Pub Date : 2024-04-01DOI: 10.4308/hjb.31.4.750-767
Hilmi Naufal Madani, N. Wijayanto, A. P. Hartoyo, A. Solikhin
The aim of this experiment is to evaluate the impact of chitosan-NPK slow-release fertilizer (CS-NPK SRF) on the germination and growth of silk tree and rice in different planting patterns, as well as to assess the nutrient release rate of the SRF. The germination test followed a complete randomized design, incorporating a single factor (fertilizer type), namely no fertilizer (F0), SRF CS 0.5% weight 0.03 g (F1), SRF CS 0.5% 0.01 g (F2), SRF CS 0.7% 0.03 g (F3), SRF CS 0.7% 0.01 g (F4), and conventional NPK fertilizer (F5). The growth test utilized a 2-factor split-plot design, with the primary factor being the planting pattern (sengon/rice monoculture-SM/RM and sengon-rice agroforestry-AF) and the second factor being the fertilizer type. Results indicate that F2 and F4 yielded the highest germination and growth values in both plants, although not significantly different from F0. These findings suggest that CS-NPK SRF has the potential to enhance plant growth. The AF pattern exhibited lower growth compared to SM/RM, attributed to plant competition. CS-NPK SRF demonstrated a slower nutrient release (47.65% N; 85.01% P; 31.80% K) compared to conventional fertilizers. This slow release could potentially reduce nutrient loss to the environment while enhancing plant nutrient absorption.
{"title":"Slow-release Fertilizer Application on Silk (Falcataria moluccana Miq.) and Rice (Oryza sativa L.) Plant Growth and Yield in Agroforestry System","authors":"Hilmi Naufal Madani, N. Wijayanto, A. P. Hartoyo, A. Solikhin","doi":"10.4308/hjb.31.4.750-767","DOIUrl":"https://doi.org/10.4308/hjb.31.4.750-767","url":null,"abstract":"The aim of this experiment is to evaluate the impact of chitosan-NPK slow-release fertilizer (CS-NPK SRF) on the germination and growth of silk tree and rice in different planting patterns, as well as to assess the nutrient release rate of the SRF. The germination test followed a complete randomized design, incorporating a single factor (fertilizer type), namely no fertilizer (F0), SRF CS 0.5% weight 0.03 g (F1), SRF CS 0.5% 0.01 g (F2), SRF CS 0.7% 0.03 g (F3), SRF CS 0.7% 0.01 g (F4), and conventional NPK fertilizer (F5). The growth test utilized a 2-factor split-plot design, with the primary factor being the planting pattern (sengon/rice monoculture-SM/RM and sengon-rice agroforestry-AF) and the second factor being the fertilizer type. Results indicate that F2 and F4 yielded the highest germination and growth values in both plants, although not significantly different from F0. These findings suggest that CS-NPK SRF has the potential to enhance plant growth. The AF pattern exhibited lower growth compared to SM/RM, attributed to plant competition. CS-NPK SRF demonstrated a slower nutrient release (47.65% N; 85.01% P; 31.80% K) compared to conventional fertilizers. This slow release could potentially reduce nutrient loss to the environment while enhancing plant nutrient absorption.","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":"140777767","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 : 2024-02-19DOI: 10.4308/hjb.31.3.603-612
R. Indrayanti, Nadia Fitria Wulandari, Agus Sutanto, Rizal Koen Asharo, Adisyahputra
In vitro medium-term storage using the alginate-encapsulation technique is essential for conserving plant genetic resources, preserving vegetatively propagated species by controlling the growth and development of explants, and maintaining plant biodiversity. The study aimed to obtain the optimum combination medium for the encapsulation of bananas and evaluate the viability of the alginate-encapsulated explants after storage. In vitro, medium- term storage of nodule-like meristem of banana cultivar ‘Barangan’ was performed using sodium alginate, paclobutrazol (PBZ), and Murashige and Skoog (MS) salt. This research consists of 3 stages: (1) Initiation and multiplication of in vitro shoots and nodule-like meristems; (2) In vitro medium-term storage of banana by encapsulation technique; (3) Regeneration of nodule-like meristem explants after in vitro storage. This research showed that the banana's number of nodule-like meristem was optimum on media supplemented with thidiazuron (TDZ) 0.22 mgL-1 and indole 3-acetic acid (IAA) 1.75 mgL-1. Encapsulation explant of nodules-like meristems using 3% sodium alginate in full and half-strength MS salt medium supplemented with PBZ 2.5 mgL-1 and incubated in liquid MS medium was able to store nodule-like meristem for six months. The color of the explants remains green, and the capsule is not damaged. Sub-culture of nodule-like meristem after storage in MS salt medium containing TDZ 0.22 mgL-1 and IAA 1.75 mgL-1 showed that nodules-like meristems could regenerate to form new shoots and nodule-like meristem three months after sub-cultured. This research concludes that encapsulated nodule-like meristem was recorded until six months of storage. PBZ was a necessary retardant in minimizing the growth during storage.
