HAYATI Journal of Biosciences
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Age and Growth Estimation of Bigeye Tuna, Thunnus obesus (Lowe, 1839) in the Eastern Indian Ocean Deduced from Otolith Microstructure
Get PDFAge-based stock assessment of globally important species, like bigeye tuna Thunnus obesus (Lowe, 1839), is urgently required to develop appropriate management plans for fisheries sustainability. This study aimed to estimate age and growth parameters using annual increments count of sectioned-otoliths, which effectively employed for age determination of tunas. Samples were collected from Indonesian tuna longline catch landed in the Port of Benoa from March until December 2017. Multi-models were employed to obtain robust growth parameters, and Akaike Information Criterion (AIC) was relied for the best fit model selection among those evaluated. Growth band formation was validated using marginal analysis (MI), indicating that one ring is deposited yearly and slow growth peaked during July (Australian winter). The von Bertalanffy growth model was selected as the best model fitting growth parameters from raw age data, as expressed as Lt = 183.49 (1-e-0.134(t+2.991)). Large variances in growth were detected at the same age, with the oldest age of 15. Over 50% of fish in the Indonesian catch were <5 years old, that may have implications for fisheries sustainability
Genetic Diversity of Gracilaria spp. in the Intertidal Zone on the South Coast of Yogyakarta, Indonesia Based on DNA Barcoding with rbcL Marker
Get PDFGracilaria spp. is a commercial seaweed utilized in various food, pharmaceutical, and health industries. Due to the high plasticity of seaweed, morphological identification must be validated by molecular identification using DNA barcoding. This study aims to identify the genetic diversity of Gracilaria spp. based on DNA barcoding with an rbcL marker. Samples were collected from six beaches, i.e., Trenggole, Drini, Siung, Wediombo, Nguyahan, and Ngedan, from September-November 2021. The methods in this study were sampling, sample preservation, morphological and tissue observations, DNA extraction, PCR and electrophoresis, and data analysis. The results showed four species of seaweed based on the rbcL marker: Gracilaria sp., G. salicornia, G. edulis, and G. vieillardii. Based on 18 samples confirmed by phylogenetics, five different species were found, namely G. salicornia, G. edulis, G. vieillardii, Gracilaria sp. 1, and Gracilaria sp. 2 The last two species, i.e., Gracilaria sp. 1 and Gracilaria sp. 2, from the intertidal zone of the south coast of Yogyakarta may have never been reported to GenBank
Effect of the Supplementation of Endogenous Probiotics in Feed on Growth Performance, Digestive Enzyme Activity, and Non-Specific Immunity Gene Expression of Sandfish, Holothuria scabra Juveniles
Get PDFThe present study aimed to evaluate the effects of endogenous compared to commercial probiotics on the growth, digestive enzyme activity, and non-specific immunity of sandfish juveniles. Treatments were: A. diet without probiotic; B. diet supplemented with endogenous probiotics Gamma proteobacterium strain M-4, Bacillus subtilis strain Q-1, Bacillus sp. strain E-2; C. diet supplemented with a commercial probiotic containing B. subtilis, B. licheniformis, and B. pumilus. The research was conducted for 4 months using 12 plastic containers, 30 juveniles each (initial weight of 2.72±0.37 g, mean ± standard deviation). From each container, ten samples were taken randomly every 14 days and weighed and three intestine samples at initial and every following month to analysis enzyme activities. At the end the study, all juveniles were counted and weighed individually, and performed a challenge test by injected a 106 CFU ml-1 Vibrio azureus strain 4C-1 at 0.1 ml/ind. Immune response observed were: total coelomate and gene expression (SOD, CAT, LZM) by Quantitative real-time PCR. The specific growth rate of juveniles fed by diet B was significantly different from treatment A (P<0.05), its final weight was higher compared to diets A and C (P<0.05). Protease, lipase, and amylase activity in treatment B was higher compared to C and A (P<0.05). The survival rate, total coelomocyte count, gene expression after being challenged were higher in treatment B compared to C and A (P<0.05). The present study showed endogenous probiotics promote growth, improve digestion enzyme activity, and stimulate non-specific immune responses
Bananas and Their Wild Relatives in Pandeglang, Indonesia
