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All Journal The Indonesian Biomedical Journal BIOLINK (Jurnal Biologi Lingkungan, Industri, Kesehatan) Jurnal Ilmiah Biologi UMA (JIBIOMA) Bioeksperimen
Yudi Gebri Foenna
Universitas Medan Area
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Public Health

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Kultur Embrio Mencit In Vitro: Studi Perbandingan Efektifitas Media M16 dan CZB Foenna, Yudi Gebri; Nasution, Jamilah
Jurnal Ilmiah Biologi UMA (JIBIOMA) Vol 6, No 2 (2024): November
Publisher : Universitas Medan Area

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31289/jibioma.v6i2.5284

Abstract

Successful embryo culture is influenced by culture methods and conditions, which have an impact on cytoplasmic factors and the ability of embryo development. This study aims to compare the effectiveness of two culture mediums, M16 and CZB, in supporting the development of DDY strain mice embryos in vitro. The research method used was an experimental study consisting of animal husbandry, medium culture preparation, superovulation, collection, and in vitro embryo culture. Data analysis in this study used descriptive statistical tests to measure embryo development in each culture medium, M16 and CZB, in observations for 96 hours with a 24-hour interval using an inverted microscope. The results showed that embryos in the CZB medium experienced 50% development of the expanded blastocyte stage after 96 hours of culture with 50% degenerative. In the M16 culture medium, 0% of embryos experienced embryonic stage development after 96 hours of culture and 100% were degenerative. This study has concluded that the development of embryos in vitro in the M16 culture medium was not better than CZB, this was evidenced by the percentage at the expanded blastocyte development stage.
miR-29 Family as Epigenetic Regulators of DNMTs in Prostate Cancer and Benign Prostatic Hyperplasia Yudi Gebri Foenna; Nilüfer Şahin Calapoğlu; Okan Sancer; Muhammet Yusuf Tepebaşı; Mustafa Calapoğlu
The Indonesian Biomedical Journal Vol 17, No 2 (2025)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v17i2.3456

Abstract

BACKGROUND: The miR-29 family (miR-29a/b/c) is recognized as a tumor suppressor, directly targeting DNA methyltransferases (DNMTs), key regulators of epigenetic gene silencing. Even though miR-29 has been implicated in tumor progression, its regulatory interaction with DNMT3A/3B, particularly in prostate cancer (PCa), has not been elucidated well. This study was conducted to explore the potential of miR-29a/b/c in targeting DNMT3A/3B in PCa and benign prostatic hyperplasia (BPH), addressing a critical gap in understanding their epigenetic role.METHODS: This study used tissue samples that were taken surgically from 30 subjects that consisted of 15 diagnosed PCa and 15 BPH patients (as the control group), aged between 18-75 years, with urinary system disorders and had a prostate specific antigen (PSA) value between 1.18 and 56.15 ng/dL. The miR-29a/b/c and DNMT3A/3B expressions were measured using quantitative real-time PCR (qRT-PCR). The variations in mean values across groups, the associations between miR-29a/b/c and DNMT3A/3B expression levels parameters, as well as the correlation between miR-29 levels and DNMT3A/3B variables were then statistically analyzed.RESULTS: The expression levels of miR-29a/b/c were significantly downregulated in the PCa subjects compared to the BPH subjects (p<0.05), and negative correlations were observed between miR-29a/b/c and DNMT3A/3B in the PCa subjects (p<0.001). In addition, a significant inverse correlation was detected only between miR-29a and DNMT3B in BPH subjects (p<0.05).CONCLUSION: The results of this study indicated that miR-29a/b/c in PCa may act as a negative regulator directly targeting DNMT3A/3B. These findings support the role of miR-29s in developing miRNA-based strategies for treating PCa.KEYWORDS: prostate cancer, benign prostatic hyperplasia, epigenetic, DNA methyltransferases-3A/3B, miR-29a/b/c
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.
MOLECULAR PHYLOGENY OF RODENTIA DERIVED FROM NRAS GENE SEQUENCES Yudi Gebri Foenna; Hartono Hartono; Imelda Maelani
BIOLINK (Jurnal Biologi Lingkungan Industri Kesehatan) Vol. 12 No. 2 (2026): Biolink February
Publisher : Universitas Medan Area

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31289/biolink.v12i2.16827

Abstract

Rodentia is the most diverse mammalian order, yet phylogenetic relationships among several rodent lineages remain incompletely resolved, particularly when inferred predominantly from mitochondrial markers. This study aims to assess the potential of the nuclear NRAS (Neuroblastoma RAS viral oncogene homolog) gene for reconstructing rodent phylogeny. A total of 18 NRAS nucleotide sequences representing major rodent families were retrieved from the NCBI GenBank database, with Equus caballus and Oryctolagus cuniculus used as outgroups. Sequence alignment and model selection were performed using MEGA 12 under Maximum Likelihood criteria. Phylogenetic reconstruction was conducted using the Maximum Likelihood method with the T92+G+I substitution model and 1,000 bootstrap replicates. Pairwise genetic distances were estimated using the p-distance method and visualized through a heatmap to examine divergence patterns. The results indicated that NRAS evolution is best explained by models incorporating invariant sites and rate heterogeneity, reflecting strong functional constraints combined with lineage-specific variation. The inferred phylogeny is largely congruent with established rodent systematics, and genetic distance patterns independently support the recovered topology. These findings suggest that NRAS represents a reliable nuclear marker that offers complementary phylogenetic information alongside mitochondrial data in Rodentia phylogenetic studies.
Co-Authors Ardhana Yulisma Calapoğlu, Nilüfer Şahin Hartono Hartono Imelda Maelani Jamilah Nasution Muhammet Yusuf Tepebaşı Mustafa Calapoğlu Nilüfer Şahin Calapoğlu Okan Sancer