{"title":"In Vitro Medium-Term Storage of Banana Cultivar ‘Barangan’ Using Alginate-Encapsulation Technique","authors":"R. Indrayanti, Nadia Fitria Wulandari, Agus Sutanto, Rizal Koen Asharo, Adisyahputra","doi":"10.4308/hjb.31.3.603-612","DOIUrl":"https://doi.org/10.4308/hjb.31.3.603-612","url":null,"abstract":"In vitro medium-term storage using the alginate-encapsulation technique is essential for conserving plant genetic resources, preserving vegetatively propagated species by controlling the growth and development of explants, and maintaining plant biodiversity. The study aimed to obtain the optimum combination medium for the encapsulation of bananas and evaluate the viability of the alginate-encapsulated explants after storage. In vitro, medium- term storage of nodule-like meristem of banana cultivar ‘Barangan’ was performed using sodium alginate, paclobutrazol (PBZ), and Murashige and Skoog (MS) salt. This research consists of 3 stages: (1) Initiation and multiplication of in vitro shoots and nodule-like meristems; (2) In vitro medium-term storage of banana by encapsulation technique; (3) Regeneration of nodule-like meristem explants after in vitro storage. This research showed that the banana's number of nodule-like meristem was optimum on media supplemented with thidiazuron (TDZ) 0.22 mgL-1 and indole 3-acetic acid (IAA) 1.75 mgL-1. Encapsulation explant of nodules-like meristems using 3% sodium alginate in full and half-strength MS salt medium supplemented with PBZ 2.5 mgL-1 and incubated in liquid MS medium was able to store nodule-like meristem for six months. The color of the explants remains green, and the capsule is not damaged. Sub-culture of nodule-like meristem after storage in MS salt medium containing TDZ 0.22 mgL-1 and IAA 1.75 mgL-1 showed that nodules-like meristems could regenerate to form new shoots and nodule-like meristem three months after sub-cultured. This research concludes that encapsulated nodule-like meristem was recorded until six months of storage. PBZ was a necessary retardant in minimizing the growth during storage.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139959214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-11DOI: 10.4308/hjb.31.2.392-403
Ruhama Maya Sari, U. Saepuloh, Rizaldi, Dyah Perwitasari-Farajallah
The long-tailed macaque (Macaca fascicularis) is a primate species recognized for its exceptional ability to adapt to urban habitat. However, urban anthropogenic activities contribute to the fragmentation of macaque natural habitat, affecting genetic variation among distinct populations. Therefore, this study aimed to assess the genetic variability of M. fascicularis populations in Padang City, West Sumatra, Indonesia. A total of 70 fecal samples from the wild long-tailed macaques in Gunung Padang (GPD), Gunung Meru (GMR), and Gunung Pangilun (GPG) were collected using a non-invasive method. Conventional PCR amplification and Sanger sequencing were conducted to examine a 1,200-bp mitochondrial DNA (mtDNA) fragment in the D-loop region. The analysis of genetic variation showed that only two haplotypes were present in the three populations. Both GPD and GMR shared the same haplotype (H1), while the GPG population had a distinct haplotype (H2). No intrapopulation variation was observed, and haplotype differences were found in ten nucleotide sites with transition substitution mutations. These results showed limited genetic variation among populations of the long-tailed macaque in Padang, thereby providing valuable insights for stakeholders when formulating genetic conservation policies.
