HAYATI Journal of Biosciences
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Optimization of Genetic Material Extraction Techniques and Application of Isothermal Amplification Method for Field Authentication of Two Thresher Sharks (Alopias pelagicus and Alopias superciliosus)
Get PDFThe pelagic thresher shark (Alopias pelagicus) and bigeye thresher shark (Alopias superciliosus) are important shark species for Indonesia\u27s consumption and finning industry. Both Alopias species are included in the CITES appendix II, thus requiring certain documents for trading. Regarding species identification for on-site application, the DNA isolation method is a crucial step. In this study, we developed a DNA isolation method suitable for on-site application based on isothermal amplification (LAMP) and species-specific COI gene markers. Three different extraction methods were applied, namely modified spin column kits and dipsticks. The quality of DNA was evaluated and tested for isothermal amplification using a reference sample, fresh fillet, and ethanol-preserved sample. The extracted sample concentration was in the range of 135.35-0.65 ng/μL. The LAMP test showed that three different DNA extraction methods successfully amplified the DNA fragments through the color changes at the end point of the LAMP reaction. The LAMP test was also sufficient to detect less than 10 ng of DNA from A. pelagicus and A. superciliosus within 30-50 min. The DNA from the modified spin column and dipstick extraction method combined with LAMP can potentially be used to detect Alopias pelagicus and Alopias superciliosus species on-site
Discovery of Simple Sequence Repeat Markers in the Endemic Durian Kura-Kura (Durio testudinarius Becc.)
Get PDFDurio testudinarius, known as Durian Kura-Kura, is a native Bornean durian species in the Malvaceae family with fruit at the base of the main stem. Recent advances in genomic-based next-generation sequencing are being used to conserve germplasm and enhance plant breeding. This method rapidly and cost-effectively sequences plant genomes, allowing for simple sequence repeat markers to be constructed in silico. This study aimed to design and evaluate novel, simple sequence repeat markers utilizing next-generation sequencing microsatellite data of D. testudinarius. A total of 20 sequences containing di-, tri-, tetra-, and penta-nucleotide motif repeats were selected and designed to generate primers using Primer3 online software. The PCR results of the twenty primers tested on D. testudinarius and 19 genomic DNA samples of species from the Malvales order showed successful amplification. These newly developed simple sequence repeat markers are crucial for genetic population analyses, determining population structure, and enhancing plant breeding programs and conservation strategies for D. testudinarius and its relative\u27s germplasm resources
Diversity of Rhizospheric Bacterial Community from Kaolin Mining Site and Their Potential as Plant Growth Promoting Bacteria
Get PDFTailing from mining activities affects soil fertility resulting in poor soil conditions that are challenging for plants to grow. Plants can interact with rhizosphere bacteria to enhance their growth in harsh environments. Rhizospheric bacteria possess numerous mechanisms that promote plant growth and induced resistance to various abiotic stress. This study aims to determine the diversity of rhizobacteria and their potential as plant growth-promoting rhizobacteria (PGPR) agents. Bacterial communities from rhizosphere soil samples from kaolin mining sites in Perawas, Tanjung Pandan district, Belitung Regency, Bangka Belitung Island, Indonesia were analyzed using Next Generation Sequencing based on the V3-V4 region of the 16S rRNA gene, while culturable bacteria were isolated from samples and screened for PGP activity. The results showed that the rhizosphere bacterial community was mostly dominated by Pseudomonadota, Acidobacteria, and Verrumicrobiota. There were 15 bacteria isolated from the sample and RKB-5 bacterial isolate had the potential to be PGP agent. The RKB-5 bacterial isolate was identified as Burkholderia cenocepacia based on its 16S rRNA sequence. The bacterial isolate produced IAA, utilized ACC, dissolved phosphate up to 209,5 mg/L, and formed a high potassium solubilizer index value of 5.00. Therefore, the B. cenocepacia RKB-5 has potential application as the PGPR to support plants growth by obtaining nutrients in ex-mining lands with poor soil conditions
Diversity and Selection of Cotton Germplasm Based on Morpho-Agronomic Character Performance
