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All Journal Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Indonesian Journal of Biotechnology The Indonesian Biomedical Journal

Dewi Kartikawati Paramita

Department Of Histology And Cell Biology, Faculty Of Medicine, Public Health And Nursing, Universitas Gadjah Mada, Jl. Farmako Sekip, Yogyakarta 55281, Indonesia

Author-ID : 2874486

Biochemistry, Genetics & Molecular Biology Immunology & microbiology Materials Science & Nanotechnology Neuroscience Public Health

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Articles

Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4 Anggi Laksmita Dewi; Dewi Kartikawati Paramita; Jajah Fachiroh
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.64933

Rs1948 A>G is a single nucleotide variation (SNV) in the 3’‐UTR of CHRNB4. Genotyping the synonymous CHRNB4 rs1948 may be useful in identifying a lung cancer susceptibility gene. The study aimed to develop a simple and easy tetra‐primer amplification refractory mutation system (ARMS PCR) for CHRNB4 rs1948. The following steps were taken to optimize tetra‐primer ARMS PCR: 1) determining the gene sequence and position of a single mutation; 2) developing outer and inner primers; 3) amplification of target gene fragments via PCR using an outer primer; 4) genotyping PCR product using Sanger sequencing; 5) determining the optimal annealing temperature and PCR cycle; 6) determining optimal outer and inner primer ratio; and 7) testing the reproducibility of the PCR program and final validation with Sanger sequencing. Genotype (PCR result) was visualized with 3% agarose gel electrophoresis. Optimum condition was determined as annealing temperature of 64.8 ºC and 35 cycles, outer and inner primer ratio of 1:6, and DNA volume of 3 µL. Sanger sequencing confirmed the results of the tetra‐primer ARMS PCR and it was shown that ARMS PCR was able to identify three different variants of CHRNB4 rs1948.

EFFECT OF 1,2-EPOXY-3[3-3[3,4-DIMETOXYI-PHENIL]-4H-1-BENZOPIRAN-4-ON] PROPANE (EPI) ON SIRTUIN-1 AND NUCLEAR FACTOR-κB EXPRESSION OF MAMMARY TUMORS INDUCED IN SPRAGUE DAWLEY RATS BY DMBA Ayyub Harly Nurung; Sri Herwiyanti; Dewi Kartikawati Paramita
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 48, No 3 (2016)
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

ABSTRACT The main factors contribute to breast cancer development is the combination of exogenous and endogenous factors. Endogenous factors include both SIRT1 and NF-kB. Exogenous factor used in this research is 7.12 dimethylbenz(a)anthracene (DMBA). 1,2-epoxy-3[3- 3[3,4-dimetoxy-phenil]-4h-1-benzophiran-4-on] propane (EPI) is a derivative of isoflavone generate from clove leaf oil. To examine the effect of EPI on SIRT1 and NF-kB expression in DMBA-induced Sprague Dawley (SD) rats, and the correlation between SIRT1 and NFkB expressions. Tissue generated form 35 Sprague Dawley female rats aged 2 weeks old were used in this study. Those rats were divided into 7 groups (5 rats/group), namely normal control group; corn oil group; DMBA group; EPI treated groups with 1 mg/kgBW (EPI I), 2 mg/kgBW (EPI II), and 4 mg/kgBW (EPI III), respectively; and doxorubicin group. EPI and doxorubicin were administered from 1st until 15th week, while DMBA were administered from 3rd until 9th week. The paraffin block was prepared from all breast organ of the rats that terminated at the end of week 15th. Examination of SIRT1 and NF-kB expression was performed using light microscope at 400x magnifications, after immunohistochemistry (IHC) staining. Expression level of SIRT1 and NF-kB were analyzed using IHC-profiler plug-in in ImageJ software. SIRT1 and NF-kB expression in EPI treated groups were not significantly different with the one in Doxorubicin group, but lower than DMBA group (p=0.000). There was a positive correlation between SIRT1 and NF-kB expression (p=0.001; r=0.773) in EPI-treated group. EPI was able to prevent an increasing of SIRT1 and NF-kB expression in SD model breast cancer that induced with DMBA. There is a positive correlation between SIRT1 and NF-kB expression in EPI-treated SD rats that were induced by DMBA

Association between HLA-B alleles and nevirapine-induced allergies among Indonesian HIV patients Angela Satiti Retno Pudjiati; Dyah Ayu Mira Oktarina; Hardyanto Soebono; Saihas Sauda; Dewi Kartikawati Paramita; Iwan Dwiprahasto; Zubairi Djoerban
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 48, No 4 (2016)
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

This study aimed to investigate the association between human leukocyte antigen-B(HLA-B) alleles and nevirapine allergy in HIV patients in Indonesia. A case control studywas conducted involving 147 HIV patients comprising of 50 patients with and 97patients without nevirapine allergy as control. The HLA-B allele typing was conducted byusing polymerase chain reaction-sequence specific oligonucleotide probes (PCR-SSOP),followed by sequencing. Bivariate analysis using Chi-square (X2) test and multivariatelogistic regression with significance level at p<0.05 were applied to analysis the data.Among 147 subjects, 34 with HLA-B alleles were identified. Bivariable analysis showedthat HLA-B*58 allele was the most significant risk factor for the nevirapine allergy (OR= 3.67; 95% CI: 1.79 to 7.54), while HLA-B*35 allele was a protective factor (OR =0.18; 95% CI: 0.08 to 0.42). Multivariate logistic regression analysis showed that youngmen and HLA-B*58 allele were the significant risk factors of nevirapine allergy (OR: 4.63;95% CI: 2.02 to 10.61), while older women with the HLA-B*35 was able to reducethe risk of nevirapine allergy approximately 81% (OR: 0.19; 95% CI: 0.08 to 0.49). Inconclusion, young male with the HLA-B*58 allele are the high risk factor for nevirapineallergy in Indonesian HIV patients.

