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All Journal HAYATI Journal of Biosciences Saintek Perikanan : Indonesian Journal of Fisheries Science and Technology BIOTROPIA - The Southeast Asian Journal of Tropical Biology Jurnal Sains Dasar Jurnal Teknosains Journal of Degraded and Mining Lands Management Biology, Medicine, & Natural Product Chemistry Bioeksperimen: Jurnal Penelitian Biologi Jurnal Pengolahan Pangan Eksakta : Berkala Ilmiah Bidang MIPA INDONESIAN JOURNAL OF MEDICAL LABORATORY SCIENCE AND TECHNOLOGY Narra J
Retnaningrum, Endah
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Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Earth & Planetary Sciences Education Energy Engineering Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Materials Science & Nanotechnology Mathematics Mechanical Engineering Medicine & Pharmacology Public Health Social Sciences Veterinary

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Journal : INDONESIAN JOURNAL OF MEDICAL LABORATORY SCIENCE AND TECHNOLOGY

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Molecular approach to the characterization of lipase encoding genes from Moraxella sp. SBE01 Soleha, Siti; Syarifah, Syarifah; Nurseha, Tito; Fatiqin, Awalul; Retnaningrum, Endah; Serang, Yitro
JURNAL INDONESIA DARI ILMU LABORATORIUM MEDIS DAN TEKNOLOGI Vol 6 No 2 (2024): Promising and Valuable Research Towards Diagnosis, Prognosis and Treatment of Dis
Publisher : Universitas Nahdlatul Ulama Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33086/ijmlst.v6i2.5596

Abstract

Lipase from Moraxella sp. SBE01 is an expression of the gene encoding lipase. Detection and characterization of the Moraxella sp. SBE01 lipase coding gene is necessary for large-scale lipase production through genetic engineering. This study aimed to observe the molecular weight, amino acid sequence, length, and conserved amino acids in the DNA encoding the lipase gene, with the goal of identifying and characterizing the lipase-coding gene from Moraxella sp. SBE01. The primer design process was conducted to amplify the lipase gene from Moraxella sp. SBE01 using specialized software for sequence alignment and phylogenetic analysis. Amplification was carried out using PCR with the designed primer, forward primer (GTC ATG ATG TAC TTC CAY GGN GGN GG), reverse primer (GGT TGC CGC CGG CDS WRT CNC C). PCR was carried out under pre-denatured conditions at 95°C (3 minutes), followed by 30 cycles of denaturation at 95°C, annealing at 66°C (30 seconds), 70°C elongations (1 minute) and final elongation of 70°C (10 minutes). The PCR results were electrophoresed using 1% agarose gel with a 1 kb DNA marker. The PCR results were sequenced and analyzed for gene and amino acid sequences and the type of lipase expressed. Sequencing resulted in 387 bp of the nucleotide sequence. The gene and amino acid sequences from Moraxella sp. SBE01 had high homology with the gene and amino acid sequences from Moraxella sp. strain TA144. The lipase gene encodes a protein consisting of 129 amino acids and contains a conserved HGG (His-Gly-Gly) motif, which is characteristic of lipases in family IV, also known as the hormone-sensitive lipase (HSL) family. This conserved sequence suggests that the lipase shares structural and functional similarities with other enzymes in the HSL family, playing a key role in lipid metabolism.
Computational Modeling of a Novel CTX-M β-Lactamase Escherichia coli Isolated from Yogyakarta, Indonesia Using I-TASSER Kinasih, Anggiresti; Retnaningrum, Endah
JURNAL INDONESIA DARI ILMU LABORATORIUM MEDIS DAN TEKNOLOGI Vol 8 No 1 (2026): Integration of Molecular Approaches in Addressing Drug Resistance and Changing Gl
Publisher : Universitas Nahdlatul Ulama Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33086/ijmlst.v8i1.7267

Abstract

Extended-spectrum β-lactamases (ESBLs), especially those of the CTX-M family, significantly contribute to antibiotic resistance in Escherichia coli. While CTX-M variants are well-characterized in clinical settings, their structural features in foodborne E. coli remain underexplored, particularly in countries like Indonesia. This study aimed to predict and validate the three-dimensional (3D) structure of a novel CTX-M β-lactamase protein from an E. coli isolate (D4DU2-ESBL-EC) culture collection at Laboratory of Microbiology, Universitas Gadjah Mada (UGM). This study reports a novel CTX-M variant from E. coli D4DU2, a locally strain originated from raw chicken meat in Yogyakarta traditional market that has been shown to adapt and thrive in Sleman Regency, Indonesia. Based on phylogenetic and structural analyses, E. coli D4DU2 evolutionary link to Indian CTX-M-15, with distinct mutations at W253L, P254A amino acid near the active site. The 3D structure of D4DU2 CTX-M β-lactamase was predicted using I-TASSER and validated using PROCHECK. Ramachandran analysis showed 78.4% of residues in the most favored regions, 20.5% in allowed regions, and only 1.2% in disallowed regions, confirming high stereochemical quality. These findings highlight potential local adaptation and emergence of a unique ESBL-producing E. coli strain. This study provides a reliable model for CTX-M β-lactamase from foodborne E. coli in Indonesia, supporting One Health-based surveillance and intervention strategies. Overall, this study demonstrates that I-TASSER, complemented by PROCHECK validation, offers a valuable in silico approach for the structural characterization of ESBL proteins from foodborne bacterial isolates in resource-limited contexts
Co-Authors Amantsura, Daimeera Anja Lulu Ardhelia Christy Anggraini Arjuna, Mesha Arte Widane, Ketut Atmandaru, Susmaya BUDI SETIADI DARYONO Burhanuddin Ihsan, Burhanuddin Chika Giyatno, Divya Daris, Pieter Jhon Joshua Daryono, Budi S. Fatiqin, Awalul Hastuti, Luthfiana Indah Khairunisa, Mutia Asri Kinasih, Anggiresti Manullang, Maria Muammar, Arief Nurseha, Tito Prastiyanto, Muhammad E. Prastiyanto, Muhammad Evy Serang, Yitro Soleha, Siti Solichah, Amalia Sri Darmawati Syarifah Syarifah, Syarifah Udasmara, Sekarani Arifah Wahyu Wilopo Warmada, Wayan Widyasari, Annisaa Yulma, Yulma