Get PDFPandeglang is one of the banana producer regencies of Banten, Indonesia, that produce 924 tons per year. However, information regarding the diversity of banana germplasm in this region is unavailable. This study explored districts Cadasari, Banjar, Jiput, Labuan, and Menes. Morphological characters were noted and used to identify the cultivars, subspecies, or varieties. In total, 22 accessions were collected from 22 collection sites. Based on morphological characters, we described 14 banana accessions of 10 cultivars, three accessions of wild Musa acuminata and one of Musa balbisiana. Considering its genome composition, five genome types we described among these banana cultivars, i.e., AA (divided into AA and AA wild), BB, AAA, AAB, and ABB. In this study, we did a principal component analysis and saw that AA wild and AAB were clearly separated, but the other genome types were clustered partially or included in one cluster. Our study expands the information on banana diversity in Indonesia. Further study on the potential of this banana germplasm to be used as a genetic resource to find resistance to banana diseases is needed
The Benthic Foraminiferal Assemblages in the Seagrass Bed of Tanjung Berakit Waters, Bintan Island
Get PDFSeagrass is the most common ecosystem in Tanjung Berakit waters. Therefore, Tanjung Berakit waters have a very important role as a benthic foraminiferal habitat. This study was conducted to describe the distribution of benthic foraminifera relating to the environmental condition of the waters. The samples were collected from eight stations by handling garb in November 2017. This study collected 18 species of shallow water benthic foraminifera dominated by Amphistegina and Heterostegina. This study recorded a correlation between the sediment texture and foraminiferal assemblages. The most common foraminifera were inhabiting fine-textured sediments, especially very fine sand and silt. Only a few foraminifers are collected from extremely fine sediments such as clay sediments, or extremely coarse including pebbles
Detection of Avirulence Gene AvrPi9 in Magnaporthe oryzae, a Rice Blast Fungus, Using a Combination of RPA and CRISPR-Cas12a Techniques
Get PDFRice blast disease is one of the most devastating diseases of rice production worldwide, which causes by an ascomycete fungus, Magnaporthe oryzae. The virulence of the rice blast fungus is determined by avirulence genes (Avr genes). Therefore, the identification of Avr genes is important for rice resistance variety improvement. Avr genes are currently identified using the pathogenicity assay with rice near-isogenic lines (NILs) or PCR amplification and gene sequencing, both of which are time-consuming and labor-intensive methods. This study aims to develop a simple method for Avr gene identification using AvrPi9 as a model. A recombinase polymerase amplification (RPA) technique was carried out to amplify AvrPi9 by incubating rice blast fungus genomic DNA with gene-specific primers at 37°C for 20 min. Cas12a-based AvrPi9 detection was performed by incubating at 37°C for 5 min. The fluorescence signal was visualized by the naked eye under an LED transilluminator. The study found that AvrPi9 can be amplified and detected using RPA and a Cas12a-based method. AvrPi9_crRNA2 has a higher efficiency than AvrPi9_crRNA1. The sensitivity of the method was 3.8 ng of DNA target for AvrPi9_crRNA1 and 1.9 ng of DNA target for AvrPi9_crRNA2. This RPA and Cas12a combination technique is a newer method for Avr gene detection in plants and has several advantages over traditional methods. It is considered easier to use and more efficient in terms of time and labor, making it a potentially useful tool for plant breeders and pathologists
Development of DNA Extraction Method for Forensics Studies of Preserved Hair and Skin Samples from Sumatran Tiger (Panthera tigris sumatrae, Pocock 1929)
Get PDFPoaching and illegal wildlife trade present severe threats to the Sumatran tiger. The high demand for tiger body parts leads to a high number of imitations in illegal markets, complicating the morphological identification of any confiscation cases. Accurate identification is essential in legal due process, given that the national protection law only regulates Indonesia\u27s native species. Identification using molecular approaches may overcome the problem. However, most illegally traded tiger body parts have been preserved for an extended period of time, reducing the quantity and quality of the recovered DNA. This study aimed to develop a fast and effective method to recover DNA from preserved forensic samples. The methods had been tested with several museum samples of arsenic-treated hairs and a tiger skin piece obtained from the National Research and Innovation Agency (BRIN, formerly LIPI), tiger hairs obtained from Conservation of Natural Resources Agency (BKSDA) of Bengkulu Province, and a confiscated tiger skin sample from BKSDA Aceh. The DNA was extracted using ion-exchange, salting out, and protease-based methods. The results showed that the protease-based extraction outperformed the others to yield applicable DNA isolates for PCR-based species identification by Cyt b and ND2 mtDNA partial genes from preserved samples. However, further works are still needed to recover sufficient DNA yields for sex identification
