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Yasir Sidiq
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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 Contribute meaningfully to the advancement of biological sciences All manuscripts must be original, unpublished, written in English, and must clearly demonstrate methodological soundness, data-driven analysis, and a significant contribution to biological sciences.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 44 Documents
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Evidence-based non-residential waste analysis to support 3R strategies and food recovery hierarchy: a case study in Solok Selatan Fauzi, Mhd.; Aziz, Rizki; Chyntia, Nanda; Titani, Fena Retyo; Afrianto, Andika Wahyu
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.16030

Abstract

The amount of waste generation that increases without being accompanied by good waste management will cause pollution and decrease the aesthetic value of the environment. Non-residential waste originating from non-residential activities is also one of the contributors to waste entering the landfill. This study aims to analyze non-residential waste generation and composition as an evidence-based reference for each source in implementing the 3R concept and the Food Recovery Hierarchy (FRH). The number of sampling sets was determined at a minimum of 10% of each type of facility following SNI 19-3964-1994. Sampling was carried out on eight consecutive days with 14 sampling points in Area 1, 14 in Area 2, and 11 in Area 3. The total non-residential waste generation was 46.79 m³/day (9.49 tons/day). Organic waste dominated the composition, accounting for 35–37% as food waste, followed by plastic (24–29%) and paper (14–20%). The high proportion of biodegradable and recyclable materials indicates significant potential for composting, recycling, and food recovery strategies at the source level. Implementing source-level 3R and FRH approaches could substantially reduce landfill dependency and extend landfill lifespan. This study addresses a knowledge gap by linking source-level non-residential waste characterization with the practical implementation of the 3R concept and the Food Recovery Hierarchy. This study provides quantitative evidence to guide localized waste minimization strategies in non-residential sectors.
Antagonistic activity of phyllosphere fungi isolated from medicinal plants against Colletotrichum sp. causing anthracnose in chilli (Capsicum annuum L.) Puspita, Ayumi Rizci; Alamsjah, Feskaharny; Mildawati, Mildawati; Agustien , Anthoni
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.16072

Abstract

Anthracnose disease caused by the fungus Colletotrichum sp. is one of the main problems in chili cultivation (Capsicum annuum L.) and can cause significant yield losses. The intensive use of chemical pesticides in controlling this disease has a negative impact on the environment and health. This study aimed to evaluate the antagonistic potential of phyllosphere fungi isolated from five medicinal plants, namely Phaleria macrocarpa, Curcuma domestica, Kleinhovia hospita, Hibiscus rosa-sinensis, and Morus macroura, against the pathogen Colletotrichum sp. Isolation was performed from leaf surfaces, and a total of 7 phyllosphere fungal isolates were tested using a double culture method with three replicates. The results showed that all isolates were able to inhibit the growth of Colletotrichum sp. through mechanisms of competition for space and nutrients as well as antibiosis, with inhibition levels ranging from high to very high. Among the tested isolates, Trichoderma sp. exhibited the highest inhibitory activity with an inhibition percentage of 92.78%, categorized as very high. Macroscopic and microscopic characterization supported the identification of several isolates belonging to the genera Trichoderma. This study concluded that phyllosphere ungi from medicinal plants have the potential as environmentally friendly biological control agents in combating anthracnose disease in chili plants.
Design and validation of PIP gene primer for quantitative PCR in Capsicum annuum using in silico and experimental approaches Nurhafitri, Amanda; Suwirmen
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.16129

Abstract

Capsicum annuum L. is an economically important horticultural crop whose productivity is strongly affected by drought stress. Plasma Membrane Intrinsic Protein (PIP), a member of the aquaporin gene family involved in water transport and osmotic regulation, represents a key target for drought stress studies, requiring highly specific and efficient primers for accurate gene expression analysis using quantitative PCR (qPCR). This study aimed to design and validate PIP gene primers for qPCR in C. annuum using integrated in silico and experimental approaches. Primer design was performed using NCBI Primer-BLAST based on the CaPIP reference sequence (XM_016711608.2), followed by in silico evaluation of primer specificity and secondary structure using Primer-BLAST and OligoAnalyzer. Nine primer pairs were initially generated and evaluated based on primer length, %GC, Tm, self3’ complementarity and amplicon size. Secondary structure analysis revealed strong self-dimer formation in pair 8, whereas pair 2 showed weak secondary structure within acceptable ΔG threshold (-9 kcal/mol). Experimental validation was conducted throught gradient PCR to optimize annealing temperature, followed by agarose gel 2%. Primer 2_CaPIP produced specific and clear amplification, with an optimal annealing temperature of 57.3oC. This study provides a validated CaPIP primer set suitable for qPCR-based gene expression analysis in C. annuum, supporting future molecular studies on drought stress tolerance.
Preliminary study of acute febrile response to crude LPS extract from Salmonella typhimurium in domestic chicken (Gallus gallus domesticus) AKY strain Wijaya, Rizky Surya; Lelono, Asmoro; Oktarianti, Rike
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.16139

