HAYATI Journal of Biosciences
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Comparative Study of DNA Barcoding and Mini-Barcoding based on COI Gene for Species Identification and Phylogeny of Formicidae Family (Insecta: Hymenoptera)
No full textDNA barcoding and mini-barcoding are widely used to study insect biodiversity, including ants (Hymenoptera: Formicidae). This study evaluated the effectiveness of both approaches for species identification and phylogenetic inference in ants, with particular attention to the performance of universal primers during PCR amplification. Full-length DNA barcode (658 bp) and mini-barcode (127 bp) regions of the mitochondrial cytochrome c oxidase subunit I (COI) gene were retrieved from GenBank, aligned, and analysed with maximum-likelihood phylogenetics (1,000 bootstrap replicates) under the Tamura-Nei model. The universal DNA barcoding primers (Folmer\u27s LCO1490 and HCO2198) showed generally good alignment with ant COI sequences. However, multiple nucleotide mismatches were observed in LCO1490, including one critical mismatch located within the GC clamp region. In contrast, the universal mini-barcoding primers (UniMinibarF1 and UniMinibarR1) showed critical mismatches at their 3′ ends, likely reducing PCR efficiency. Despite limitations associated with primer mismatches, both DNA barcoding and mini-barcoding are reliable for species identification. DNA barcoding and mini barcoding are both capable of distinguishing ants at the species level, regardless of the length of the sequences being compared. The same sequences have also been used for phylogenetic analysis, showing good ability to distinguish ant species based on phylogenetic tree reconstruction. The comparison of DNA barcoding and mini-barcoding in ants showed that longer sequences offered superior resolution for species identification and phylogenetic reconstruction. These findings underscore the need for primer optimisation in ant-specific applications and highlight the utility of both barcoding strategies for taxonomic and evolutionary studies
Eugenol Exhibits Antimutagenic Activity in Model Yeast Schizosaccharomyces pombe by Regulating DNA Damage Repair System: A Transcriptomic Analysis
No full textFree radicals that accumulate in cells can cause oxidative imbalance and trigger oxidative stress at the cellular level. Such conditions lead to damage to genetic material that accelerates cellular aging. Plant secondary metabolites have been reported to exhibit antioxidant activities that have the potential to overcome oxidative stress. Eugenol, derived from cloves (Syzygium aromaticum), has been shown to possess antioxidant activity in vitro. However, there is no information on the antioxidative activity of eugenol at the cellular level. Our study focused on the effect of eugenol as an antigenotoxic agent in preventing DNA damage caused by oxidative stress treatment. Further analysis on the cellular levels of eugenol was done through a transcriptomics study in the model yeast Schizosaccharomyces pombe. Treatment with eugenol may increase the cell viability of yeast exposed to mutagenic UV and EMS, suggesting that eugenol can act as an antigenotoxic agent. Indeed, eugenol treatment can repair DNA damage as indicated by the DNA nicking assay. Eugenol showed potential as an antiaging agent by regulating the cell cycle of S. pombe, specifically by slowing down at the G1 phase and progressing towards the S phase. Transcriptomics analysis revealed that eugenol treatment can regulate genes related to DNA damage response, specifically mismatch repair, base excision repair, and Nucleotide excision repair, in the yeast S. pombe. Our data suggest that eugenol has the potential to regulate the oxidative stress-induced DNA damage response in yeast S. pombe, which supports cell longevity
Cadmium (Cd) Contamination Status in Cisanti Lake (West Java, Indonesia) Analysis on Water, Sediment, and Bioaccumulation in Invasive Mussels Sinanodonta pacifica (Heude, 1878)
No full textCisanti Lake, the strategic zero point of the Citarum River, faces the threat of cadmium (Cd) pollution from surrounding agricultural activities. Conducted during the dry season of 2024, this pioneering study assesses the Cd pollution status using a multicompartment approach (water, sediment, and bioindicator organism Sinanodonta pacifica, Heude 1878). Samples from the three stations were analyzed using Atomic Absorption Spectrophotometry (AAS). The concentration of Cd in water was very low (0.0012–0.0030 mg/L), but it accumulated significantly in sediment (0.37–0.65 mg/kg) and mussel tissue (0.20–0.30 mg/kg). Although the concentration in water and biota was below quality standards, ecological risk analysis revealed that the sediment has moderate contamination (Contamination Factor: 1.25–2.15) and acts as a long-term pollutant sink. S. pacifica proved effective in accumulating Cd from the water column, demonstrated by a high Bioconcentration Factor from water to biota (BCF b-w >75), making it a reliable bioindicator of Cd pollution. This study provides crucial baseline data on environmental management in the upstream Citarum and establishes sediment monitoring as a vital early warning tool for future pollution risks
Morphological and Molecular Characterization of Entomopathogenic Fungi Beauveria spp. Bengkulu Isolate
