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All Journal HAYATI Journal of Biosciences SAINS MEDIKA : JURNAL KEDOKTERAN DAN KESEHATAN Jurnal Ilmiah Aplikasi Isotop Radiasi Microbiology Indonesia Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Medical Journal of Indonesia Journal of Biomedicine and Translational Research The Indonesian Biomedical Journal Universa Medicina Indonesian Journal of Biotechnology and Biodiversity The Indonesian Journal of Infectious Diseases Eksakta : Berkala Ilmiah Bidang MIPA Majalah Kedokteran Andalas Health Information : Jurnal Penelitian Jurnal Ners East Asian Journal of Multidisciplinary Research (EAJMR) Journal of Comprehensive Science Makara Journal of Health Research Makara Journal of Science Journal of Clinical Microbiology and Infectious Diseases Indonesian Journal of Biomedicine and Clinical Sciences

Andi Yasmon

Department Of Microbiology, Faculty Of Medicine Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta

Author-ID : 422494

Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Decision Sciences, Operations Research & Management Dentistry Earth & Planetary Sciences Economics, Econometrics & Finance Education Electrical & Electronics Engineering Energy Engineering Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Languange, Linguistic, Communication & Media Library & Information Science Materials Science & Nanotechnology Mathematics Mechanical Engineering Medicine & Pharmacology Neuroscience Nursing Public Health Other

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Articles

Title

In vitro transcription of HIV-1 RNA for standard RNA Yasmon, Andi; Bela, Budiman; Ibrahim, Fera; Syahruddin, Elisna
Medical Journal of Indonesia Vol 20, No 3 (2011): August
Publisher : Faculty of Medicine Universitas Indonesia

Background: The quantitative assays are important tests in the management of patients with HIV-1/AIDS. The importantÂ step in developing the assay is the availability of the standard HIV-1 RNA. For this purpose, we optimized in vitro HIV-1Â RNA transcription to produce the standard HIV-1 RNA.Methods: The HIV-1 DNA was amplified from pNL43 by PCR using a primer pair that was specific for conserved region ofÂ HIV-1 Gag gene. The PCR product was further cloned into pBluescript II KS. The recombinant plasmid was restricted withÂ EcoRI enzyme. Then, the linearized plasmid was used as template for RNA transcription. RT-PCR and PCR were performedÂ simultaneously for confirmation of synthesized RNA fragment.Results: A 115 bp DNA of HIV-1 Gag gene has been cloned into pBluescript II SK with the exact true orientation. TheÂ reaction of the RNA transcription was also successfully performed. The RNA transcripts have been confirmed and showedÂ the accuracy of the transcripts.Conclusion: We successfuly constructed the recombinant plasmid containing a conserved region of HIV-1 Gag gene, andÂ the HIV-1 RNA has been transcribed in vitro as well. (Med J Indones. 2011; 20:185-9)Keywords: HIV-1/AIDS, Quantitative assay, RNA transcription

Applicability of an oligonucleotide probe in radioisotope 32P-based dot blot hybridization for detection of hepatitis C virus in large sample numbers: a preliminary study Rosilawati, Maria L.; Yasmon, Andi
Medical Journal of Indonesia Vol 21, No 2 (2012): May
Publisher : Faculty of Medicine Universitas Indonesia

