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Development of an inactivated viral transport medium for diagnostic testing in low-resource countries Rahmani, Silmi; Meitha, Karlia; Septiani, Popi; Priharto, Neil; Kamarisima, Kamarisima; Ningrum, Ratih A.; Angelina, Marissa; Agustiyanti, Dian F.; Wisnuwardhani, Popi H.; Nugroho, Herjuno A.; Tan, Marselina I.
Narra J Vol. 5 No. 3 (2025): December 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i3.2068

Viral transport medium (VTM) is crucial for retaining clinical specimens, such as the virus or its genetic material from the mucus of respiratory tract of coronavirus disease 2019 (COVID-19) suspected patients. However, the locally produced VTM in Indonesia lacks the ability to inactivate the virus, risking the safety of diagnostic personnel. The aim of this study was to formulate inactive VTM (iVTM) incorporating chaotropic agents like guanidine salt, along with anionic detergents, chelators, buffers, and surfactants, to inactivate the virus while maintaining RNA integrity. Viral RNA stability in iVTM (pH 4 and pH 6) was evaluated for 30 days at 4°C and 25–28°C. In vitro inactivation test was performed on SARS-CoV-2 isolate (variant B1). The stability test revealed that storing the clinical specimens in iVTM at pH 6 maintained severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) detectability by qPCR for up to 30 days at cold and room temperatures. Stability assessments conducted over a 4-month period (at 25–28°C) on iVTM with a pH of 6 revealed clear appearance, consistent pH stability, no alteration in the solution color, and no indications of bacterial or fungal contamination. Results from an in vitro inactivation assay demonstrated that iVTM pH 6 eliminated SARS-CoV-2 infectivity within just five minutes of contact. These findings suggest that iVTM pH 6 offers a safer and cost-effective alternative for handling and transportation of clinical specimens.

Gama Melon Parfum, a Potential Melon Genotype Tolerant of Salinity Stress Nugroho, Giri; Chikmawati, Tatik; Sartika, Dian; Yusuf, Adib Fakhruddin; Putro, Karso Suryo; Latifah, Vida Rahma; Daryono, Budi Setiadi; Wibowo, Anjar Tri; Nurhayati, Awik Puji Dyah; Meitha, Karlia; Miftahudin, Miftahudin
Makara Journal of Science Vol. 29, No. 3
Publisher : UI Scholars Hub

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Melona, Tacapa Gold, and Gama Melon Parfum are novel Melon genotypes that have been introduced for cultivation in the saline-prone coastal region of Bocor Beach, Kebumen, Central Jawa. Elevated salt concentrations in the area pose challenges, impacting yield. The potential of these new genotypes for saline land remains unexplored. This study aimed to assess the morphophysiological and molecular responses of these genotypes to salinity stress. Seeds were germinated in cocopeat and ABmix 3000 solution and treated with 220 mM NaCl until harvest. The analysis included morphology, chlorophyll content, proline accumulation, malondialdehyde levels, and gene expression were analyzed. After 1 week of salinity stress, the results showed reduced plant height, leaf number, stomatal density, percentage of opened stomata, and width and length of leaves. The malondialdehyde, proline, and root-shoot dry mass ratio increased. The expression of CSD1-1, P5CR, and late embryogenesis abundant genes increased under salinity treatment. Gama Melon Parfum exhibits salt tolerance, as indicated by higher P5CR gene expression, proline accumulation, and leaf-relative water content. P5CR gene expression, proline accumulation, and leaf-relative water content are valuable indicators of salt tolerance for assessing melon genotypes.