Abstract

Salmonella is a genus that commonly attacks the health of poultry, especially chickens. One type of poultry that is widely attacked by S. typhimurium is chickens. S. typhimurium infects the host with Lipopolysaccharides (LPS). This study aims to determine the innate immune response of domestic chickens to LPS-based vaccines S. typhimurium as the first step in vaccine development. The sample was in the form of female domestic chickens of the AKY strain which was divided into 3 groups, the control group was injected using 0.1ml of PBS (Phosphate Buffer Saline) treatment group 1 was injected with LPS with an adjuvant with a concentration of 0.5mg/kg as much as 0.1ml. Treatment group 2 was injected with LPS with an adjuvant with a concentration of 1mg/kg of 0.1ml. Injection treatment group using Incomplete Freund Adjuvant (IFA). The results obtained were that the treatment groups had an increase in temperature at the 1st hour to the highest in the 3rd hour with a temperature range of 42.5°C to 42.6°C, contrast to the control group which has a static temperature with a range of 41°C to 41.8°C. The comparison of chicken body temperature among treatment groups using a Liner Mixed Model revealed a significant difference (p < 0.001) between the treatment groups and the control group. These results indicate that subcutaneous LPS administration induces a controlled acute febrile response, which is consistent with involvement of innate inflammatory pathways.
Daily dynamics and structure of zooplankton communities as bioindicators in Merdada Lake, Dieng Plateau, Central Java, Indonesia Wahyu Febriani; Suwarno Hadisusanto
Bioeksperimen: Jurnal Penelitian Biologi Vol. 12 No. 2: September 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i2.16113

Abstract

Prolonged anthropogenic disturbance contributes to the degradation of Merdada Lake. Tourism development, intensive water extraction, fertilizer and pesticide application, and the conversion of land into agricultural areas have accelerated soil erosion, sediment accumulation, nutrient loading, and siltation, which ultimately reduce water quality and influence zooplankton communities. This study assessed the suitability of zooplankton as a bioindicator by examining community composition, abundance, daily variation, ecological indices, and key environmental constraints as indicators of trophic conditions. Sampling was carried out randomly in May 2021 at five observation sites with three replicates, conducted during nighttime (7:00 PM), early morning (5:00 AM), and morning (9:00 AM). The zooplankton community consisted of several functional groups, including Cladocerans, Copepods, Nauplius, Protozoa, and Rotifers. Abundance ranged from 5.51 to 22.47 individuals per liter, with Rotifers, particularly Philodina sp., being the most dominant group. Peak abundance was recorded at night, reflecting diel movement patterns associated with vertical migration and food availability. Ecological index analysis revealed poor-moderate diversity (H’ = 1.76–1.90), moderate -high evenness (E = 0.72–0.80), and high dominance (C = 0.79–0.82), which indicates an unstable community structure and ecological. Variations in zooplankton structure and daily dynamics were strongly associated with light intensity, nitrate concentration, dissolved oxygen, and alkalinity. Overall, the findings demonstrate that zooplankton communities are sensitive to environmental changes and can serve as effective bioindicators of water quality in Merdada Lake. Overall, zooplankton communities are responsive to water quality conditions in Merdada Lake.
Effect of chicken feet collagen ointment (Gallus gallus domesticus L.) on incision wound healing in mice (Mus musculus L.) Zulfa Hafidzah; Rudy Agung Nugroho; Retno Aryani; Reni Kurniati; Eko Kusumawati
Bioeksperimen: Jurnal Penelitian Biologi Vol. 12 No. 2: September 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i2.16402

