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Bioeksperimen
Published by Universitas Muhammadiyah Surakarta
ISSN : 24601365     EISSN : 25272799     DOI : -
Core Subject : Science,
Biochemistry, Genetics & Molecular Biology
Aim Bioeksperimen: Jurnal Penelitian Biologi is a peer-reviewed, open-access scientific journal dedicated to advancing knowledge across a broad spectrum of biological sciences through the publication of high-quality original research articles. The journal promotes rigorous experimental and exploratory research that advances fundamental and applied understanding in biological sciences. Bioeksperimen provides an international platform for researchers, academics, and practitioners to disseminate innovative empirical findings and scientifically robust investigations that contribute to the development of biological sciences at regional and global levels. The journal welcomes manuscripts that: 1. Present original experimental or exploratory research in biological sciences 2. Demonstrate strong methodological design and scientific rigor 3. Contribute novel data, findings, or biological insights 4. Address contemporary biological challenges and emerging scientific issues 5. Integrate laboratory, field, and computational approaches 6. Contribute meaningfully to the advancement of biological sciences All manuscripts must be original, unpublished, written in English, and must clearly demonstrate methodological soundness, data-driven analysis, and a significant contribution to biological sciences. Since March 2026, Bioeksperimen does not publish literature review articles, conceptual papers, or purely theoretical manuscripts. Focus The primary focus of Bioeksperimen: Jurnal Penelitian Biologi is on empirical biological research based on experimental, observational, or exploratory approaches. The journal prioritizes studies that: 1. Apply molecular, physiological, ecological, microbiological, or genetic techniques 2. Utilize omics-based and bioinformatics approaches to generate primary data 3. Conduct laboratory experiments, field investigations, or integrative biological exploration 4. Produce reproducible and evidence-based scientific findings Scope Bioeksperimen: Jurnal Penelitian Biologi publishes original research in the following areas: Main Topics: 1. Ecology and Environmental Sciences 2. Molecular Biology of Plants, Animals, and Microorganisms 3. Bioinformatics and Computational Biology 4. Omics-Based Studies (Genomics, Transcriptomics, Metagenomics, Proteomics, Metabolomics) 5. Basic and Applied Microbiology 6. Plant and Animal Physiology 7. Animal Behavior 8. Plant and Animal Systematics and Taxonomy 9. Genetics of Plants, Animals, and Microorganisms 10. Human Physiology
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Biokimia, Genetika dan Biologi Molekuler (Lain-Lain)
Articles 34 Documents
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The Phylogenetic analysis of representative mammalian MUC16 supported by comparative SEA domain and tandem repeat variation Foenna, Yudi Gebri; Yulisma, Ardhana; Calapoğlu, Nilüfer Şahin
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.14233

Abstract

MUC16 is one of the largest mammalian mucins and exhibits substantial evolutionary variation in both sequence composition and structural modularity. Comparative analysis of SEA domain composition and tandem repeat architecture is therefore essential for understanding the evolutionary diversification of this gene across mammals. This study investigates the phylogenetic relationships of mammalian MUC16 and examines how variation in SEA domains and tandem repeats contributes to lineage-specific structural divergence. MUC16 nucleotide and protein sequences from 20 mammalian species representing Primates and Rodentia were retrieved from public databases. Multiple sequence alignment and phylogenetic reconstruction were conducted using the Neighbor-Joining method with 1,000 bootstrap replicates. SEA domains were annotated using the SMART database, while tandem repeats were identified with Tandem Repeats Finder. Structural features were evaluated using descriptive statistics, hierarchical clustering, and Spearman’s rank correlation analysis. Phylogenetic reconstruction revealed a clear molecular separation between Primates and Rodentia with strong bootstrap support. Primate species generally exhibited conserved sequences and expanded SEA domain and tandem repeat architectures, whereas rodents displayed higher sequence divergence and reduced structural complexity. A moderate positive association between SEA domain number and tandem repeat count (ρ = 0.44) was observed, although this relationship did not reach statistical significance and is therefore interpreted as a biologically suggestive trend rather than evidence of coordinated evolution. Overall, the results indicate that MUC16 evolution follows lineage-dependent patterns shaped by both sequence divergence and domain-level remodeling. This comparative framework provides an evolutionary context for understanding structural diversity in mammalian mucins and offers a foundation for future functional and genomic investigations.
Isolation and screening of halotolerant protease-producing bacteria from Lampung fermented shrimp paste Istiadi, Khaerunissa Anbar; Ningsih; Suryanti, Erma; Imaniar, Lisana Husna
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.14593