In silico–guided Design and Endonuclease-Based Functional Validation of sgRNAs Targeting ERBB2 Transmembrane and Kinase Domains Gunsi, Via Susana; Dirgahyu, Anugrah Prima; Meitha, Karlia; Christianto, Antonius; Tan, Marselina Irasonia
The Indonesian Biomedical Journal Vol 18, No 2 (2026)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v18i2.4048

BACKGROUND: Erythroblastic oncogene B2 (ERBB2) overexpression promotes breast cancer progression through activation of phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) and mitogen-activated protein kinase (MAPK) signaling pathways. Although CRISPR–Cas9 enables precise gene disruption, sgRNA efficiency is strongly influenced by target sequence and structural features, necessitating careful in silico design and validation. This study aimed to design and evaluate sgRNAs targeting the transmembrane- and tyrosine kinase–encoding regions of ERBB2.METHODS: Candidate sgRNAs were selected using CHOPCHOP, CRISPOR, and CRISPR RGEN, followed by secondary structure analysis with RNAfold to assess folding stability and scaffold integrity. sgRNAs were synthesized via in vitro transcription and assembled with Cas9 protein to form ribonucleoprotein (RNP) complexes. In vitro endonuclease assays were performed using PCR-amplified ERBB2 fragments derived from SK-OV3 genomic DNA, corresponding to exon 22 (523 bp) and exon 25 (933 bp). sgRNAs targeting eIF4E1 served as positive controls.RESULTS: Two sgRNAs meeting all in silico criteria were selected. Secondary structure prediction confirmed that both sgRNAs possessed essential structural elements required for Cas9 interaction including the repeat–anti-repeat region and three stem–loop structures. In vitro endonuclease assays demonstrated that the sgRNA targeting exon 22 of ERBB2 successfully cleaved its target DNA, producing fragments of 266 bp and 257 bp. Similar cleavage activity was observed in the two control sgRNAs, which generated fragments of 384 bp and 303 bp, and 486 bp and 201 bp, respectively. In contrast, the sgRNA targeting exon 25 of ERBB2 exhibited no detectable cleavage activity.CONCLUSION: The sgRNA targeting exon 22 of ERBB2 demonstrated effective DNA cleavage activity in vitro, whereas the sgRNA targeting exon 25 showed no endonuclease activity.KEYWORDS: CRISPR–Cas9, endonuclease, ERBB2, in vitro, breast cancer, RNP, sgRNA

Development of an inactivated viral transport medium for diagnostic testing in low-resource countries Rahmani, Silmi; Meitha, Karlia; Septiani, Popi; Priharto, Neil; Kamarisima, Kamarisima; Ningrum, Ratih A.; Angelina, Marissa; Agustiyanti, Dian F.; Wisnuwardhani, Popi H.; Nugroho, Herjuno A.; Tan, Marselina I.
Narra J Vol. 5 No. 3 (2025): December 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i3.2068

Viral transport medium (VTM) is crucial for retaining clinical specimens, such as the virus or its genetic material from the mucus of respiratory tract of coronavirus disease 2019 (COVID-19) suspected patients. However, the locally produced VTM in Indonesia lacks the ability to inactivate the virus, risking the safety of diagnostic personnel. The aim of this study was to formulate inactive VTM (iVTM) incorporating chaotropic agents like guanidine salt, along with anionic detergents, chelators, buffers, and surfactants, to inactivate the virus while maintaining RNA integrity. Viral RNA stability in iVTM (pH 4 and pH 6) was evaluated for 30 days at 4°C and 25–28°C. In vitro inactivation test was performed on SARS-CoV-2 isolate (variant B1). The stability test revealed that storing the clinical specimens in iVTM at pH 6 maintained severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) detectability by qPCR for up to 30 days at cold and room temperatures. Stability assessments conducted over a 4-month period (at 25–28°C) on iVTM with a pH of 6 revealed clear appearance, consistent pH stability, no alteration in the solution color, and no indications of bacterial or fungal contamination. Results from an in vitro inactivation assay demonstrated that iVTM pH 6 eliminated SARS-CoV-2 infectivity within just five minutes of contact. These findings suggest that iVTM pH 6 offers a safer and cost-effective alternative for handling and transportation of clinical specimens.

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