasonia Tan, Novia Syari Intan, Putri Ayu Fajar, Gladys Emmanuella, Putri Wojciechowska, R. Hertadi, Debbie Soefie","doi":"10.4308/hjb.31.5.1007-1018","DOIUrl":"https://doi.org/10.4308/hjb.31.5.1007-1018","url":null,"abstract":"Hepatitis B virus (HBV) remains an important healthcare challenge, leading to liver diseases like cirrhosis and cancer. In response, we created a prophylactic and therapeutic HBV vaccine by integrating HBcAg and HBsAg from HBV genotype B into Norovirus (NoV) GII.2 P domain (PdomGII.2-HBV) for enhanced intranasal delivery. This vaccine also aimed to simultaneously prevent NoV infection, which causes gastroenteritis. Since the selected HBV epitopes have undergone extensive research and are tailored to the Indonesian population, this study focused on identifying NoV epitopes and assessing T cell epitopes coverage of the PdomGII.2-HBV for the Indonesian population. Following that, we expressed the PdomGII.2-HBV protein using Escherichia coli BL21(DE3) and employed a gentle solubilization technique for protein purification. Our in-silico analysis identified two B cell epitopes, along with 15 CD4+T cell epitopes and 35 CD8+T cell epitopes within the GII.2 P domain. These T cell epitopes cover 100% of the Javanese-Sundanese population's HLA allele variations, which constituted the largest demographic group in Indonesia. Subsequently, we successfully purified the presumed PdomGII.2-HBV protein, revealing a molecular weight of 39.5 kDa. Following the successful expression and purification of the presumed PdomGII.2-HBV protein, it is evident that this vaccine design has significant potential, warranting further study.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141681027","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 : 2024-04-04DOI: 10.4308/hjb.31.4.803-810
Djaja Rusmana, H. Tiono, Wahyu Widowati, Johan Lucianus, Lusiana Darsono, Philips Onggowidjaja, R. Tjokropranoto, Vera Vera, Edwin Setiabudi, S. Obeng, H. Kusuma, Agung Novianto
Metabolic abnormalities caused by the accumulation of human, environmental, genetic and lifestyle variables can be found in diabetes mellitus (DM). An increase in blood glucose carried on by a reduction in insulin production can also result in DM. Insulin resistance often occurs as a result of obesity and a lack of physical activity and aging. Telang flower extract (Clitoria ternatea L.) is reported to have several qualities such as being able to treat DM, chronic bronchitis, goiter, mucosal disorders and leprosy. This study’s objective was to elucidate anti-dibetic effect of C. ternatea extract (CTE) in rats with diabetic complications related to dyslipidemia. Rats suffering from diabetes will be examined after being given oral doses of Simvastatin 0.9 mg/kg BW, Glibenclamide 0.45 mg/kg BW, and 200, 400, and 800 mg/kg BW CTE, model induced by streptozotocin. The expression of the insulin gene (INS-1) was investigated by qRTPCR, Tumor Necrosis Factor-α (TNF-α), and Interleukin-1β (IL-1β) pancreatic DM rats model using the Immunohistochemistry (IHC) test. Both descriptive and quantitative data were acquired for the data. After utilizing ANOVA to evaluate quantitative data, the Tukey post hoc test was used to analyze the data, the expression of TNF-α and IL-1β was found to decrease while INS-1 expression increased in response to CTE. This effect was attributed to the modulation of TNF-α, IL-1β, and INS-1 expression. These findings suggest that CTE possesses antidiabetic properties.