Abstract

Protease are class of degradative enzymes that hydrolyze proteins, breaking its peptide bond, into smaller peptides and amino acids. Microbial proteases have gained increasing attention due to its productivity and utilization in various industries. Proteolytic bacteria derived from fermented shrimp paste from Lampung have great potential to meet this need. However, studies on these bacteria are still limited, so further research is needed to explore and optimally utilize their potential. This study aims to explore the diversity of proteolytic bacteria from Lampung terasi.. The methods employed included isolation stages using Nutrient Agar supplemented with 5% and 10% NaCl (w/v), followed by proteolytic screening properties using Skim Milk Agar media. A total of 20 bacterial isolates were obtained from terasi using Nutrient Agar supplemented with 5% (w/v) NaCl, and 15 isolates were obtained from Nutrient Agar (NA)  supplemented with 10% (w/v) NaCl. Screening results showed that 85% and 67% of the isolates obtained from NA supplemented with 5% and 10% NaCl, respectively, exhibited proteolytic activity. Halotolerant bacterial isolates isolated using NA + 5% NaCl exhibited a proteolytic index ranging from 0.3 – 3.0, while those isolated with NA + 10% NaCl showed values ranging from 0.18 to 3.06. The screening results revealed that isolates BTCL5-07 and BTCL10-05 exhibited the highest proteolytic activity, with proteolytic indices of 3.0 and 3.06, respectively. These findings indicate that halotolerant bacteria from Lampung terasi represent a promising source of potential proteolytic enzymes. Further research is required to optimize enzyme production.
Morphological and genetic identifications of Spirulina based on 16S rRNA gene Dito, Bahana Safiria; Sajidan, Sajidan; Susilowati, Ari; Sidiq, Yasir
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.14879

Abstract

Spirulina is a microalga with spiral or linear trichome shapes that has potential in industrial and food sectors due to its rich nutritional content. Spirulina can live in various aquatic habitats with different environmental conditions. Differences in cultivation environments can affect the morphological characteristics of Arthrospira due to phenotypic plasticity, making morphology-based identification prone to errors. Therefore, molecular identification using the 16S rRNA gene for phylogenetic analysis is necessary. This study aims to identify and analyze the genetic relationships of Spirulina from freshwater and brackish water based on 16S rRNA gene sequences. Freshwater Spirulina samples were taken from Bogor (BGR) and Yogyakarta (MRP), while brackish water Spirulina was taken from Jepara (JPR). DNA extraction was performed using the Zymo Research Quick-DNA Fungal/Bacterial Miniprep Kit, amplification of the 16S rRNA gene was conducted through PCR, followed by DNA sequencing. Phylogenetic analysis was carried out using MEGA11 to construct the phylogenetic tree. The morphology of strains BGR and MRP showed straight and thin filaments, whereas JPR had spiral and relatively long filaments. Sequencing analysis results showed that strains JPR and MRP had the closest homology similarity to Arthrospira sp. IAQUASC-C0001 with percentages of 99.34% and 99.12%, respectively. Meanwhile, Spirulina from BGR had the closest homology similarity to Arthrospira fusiformis strain AICB 668 with a percentage of 99.78%. Phylogenetic analysis indicated that strains BGR, JPR, and MRP are more closely related to Arthrospira than to Limnospira.
Potential of butterfly pea (Clitoria ternatea) nanoherbal on spermatozoa quality in hyperglycemic rats Putri, Komala Amelia; Christijanti, Wulan; Marianti, Aditya
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.15239

Abstract

Hyperglycemia is a condition characterized by elevated blood glucose levels that induce free radical formation, leading to reduced spermatozoa quality. Butterfly pea (Clitoria ternatea) contains antioxidant compounds and is formulated as a nanoherbal to enhance bioavailability. This study aimed to evaluate the potential of butterfly pea nanoherbal in improving spermatozoa quality in hyperglycemic rats. This experimental study employed a post-test only control group design using 25 male Wistar rats divided into a healthy control group and hyperglycemic groups induced by alloxan (125 mg/kg BW). The hyperglycemic groups consisted of a metformin control (400 mg/kg BW) and butterfly pea nanoherbal treatment groups at doses of 12.5, 25, and 50 mg/kg BW administered for 28 days. Data were analyzed using One-Way ANOVA followed by the Least Significant Difference (LSD) post hoc test. The results showed that spermatozoa concentration in the healthy control group differed significantly from the positive control, P1, and P2 groups (p<0.05), but not from the P3 group. Spermatozoa motility and viability also showed significant differences among groups (p<0.05). It can be concluded that butterfly pea flower nanoherbal significantly improves spermatozoa quality in hyperglycemic rats.
Waterbirds as bioindicators of ecosystem health: seasonal dynamics in Tondano Lake, Indonesia Djarang, Rievo; Harindah, Gerry; Suriani, Ni Wayan; Taulu, Marthy Lingkan Stella
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.15450