长尾猕猴（Macaca fascicularis）是一种灵长类动物，因其适应城市栖息地的卓越能力而受到认可。然而，城市人为活动导致猕猴自然栖息地的破碎化，影响了不同种群之间的遗传变异。因此，本研究旨在评估印度尼西亚西苏门答腊巴东市猕猴种群的遗传变异。本研究采用非侵入式方法收集了70份野生长尾猕猴的粪便样本，这些样本分别来自巴东山（GPD）、梅鲁山（GMR）和庞吉伦山（GPG）。通过传统的 PCR 扩增和 Sanger 测序，对 D 环区域的 1200 bp 线粒体 DNA（mtDNA）片段进行了检测。遗传变异分析表明，三个种群中只有两种单倍型。GPD 和 GMR 具有相同的单倍型（H1），而 GPG 群体则具有独特的单倍型（H2）。没有观察到种群内的变异，而在 10 个核苷酸位点的过渡取代突变中发现了单倍型差异。这些结果表明巴东长尾猕猴种群间的遗传变异有限，从而为利益相关者制定遗传保护政策提供了宝贵的见解。
{"title":"Genetic Variability of the Long-Tailed Macaque (Macaca fascicularis) Populations in Urban Habitat in Padang City, West Sumatra, Indonesia","authors":"Ruhama Maya Sari, U. Saepuloh, Rizaldi, Dyah Perwitasari-Farajallah","doi":"10.4308/hjb.31.2.392-403","DOIUrl":"https://doi.org/10.4308/hjb.31.2.392-403","url":null,"abstract":"The long-tailed macaque (Macaca fascicularis) is a primate species recognized for its exceptional ability to adapt to urban habitat. However, urban anthropogenic activities contribute to the fragmentation of macaque natural habitat, affecting genetic variation among distinct populations. Therefore, this study aimed to assess the genetic variability of M. fascicularis populations in Padang City, West Sumatra, Indonesia. A total of 70 fecal samples from the wild long-tailed macaques in Gunung Padang (GPD), Gunung Meru (GMR), and Gunung Pangilun (GPG) were collected using a non-invasive method. Conventional PCR amplification and Sanger sequencing were conducted to examine a 1,200-bp mitochondrial DNA (mtDNA) fragment in the D-loop region. The analysis of genetic variation showed that only two haplotypes were present in the three populations. Both GPD and GMR shared the same haplotype (H1), while the GPG population had a distinct haplotype (H2). No intrapopulation variation was observed, and haplotype differences were found in ten nucleotide sites with transition substitution mutations. These results showed limited genetic variation among populations of the long-tailed macaque in Padang, thereby providing valuable insights for stakeholders when formulating genetic conservation policies.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138978731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-11DOI: 10.4308/hjb.31.2.404-413
W. Lim, A. R. Mojiol, Henry Bernard, Christopher A. Matunjau, G. V. Nair
The information related to the species of terrestrial mammals that can be detected along the nature trails established in the lowland tropical forests of Western Sabah remains scarce at this moment. The camera trapping surveys were commenced at the Tenghilan Community Forest (TCF), Kawang Forest Reserve (KFR), and the urban forest of Universiti Malaysia Sabah (UMS) to investigate the terrestrial mammal species that could be observed along the local trails. A total of 20 terrestrial mammal species belonging to 13 different families were observed in 2,077 trap nights, where most of them were validated to be non-threatened (n = 16 or 80.0%) and omnivorous (n = 13 or 65.0%) species. Twelve species were found along the nature trails in TCF (H’ = 2.223; 1-D = 0.8650) and KFR (H’ = 1.730; 1-D = 0.7078), whereas seven species were detected along the trails in the urban forest of UMS (H’ = 1.217; 1-D = 0.5567). The differences in the mammalian composition, diversity richness, and distribution evenness between these three study sites were validated as significant (p<0.05). The present findings emphasize that these three study sites are favorable habitats for four threatened species. Hence, conservation efforts are needed to protect these terrestrial mammal species from facing extinction risks in future.
目前，有关在沙巴州西部低地热带森林的自然路径上可发现的陆生哺乳动物种类的信息仍然很少。我们在腾吉兰社区森林（Tenghilan Community Forest，简称TCF）、卡旺森林保护区（Kawang Forest Reserve，简称KFR）和马来西亚沙巴大学（Universiti Malaysia Sabah，简称UMS）的城市森林开始了相机诱捕调查，以调查在当地小径上可以观察到的陆生哺乳动物物种。在2,077个诱捕夜中，共观察到隶属于13个不同科的20种陆生哺乳动物，其中大部分被证实为无威胁物种（16种，占80.0%）和杂食物种（13种，占65.0%）。在TCF（H'=2.223；1-D=0.8650）和KFR（H'=1.730；1-D=0.7078）的自然小径上发现了12个物种，而在UMS城市森林的小径上发现了7个物种（H'=1.217；1-D=0.5567）。这三个研究地点的哺乳动物组成、多样性丰富度和分布均匀度差异显著（P<0.05）。本研究结果表明，这三个研究地点是四种濒危物种的有利栖息地。因此，需要努力保护这些陆生哺乳动物物种，以免它们在未来面临灭绝的危险。
{"title":"Viewable Terrestrial Mammals along the Nature Trails at the Lowland Tropical Forests of Western Sabah, Malaysia Borneo","authors":"W. Lim, A. R. Mojiol, Henry Bernard, Christopher A. Matunjau, G. V. Nair","doi":"10.4308/hjb.31.2.404-413","DOIUrl":"https://doi.org/10.4308/hjb.31.2.404-413","url":null,"abstract":"The information related to the species of terrestrial mammals that can be detected along the nature trails established in the lowland tropical forests of Western Sabah remains scarce at this moment. The camera trapping surveys were commenced at the Tenghilan Community Forest (TCF), Kawang Forest Reserve (KFR), and the urban forest of Universiti Malaysia Sabah (UMS) to investigate the terrestrial mammal species that could be observed along the local trails. A total of 20 terrestrial mammal species belonging to 13 different families were observed in 2,077 trap nights, where most of them were validated to be non-threatened (n = 16 or 80.0%) and omnivorous (n = 13 or 65.0%) species. Twelve species were found along the nature trails in TCF (H’ = 2.223; 1-D = 0.8650) and KFR (H’ = 1.730; 1-D = 0.7078), whereas seven species were detected along the trails in the urban forest of UMS (H’ = 1.217; 1-D = 0.5567). The differences in the mammalian composition, diversity richness, and distribution evenness between these three study sites were validated as significant (p<0.05). The present findings emphasize that these three study sites are favorable habitats for four threatened species. Hence, conservation efforts are needed to protect these terrestrial mammal species from facing extinction risks in future.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138980390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-08DOI: 10.4308/hjb.31.2.382-391