{"title":"Potential of Clitoria ternatea L. Extract Towards Insulin Receptor Expression and Marker of Inflammation in Diabetes Mellitus Rats Model","authors":"Djaja Rusmana, H. Tiono, Wahyu Widowati, Johan Lucianus, Lusiana Darsono, Philips Onggowidjaja, R. Tjokropranoto, Vera Vera, Edwin Setiabudi, S. Obeng, H. Kusuma, Agung Novianto","doi":"10.4308/hjb.31.4.803-810","DOIUrl":"https://doi.org/10.4308/hjb.31.4.803-810","url":null,"abstract":"Metabolic abnormalities caused by the accumulation of human, environmental, genetic and lifestyle variables can be found in diabetes mellitus (DM). An increase in blood glucose carried on by a reduction in insulin production can also result in DM. Insulin resistance often occurs as a result of obesity and a lack of physical activity and aging. Telang flower extract (Clitoria ternatea L.) is reported to have several qualities such as being able to treat DM, chronic bronchitis, goiter, mucosal disorders and leprosy. This study’s objective was to elucidate anti-dibetic effect of C. ternatea extract (CTE) in rats with diabetic complications related to dyslipidemia. Rats suffering from diabetes will be examined after being given oral doses of Simvastatin 0.9 mg/kg BW, Glibenclamide 0.45 mg/kg BW, and 200, 400, and 800 mg/kg BW CTE, model induced by streptozotocin. The expression of the insulin gene (INS-1) was investigated by qRTPCR, Tumor Necrosis Factor-α (TNF-α), and Interleukin-1β (IL-1β) pancreatic DM rats model using the Immunohistochemistry (IHC) test. Both descriptive and quantitative data were acquired for the data. After utilizing ANOVA to evaluate quantitative data, the Tukey post hoc test was used to analyze the data, the expression of TNF-α and IL-1β was found to decrease while INS-1 expression increased in response to CTE. This effect was attributed to the modulation of TNF-α, IL-1β, and INS-1 expression. These findings suggest that CTE possesses antidiabetic properties.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140741795","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 : 2024-04-04DOI: 10.4308/hjb.31.4.793-802
Víctor Javier Vásquez Villalobos, Angely Meryl Alessandra Hidalgo-Arteaga, Roxana Beatriz Sosa-Becerra, Bertha Soledad Soriano-Bernilla, Maurício Alexander de Moura Ferreira, Wendel Batista da Silveira
Genomes of oleaginous yeast strains Rhodotorula glutinis CON-5 and Rhodotorula kratochvilovae POR-3, isolated from areas in the northern Peruvian Andes using SPAdes, were sequenced and assembled applying Illumina and de novo. Genomes of 20,515,696 and 20,738,185 bp, respectively, were determined. From the structural and functional annotations, the Basidiomycota phylum showed a similarity of 76.8% and 86.5% with 6,976 and 8,124 pairs of proteins in both yeasts respectively, with homologues in the UniProt data bank. Using OrthoVenn, a relationship between both yeasts was obtained from 450 orthologous groups. Likewise, the above-mentioned yeasts and R. toruloides (oleaginous Basidiomycota) showed 1,574 orthologous groups, indicating a good relationship. Construction of phylogenetic trees of genes encoding metabolic enzymes was also carried out, based on the ITS sequences which showed that CON-5 and POR-3 have a greater relationship with R. graminis. Their phylogenetic relationship was ascertained and determined that the enzymes involved in the metabolism of CON-5 and POR-3 are related to each other. It was also found that the protein sequences of the Basidiomycota phylum differ from Ascomycota. The study showed functional evidence regarding the lipid accumulation phenotype, an important aspect in the context of obtaining lipids or oleochemicals.
{"title":"Genomics and Phylogeny of Rhodotorula glutinis and Rhodotorula kratochvilovae Isolated from the Northern Peruvian Andes","authors":"Víctor Javier Vásquez Villalobos, Angely Meryl Alessandra Hidalgo-Arteaga, Roxana Beatriz Sosa-Becerra, Bertha Soledad Soriano-Bernilla, Maurício Alexander de Moura Ferreira, Wendel Batista da Silveira","doi":"10.4308/hjb.31.4.793-802","DOIUrl":"https://doi.org/10.4308/hjb.31.4.793-802","url":null,"abstract":"Genomes of oleaginous yeast strains Rhodotorula glutinis CON-5 and Rhodotorula kratochvilovae POR-3, isolated from areas in the northern Peruvian Andes using SPAdes, were sequenced and assembled applying Illumina and de novo. Genomes of 20,515,696 and 20,738,185 bp, respectively, were determined. From the structural and functional annotations, the Basidiomycota phylum showed a similarity of 76.8% and 86.5% with 6,976 and 8,124 pairs of proteins in both yeasts respectively, with homologues in the UniProt data bank. Using OrthoVenn, a relationship between both yeasts was obtained from 450 orthologous groups. Likewise, the above-mentioned yeasts and R. toruloides (oleaginous Basidiomycota) showed 1,574 orthologous groups, indicating a good relationship. Construction of phylogenetic trees of genes encoding metabolic enzymes was also carried out, based on the ITS sequences which showed that CON-5 and POR-3 have a greater relationship with R. graminis. Their phylogenetic relationship was ascertained and determined that the enzymes involved in the metabolism of CON-5 and POR-3 are related to each other. It was also found that the protein sequences of the Basidiomycota phylum differ from Ascomycota. The study showed functional evidence regarding the lipid accumulation phenotype, an important aspect in the context of obtaining lipids or oleochemicals.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140742317","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 : 2024-04-03DOI: 10.4308/hjb.31.4.781-792