Background: This study aimed to design and analyze the applicability of an oligonucleotide probe in radioisotope 32P-based dot blot hybridization for detection of hepatitis C virus.Methods: Forty-six of plasma samples were used. The plasma was extracted to obtain viral RNA genome as template for RT-PCR and the amplicon was used for nested PCR. Twenty-four HCV genomes were retrieved from GeneBank DNA sequence and alignment was performed by Bio Edit Software version 7.0.9.0. An oligonucleotide probe was designed based on a highly conserved region that is located on internal sequence between two primers used for nested PCR. Blast analysis on GeneBank was performed to obtain homology of the oligonucleotide for HCV. The oligonucleotide was then labeled with 32P and dot blot hybridization was applied for nested PCR products. DNA Sequencing was performed to confirm the amplicon and dot blot hybridization results.Results: Blast analysis showed high homology (100%) for HCV. Nested PCR resulted in three patterns of DNA fragments representing HCV genotypes 1, 2, and 3, respectively. The primers used in nested PCR were not specific and resulted in DNA fragments difficult to be interpreted. Dot blot hybridization using the designed oligonucleotide showed high intensity dots. All nested PCR fragments showed the dot blot positive. The dot blot results were in accordance with DNA sequencing that confirmed three patterns of DNA fragments as different HCV genotypes.Conclusion: The oligonucleotide showed excellent bioinformatically criteria. 32P-based dot blot hybridization yielded high intensity dots and was easier to be interpreted than nested PCR assay. (Med J Indones. 2012;21:71-6)Keywords: Dot blot hybridization, hepatitis C virus, oligonucleotide, radioisotope

A second generation of RT-PCR assay for detection of human immunodeficiency virus type 1 (HIV-1) infection Yasmon, Andi; Fatmawati, Ni N.D.; Ibrahim, Fera; Bela, Budiman
Medical Journal of Indonesia Vol 19, No 3 (2010): August
Publisher : Faculty of Medicine Universitas Indonesia

Aim A spesific and rapid diagnosis such as RT-PCR assay is the most needed to minimize transmission of HIV-1Â infection. Therefore, in this study we developed the RT-PCR assay that was spesific against the gag gene of HIV-1.Methods The developed RT-PCR assay was evaluated against 46 specimens that were obtained from voluntaryÂ counseling and testing for HIV (VCT) in Rumah Sakit Umum Pemerintah (RSUP) Sanglah, Bali. To get the sensitivityÂ and specificity of RT-PCR assay, the results of assays were compared with the results of commercially serologic teststhat were commonly used in Indonesia.Results The RT-PCR assay could detect 21 of 26 serologic test-positive specimens and showed 19 negative results of 20Â serologic test-negative specimens. There was one specimen that was positive in RT-PCR but negative in serologic assay,Â which might depict a true yield at particular condition when the serologic assay was unable to detect. Five serologicÂ positive-test specimens were negative by RT-PCR that was possibly caused by low detection level of the assay.Conclusion The RT-PCR assay is potential to be used for the detection of HIV-1 infection with a sensitivity andÂ specificity of 80.8% and 95.0% respectively. (Med J Indones 2010;19:154-7)Key words: AIDS, diagnosis, PoL, sensitivity, specificity

Optimizing real-time PCR method to detect Leptospira spp. in human blood and urine specimens Karuniawati, Anis; Yasmon, Andi; Ningsih, Ika
Medical Journal of Indonesia Vol 21, No 1 (2012): February
Publisher : Faculty of Medicine Universitas Indonesia

Background: Leptospirosis is an acute infectious disease in humans caused by Leptospira spp. and classified as a zoonosis. Clinical symptoms of leptospirosis are nonspecific and the current available laboratory method for detecting Leptospira spp. is difficult, which resulted to the misdiagnosis of this disease. Therefore, the rapid and accurate method is needed to diagnose the disease. This study was aimed to optimize molecular diagnostic test using real-time PCR assay as a rapid, sensitive and specific method for the detection of pathogenic Leptospira spp. in humans.Methods: Bacterial DNA was extracted by DNA extraction kit according to the manufacturerâs instructions. Primers and probes used in this study was based on previous and published research. The assay is performed using PCR-IQTM5, iCycler Multicolor real-time PCR detection system. Specificity of the primer used was evaluated towards some bacterial pathogens.Results: Limit detection of the DNA was 0.375 fg/ml and the primers used does not cross-react with the genomes of the pathogens tested. Limit detection of DNA in blood is 150 fg/Î¼l, and in urine is 1470 fg/Î¼l.Conclusion: Real-time PCR test is a rapid and accurate method for detecting pathogenic Leptospira spp. in human specimens. Further research is needed to determine the sensitivity and specificity of real-time PCR tests compared with other diagnostic methods in clinical settings. (Med J Indones 2012;21:13-7)Keywords: Leptospirosis, Leptospira, optimization, real-time PCR