Full text linkBeuveria is a genus of entomopathogenic fungi that plays an important role in controlling agricultural pests. Pest control with entomopathogenic fungi is an alternative to reduce influence the use of chemical insecticides. The diversity of entomopathogenic fungi intraspecies is by the genetic diversity of isolates, a high diversity of isolates can result diversity of fungus virulence. The purpose of this study was to perform the characterization molecular of entomopathogenic fungi Beauveria spp. Bengkulu isolate. Polymerase chain reaction (PCR) was performed for molecular identification Beauveria isolates were obtained from infected larvae in the field (1. Isolate from Coleoptera in Kepahiang, Bengkulu (BBC), 2. Isolate from Hemiptera: Pentatomidae in Rejang Lebong, Bengkulu (BBL), and 3. Isolate from Hemiptera: Alydidae in Taba Mulan, Merigi District, Kepahiang, Bengkulu (MT). The results of the amplification of the entomopathogen Beauveria samples produce DNA bands around ±580 bp. The DNA sequence analysis of ITS 5F and ITS 4R primers showed that the isolates BBC, MT and BBL have fairly high similarity with the Beauveria bassiana isolate 1397, Beauveria bassiana isolate SBI TNSPI, Beauveria bassiana strain B-Bug, Beauveria bassiana voucher TSJBB, Beauveria bassiana isolate SASRI C2, Beauveria bassiana isolate IMI 382764, Beauveria bassiana BCRC:FU31669, Beauveria bassiana isolate B098, Beauveria bassiana isolate INRS-CFL, Beauveria sp. JS-2009a isolate B4B, Beauveria bassiana isolate KACC with the homology of 99.83%, 99.83%, and 98.61%
Expression of the BAX Gene, CO1 Gene, and their Relationship to the Motility and Spermatozoa Concentration of Rats Treated with Moringa oleifera Leaf Extract
Full text linkSpermatogenesis is the process of spermatozoa formation. An increase in free radicals, such as in hyperglycemia conditions, causes oxidative stress, which can interfere with spermatogenesis. Oxidative stress is an inequality condition between the body’s capacity to produce antioxidants and the rise of free radicals. Antioxidants such as flavonoids are contained in plants such as Moringa oleifera leaves. During spermatogenesis, an apoptosis process involves the BAX gene. BAX is a gene that functions as pro-apoptosis. There is also a CO1 gene in mitochondria, which plays a role in cellular metabolism. Gene expression examination assesses the comparative threshold cycle (CT) with RT-PCR, and spermatozoa quality examination includes assessing spermatozoa concentration and motility. This study used 30 male white Sprague Dawley rats as the test animals, which were divided into five treatment groups: treatment of moringa leaf extract dose 200 mg/kg BW, treatment dose 300 mg/kg BW, treatment dose 400 mg/kg BW, normal control group, and positive control group. The results showed a decrease in BAX gene expression and CO1 gene expression in the treatment group of test animals. The results of sperm analysis showed an increase in spermatozoa concentration in all treatment groups compared to the control group. For sperm motility in the 400 mg/KgBB dose treatment, an increase in sperm motility compared to the control group. This study concludes that administering moringa leaf extract reduced the expression of the Bax and CO1 genes. However, no significant changes were observed in sperm concentration and motility within the treatment group
Impact of Dietary Variation on Gut Microbiota Composition in Macaca fascicularis at the Primate Research Center, IPB University
Full text linkLong-tailed macaques (Macaca fascicularis: LTMs) are widely distributed, adaptable primates commonly used as animal models in biomedical research. At primate facilities such as the Dramaga Captive Breeding Facility and the Tinjil Island Natural Habitat Breeding Facility at the Primate Research Center, IPB University, LTMs experience varying diets depending on their captive or semi-wild environments. At Dramaga Captive Breeding Facility, LTMs housed in individual and group cages are provided with different feeding regimens, whereas the semi-wild LTMs on Tinjil Island feed primarily on natural food sources with occasional, very modest provisioning of bananas. Our study\u27s objective is to evaluate these diets\u27 influence on the gut microbiota and overall health of LTMs. Through comparative analysis of fecal microbiomes using 16S rRNA sequencing, we identified distinct gut microbiota profiles between captive and semi-wild LTMs. Semi-wild LTMs displayed a predominance of Proteobacteria, notably Succinivibrio, associated with a high-fiber diet derived from wild plant consumption. In contrast, captive LTMs housed in individual and group cages exhibited dominance of Firmicutes and Bacteroidota, respectively. These findings suggest that diet is pivotal in shaping gut bacterial profiles, potentially impacting metabolic functions. Our study provides insight into the relationship between certain diets and gut bacterial composition in LTMs across different breeding facilities at the Primate Research Center, IPB University, thereby offering valuable implications for LTMs\u27 welfare and management strategies
DNA Barcoding of Commercially Important Groupers (Epinephelidae) in Simeulue and Banyak Islands, Aceh, Indonesia
