Tropical Genetics

In Silico Analysis of Non-synonymous Mutations in the durA Gene and Their Effects on the Stability and Physicochemical Properties of Duramycin

Yulianto Ade Prasetya — 2025-11-30

Duramycin is a lantibiotic peptide encoded by the durA gene, known for its antimicrobial activity against Gram-positive bacteria. This study aimed to evaluate the effects of single-point mutations on the stability and structural integrity of duramycin using a comprehensive in silico approach. Five variants—C1S, F7A, T11Y, D15E, and K19V—were designed and assessed using I-Mutant2.0 to predict their impact on protein stability. ProtParam analysis was conducted to determine molecular weight, isoelectric point (pI), net charge at pH 7, instability index, aliphatic index, and hydropathicity (GRAVY). In addition, PEP-FOLD3 was employed to model the 3D conformations of each mutant peptide. Results showed that K19V improved peptide stability and increased aliphatic index and GRAVY score, indicating enhanced hydrophobicity and potential thermal stability. In contrast, F7A led to a major structural shift marked by an α-helical conformation and reduced stability. C1S and T11Y induced minor destabilizing effects, while D15E offered a moderately stabilizing substitution with minimal structural deviation. Overall, this study highlights the functional relevance of C-terminal and hydrophobic residues in maintaining duramycin’s structural compactness and provides a framework for future design of optimized antimicrobial peptides through rational mutation

Phylogenetic and Genetic Distance Analysis of the Mangrove Worm (Namalycastis) Based on the 18S rRNA Gene Using in Silico Methods

Arielda Putri Aditya — 2025-11-30

Namalycastis is a polychaete worm that inhabits dynamic aquatic environments and exhibits high genetic and morphological variability. This study investigates the phylogeny of the genus Namalycastis through an in silico analysis using the 18S ribosomal RNA (rRNA) gene. This genetic marker is considered ideal as it combines conserved and variable regions, both essential for taxonomic and evolutionary analyses. The objective of this research was to examine the phylogenetic relationships and genetic distances among 12 species of the genus Namalycastis based on their 18S rRNA gene sequences. DNA sequences were obtained from the NCBI database and aligned using Clustal-W in MEGA XI software. Phylogenetic reconstruction was performed using the Neighbor-Joining method with 1000 bootstrap replications, applying the Kimura 2-Parameter (K2P) model. The results revealed that Namalycastis jaya shares a very close evolutionary relationship with Namalycastis abiuma, forming a monophyletic clade that is distinct from Namalycastis hawaiiensis. The genetic distances among N. jaya, N. abiuma, and N. abiuma group sp. indicate a close evolutionary affinity, whereas N. hawaiiensis displays greater genetic divergence from the other two species. Overall, this study demonstrates that the 18S rRNA gene is an effective molecular marker for identifying phylogenetic relationships among Namalycastis species. The findings also highlight the potential of in silico methods in elucidating evolutionary patterns within the genus Namalycastis.

Genetic Diversity and Relationships of Dendrobium Based on TrnL-F Markers: An Approach In-silico

Ikhwan Ismail — 2025-11-27

The development of DNA sequencing technologies has deepened our understanding of genetic variation within Dendrobium species and revealed evolutionary relationships among them. in-silico methods facilitate efficient phylogenetic determination, leveraging computational advantages to process sequence data with high accuracy. This study aims to significantly contribute to the understanding of genetic diversity within the genus Dendrobium based on the TrnL-F marker, with potential implications for the conservation and management of these plant genetic resourcesThis paper presents nucleotide diversity analysis and phylogenetic analysis to determine the kinship relationships among Dendrobium species. The analysis revealed a high degree of relatedness among the Dendrobium species, with kinship relationships dividing them into three distinct groups.

Analisis Filogenetik Bakteri Escherichia coli Berdasarkan DNA Genomik Gen BlaTEM Dari Data Sekuens NCBI

Indria Palupi — 2025-12-01

Resistensi antibiotik yang disebabkan oleh bakteri penghasil β-laktamase, seperti Escherichia coli, menjadi permasalahan global yang serius. Gen blaTEM merupakan salah satu gen utama yang berkontribusi terhadap resistensi tersebut. Penelitian ini bertujuan untuk menganalisis hubungan filogenetik antar isolat Escherichia coli berdasarkan sekuens DNA gen blaTEM yang diambil dari database NCBI dalam rentang waktu 2016 hingga 2025. Data sekuens diselaraskan menggunakan metode ClustalW dalam perangkat lunak MEGA X, kemudian dianalisis menggunakan metode Neighbor-Joining dan 1000 bootstrap. Hasil analisis menunjukkan pembentukan beberapa klade utama dengan tingkat kedekatan genetik yang bervariasi. Kelompok isolat tahun 2021–2024 memiliki kedekatan genetik tinggi, sedangkan isolat tahun 2020 dan 2025 menunjukkan divergensi yang signifikan. Temuan ini mengindikasikan adanya variasi evolusioner dalam gen blaTEM yang penting untuk dipantau sebagai bagian dari strategi pengendalian resistensi antibiotik.

Evaluating Misconceptions in the Representation of Mendelian Genetic Inheritance in High School Biology Textbooks

Kusniawati Kusniawati — 2025-12-03

Genetics learning is prone to misconceptions due to complex concepts, abstract reasoning, and inconsistencies in textbook presentations, which can hinder students’ understanding of inheritance patterns such as Mendelian genetics. This study analyzes the potential misconceptions in high school biology textbooks regarding Mendel’s Laws and dominance–recessive inheritance using Dikmenli et al.’s categorization, aiming to provide references for teachers in selecting and supplementing instructional materials. This is a descriptive qualitative research using content analysis method. Four textbooks, selected through a survey of biology teachers in Pontianak City, were analyzed by comparing key concepts in the textbooks with scientifically accurate explanations from authoritative references. The findings were systematically examined, categorized, and validated through member-checking to ensure accuracy, highlighting the most common types of misconceptions in the textbooks. The analysis revealed variations in the coverage and accuracy of 13 key concepts related to Mendel’s Laws and dominance–recessive inheritance, with Books A–C containing several potential misconceptions while Book D showed none. The most frequent types of misconceptions identified were misidentifications, followed by oversimplifications and overgeneralizations, often involving definitions of gene, genotype, phenotype, and independent assortment. These findings highlight the importance of accurate textbook content and suggest that educators must critically evaluate and clarify textbook explanations to prevent persistent misunderstandings in students’ conceptual understanding of genetics.