Aviesta Linggabuwana, Saifa Usni Putri, F. Y. Kurniawan, E. Semiarti
Variegated flowers, characterized by the presence of different colors in flowers, have high economic and aesthetic values. The main pigment in the orchid's purple flowers is anthocyanin, while the chalcone synthase (CHS) gene is the key to anthocyanin biosynthesis. Analysis of the CHS gene can reveal some changes, including mutations, in the process of color patterning in flowers. This study aims to determine the structure of the CHS gene related to color patterning in Dendrobium 'Enobi' and Phalaenopsis hybrid with variegated flowers. The methods applied in this study are floral morphology observation, DNA isolation, CHS gene amplification, anthocyanin measurement, and bioinformatic analysis. Morphologically, the variegated pattern has appeared since the flowers were still in the bud on both orchids. Based on the anthocyanin content analysis, the difference in the genus is not directly related to the differences in the flower's anthocyanin content. In addition, the purple zone in the D. 'Enobi' and Phalaenopsis hybrid has a longer fragment of CHS than the white zone. Our analysis suggested several mutations in the white zone and differences in the type and location of several conserved domain proteins. Mutations at the CHS gene fragment might cause decreased anthocyanin pigment formation in the white region.
{"title":"Isolation and Characterization of Chalcone Synthase (CHS) Gene in Variegated-Flower of Dendrobium 'Enobi' and Phalaenopsis Hybrid Orchids","authors":"Aviesta Linggabuwana, Saifa Usni Putri, F. Y. Kurniawan, E. Semiarti","doi":"10.4308/hjb.31.2.382-391","DOIUrl":"https://doi.org/10.4308/hjb.31.2.382-391","url":null,"abstract":"Variegated flowers, characterized by the presence of different colors in flowers, have high economic and aesthetic values. The main pigment in the orchid's purple flowers is anthocyanin, while the chalcone synthase (CHS) gene is the key to anthocyanin biosynthesis. Analysis of the CHS gene can reveal some changes, including mutations, in the process of color patterning in flowers. This study aims to determine the structure of the CHS gene related to color patterning in Dendrobium 'Enobi' and Phalaenopsis hybrid with variegated flowers. The methods applied in this study are floral morphology observation, DNA isolation, CHS gene amplification, anthocyanin measurement, and bioinformatic analysis. Morphologically, the variegated pattern has appeared since the flowers were still in the bud on both orchids. Based on the anthocyanin content analysis, the difference in the genus is not directly related to the differences in the flower's anthocyanin content. In addition, the purple zone in the D. 'Enobi' and Phalaenopsis hybrid has a longer fragment of CHS than the white zone. Our analysis suggested several mutations in the white zone and differences in the type and location of several conserved domain proteins. Mutations at the CHS gene fragment might cause decreased anthocyanin pigment formation in the white region.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139011599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-06DOI: 10.4308/hjb.31.2.374-381
R. Agus, Sjafaraenan, Yulianti Samara, Muhammad Nasrum Massi
The main challenge in the management of Tuberculosis (TB) is diagnosing quickly and accurately, especially Latent Tuberculosis Infection (LTBI). LTBI detection was carried out using the Tuberculin Skin Test (TST) and Interferon Gamma Release Assay (IGRA). In TB endemic areas, these two examinations have limitations, so current research is directed at finding specific antigens for the diagnosis of LTBI. One of the potential proteins is Antigen 85A (Ag85A) Mycobacterium tuberculosis (Mtb) encoded by Fibronectin-binding protein A (FbpA). The Ag85 complex induces the proliferation of T-cells and interferon-gamma in most healthy individuals infected with Mycobacterium tuberculosis, Mycobacterium leprae, and BCG-vaccinated mice, making it a potential antigen. This study aims to clone and produce recombinant protein Ag85A from Mtb in Escherichia coli BL21. The methods used were ligation to the pET-32a expression vector, transformation to Escherichia coli BL21, and production of protein by IPTG induction. Characterization of recombinant clones by colony PCR and sequencing. The results obtained were that the fbpA gene isolated from Mtb clinical isolate had been amplified, and the PCR product was 900 bp. The production of Antigen 85A has been successfully carried out and produces 44 kDa.