I. K. Abywijaya, R. Rindyastuti, Fira Fitria Jihans, A. T. Wibowo
The endemic Diospyros celebica and widely spread D. blancoi are two valuable species of Diospyros (the genus of persimmons and ebonies) that have been conserved at botanic gardens in Indonesia. Understanding the biological contrasts between endemic and widely spread species is essential for plant conservation. This study aims to compare the phenotypic and estimated genetic variability between the endemic D. celebica and the widely spread D. blancoi to support their conservation. Fifty-three morphological characters from fifteen selected living plant specimens at Purwodadi Botanic Garden were measured directly or using variable encoding methods. Unpaired two-samples Wilcoxon test and hierarchical cluster analysis were used to compare morphological variations between both species. Further, genetic variabilities were estimated from encoded morphological characters using GenAlEx 6.503 software. The two Diospyros’ morphological characters were significantly different, except for the lamina length, pairs of leaf vein, number of flowers in each inflorescence, and the fruit sulci presence. The cluster analysis successfully distinguished D. celebica from D. blancoi according to thirteen comparable morphological characters. The endemic D. celebica has lower genetic variability (female/bisexual %P = 86.21%, He = 0.259, uHe = 0.277; male P = 54.29%, He = 0.195, uHe = 0.234) than the widely spread D. blancoi (female/bisexual %P = 86.76, He = 0.311, uHe = 0.355). Due to the importance of genetic diversity in plant conservation, both species’ population size needs to be maintained, if not increased, to preserve the existing phenotypic and genetic variabilities within the cultivated populations at the botanic garden.
印度尼西亚植物园保护的两种珍贵的柿树（柿属和乌骨木属）物种--Diospyros celebica（特有种）和广泛分布的 D. blancoi（广布种）。了解特有种和广布种之间的生物学对比对植物保护至关重要。本研究旨在比较特有种 D. celebica 和广泛分布的 D. blancoi 之间的表型和估计遗传变异性，以支持它们的保护工作。研究人员直接或使用变量编码方法测量了普沃达迪植物园中 15 个活体植物标本的 53 个形态特征。采用非配对双样本 Wilcoxon 检验和分层聚类分析来比较两个物种之间的形态变异。此外，还使用 GenAlEx 6.503 软件根据编码的形态特征估算遗传变异率。结果表明，除叶片长度、叶脉对数、每花序的花朵数和果实沟外，两种果树的形态特征存在显著差异。聚类分析根据 13 个可比较的形态特征成功地将 D. celebica 与 D. blancoi 区分开来。D. celebica的遗传变异性（雌性/双性%P = 86.21%，He = 0.259，uHe = 0.277；雄性P = 54.29%，He = 0.195，uHe = 0.234）低于广泛分布的D. blancoi（雌性/双性%P = 86.76，He = 0.311，uHe = 0.355）。由于遗传多样性在植物保护中的重要性，这两个物种的种群数量即使不能增加，也需要保持，以保护植物园栽培种群中现有的表型和遗传变异。
{"title":"Phenotypic and Estimated Genetic Variability in Endemic Diospyros celebica Bakh. and Widely-spread D. blancoi A.Dc. Cultivated at Purwodadi Botanic Garden, Indonesia","authors":"I. K. Abywijaya, R. Rindyastuti, Fira Fitria Jihans, A. T. Wibowo","doi":"10.4308/hjb.31.4.781-792","DOIUrl":"https://doi.org/10.4308/hjb.31.4.781-792","url":null,"abstract":"The endemic Diospyros celebica and widely spread D. blancoi are two valuable species of Diospyros (the genus of persimmons and ebonies) that have been conserved at botanic gardens in Indonesia. Understanding the biological contrasts between endemic and widely spread species is essential for plant conservation. This study aims to compare the phenotypic and estimated genetic variability between the endemic D. celebica and the widely spread D. blancoi to support their conservation. Fifty-three morphological characters from fifteen selected living plant specimens at Purwodadi Botanic Garden were measured directly or using variable encoding methods. Unpaired two-samples Wilcoxon test and hierarchical cluster analysis were used to compare morphological variations between both species. Further, genetic variabilities were estimated from encoded morphological characters using GenAlEx 6.503 software. The two Diospyros’ morphological characters were significantly different, except for the lamina length, pairs of leaf vein, number of flowers in each inflorescence, and the fruit sulci presence. The cluster analysis successfully distinguished D. celebica from D. blancoi according to thirteen comparable morphological characters. The endemic D. celebica has lower genetic variability (female/bisexual %P = 86.21%, He = 0.259, uHe = 0.277; male P = 54.29%, He = 0.195, uHe = 0.234) than the widely spread D. blancoi (female/bisexual %P = 86.76, He = 0.311, uHe = 0.355). Due to the importance of genetic diversity in plant conservation, both species’ population size needs to be maintained, if not increased, to preserve the existing phenotypic and genetic variabilities within the cultivated populations at the botanic garden.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140749552","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 : 2024-04-01DOI: 10.4308/hjb.31.4.733-743