Optimizations of expression and purification of recombinant HIV-1 CRF01_AE p24 protein in Escherichia coli for development of immunodiagnostic assay Simaremare, Ade P.R.; Bela, Budiman; Yasmon, Andi; Ibrahim, Fera
Medical Journal of Indonesia Vol 24, No 1 (2015): March
Publisher : Faculty of Medicine Universitas Indonesia

Background: Conventional method for confirmation of HIV infection is Western blot. However, it has limitations because of contamination by human cellular antigen and genetic diversity among the HIV-1 subtypes that show indeterminate result and inaccuracy for the diagnosis of different strains. Most of Western blot developed are based on HIV-1 B subtype. In Indonesia HIV-1 CRF01_AE subtype is dominantly circulated. Therefore, we optimized the expression, purification of the recombinant HIV-1 CRF01_AE p24 protein for development of immunodiagnostic assay.Methods: Optimization of protein expression in Escherichia coli strain BL21CP was performed including induction time, isopropyl-1-thio-d-galactopyranoside (IPTG) and immidazole consentrations, and induction temperature. Purification of the recombinant p24 protein was used by using Ni-NTA (Qiagen) purification system in native condition. Results: Expression and purification of HIV-1 CRF01_AE p24 protein have been performed. Confirmation of the recombinant protein by Western blot showed the expression and purification of recombinant p24 protein has been optimized well and reactive with sera of patients with HIV-1 CRF01_AE subtype positive.Conclusion: The recombinant HIV-1 CRF01_AE p24 protein has been expressed and purified successfully, and it is potential to be used as antigen for immunodiagnostic assay.

Simultaneous detection of Legionella species and Legionella pneumophila by duplex PCR (dPCR) assay in cooling tower water samples from Jakarta, Indonesia Yasmon, Andi; Yusmaniar, Yusmaniar; Anis, Anis; Bela, Budiman
Medical Journal of Indonesia Vol 19, No 4 (2010): November
Publisher : Faculty of Medicine Universitas Indonesia

Aim: Since culture method is time-consuming and has lowÂ sensitivity, we developed a duplex PCR (dPCR) assay for the detection of Legionella sp. and L. pneumophila in cooling tower samples. We used culture method as a gold standard.Methods: Optimization of dPCR method was performed to obtain an assay with high sensitivity and specifi city. The optimized method was used to detect Legionella sp. dan L. pneumophila in 9 samples obtained from 9 buildings in Jakarta. For culture method, the bacteria were grown or isolated on selective growth factor supplemented-buffered charcoal yeast extract (BCYE) media.Results: Of 9 samples tested by dPCR assay, 6 were positive for Legionella species,1 was positive for L. pneumophila, and 2 showed negative results. For the same samples, no Legionella sp. was detected by the culture method.Conclusion: dPCR assay was much more sensitive than the culture method and was potentially used as a rapid, specifi c and sensitive test for routine detection of Legionella sp. dan for L. pneumophila in water samples. (Med J Indones 2010; 19:223-7)Keywords: BCYE media, mip gene, 16S-rRNA gene

Development of multiplex-PCR assay for rapid detection of Candida spp. Tarini, Ni Made A.; Wahid, Mardiastuti H.; Ibrahim, Fera; Yasmon, Andi; Djauzi, Samsuridjal
Medical Journal of Indonesia Vol 19, No 2 (2010): May
Publisher : Faculty of Medicine Universitas Indonesia

