HAYATI Journal of Biosciences
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A Possible Mixing Genetic Pool of Eastern Little Tuna Euthynnus affinis Cantor (1849) from the Western and Southern Part of Indonesian Waters
Get PDFEastern little tuna (Euthynnus affinis) is a commercially important species for coastal communities in the western and southern part of Indonesia. However, little is known about its characteristics. Therefore, a comprehensive and broader research of its population structure is imminent in response to conserve and manage the fishery sustainably. This study aimed to fill the gap of the lacking information on the stock separation of eastern little tuna within the Indonesian archipelagic waters and its Economic Exclusive Zone (EEZ). Population genetic approaches were used to examine population structure using the mitochondrial DNA (mtDNA) control region marker. A total of 94 samples were collected from nine landing sites between January to September 2020. Polymerase chain reaction (PCR) was used to amplify the samples, and Sanger sequencing was used to sequence them. The findings showed a mean value of 0.922 for genetic diversity (Hd) and 0.009 for nucleotide diversity (π). Both of these numbers pointed to a high level of genetic diversity. A further population analyses using Analysis of Molecular Variance (AMOVA) and Discriminant Analysis of Principal Component (DAPC) confirmed a mixing gene pool with no distinct population structure detected (ΦST value of 0.097 and p-value>0.05)
Salt and Heat Stress Trigger Morpho-Physiological Changes, Antioxidant Enzyme and Secondary Metabolites Gene Expression in Rice (Oryza sativa L.)
Get PDFClimate change significantly increases salt and heat stress in rice plants. This condition causes plants to activate antioxidant enzymes and produce secondary metabolites. This study aimed to determine the morpho-physiological changes and gene expression profiles of antioxidant enzymes and secondary metabolites. This study used a completely randomized design factorial. The first factor was local rice varieties (IR64, Silaun, and Cigeulis), and the second factor was stress treatments (control, NaCl 150 mM, 40°C, and NaCl 150 mM + 40°C). The results showed that multiple stress significantly affected the plant height, stem length, stem diameter, leaf area, root length, total main root, plant biomass, necrotic length, chlorophyll content, relative water content, and plant ROS production. Multiple stress could up-regulate the gene expression of antioxidant enzymes (Mn-SOD, Cu/Zn SOD, Cytosolic APX, OsAPX1, CAT, OsCATA, and GPOD) in rice after stress combination treatments and increase the secondary metabolites gene expression (P5CS and GABA-T) in all rice varieties. Still, the OsNOMT gene was only active in the Cigeulis variety
Isolation and Characterization of Chalcone Synthase (CHS) Gene in Variegated-Flower of Dendrobium \u27Enobi\u27 and Phalaenopsis Hybrid Orchids
Get PDFVariegated flowers, characterized by the presence of different colors in flowers, have high economic and aesthetic values. The main pigment in the orchid\u27s 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 \u27Enobi\u27 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\u27s anthocyanin content. In addition, the purple zone in the D. \u27Enobi\u27 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
Population Management of Samia cynthia ricini Boisduval (Lepidoptera: Saturniidae) by Eggs Refrigeration and Its Effect on Hatchability, Development, and Fecundity
Get PDFEgg viability, hatchability, and development are significant factors in the natural silk industry. Life cycle modification is an important aspect that must be considered to perform effective and efficient mass-rearing and quality control. This study aimed to improve the mass rearing efficiency of Samia chintya ricini through a life cycle modification technique by refrigeration. The study was conducted by storing S. c. ricini eggs in the refrigerator at a temperature of 5°C for one to seven days. Observations were made on the hatchability, development time, cocoon shell weight, and adult female fecundity. The results showed that the egg refrigeration period affected the hatchability of the eggs. A more extended period of egg refrigeration significantly decreased hatchability. The eggs could develop into adult insects after being stored for one to five days. Meanwhile, none of the eggs hatched successfully after going through a cold storage period of six and seven days. Furthermore, the egg refrigeration period affected the development time of the egg, larvae, pupae, and adult. A more extended period of egg refrigeration results in slower egg and larval development time. But a faster cocoon development time. The refrigeration period did not significantly affect the cocoon shell weight. However, it was affecting adult female fecundity. Total fecundity decreased as the refrigeration period increased with different daily oviposition patterns. This study implies that when the egg population is excessive, the life cycle of S. c. ricini can be delayed for 1-5 days. This method can be implied as a simple life cycle modification technique for eri silkworm cultivation