Abstract

Chicken feet (Gallus gallus domesticus L.) are a by-product of a chicken slaughterhouse that has the potential to be a source of collagen for wound healing therapy. Collagen plays an important role in skin tissue regeneration, protein synthesis, and connective tissue formation during the healing process. This study aimed to characterize chicken feet collagen using Fourier Transform Infrared (FTIR), evaluate the physicochemical properties of collagen ointment preparations, and analyze their effect on the percentage of incision wound closure, protein levels, and hydroxyproline in mice (Mus musculus L.). The study was conducted as a laboratory experiment with a complete randomized design, including negative controls, two positive controls, and three groups of collagen ointment at concentrations of 5%, 10%, and 15%. Collagen is extracted using the Acid Soluble Collagen (ASC) method and is formulated in the form of an ointment. FTIR characterization shows the presence of amide groups A, B, I, II, and III as characteristic of collagen. The ointment preparation meets physical and chemical requirements, including homogeneity, semi-solid consistency, and pH according to the skin. Collagen ointment increased the percentage of incision wound closure across all groups without a significant difference among treatments. Tissue protein levels declined progressively from the untreated control through the treated groups, reaching the lowest value at the 5% concentration (P1). Hydroxyproline levels, by contrast, did not follow a uniform pattern: the 5% ointment (P1) showed hydroxyproline levels comparable to the positive controls, whereas the 10% and 15% ointments (P2, P3) showed hydroxyproline levels comparable to the untreated negative control, suggesting that healing in the P2 and P3 groups remained in an active, collagen-synthesizing phase at the time of sampling. These results suggest that chicken feet collagen has the potential to be an active ingredient in topical preparations to support the healing of incision wounds.
Effect of topical collagen extract ointment from Oreochromis niloticus L. scales on incision wound healing in Mus musculus L. Liliana Devita Sari; Rudy Agung Nugroho; Retno Aryani; Reni Kurniati; Eko Kusumawati
Bioeksperimen: Jurnal Penelitian Biologi Vol. 12 No. 2: September 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i2.16418

Abstract

Nile tilapia (Oreochromis niloticus L.) ranks among Indonesia’s most heavily farmed freshwater fish, and the scales discarded during its processing are a rich, underused source of type I collagen, a structural protein of the extracellular matrix that supports skin repair and could serve as a natural ingredient in wound-care ointments. This study evaluated the physical properties of an ointment formulated with tilapia scale collagen extract and examined its effect on incision wound healing in mice (Mus musculus L.). Six groups were compared: K- (untreated), K+1 (bioplacenton), K+2 (ointment base only), and three collagen-ointment concentrations, P1 (5%), P2 (10%), and P3 (15%). Collagen was isolated by the acid-soluble collagen (ASC) method and characterized by Fourier-transform infrared (FTIR) spectroscopy; wound closure, tissue protein content (Lowry method), and hydroxyproline content were assessed over 14 days. All three ointment formulations met the general pharmaceutical standards for topical preparations. Wounds in every group closed gradually, reaching a mean closure of 87.4-98.2% by day 14 without a statistically significant difference among treatments, whereas protein and hydroxyproline assays showed that the 15% collagen ointment produced the lowest tissue protein (397.0 ± 8.55 μg/mL) and hydroxyproline (82.05 ± 4.45 μg/mL) levels, consistent with an accelerated transition into the tissue remodeling phase.
Prediction of hemoglobin protein structure and function of the α4.2 deletion mutation and αα/-α4.2/βCD8 (-AA)/βN co-inheritance Nurul Fitri T Tagunu; Tri Ratnaningsih; Nur Imma Fatimah Harahap; Indra Lesmana; Niken Satuti Nur Handayani
Bioeksperimen: Jurnal Penelitian Biologi Vol. 12 No. 2: September 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i2.16912