The expression of COX-2 and iNOS in ethanol and aspirin induced gastric ulcer rat models sherly usman; Dewi Kartikawati Paramita; Yustina Andwi Ari Sumiwi
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 50, No 3 (2018)
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

Aspirin or ethanol induced gastric ulcer rat models are the most frequently used in studies.Aspirin and ethanol induced gastric ulcers through different pathways involving COX-2 andiNOS. The aim of this study was to examine the expression of COX-2 and iNOS in gastriculcer rat model induced by ethanol and aspirin. Twenty-one Sprague Dawley rats weredivided into 7 groups i.e. control group (CA), ethanol 1st day (ED1), ethanol 3rd day (ED3),ethanol 5th day (ED5), aspirin 4th day (AD4), aspirin 6th day (AD6), and aspirin 8th day (AD8).Oral administration of aspirin was at 200mg/kgBW and the 100% ethanol at 1mL/200gBW.Macroscopic and microscopic observations were done to examine the gastric mucosaldamage, COX-2 and iNOS expressions. Severe gastric ulcers were observed in ED1and AD4 groups and mild gastric mucosal damage was observed in ED3, ED5, AD6 andAD8 groups. Microscopically, light erosion was shown by the CA and AD8 groups. Erosionwas also shown by ED3, ED5, and AD6 groups. The most severe damage with ulcers andheavier bleeding were shown by the ED1 and AD4 groups. Weak COX-2 expression wasfound in the CA, while the highest COX-2 expression was found in the ED1. The iNOSexpression in the ethanol groups was still increasing until the 5th day (ED5). In the aspiringroups, it reached the peak on the 3rd day (AD6), and already declined on the 5th day (AD8).In conclusion, the damage process of ethanol induced gastric ulcer occurred faster thanthat by aspirin. The highest COX-2 expression in the ethanol and aspirin groups wereshown at the onset begin. iNOS expression in ethanol induced ulcer groups still increaseduntil the 5th day, while in the aspirin induced ulcer groups already declined in the 5th day.

Review of immune responses correlated with COVID-19 outcomes: the fight, debacle and aftermath in the Indonesian context. Dian Eurike Septyaningtrias; Jajah Fachiroh; Dewi Kartikawati Paramita; Dewajani Purnomosari; Rina Susilowati
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 52, No 3 (2020): Special Issue: COVID-19
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

In the current pandemic, the highly contagious nature of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) leads to an enormous burden for the global health care system and creates challenging socioeconomic problems. Respiratory mucosa, the main entrance of SARS-CoV-2 infection, are equipped with an innate immune defense system as the initial response against infection. Activation of the adaptive immune system facilitates viral clearance as well as providing immunological memory for prevention from subsequent exposure. However, despite repeated efforts at implementing appropriate interventions, severe and fatal cases are continuing to occur and reports of recurrent cases need clarification. Host factors may contribute to the severity of the diseases while viral immune evasion is a common phenomenon leading to severe outcomes and recurrent infection. Discussions of immunological-based tests for screening, herd immunity, along with the possible advantages or potentially futile efforts of development of vaccine and alternative immunotherapy have become a part of daily household conversations. In this review, evidence of innate and adaptive immune responses or lack of them, and immunological problems relevant for SARS-CoV-2 will be summarized. Finally, perspectives for future studies especially in the Indonesian population will be sketched.

Development of Tetra-primer Amplification Refractory Mutation System (ARMS) PCR for Detection of CHRNA3 rs8040868 Anggi Laksmita Dewi; Dewi Kartikawati Paramita; Jajah Fachiroh
The Indonesian Biomedical Journal Vol 13, No 2 (2021)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v13i2.1463

BACKGROUND: Single nucleotide variations (SNV) have been mapped to be associated with several human conditions and diseases. To validate the association between SNV to certain human traits or diseases, a large number of subjects must be included. Thus, in need of a fast, relatively economic, and reliable genotyping method. This can be achieved through the use of tetra-primer amplification refractory mutation system polymerase chain reaction (Tetra-primer ARMS PCR). This study reports strategy to develop Tetra-primer ARMS PCR-based genotyping of CHRNA3 rs8040868.METHODS: The optimization of Tetra-primer ARMS PCR was done through these steps: identification of gene sequence and position of single mutation; designing outer and inner PCR primers; amplification of target gene fragments through PCR by using outer primer; confirming genotype of the PCR product by using sequencing; determining an optimum ratio of outer and inner primer; and determining optimum annealing temperature and cycles for the PCR program. The PCR products were run in 2% gel agarose electrophoresis and visualized under UV illumination.RESULTS: Outer and inner primer ratio of 1:3 with annealing temperature of 64.4°C and 40x cycles was found to be the most optimum condition. Tetra-primer ARMS PCR was able to confirm the results of the DNA sequence of 2 samples, confirming wild-type variants (TT allele) and the heterozygous mutant (CT allele).CONCLUSION: Tetra-primer ARMS PCR was able to genotype rs8040868 of the CHRNA3 gene.KEYWORDS: tetra-primer ARMS PCR, CHRNA3, rs8040868, genotyping

Co-Authors Angela Satiti Retno Pudjiati Anggi Laksmita Dewi Anggi Laksmita Dewi Dewajani Purnomosari Dian Eurike Septyaningtrias Hardyanto Soebono Iwan Dwiprahasto Jajah Fachiroh, Jajah Nurung, Ayyub Harly Oktarina, Dyah Ayu Mira Rina Susilowati Saihas Sauda Sherly Usman Sri Herwiyanti, Sri Yustina Andwi Ari Sumiwi Zubairi Djoerban

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