{"title":"Cloning and Production of Antigen 85A Mycobacterium tuberculosis for Diagnostic Latent Tuberculosis: a Preliminary Study","authors":"R. Agus, Sjafaraenan, Yulianti Samara, Muhammad Nasrum Massi","doi":"10.4308/hjb.31.2.374-381","DOIUrl":"https://doi.org/10.4308/hjb.31.2.374-381","url":null,"abstract":"The main challenge in the management of Tuberculosis (TB) is diagnosing quickly and accurately, especially Latent Tuberculosis Infection (LTBI). LTBI detection was carried out using the Tuberculin Skin Test (TST) and Interferon Gamma Release Assay (IGRA). In TB endemic areas, these two examinations have limitations, so current research is directed at finding specific antigens for the diagnosis of LTBI. One of the potential proteins is Antigen 85A (Ag85A) Mycobacterium tuberculosis (Mtb) encoded by Fibronectin-binding protein A (FbpA). The Ag85 complex induces the proliferation of T-cells and interferon-gamma in most healthy individuals infected with Mycobacterium tuberculosis, Mycobacterium leprae, and BCG-vaccinated mice, making it a potential antigen. This study aims to clone and produce recombinant protein Ag85A from Mtb in Escherichia coli BL21. The methods used were ligation to the pET-32a expression vector, transformation to Escherichia coli BL21, and production of protein by IPTG induction. Characterization of recombinant clones by colony PCR and sequencing. The results obtained were that the fbpA gene isolated from Mtb clinical isolate had been amplified, and the PCR product was 900 bp. The production of Antigen 85A has been successfully carried out and produces 44 kDa.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138984308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-05DOI: 10.4308/hjb.31.2.367-373
I. Rizkiya, B. Juliandi, Kukuh Nirmala, D. Puspaningsih, Imam Taufik
Mahseer (Neolissochilus soro) grows and develops in Indonesian lakes and rivers. However, in line with the increase in population, the pollution load that enters water bodies is increasing due to anthropogenic activities along the river. One of the chemicals that can potentially be a source of water pollution is Linear Alkylbenzene Sulfonate (LAS). This study aims to determine the lethal toxicity of LAS surfactant to mahseer and to analyze the sub-lethal effect of this surfactant on the biological, physiological, and histological conditions of mahseer seeds. Parameters studied included lethal toxicity (LC50), sub-lethal toxicity, and biological, histological, and hematological conditions. The results showed that the LAS surfactant had an LC50-96 hour value of 6.14 mg/L in mahseer and was classified as highly toxic. Fish exposed to LAS for 40 days experienced a decrease in specific growth rate and feed efficiency as the surfactant concentration increased. Exposure to LAS also decreases the number of erythrocytes, hemoglobin, hematocrit, and blood sugar levels while increasing the number of leukocytes. There was also damage to the gills of fish exposed to LAS. In general, the sub-lethal concentration of LAS negatively affected mahseer seeds.