Abstract

The α4.2 deletion is typically characterized as a silent mutation. The clinical impact of this mutation can vary, particularly when inherited alongside other globin gene mutations, for example co-inheritance with β-thalassemia mutations, such as βCD8 (-AA)/βᴺ. This study aims to determine the α4.2 deletion breakpoint and analyze the structural and functional impact of α-thalassemia heterozygous mutation associated with α4.2 deletion and co-inheritance of αα / -α4.2/ βCD8 (-AA) / βN on the resulting hemoglobin protein. DNA sample was sequenced using the Sanger method by 1st BASE laboratory. Sequence alignment was performed via Clustal Omega, while hemoglobin structure prediction and analysis were conducted using UCSF Chimera (Chimera-1.19) and BIOVIA Discovery Studio. The results identified the α4.2 deletion breakpoint between nucleotide 26 of the X2 box and nucleotide 347 of the X1 box. Despite the mutations, the α4.2 deletion and the αα / -α4.2/ βCD8 (-AA) / βN co-inheritance resulted in a protein structure identical to normal residues, maintaining all stabilizing interactions. Therefore, we conclude that in silico predictions indicate no major structural deviations from wild-type hemoglobin A for both the α4.2 deletion and the co-inheritance of αα/-α4.2 with βCD8 (-AA)/βN. This is consistent with the molecular nature of α-thalassemia deletions, which primarily affect globin gene dosage rather than amino acid sequence, although this observation is limited to computational analysis and has not been experimentally confirmed.
The effect of coconut water on the in vitro growth of Phalaenopsis amabilis (L.) Blume plantlets Elvina Adinda Triansyah; Nintya Setiari; Yulita Nurchayati
Bioeksperimen: Jurnal Penelitian Biologi Vol. 12 No. 2: September 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i2.16917

Abstract

Phalaenopsis amabilis is an Indonesian native orchid listed in Appendix II, therefore, appropriate cultivation strategies, including tissue culture techniques, are required to support its sustainable propagation. However, Murashige and Skoog (MS) medium does not contain sufficient natural growth-promoting substances; thus, organic supplementation such as coconut water is needed to enhance plantlet development. This study aimed to evaluate the effect of coconut water supplementation in MS medium and to determine the optimal concentration for promoting the growth of P. amabilis plantlets during the subculture stage. Plantlets were subcultured onto MS medium supplemented with coconut water at concentrations of 0%, 15%, and 30% using a Completely Randomized Design with five replications. Data were analyzed using ANOVA followed by Duncan’s Multiple Range Test at a 5% significance level. Observations were conducted for two months on leaf emergence time, leaf length and width, number of leaves, shoot emergence time, number of shoots, root emergence time, number of roots, and leaf color. The results showed that 15% coconut water was the optimal concentration for improving plantlet growth, particularly in new leaf length (8 mm), number of shoots (1,66 shoots), and number of leaves (1,33 leaves). whereas 30% coconut water increased leaf width (3,2 mm). Overall, supplementation with 15% coconut water effectively enhanced the vegetative growth of P. amabilis plantlets, so it can be applied to successfully cultivate this plant.
Colonization of Streptomyces enissocaesilis on the root system of Zea mays var ceratina Velma Agtavia; Yuliana Retnowati; Novri Youla Kandowangko; Jusna Ahmad; Abubakar Sidik Katili
Bioeksperimen: Jurnal Penelitian Biologi Vol. 12 No. 2: September 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i2.17484

Abstract

Streptomyces enissocaesilis is a microorganism with diverse biological activities; it is capable of colonizing plant root systems by forming mycelium and adhering to root surfaces.. This study aimed to analyze the colonization of Streptomyces enissocaesilis in the root system of Zea mays var ceratina based on root infection ability, metabolite profiles in growth media, and plant vegetative growth. Zea mays var ceratina was grown hydroponically using the Deep Flow Technique (DFT) for 30 days with inoculation (1.1 × 10⁸ CFU/g) and without inoculation of Streptomyces enissocaesilis as a control. Plant growth was monitored at 7-day intervals, while infectivity and metabolite profiles were assessed at the end of the growth period; metabolite screening in the growth medium was performed using LC-MS.The results showed that Streptomyces enissocaesilis was able to infect plant root tissue, as well as interact on the root surface, as indicated by filamentous structures resembling hyphae on the epidermis of treated plant roots. Analysis of the metabolite profile in growth media inoculated with Streptomyces enissocaesilis using LC-MS revealed peaks detected at retention times of 0.72 and 1.18 minutes. Inoculation of Streptomyces enissocaesilis during the vegetative growth of Zea mays var ceratina, based on plant height and root length data, showed significantly higher values compared to the control; however, no significant differences were observed for the parameters of leaf number, dry weight, and root-to-shoot ratio. Based on these data, inoculation with Streptomyces enissocaesilis has the potential to function as a Plant Growth Promoting Rhizobacteria (PGPR). Based on the research findings, Streptomyces enissocaesilis has the potential to be developed as a plant growth promoter. However, its effectiveness in increasing biomass and overall plant growth still requires further study.

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