The First Evidence of Potential Antibacterial Activity of Laccase Enzyme from Indonesian White Rot Fungi against Pathogenic Bacteria
Get PDFThe antibacterial agent can be extracted from plants, animals, and microorganisms such as fungi. The potential antibacterial activity of laccase derived from fungi remains limited in current reports. This study aimed to investigate the characteristics of laccase from Indonesian white rot fungi (WRF) and explore its potential as an antibacterial agent. The laccases were produced by Trametes hirsuta D7, Trametes hirsuta EDN 082, Leiotrametes menziesii BRB 73, and Lentinus sajor-caju BRB 12 using oil palm empty fruit bunch as a substrate. The results showed that the Indonesian WRF tested produced brownish-yellow laccase. FTIR analysis demonstrated similar peak patterns but distinct absorption intensities among the laccases. Trametes hirsuta D7 gained 0.044 U/ml of the greatest laccase activity. Laccase, with minimal activity of 0.001 U/ml–0.026 U/ml, suppressed the propagation of Propionibacterium acnes and Staphylococcus aureus. Escherichia coli and Pseudomonas aeruginosa could be inhibited by the laccase with a minimum activity of 0.002 U/ml–0.044 U/ml. However, S. aureus and E. coli showed the Minimum Bactericidal Concentration in the laccase activity range of 0.018 U/ml–0.308 U/ml. Gram-positive and Gram-negative bacteria grow more slowly when the laccase is present, supposed the laccase as a potential antibacterial agent
A Study of Chemical Constituents in Platinum Fast-Grown Teak Wood (Tectona grandis) with Age Differences Using Py-GCMS Coupled with Interdependence Multivariate Analysis
Get PDFPyrolysis gas chromatography-mass spectrometry (Py-GCMS) is a simple, rapid, and reliable analytical technique to assay lignocellulose biomass. This study aims to analyze the chemical content of various ages of platinum fast-grown teak wood using PyGCMS coupled with interdependence multivariate analysis. Fifty-eight peaks were shown in the pyrogram originating from carbohydrates, lignin, and extractive derivatives. Along with age, platinum fast-grown teak wood showed higher carbohydrate derivatives in heartwood than sapwood. Compared to teak wood grown in conventional (between 36.72-45.69%), platinum fast-grown teak wood has a higher content of carbohydrates (42.82-48.04%). A substantial amount of G-unit lignin was detected in the sapwood, while the S-unit lignin dominated the heartwood. The extractive content of 10-years-old teak wood heartwood was 4.82%, higher than 10- and 20-years-old heartwood from conventional wood (2.23% and 8.88%, respectively). Multivariate analysis of the chemical compound showed that Py-GCMS could be utilized to classify platinum fast-grown and conventional teak wood. 2-methyl anthraquinone (MAQ) content of 10-year-old fast-grown teak wood was 2.5 times higher than 20-year-old conventional teak wood. Based on the study, platinum fast-grown teak wood is promising as alternative wood material to fulfill the market demand for conventional teak wood
Prospects of Indigenous Bacillus subtilis Strain LS9.1 as a Potential Biocontrol Agent against Aedes aegypti Larvae
Get PDFBiocontrol is one way that can be developed to overcome public health and agricultural problems. Biocontrol agents could be a microorganism, for example, from the Bacillus group. This study aims to determine the larvicidal toxicity of the Bacillus subtilis strain LS9.1 against Aedes aegypti larvae. The mode of action of the isolate caused larval death, which was detected with parasporal inclusions and secondary metabolites. Larvicidal toxicity with the bioassay method. Parasporal inclusion proteins were detected with the SDS-PAGE method. The Cry toxin coding gene with the PCR method and cell ultrastructure with transmission and scanning electron microscopy (TEM and SEM). The action of secondary metabolites was detected with hemolytic activity test. The isolate high toxicity to A. aegypti larvae. Parasporal inclusion proteins with molecular weights ranging from 72-7 kDa and the gene encoding a protein toxin in size 300 bp. The TEM and SEM results did not Cry-IV toxin. The hemolytic activity test showed a positive reaction correlated with biosurfactant production. Based on this study, the death of larvae is probably caused by secondary metabolites produced by Bacillus subtilis strain LS9.1. Thus, this isolate has the prospect of being an environmentally friendly biocontrol agent to disease vectors and insect pests