鲯鳅（Neolissochilus soro）生长在印度尼西亚的湖泊和河流中。然而，随着人口的增加，由于河流沿岸的人为活动，进入水体的污染负荷也在增加。线性烷基苯磺酸盐（LAS）是可能成为水污染源的化学物质之一。本研究旨在确定 LAS 表面活性剂对马尾藻的致死毒性，并分析这种表面活性剂对马尾藻种子的生物、生理和组织学状况的亚致死效应。研究参数包括致死毒性（LC50）、亚致死毒性以及生物、组织学和血液学状况。结果表明，LAS 表面活性剂对麻子鱼的 LC50-96 小时值为 6.14 毫克/升，属于剧毒。鱼类接触 LAS 40 天后，随着表面活性剂浓度的增加，特定生长率和饲料效率都有所下降。接触 LAS 还会降低红细胞数量、血红蛋白、血细胞比容和血糖水平，同时增加白细胞数量。接触过 LAS 的鱼鳃也会受损。总的来说，亚致死浓度的氯化氨对马赛克鱼籽有负面影响。
{"title":"Effects of Surfactants on Biological, Physiological, and Histological Performance of Mahseer Seeds, Neolissochilus soro","authors":"I. Rizkiya, B. Juliandi, Kukuh Nirmala, D. Puspaningsih, Imam Taufik","doi":"10.4308/hjb.31.2.367-373","DOIUrl":"https://doi.org/10.4308/hjb.31.2.367-373","url":null,"abstract":"Mahseer (Neolissochilus soro) grows and develops in Indonesian lakes and rivers. However, in line with the increase in population, the pollution load that enters water bodies is increasing due to anthropogenic activities along the river. One of the chemicals that can potentially be a source of water pollution is Linear Alkylbenzene Sulfonate (LAS). This study aims to determine the lethal toxicity of LAS surfactant to mahseer and to analyze the sub-lethal effect of this surfactant on the biological, physiological, and histological conditions of mahseer seeds. Parameters studied included lethal toxicity (LC50), sub-lethal toxicity, and biological, histological, and hematological conditions. The results showed that the LAS surfactant had an LC50-96 hour value of 6.14 mg/L in mahseer and was classified as highly toxic. Fish exposed to LAS for 40 days experienced a decrease in specific growth rate and feed efficiency as the surfactant concentration increased. Exposure to LAS also decreases the number of erythrocytes, hemoglobin, hematocrit, and blood sugar levels while increasing the number of leukocytes. There was also damage to the gills of fish exposed to LAS. In general, the sub-lethal concentration of LAS negatively affected mahseer seeds.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138985276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-01DOI: 10.4308/hjb.31.2.348-356
Khomaini Hasan, Maria Ulfah, N. Nurhayati, Gabriela Christy Sabbathini, Sri Rezeki Wulandari, I. Gede, Eka Perdana Putra, I. Helianti
Protein structure has a direct impact on thermostability. Deviations in the primary sequence can affect structural changes, leading to alterations in thermostability properties. However, the molecular basis of protein thermostability is unspecified; thus, elucidation of key factors that role particular protein thermostability is required when engineering proteins to be thermostable. To address this challenge, the amino acid composition, hydrophobicity/hydrophilicity ratio, cysteine bridges, and intrinsic features of two structurally homologous but different thermostability, poly(ethylene terephthalate) hydrolase (PETase) were compared. According to the findings, thermostable and thermolabile PETases have similar folds, compactness, and disulfide bridges. Interestingly, an abundance gap of aromaticity, hydrophobic cluster area, polar amino acid and hydrogen bond network compositions demonstrated dominant trends of variations for both PET hydrolases, indicating a pivotal role of these features in the thermostability of PET hydrolase. Furthermore, increased hydrophobic amino acid frequency in the inner surface of thermostable proteins contributed significantly to thermostability by forming more internal hydrophobic interactions and a less hydrophobic patch. There are no consistent trends in insertions and deletions between both PETases. Taken together, these observations demonstrate that hydrophobicity and hydrogen bond networks are essential factors in thermostability of thermostable PETase.
蛋白质结构对恒温性有直接影响。主序列的偏差会影响结构变化，从而导致恒温特性的改变。然而，蛋白质热稳定性的分子基础尚不明确；因此，在对蛋白质进行热稳定性工程设计时，需要阐明对特定蛋白质热稳定性起作用的关键因素。为了应对这一挑战，我们比较了两种结构同源但热稳定性不同的聚对苯二甲酸乙二醇酯水解酶（PETase）的氨基酸组成、疏水性/亲水性比例、半胱氨酸桥和内在特征。研究结果表明，耐热和不耐热的聚对苯二甲酸乙二醇酯水解酶具有相似的褶皱、紧密度和二硫桥。有趣的是，两种 PET水解酶的芳香度、疏水簇面积、极性氨基酸和氢键网络组成的丰度差距呈现出主要的变化趋势，表明这些特征在 PET水解酶的耐热性中起着关键作用。此外，热稳定性蛋白内表面疏水氨基酸频率的增加通过形成更多的内部疏水相互作用和更小的疏水斑块，对热稳定性有显著的促进作用。两种 PET 酶之间的插入和缺失趋势并不一致。综上所述，这些观察结果表明，疏水性和氢键网络是影响恒温 PET 酶耐热性的重要因素。