Abstract

Waterbird diversity in Tondano Lake reflects ecological degradation caused by water-hyacinth invasion and sedimentation. This study analyzed the diversity and abundance of waterbirds in Tondano Lake, Indonesia, across wet (February-May) and dry (June-October) seasons in 2025 to assess their role as bioindicators of ecosystem health. Multi-season observations were carried out monthly along a 6.5 km transect at ten strategic points. Eight waterbird species from three families were recorded, with Egretta garzetta being the most abundant (29.1%) and Alcedo atthis the least (4.8%). The Shannon-Wiener diversity index (H' = 1.92) indicates a moderate level of species diversity, which reflects a pattern of ecological simplification when compared to pristine tropical lakes such as Lake Sentarum (H' = 2.5). Waterbird abundance showed significant negative correlations with water hyacinth density (r = -0.68, p = 0.032) and water depth (r = -0.72, p = 0.019), revealing that invasive vegetation and shoaling are primary drivers of habitat loss. These findings demonstrate that waterbirds function as sensitive bioindicators of ecological stress, highlighting the urgent need for integrated watershed management to prevent further community collapse.
Assessment of genetic diversity in EMS-induced porang (Amorphophallus muelleri Blume) revealed by RAPD markers Haritzah, Rendha Maulana; Radita, Novia Fitri; Ramadanti, Isma Salsabila; Azzahro, Yusri Despa; Wahyudi, Didik; Resmisari, Ruri Siti; Suyono
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.15768

Abstract

Increasing genetic diversity of porang through mutation is urgently needed since porang has low genetic diveristy. Therefore, this study aims to increase the genetic diversity of porang using ethyl methanesulfonate (EMS) and analyze the genetic diversity of porang using RAPD markers. Porang explants were subjected to in vitro EMS induction at various concentrations (control, 0.1%, 0.2%, 0.3%, 0.4%, and 0.5%) and evaluated after 35 days. DNA amplification was carried out using 20 RAPD primers. Genetic diversity within and between porang populations was analyzed using POPGENE software, while cluster analysis was performed using PAST software to identify genetic diversity patterns. The results showed that EMS mutation induction effectively increased the genetic diversity of porang. Primers OPA-2 and OPA-9 were identified as the most effective primers for detecting genetic diversity resulting from mutation induction. The 0.2% EMS treatment is recommended because it produced the most notable genetic changes compared to the control and shows potential for generating superior mutants to support porang breeding programs.
Integrating field inventory and in silico phylogenetic analysis of pteridophytes at Gandul Mount, Indonesia Candra, Sri Devi Galuh; Kinasih, Anggiresti; Khotimperwati, Lilih
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.15947

Abstract

Pteridophytes are vascular plants that are considered the most primitive plants because they only use spores to reproduce. Several major fern families exhibit distinctive morphological and ecological characteristics that support their taxonomic recognition. Pteridophytes represent an important component of tropical biodiversity, yet their diversity and evolutionary relationships in karst ecosystems remain poorly documented. This study aimed to integrate field inventory and in silico phylogenetic analysis to assess pteridophyte diversity in Gandul Mount, Wonogiri, Central Java. Field data were collected using the cruise method, followed by morphological identification and habitat characterization. Phylogenetic relationships were inferred using matK gene sequences retrieved from the NCBI database and analyzed with the Maximum Likelihood method. The inventory recorded 17 species belonging to eight families, with Pteridaceae as the most dominant. Most species were lithophytic, indicating strong adaptation to rocky substrates. Two species were categorized as Least Concern, while the remaining species have not been evaluated by the IUCN. Eleven species showed ethnobotanical potential as medicinal plants, ornamentals, and phytoremediation agents. Phylogenetic analysis revealed clustering patterns consistent with taxonomic classification. These results demonstrate that Gandul Mount harbors considerable pteridophyte diversity and confirm that combining field-based inventory with in silico phylogenetic analysis provides a robust approach for biodiversity assessment and evolutionary interpretation.
Insect diversity at vegetative maize phase (Zea mays L.) in caturharjo village Putri, Dila Savira Mayang; Putra, Ichsan Luqmana Indra
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.15963