Molecular Docking and Dynamics of SARS-CoV-2 Programmed Ribosomal Frameshifting RNA and Ligands for RNA-Targeting Alkaloids Prospecting
Get PDFRNA-ligand docking is a part of computational biology, which is currently lowly recognized compared to the protein-ligand docking procedure commonly applied for drug discovery. This in silico study aims to create a simplified protocol for RNA-ligand docking, which is applicable to RNA-targeting small molecular drug screening. Four alkaloids (berberine, colchicine, nicotine, and tomatine) were subjected to this study and contended against the SARS-CoV-2 genomic RNA -1 PRF component targeting control drug, merafloxacin, including two known intercalator berberine and colchicine, a small alkaloid nicotine and a large alkaloid tomatine. The alkaloids were screened for drug-likeness properties (Lipinski’s Rules of 5 or LRo5), bioavailability indexes, and synthetic accessibility values using SwissADME before docking. The docking used PyRx – Autodock Vina and re-scored for RNA-ligand scoring using AnnapuRNA. The docking results have the interactions mapped using fingeRNAt and visualized using Discovery Studio. Molecular dynamics using CHARMM36 and AMBER forcefields were simulated in NAMD. The molecular dynamics 1 ns simulation results showed that the ligand interaction over time did not cause much interference with the RNA, indicated by the low number of RMSD changes between RNA itself and the RNA-ligand complex. Additionally, CHARMM36 forcefield provided more stable fluctuation compared to AMBER. The results indicated that tomatine disobeyed LRo5 and had a low bioavailability index and bad synthetic accessibility value, while the rest alkaloids passed. In the end, berberine has an even higher docking score than the control drug. The study also shows that this protocol can be useful for future RNA-ligand computational studies
Study on the Mitochondrial Genome of Variants Carrying mt.3243A>G from Type-2 Diabetes Mellitus and Cataract Patients in Indonesia
Get PDFThe association of type-2 diabetes mellitus (T2DM) and cataract with mtDNA mutation has been reported before. Despite the high prevalence of DM and cataract in Indonesia, a study of the mtDNA variants in Indonesia in correlation with the two diseases is still limited. MT.3243A>G is one of the hotspots mutations for mitochondrial diseases, but the explanation for its occurrence in patients with pure cataract is still elusive. Therefore, the objective of this study was to analyze the mitochondrial genome variants from T2DM and cataract patients in Indonesia using the direct sequencing method. The homology analysis of the genome to the Cambridge reference sequence resulted in 86 variants, including 20 variants that cause amino acid substitutions. Based on the Mitomap data, 17 of the 20 variants were novel. Upon comparison with the 12 normal variant genomes, 11 of 17 variants were suggested to be associated with T2DM and cataract diseases since they code the protein in complex-I (ND4L, ND5, and ND6), complex-III (cytb), and complex-V (ATP6) of the respiratory complex. Interestingly, MT.3316G>A, for the first time, is shown in a pure cataract patient. In addition, the novel phenotype of MT.5460G>A and MT.10398A>G were revealed, which are T2DM and cataract in one patient. Based on our study, these diseases might be related to the disruption of the ATP metabolism due to the structure and function changes of proteins involved in the respiratory complex. This discovery is expected to offer an understanding of the origins of gene-level clinical differences, particularly in Indonesia
Haplotype Diversity in the Mitochondrial COI Gene of Barred Rainbowfish (Chilaterina fasciata) from Mamberamo River of Western New Guinea, Indonesia