Sari Nurulita, Sofi Mawarni, S H Hidayat
Virus infection is one of the major constraints in garlic production since the viruses are readily accumulated on vegetative propagation material (bulbs). This research aimed to detect garlic common latent virus (GCLV), shallot latent virus (SLV), onion yellow dwarf virus (OYDV), and leek yellow stripe virus (LYSV) infecting local garlic as seed bulb and imported garlic as consumption bulb. Seed bulb samples were obtained from seed breeders in several garlic growing centers in Indonesia. In contrast, consumption bulb samples were obtained from plant quarantine warehouses and three local markets in Bogor. Some bulb samples were used for morphological observations, and some were germinated in the laboratory until the leaves emerged. Leaves were collected for virus detection by RT-PCR using specific primers for GCLV, SLV, OYDV, and LYSV. Seed and consumption bulbs have differences in their morphological characteristics, especially in the type of neck hardness and the size of the bulb diameter. OYDV and LYSV infections were successfully detected in seed and consumption bulbs, while SLV was only found in consumption bulbs. Nucleotide sequence analysis showed that SLV from consumption bulbs formed one group, GCLV from seed bulbs formed one group, while OYDV and LYSV from seed and consumption bulbs were in different groups, indicating that the viruses came from different strains. Further research through high-throughput detection methods and providing virus-free planting material are needed to anticipate the spread of new strains of garlic viruses in Indonesia.
{"title":"Identification of Garlic Viruses Associated with Seed Bulbs and Consumption Bulbs from Several Locations in Indonesia","authors":"Sari Nurulita, Sofi Mawarni, S H Hidayat","doi":"10.4308/hjb.31.4.733-743","DOIUrl":"https://doi.org/10.4308/hjb.31.4.733-743","url":null,"abstract":"Virus infection is one of the major constraints in garlic production since the viruses are readily accumulated on vegetative propagation material (bulbs). This research aimed to detect garlic common latent virus (GCLV), shallot latent virus (SLV), onion yellow dwarf virus (OYDV), and leek yellow stripe virus (LYSV) infecting local garlic as seed bulb and imported garlic as consumption bulb. Seed bulb samples were obtained from seed breeders in several garlic growing centers in Indonesia. In contrast, consumption bulb samples were obtained from plant quarantine warehouses and three local markets in Bogor. Some bulb samples were used for morphological observations, and some were germinated in the laboratory until the leaves emerged. Leaves were collected for virus detection by RT-PCR using specific primers for GCLV, SLV, OYDV, and LYSV. Seed and consumption bulbs have differences in their morphological characteristics, especially in the type of neck hardness and the size of the bulb diameter. OYDV and LYSV infections were successfully detected in seed and consumption bulbs, while SLV was only found in consumption bulbs. Nucleotide sequence analysis showed that SLV from consumption bulbs formed one group, GCLV from seed bulbs formed one group, while OYDV and LYSV from seed and consumption bulbs were in different groups, indicating that the viruses came from different strains. Further research through high-throughput detection methods and providing virus-free planting material are needed to anticipate the spread of new strains of garlic viruses in Indonesia.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140795522","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 : 2024-04-01DOI: 10.4308/hjb.31.4.744-749
I. Indrayani, Sri Ambardini, A. Pariakan, Indriyani Nur
Flying fish (Exocoetidae) is a pelagic fishery commodity that holds economic value among the people of eastern Indonesia. Flying fish are advantageous as they are abundant in Indonesian sea waters, making them an affordable source of omega-3, which is beneficial for human health. However, the high demand for flying fish has resulted in overfishing, which poses a risk of reducing their natural population. Proper management of this commodity is necessary to minimize these risks. Effective management requires adequate information, including genetic diversity data. This study aims to determine the genetic diversity of flying fish in Southeast Sulawesi, specifically in the Banda Sea and Bone Bay populations. Tissue samples were collected from flying fish in the two populations during the study in March 2022. The results show that the genetic diversity values of flying fish in Bone Bay and the Banda Sea were 0.984 and 1.00, respectively, while the nucleotide diversity values were 0.021 and 0.018. High genetic diversity values and nucleotide diversity values were found between the two populations, with values of 0.990 and 0.020, respectively. Based on phylogenetic analysis, the two populations in Southeast Sulawesi are genetically similar.