Full text linkThe groupers are a group of demersal fish that live in tropical and subtropical areas and are mostly linked to coral reefs. The fish are highly valued in international markets and are subjected to overfishing in the wild. Accurate fish resource identification knowledge is essential for sustainable fisheries management. This research is aimed to generate a reference COI sequence library of grouper species caught in Simeulue and Banyak Islands, Aceh. The study was conducted from April-September 2021 at sixteen fish landing sites in Simeulue and Banyak Islands. In total, this study generated 70 COI sequences representing 20 grouper species. Epinephelus (54%) was the most prevalent grouper genus at the study site, followed by Cephalopholis (19%), Plectropomus (13%), Variola (12%), Hyporthodus (1%), and Anyperodon (1%). According to the IUCN classification, 17 species (85%) fall into the category of Least Concern, two (10%) fall into the category of Vulnerable, and one (5%) falls into the category of Data Deficient. The average genetic distance based on the Kimura-2-Parameter (K2P) between specimens was 0.51% at the species level and 8.34% at the genus level. Overall, this study has provided the COI sequence database of grouper for the Simeulue and Banyak Islands
Evaluation of the 90-Day Administration of Cyperus rotundus Tubers on Nrf2, SOD, and MDA Profiles by Flow Cytometry
Full text linkNuclear factor erythroid 2-related factor 2 (Nrf2), superoxide dismutase (SOD), and malondialdehyde (MDA) are components involved in the antioxidant system and the body\u27s response to oxidative stress. The bioactive compounds of Cyperus rotundus tuber (CRT) have pharmacological effects as antioxidants and anti-inflammatory. This study aimed to evaluate the impact of CRT administration for 90 days on the profiles of Nrf2, SOD, and MDA. 24 male Wistar rats were used in this study and divided into 4 treatment groups: Control, dose 1 (300 mg/kg BW), dose 2 (600 mg/kg BW), and dose 3 (900 mg/kg BW). Oral administration of CRT was carried out for 90 days. On day 91, liver isolation was performed to determine the profiles of Nrf2, SOD, and MDA using Flow Cytometry. Statistical analysis using One-Way ANOVA with P<0.05 was conducted using SPSS. The administration of CRT to Wistar rats for 90 days did not induce toxic or harmful effects. The Nrf2 and MDA profiles did not show excessive activation with CRT administration. The SOD profile increased with D1 administration compared to the control and other doses. The administration of CRT for 90 days has the potential to be used as a natural alternative to address diseases related to oxidative stress
Evaluation of Lantana camara Leaf Extract as Biopesticide for Lifecycle Disruption in Spodoptera litura
Full text linkSpodoptera litura is a destructive agricultural pest whose management is hindered by synthetic pesticides\u27 ecological and health risks. Plant-based biopesticides, such as Lantana camara leaf extract, provide a sustainable alternative due to the presence of bioactive phytochemicals with pesticidal properties. Therefore, this study aimed to evaluate the efficacy of L. camara extract in disrupting the lifecycle of S. litura. A completely randomized design was adopted, and six treatment concentrations of L. camara extract, namely 0%, 6.25%, 12.5%, 25%, 50%, and 100%, were applied to second-instar larvae. Observations included larval development time, leaf consumption, pupation rate, pupal weight, moth emergence, and fecundity. Data were analyzed using ANOVA, and the result showed that the extract had strong dose-dependent effects on all variables. Pupation, moth development, and fecundity were inhibited by concentrations greater than 25%. Feeding activity was significantly reduced at higher concentrations, with a 100% concentration achieving a 3.67% leaf consumption rate after 48 hours. Larval development was delayed or halted entirely at critical thresholds. In conclusion, L. camara extract effectively disrupted the lifecycle of S. litura, providing immediate suppression and long-term population control. The dual-action potential, biodegradability, and natural origin made extract a sustainable alternative to synthetic pesticides. Future studies are recommended to validate these results under field conditions and evaluate impacts on non-target species
Characteristics of Microplastic in Selected Marine Sponges from Pasir Putih Situbondo, East Java, Indonesia
No full textMicroplastics (MPs) are global concern due to their presence in various ecosystems and their tendency to have a negative impact on organisms. MPs are plastic fragments with a small size ranging from >1 μm to <5 mm, which are easily ingested by marine organisms, including marine sponges. As filter-feeding organisms, sponges can accumulate MPs in their bodies. This study aims to analyze the physical and chemical characteristics and the abundance of MPs in seawater and sponges. Three species of marine sponges (Xestospongia testudinaria/XT, Aaptos suberitoides/AS, and Clathria sp./CR) with ten replicate samples were collected from Batu Lawang reef in Pasir Putih, Situbondo, East Java, Indonesia. MPs samples were also collected from the water column (surface and sea bottom at a depth of ±6-7 m). Analysis of physical characteristics (shape, color, and size) performed using a stereo microscope and Optilab, whilst chemical characteristics (type of polymer) was analyzed using ATR-FTIR. A one-way ANOVA test followed by Tukey\u27s HSD (both at p = 0.05) were performed to determine the difference in MPs density from each species. There was no significant difference in term of density in XT and AS, with average density of 60.6 and 66.9 particles/g wet weight (ww), respectively. The density in CR was significantly higher, with the value of 86.7 particles/g (ww). In the water column, the density was 20-27 particles/L (surface sample) and 37-84 particles/L (sea bottom). All particles dominated by black fragments with sizes ranging from 0 to 60 μm, and the polymer type is polypropylene (PP)