Abstract

This study aims to analyse the diversity and dominance of insect species in maize fields in Caturharjo Village, Sleman District, Yogyakarta. The research was conducted from March to August 2025 on 1,000 m² of maize fields divided into three plots, each measuring 10 × 15 m. Light traps were installed in the centre of each plot, and insects were captured manually (direct capture) every three days. Species diversity was calculated using the Shannon-Wiener Index, dominance using the Simpson Index, and the data were analysed for correlation with abiotic factors. The results showed that the total number of insect individuals in the vegetative phase of maize plants was 19,874 individuals, consisting of 6 orders, 24 families, and 30 species. The largest proportion of insects were predators (33.33%), followed by herbivores (26.67%), maize pests (16.67%), visitors (10%), detritivores (10%), and pollinators (3.33%). The insect diversity index was (H') = 0.83, which was classified as low diversity, and the dominance index was (D) = 0.18, indicating low dominance. The conclusion of this study is that the insect species diversity at the study site was low, with no dominant species found, and a total of 30 insect species found.
Diversity of plankton species in different ecosystems on Beras Basah Island, Bontang, East Kalimantan Imam Fadila, Muhammad; Anjasmara, Aang Setyawan; Rizal, Daisy Rahma; Rusdi, Rismawaty; Reynalta, Ricko
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.15978

Abstract

Beras Basah Island, located in the coastal waters of Bontang City, East Kalimantan, is a marine conservation area characterized by diverse coastal ecosystems, including marine waters, coral reefs, and seagrass beds. These ecosystems support various aquatic organisms, including plankton communities that play a key role in marine food webs. This study aimed to examine the composition, abundance, and diversity of plankton across three different ecosystems around Beras Basah Island. Sampling was conducted in May 2025 using a purposive sampling method at three stations representing marine waters, coral reefs, and seagrass bed. Plankton samples were collected using a 20 µm mesh plankton net and preserved with Lugol’s solution. The data were analyzed to determine plankton abundance, Shannon–Wiener diversity index (H’), and evenness index (E). A total of 13 plankton species were identified, consisting of 10 phytoplankton species (Bacillariophyceae and Dinophyceae) and 3 zooplankton species (Ciliata and Crustacea). The Shannon–Wiener diversity index ranged from 2.17 to 2.30, indicating moderate diversity, while evenness values ranged from 0.94 to 0.98, suggesting a relatively uniform distribution of individuals among species. Phytoplankton dominated the plankton community across all ecosystems, with the highest abundance recorded in the seagrass ecosystem (1,732 individuals L⁻¹). These findings indicate that plankton communities are relatively consistent across different coastal ecosystems in the waters of Beras Basah Island.
Pharmacological prediction of Marchantia polymorpha: GC-MS and molecular docking approaches Farhan, Abdillah Maulana
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.15983

Abstract

Marchantia polymorpha is the liverworts that can be found abundantly in the Mount Pasang Jember area. The metabolite profiling of M. polymorpha has not yet been conducted.  The method used in this study was untargeted metabolite profiling using GC-MS, and the results of the metabolite compound profiling were analyzed in silico using bioinformatics-based, namely PASS Online, SwisADME, and Molecular Docking using PyRx 8.0 with AutodockVina. The aims  of docking with this protein was adjusted to the PASS Online results, namely alkenylglycerophosphocholine hydrolase inhibitor and antiseborrheic, which are closely related to antifungals. The natural metabolite compounds detected from M. polymorpha were fatty acids (20%), terpenoids (16%), and phenolics (10%). Terpenoids-phenolics compounds were analyzed in silico to predict pharmacological potential. Terpenoids showed that the compound with the highest Pa value was 3,7-Cyclodecadiene (Pa=0.920), predicted to be an alkenylglycerophosphocholine hydrolase inhibitor, while the phenolic compound with the highest Pa value was hydroquinone (Pa=0.927), predicted to be an antiseborrheic. Based on SwissADME in silico Druglikeness, five compounds out of a total of six terpenoid and phenolic compounds showed compliance with Lipinski's theory. In addition, the in silico results also showed a bioavailability score of 0.55. Molecular docking was performed on the target protein sterol 14-α-demethylase (CYP51) from Candida albicans (PDB ID: 5TZ1). This protein is representative of antifungal agents. The results of molecular docking showed that the compound 3,7-Cyclodecadiene consistently had the strongest binding affinity value of -10.1 kcal/mol with residues ILE A:55, ALA A:62, PHE A:58, and TRP B:5  These results  imply that further research on M. polymorpha metabolites should be conducted using comprehensive methods to explore their potential in the field of health.

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