{"title":"Genetic Diversity of Flying Fish (Exocoetidae) in Southeast Sulawesi, Indonesia","authors":"I. Indrayani, Sri Ambardini, A. Pariakan, Indriyani Nur","doi":"10.4308/hjb.31.4.744-749","DOIUrl":"https://doi.org/10.4308/hjb.31.4.744-749","url":null,"abstract":"Flying fish (Exocoetidae) is a pelagic fishery commodity that holds economic value among the people of eastern Indonesia. Flying fish are advantageous as they are abundant in Indonesian sea waters, making them an affordable source of omega-3, which is beneficial for human health. However, the high demand for flying fish has resulted in overfishing, which poses a risk of reducing their natural population. Proper management of this commodity is necessary to minimize these risks. Effective management requires adequate information, including genetic diversity data. This study aims to determine the genetic diversity of flying fish in Southeast Sulawesi, specifically in the Banda Sea and Bone Bay populations. Tissue samples were collected from flying fish in the two populations during the study in March 2022. The results show that the genetic diversity values of flying fish in Bone Bay and the Banda Sea were 0.984 and 1.00, respectively, while the nucleotide diversity values were 0.021 and 0.018. High genetic diversity values and nucleotide diversity values were found between the two populations, with values of 0.990 and 0.020, respectively. Based on phylogenetic analysis, the two populations in Southeast Sulawesi are genetically similar.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140761937","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 : 2024-04-01DOI: 10.4308/hjb.31.4.725-732
Vincentia Fenice Angger Maherani, N. R. Mubarik, J. A. Priyanto, Ivan Permana Putra
Biosurfactants are a class of amphipathic molecules that various microorganisms can produce. Biosurfactants are used as biopesticides and biocontrol agents because they have antimicrobial activity, especially as antifungal agents in several species of fungal pathogens such as Ganoderma boninense and Fusarium sp. that attack crops. This study aims to detect the biosurfactant activity of Bacillus sp. and its potential as an antifungal agent against the fungi Ganoderma boninense and Fusarium sp. Biosurfactants were produced in mineral salt medium (MSM) by harvesting cell-free supernatants. Screening of biosurfactant-producing isolates was carried out using an oil-spreading assay, a hemolysis assay, and an emulsification index. The antifungal activity of the isolates was then tested using the agar diffusion method. The LP04 isolate was closely related to Bacillus thuringiensis with a 99% similarity level. It has the potential to have biosurfactant activity, which is characterized by a positive result on the oil spreading assay test and has an emulsification index of 48.33±2.87%. The cell-free supernatants of the bacterial isolate were able to inhibit the growth of Ganoderma boninense and Fusarium sp. with growth inhibition rates of 51.11% and 56.92%, respectively.