{"title":"Sequence-Structure Based Comparison of Structurally Homologous Thermophilic and Mesophilic Polyethylene Terephthalate (PET) Hydrolases","authors":"Khomaini Hasan, Maria Ulfah, N. Nurhayati, Gabriela Christy Sabbathini, Sri Rezeki Wulandari, I. Gede, Eka Perdana Putra, I. Helianti","doi":"10.4308/hjb.31.2.348-356","DOIUrl":"https://doi.org/10.4308/hjb.31.2.348-356","url":null,"abstract":"Protein structure has a direct impact on thermostability. Deviations in the primary sequence can affect structural changes, leading to alterations in thermostability properties. However, the molecular basis of protein thermostability is unspecified; thus, elucidation of key factors that role particular protein thermostability is required when engineering proteins to be thermostable. To address this challenge, the amino acid composition, hydrophobicity/hydrophilicity ratio, cysteine bridges, and intrinsic features of two structurally homologous but different thermostability, poly(ethylene terephthalate) hydrolase (PETase) were compared. According to the findings, thermostable and thermolabile PETases have similar folds, compactness, and disulfide bridges. Interestingly, an abundance gap of aromaticity, hydrophobic cluster area, polar amino acid and hydrogen bond network compositions demonstrated dominant trends of variations for both PET hydrolases, indicating a pivotal role of these features in the thermostability of PET hydrolase. Furthermore, increased hydrophobic amino acid frequency in the inner surface of thermostable proteins contributed significantly to thermostability by forming more internal hydrophobic interactions and a less hydrophobic patch. There are no consistent trends in insertions and deletions between both PETases. Taken together, these observations demonstrate that hydrophobicity and hydrogen bond networks are essential factors in thermostability of thermostable PETase.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139018703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-30DOI: 10.4308/hjb.31.2.336-347
E. P. Septisetyani, P. W. Prasetyaningrum, K. A. Paramitasari, A. Suyoko, Alayna Lillahida Indri Himawan, Salsabila Azzahra, P. H. Wisnuwardhani, Khairul Anam, Ratna D. Ramadani, Adi Santoso, R. A. Ningrum, N. Herawati, Y. Rubiyana
A molecular docking study demonstrates the interaction between naringin, a citrus flavonoid, with SARS-CoV-2 spike RBD. Nevertheless, in vitro investigation of the inhibitory effect of naringin on SARS-CoV-2 entry and syncytia models has yet to be carried out. We synthesized VSV∆G-GFP/Spike* pseudovirus (PSV) as a SARS-CoV-2 model by pseudotyping VSV∆G-GFP/S* in BHK-21 cells overexpressing the SARS-CoV-2 spike glycoprotein. In the SARS-CoV-2 PSV entry assay, we utilized CHO-K1 cells transfected with hACE2 plasmid, which were then treated with naringin and SARS-CoV-2 PSV/naringin. After 16-18 h incubation, PSV internalization represented by the GFP signal was observed under a fluorescence microscope. Immunofluorescence staining was also performed to probe the SARS-CoV-2 spike and confirm the PSV entry. We performed a syncytia assay using 293T cells co-transfected with SARS-CoV-2 spike/hACE2. Six hours after transfection, the cells were treated with naringin and incubated for another 16-18 hours. Then, we observed syncytia using a phase contrast microscope. Based on fluorescence foci quantification, the results indicated that naringin might inhibit SARS-CoV-2 PSV entry at a concentration of 100 µM (P<0.05). However, naringin did not prevent syncytia formation compared to solvent control. These PSV entry and syncytia assay results suggested that naringin potentially inhibited SARS-CoV-2 viral infection but not cell-to-cell viral transmission.
{"title":"Naringin Effect on SARS-CoV-2 Pseudovirus Entry and Spike Mediated Syncytia Formation in hACE2-overexpressing Cells","authors":"E. P. Septisetyani, P. W. Prasetyaningrum, K. A. Paramitasari, A. Suyoko, Alayna Lillahida Indri Himawan, Salsabila Azzahra, P. H. Wisnuwardhani, Khairul Anam, Ratna D. Ramadani, Adi Santoso, R. A. Ningrum, N. Herawati, Y. Rubiyana","doi":"10.4308/hjb.31.2.336-347","DOIUrl":"https://doi.org/10.4308/hjb.31.2.336-347","url":null,"abstract":"A molecular docking study demonstrates the interaction between naringin, a citrus flavonoid, with SARS-CoV-2 spike RBD. Nevertheless, in vitro investigation of the inhibitory effect of naringin on SARS-CoV-2 entry and syncytia models has yet to be carried out. We synthesized VSV∆G-GFP/Spike* pseudovirus (PSV) as a SARS-CoV-2 model by pseudotyping VSV∆G-GFP/S* in BHK-21 cells overexpressing the SARS-CoV-2 spike glycoprotein. In the SARS-CoV-2 PSV entry assay, we utilized CHO-K1 cells transfected with hACE2 plasmid, which were then treated with naringin and SARS-CoV-2 PSV/naringin. After 16-18 h incubation, PSV internalization represented by the GFP signal was observed under a fluorescence microscope. Immunofluorescence staining was also performed to probe