Get PDFCotton is a plant that produces natural fibers of high economic value. Developing a new superior variety of cotton is expected to support fiber demand in Indonesia. The purpose of this study was to determine the diversity of morpho-agronomic characters and obtain secondary characters and cotton accessions that support the development of a new superior cotton variety. The genetic material used was 266 cotton accessions from the ISFCRI germplasm collection. Primary data of the 16 quantitative morphological characters were observed and analyzed using descriptive data, correlation analysis, path analysis, scatterplot, and grouping. The fiber length character has a very low diversity with a value of 0.01, and the plant height character has the highest variance, which is 637.42. The lint percentage with a variance value of 9.37 is influenced by duplicate epistasis genes and controlled by many genes. The fiber\u27s fineness character has a positive and very significant correlation value to the character of the lint percentage. It has fairly high direct and total effect values of 0.156 and 0.134, respectively. Four accession groups can potentially support developing a new superior variety; accession CEA N 268, CEDIX, or L21999-10-71 can be used as the parent of new superior cotton varieties
Slow-release Fertilizer Application on Silk (Falcataria moluccana Miq.) and Rice (Oryza sativa L.) Plant Growth and Yield in Agroforestry System
Get PDFThe 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
Genetic Relationship and the Putative Occurrence of A Species Complex Within the Indonesian Calotes (Daudin, 1802) (Squamata, Agamidae) Genus Based on COI Gene Sequences
Get PDFThe 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
Expression of Immunoglobulin M (IgM) and Immunoglobulin G (IgG) in Normal Wistar Rat Post-Cheral® Administration
Get PDFMaintaining 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®\u27s ability to prevent infections and maintain the immune system of the rats throughout the treatment period
Molecular Analysis of Cry1Ab-Cry1Ac Gene Fusion in Transgenic Sugarcane Resistant to Shoot Borer Scircophaga excerptalis (Lepidoptera: Pyralidae) and Stem Borer Chilo sacchariphagus (Lepidoptera: Pyralidae)
Get PDFSugarcane (Saccharum officinarum) is a plant with high economic value because it can produce sugar. Shoot borer Scircophaga excerptalis (Lepidoptera: Pyralidae) and stem borer Chilo sacchariphagus (Lepidoptera: Pyralidae) attacks are one of the issues that limit sugarcane productivity. Establishing transgenic sugarcane is one of the most efficient ways to prevent borer damage. Previously, Cry1Ab and Cry1Ac genes were successfully used to create transgenic sugarcane plants. This study aimed to detect the presence of transgenes and analyze the expression level of the Cry1Ab-Cry1Ac gene fusion in transgenic sugarcane using RT-PCR. The methods used in this study are transgene detection with PCR and gene expression analysis in normalized expression (2-ΔΔCq) with RT-PCR. The Cry1Ab-Cry1Ac gene has been integrated into all lines with varied expression levels. In 311 GV and 333 GV lines, the Cry1Ab-Cry1Ac gene was expressed in the leaf but not in the stem. Shoot and stem borer attack percentage values showed that all lines were lower than the control, with 222 EH as the lowest and 311 GV as the highest. Leaf and stem borer attack levels were compared to gene expression values of Cry1Ab-Cry1Ac. Results may indicate that the 222 EH line was resistant, but the 311 GV and 333 GV lines were not
Isolation of Endophytic Bacteria from Melon Root and Evaluation of Their Antagonistic Activity Against Acidovorax citrulli
Get PDFEndophytic bacteria are a potential biocontrol agent to control plant diseases. Controlling plant disease using bactericides has negative impacts, including the death of other organisms on plants. This research aimed to identify potential endophytic bacteria from melon roots for biocontrol against Acidovorax citrulli, the pathogen causing Bacterial Fruit Blotch (BLB) disease in the Cucurbitaceae family. A total of 11 endophytic bacteria were isolated from healthy melon roots. The isolates exhibited similar colony morphology with white, circular, convex elevation. Physiology and biochemistry tests revealed 8 isolates as Gram-negative and catalase-positive, while the remaining 3 were identified as Gram-positive and catalase-negative. A fluorescence test on King\u27s B media indicated that the Gram-negative isolates could belong to the Pseudomonas genus. This study also confirmed Acidovorax sp. cultures isolated from infected melon plants many years ago as A. citrulli. Assessment of pathogenicity in the melon plants showed that A. citrulli isolate N2 was the most pathogenic. Based on the in vitro inhibition test, all the Gram-negative isolates formed inhibition zones ranging from 1.94-4.41 mm, suggesting their potential to inhibit the growth of A. citrulli. The EB6 isolate exhibited the highest inhibition zone at 4.41 mm ±0.28. five of the eight isolates tested (EA1, EB1, EB3, EB4, and EB6) did not exhibit any Hypersensitive Response (HR) reaction in the tobacco leaves, thus can potentially be used as a biocontrol agent against BLB disease in melon plants. Further studies are required to determine the species identity of the isolates and explore their application as biocontrol agents
Potential of Clitoria ternatea L. Extract Towards Insulin Receptor Expression and Marker of Inflammation in Diabetes Mellitus Rats Model
Get PDFMetabolic 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