Get PDFA Barred rainbowfish (Chilatherina fasciata) is one of the native fish species found in Western New Guinea of Indonesia. This study aimed to observe the levels of haplotype diversity in the partial Cytochrome-c oxidase subunit I (COI) gene of Barred rainbowfish. For the DNA analysis, thirty (30) Barred rainbowfishes were caught from the Mamberamo River. Three (3) molecular packages of BioEdit, MEGA, and DNAsp were used to analyze twenty (30) forward sequences of the COI gene (502 bp). The research showed four (4) haplotypes for the examined population, a total of seven (7) mutations, and low genetic diversity detected in the partial COI gene with the haplotype diversity (Hd) = 0.405 and nucleotide diversity (pi) = 0.003. Meanwhile, the Fu\u27s and Tajima\u27s tests were 1.21 and -0.69, respectively. The UPGMA tree with 1,000 × bootstrap replications revealed that Barred rainbowfishes are grouped into similar clusters with Melanotaenia vanheurni, Chilatherina alleni, and Chilatherina bleheri. In conclusion, haplotype 3 (77%) was detected as the common haplotype for Barred rainbowfishes at the Mamberamo River of Western New Guinea
Enhancing Solubility of Recombinant Plasmodium Lactate Dehydrogenase (pLDH) Using Combination of Cold-Inducible Expression System and Cold-Stirred Bioreactor
Get PDFA major drawback associated with an expression of a high-level Plasmodium Lactate Dehydrogenase (pLDH) using Escherichia coli is the low solubility due to the formation of an inclusion body (IB). This study aimed to develop a suitable protocol for enhancing the solubility of pLDH expressed in E. coli. Firstly, a pLDH-encoding gene was amplified from the blood sample of malaria-infected patients and ligated into pBlueScript II KS+ for sequencing. Afterward, the pLDH gene was digested and cloned into pColdTF for expression. The recombinant plasmid was transformed into the E. coli BL21 (DE3) RIPL Codon Plus Strain. Then, the bacterial host was initially cultured at 37°C until reaching optical density (OD) at 600 nm: 0.5. Thereafter, the growth temperature was lowered to 15°C, followed by the addition of 0.1 mM IPTG into the culture medium for inducing pLDH expression. Thereafter, the bacterial hosts were cultured in a cold-stirred bioreactor (15°C). The result showed that a combination of the low culture conditions (15°C) and a low amount of IPTG increased the solubility of pLDH. This result suggests that this protocol can be a convenient method for generating high-quality recombinant protein using the E. coli system
COI Gene Analysis of Asian Horseshoe Crab in Banyuasin Estuarine Waters, Sumatra, Indonesia
Get PDFThere is limited study on DNA barcoding of horseshoe crabs in South Sumatra, Indonesia. The present study was the first to record horseshoe crabs\u27 COI DNA barcoding in three localities of Banyasin estuarine waters. The nucleotide composition was in a strong adenine thymine bias (AT = 63.90%) with high haplotypic diversity (Hd = 0.858) relative to low nucleotide diversity (π = 0.0534). A total of 16 haplotypes were recorded, of which two were in Carat Cape, 4 in Makati Jaya, and 12 in the Banyuasin river estuary (BRE), and Hap 1 was a dominant type (62.5%). The population differentiation (FST) value was varied, and only in the comparison of BRE-Carat Cape was significant (FST = 0.637), while the gene flow (Nm) value in Makati Jaya-BRE was high (6.563). The neutrality test, Tajima\u27s D (0.4142), and Fu\u27s Fs values were negative (-0.492), suggesting these populations have experienced a current bottleneck or multiplication. Analysis of molecular variation (AMOVA) suggested that 68% was distributed within populations. The haplotype network, PCoA, and phylogenetic of COI DNA sequences clustered in three groups correspond to Carcinoscorpius rotundicauda, Tachypleus gigas, and Tachypleus tridentatus. This finding is a matter of concern for managing and conserving horseshoe crab species in Banyuasin estuarine waters
Growth Patterns and Mortality of Lobster Panulirus ornatus from the Catch of Bottom Gill Net Fishers in the Western Waters of Tarakan Island
Get PDFLarge-bodied Panulirus ornatus lobsters are economically important because they are an aquatic biota. It is one of the most important commodities in the city of Tarakan. The aim is to analyze the growth patterns and mortality of P. ornatus from the West Waters of Tarakan City. Method using a quantitative descriptive. The purposive sampling method was used by dragging the gill net fishing gear to the P. ornatus lobster ground area, and the collection was carried out 16 times in 7 months (December 2021-July 2022). The results of P. ornatus showed that the male sex ratio was higher than the female. The growth model was allometrically negative, and the criteria for the condition index were fat and thin. The growth pattern of Model Von Bertalanffy males is slower than females. However, the growth rate to achieve asymptotic growth for males is faster than for females. The total mortality, catch mortality, and exploitation rate of males was higher than females. However, the mortality of the female nature was higher than that of males. P. ornatus should be managed in the waters of West Tarakan using the domestication and restocking technique to increase sustainability