the SARS-CoV-2 spike and confirm the PSV entry. We performed a syncytia assay using 293T cells co-transfected with SARS-CoV-2 spike/hACE2. Six hours after transfection, the cells were treated with naringin and incubated for another 16-18 hours. Then, we observed syncytia using a phase contrast microscope. Based on fluorescence foci quantification, the results indicated that naringin might inhibit SARS-CoV-2 PSV entry at a concentration of 100 µM (P<0.05). However, naringin did not prevent syncytia formation compared to solvent control. These PSV entry and syncytia assay results suggested that naringin potentially inhibited SARS-CoV-2 viral infection but not cell-to-cell viral transmission.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139203574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-29DOI: 10.4308/hjb.31.2.328-335
Nur Fadli, Sri Jumiati, N. M. Razi, Adrian Damora, Z. Muchlisin, Irma Dewiyanti, M. Ramadhaniaty, Essy Harnelly, Ahasan Habib, M. N. Siti-Azizah
Groupers are among the fish groups that are difficult to recognize due to their high morphological similarities. Therefore, molecular techniques, particularly DNA barcoding, are extensively utilized to differentiate this fish group. This study aimed to analyze and validate six grouper species belonging to the Epinephelidae family that were harvested from Langsa district waters in Aceh province, Indonesia, based on DNA barcode data. It was conducted from June to December 2021, with the fish specimens collected from fishers at fish landing sites and the fish market in Langsa City, Aceh province. A total of 22 grouper sequences belonging to six species were generated, namely Epinephelus coioides, E. bleekeri, E. malabaricus, E. erythrurus, E. sexfasciatus and Mycteroperca poecilonotus (formerly Epinephelus poecilonotus). Genetic distance within these species ranged from 0.10 to 0.73% (average: 0.40%). Notably, E. malabaricus and E. coioides exhibited the closest genetic kinship (4.07%), while E. sexfasciatus and M. poecilonotus displayed the greatest genetic distance (19.33%). This study provides the first DNA reference for grouper in Langsa district, Indonesia, with significant implications for future sustainable grouper management.
石斑鱼是一种因形态高度相似而难以识别的鱼类。因此，分子技术（尤其是 DNA 条形码）被广泛用于区分这一鱼类。本研究旨在根据DNA条形码数据，分析和验证从印度尼西亚亚齐省兰萨地区水域捕捞的属于石斑鱼科的六个石斑鱼物种。研究于2021年6月至12月进行，鱼类标本从亚齐省兰萨市的鱼类上岸点和鱼类市场的渔民处采集。共产生了 22 个石斑鱼序列，分别属于 6 个物种，即 Epinephelus coioides、E. bleekeri、E. malabaricus、E. erythrurus、E. sexfasciatus 和 Mycteroperca poecilonotus（原 Epinephelus poecilonotus）。这些物种之间的遗传距离从 0.10% 到 0.73%（平均：0.40%）不等。值得注意的是，E. malabaricus 和 E. coioides 的遗传亲缘关系最近（4.07%），而 E. sexfasciatus 和 M. poecilonotus 的遗传距离最大（19.33%）。这项研究首次为印度尼西亚浪沙地区的石斑鱼提供了DNA参考，对未来石斑鱼的可持续管理具有重要意义。
{"title":"DNA Barcoding of Six Commercially Important Groupers (Epinephelidae) from Langsa, Aceh, Indonesia","authors":"Nur Fadli, Sri Jumiati, N. M. Razi, Adrian Damora, Z. Muchlisin, Irma Dewiyanti, M. Ramadhaniaty, Essy Harnelly, Ahasan Habib, M. N. Siti-Azizah","doi":"10.4308/hjb.31.2.328-335","DOIUrl":"https://doi.org/10.4308/hjb.31.2.328-335","url":null,"abstract":"Groupers are among the fish groups that are difficult to recognize due to their high morphological similarities. Therefore, molecular techniques, particularly DNA barcoding, are extensively utilized to differentiate this fish group. This study aimed to analyze and validate six grouper species belonging to the Epinephelidae family that were harvested from Langsa district waters in Aceh province, Indonesia, based on DNA barcode data. It was conducted from June to December 2021, with the fish specimens collected from fishers at fish landing sites and the fish market in Langsa City, Aceh province. A total of 22 grouper sequences belonging to six species were generated, namely Epinephelus coioides, E. bleekeri, E. malabaricus, E. erythrurus, E. sexfasciatus and Mycteroperca poecilonotus (formerly Epinephelus poecilonotus). Genetic distance within these species ranged from 0.10 to 0.73% (average: 0.40%). Notably, E. malabaricus and E. coioides exhibited the closest genetic kinship (4.07%), while E. sexfasciatus and M. poecilonotus displayed the greatest genetic distance (19.33%). This study provides the first DNA reference for grouper in Langsa district, Indonesia, with significant implications for future sustainable grouper management.","PeriodicalId":12927,"journal":{"name":"HAYATI Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139211571","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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