{"title":"Biosurfactant Activity of Bacillus sp. Strain LP04 Isolate and Its Antifungal Potency against Ganoderma boninense and Fusarium sp.","authors":"Vincentia Fenice Angger Maherani, N. R. Mubarik, J. A. Priyanto, Ivan Permana Putra","doi":"10.4308/hjb.31.4.725-732","DOIUrl":"https://doi.org/10.4308/hjb.31.4.725-732","url":null,"abstract":"Biosurfactants are a class of amphipathic molecules that various microorganisms can produce. Biosurfactants are used as biopesticides and biocontrol agents because they have antimicrobial activity, especially as antifungal agents in several species of fungal pathogens such as Ganoderma boninense and Fusarium sp. that attack crops. This study aims to detect the biosurfactant activity of Bacillus sp. and its potential as an antifungal agent against the fungi Ganoderma boninense and Fusarium sp. Biosurfactants were produced in mineral salt medium (MSM) by harvesting cell-free supernatants. Screening of biosurfactant-producing isolates was carried out using an oil-spreading assay, a hemolysis assay, and an emulsification index. The antifungal activity of the isolates was then tested using the agar diffusion method. The LP04 isolate was closely related to Bacillus thuringiensis with a 99% similarity level. It has the potential to have biosurfactant activity, which is characterized by a positive result on the oil spreading assay test and has an emulsification index of 48.33±2.87%. The cell-free supernatants of the bacterial isolate were able to inhibit the growth of Ganoderma boninense and Fusarium sp. with growth inhibition rates of 51.11% and 56.92%, respectively.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140773711","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 : 2024-04-01DOI: 10.4308/hjb.31.4.768-780
Juniarto Gautama Simanjuntak, W. Priawandiputra, R. Raffiudin, N. I. Shullia, Jauharlina Jauharlina, Mahardika Gama Pradana, Araz Meilin, J. Jasmi, Yulia Pujiastuti, Puji Lestari, Rustem Ilyasov, Rahmadi Sitompul, T. Atmowidi
Honey bee Apis cerana is widely distributed in Asia and the Indonesian archipelago, including Sumatra. We studied the molecular variations of A. cerana using cytochrome c oxidase subunits 1 and 2 genes (cox1 and cox2) and the cox1/cox2 intergenic spacers (igs) in several altitudes in the six provinces of Sumatra. We explored the haplotype distributions of those three mtDNA markers for A. cerana in the low-, mid-, and highlands of Sumatra. We also analyzed their relationship with A. cerana in Sundaland and Asia using those markers. Our study revealed 12 new haplotypes of A. cerana cox1 in Sumatra, while nine and eight new haplotypes for cox2 and igs, respectively. Apis cerana in North Sumatra, Lampung, and South Sumatra had the three highest haplotype variations. Most of the specific haplotypes of inter-colony A. cerana from Sumatra were found in the lowlands, while most were in the highlands for intra-colony variations. We found low gene flow among populations of A. cerana in Sumatra. One haplotype, Sumatra4 cox2 from North Sumatra, was the same as Java3 haplotype, presumably due to anthropogenic impact. The molecular phylogenetic tree of A. cerana in the Sundaland revealed that A. cerana from Sumatra has a close relationship to those of Borneo compared to Java.
{"title":"Apis cerana Fabricius, 1793 in Sumatra: Haplotype Variations of Mitochondrial DNA and the Molecular Relationship with the Asian Honey Bees (Hymenoptera: Apidae)","authors":"Juniarto Gautama Simanjuntak, W. Priawandiputra, R. Raffiudin, N. I. Shullia, Jauharlina Jauharlina, Mahardika Gama Pradana, Araz Meilin, J. Jasmi, Yulia Pujiastuti, Puji Lestari, Rustem Ilyasov, Rahmadi Sitompul, T. Atmowidi","doi":"10.4308/hjb.31.4.768-780","DOIUrl":"https://doi.org/10.4308/hjb.31.4.768-780","url":null,"abstract":"Honey bee Apis cerana is widely distributed in Asia and the Indonesian archipelago, including Sumatra. We studied the molecular variations of A. cerana using cytochrome c oxidase subunits 1 and 2 genes (cox1 and cox2) and the cox1/cox2 intergenic spacers (igs) in several altitudes in the six provinces of Sumatra. We explored the haplotype distributions of those three mtDNA markers for A. cerana in the low-, mid-, and highlands of Sumatra. We also analyzed their relationship with A. cerana in Sundaland and Asia using those markers. Our study revealed 12 new haplotypes of A. cerana cox1 in Sumatra, while nine and eight new haplotypes for cox2 and igs, respectively. Apis cerana in North Sumatra, Lampung, and South Sumatra had the three highest haplotype variations. Most of the specific haplotypes of inter-colony A. cerana from Sumatra were found in the lowlands, while most were in the highlands for intra-colony variations. We found low gene flow among populations of A. cerana in Sumatra. One haplotype, Sumatra4 cox2 from North Sumatra, was the same as Java3 haplotype, presumably due to anthropogenic impact. The molecular phylogenetic tree of A. cerana in the Sundaland revealed that A. cerana from Sumatra has a close relationship to those of Borneo compared to Java.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140781054","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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