AimÂ Candida spp. infection commonly occur in immunocompromised patients. Biochemical assay for identificationÂ of Candida spp. is time-consuming and shows many undetermined results. Specific detection for antibody, antigen andÂ metabolites of Candida spp. had low sensitivity and specificity. In this study, we developed a rapid diagnostic method,Â Multiplex-PCR, to identify Candida spp.Methods Five Candida spp. isolates were cultured, identifi ed with germ tube and APIÂ® 20 C AUX (BioMerieuxÂ® SA) kit.Â Furthermore, DNA was purified by QIAamp DNA mini (QiagenÂ®) kit for Multiplex-PCR assay.Results DNA detection limit by Multiplex-PCR assays for C. albicans, C. tropicalis, C. parapsilosis, C. krusei and C.Â glabrata were 4 pg, 0.98 pg, 0.98 pg, 0.5 pg and 16 pg respectively. This assay was also more sensitive than culture inÂ that Multiplex-PCR could detect 2.6-2.9 x 100 CFU/ml, whereas culture 2.6-2.9 x 102 CFU/ml.Conclusion Multiplex-PCR is much more sensitive than culture and thus, can be recommended as a sensitive andÂ specific assay for identification of Candida spp. (Med J Indones 2010; 19:83-7)Keywords: Candida spp., multiplex-PCR

Detection and identification of azithromycin resistance mutations on Treponema pallidum 23S rRNA gene by nested multiplex polymerase chain reaction Gultom, Desy A.; Rosana, Yeva; Efendi, Ida; Indriatmi, Wresti; Yasmon, Andi
Medical Journal of Indonesia Vol 26, No 2 (2017): June
Publisher : Faculty of Medicine Universitas Indonesia

Background: Azithromycin-resistant strains of Treponema pallidum is associated with the mutation of 23S rRNA gene of T. pallidum. Although these strains are now prevalent in many countries, there is no laboratory test kit to detect and identify these mutations. Thus, in this study we developed a nested multiplex polymerase chain reaction (PCR) to detect and identify A2058G and A2059G mutations in 23S rRNA gene.Methods: Three primer sets were designed for nested PCR reactions. To obtain maximum PCR reaction, all parameters were optimized. The specificity of the primer sets was evaluated towards some microorganisms. A sensitivity test was conducted to get detection limit of deoxyribonucleic acid (DNA). Forty-five whole blood specimens were tested by PCR, and positive results were confirmed by the DNA sequencing.Results: The assay could detect at least 4,400 DNA copy number and showed no cross reaction with other microorganisms used in the specificity test. A total 13 of 45 whole blood specimens were PCR positive for T. pallidum, and no single mutations (either A2058G or A2059G) were detected. Two positive specimens were confirmed by the DNA sequencing and showed no mutation.Conclusion: Nested multiplex PCR developed in this study showed a specific and sensitive test for the detection and identification of A2058G and/or A2059G mutations of 23S rRNA T. pallidum gene.

Co-Authors . Andriansjah Abror Irsan Ade P.R. Simaremare Agustini, Riani Anis Anis Anis Karuniawati Ardiana Kusumaningrum Ariyani Kiranasari ASRI SULFIANTI Beti Ernawati Dewi Budiman Bela Burhanuddin Burhanuddin Burhanuddin Burhanuddin Delly Chipta Lestari Delly Chipta Lestari Dewi Murniati Diah Dwi Utami Diana Natalia Diana Natalia Efendi, Ida Effendi, Ida Effiana Effiana Effiana, Effiana Elisabeth D. Harahap Elisna Syahruddin Erlina, Linda Fadilah Fadilah Fadilah FERA IBIRAHIM Fera Ibrahim Fithriyah Fithriyah Fithriyah Fithriyah Fithriyah Fithriyah Gultom, Desy A. Hanifah, Rifdah Heri Wibowo Ibnu Agus Ariyanto Ika Ningsih Junita Indarti Ketut Tuti Parwati Linosefa Linosefa Lisnawati Rachmadi Lola Febriana Dewi Louisa Ivana Utami Lucky H Moehario Mardhia, Mardhia Mardhia, Mardhia Mardiastuti H Wahid Maria L. Rosilawati Maria L. Rosilawati Maria Lina R. Maria Lina Rosilawati Maya Ulfah Moehario, Lucky Hartati Murti, Anissa Wari Ni Made Adi Tarini Ni Nengah Dwi Fatmawati Normasari Normasari Oktania Sandra Puspita Paramita, Rafika Indah Pramita G. Dwipoerwantoro Pratiwi Pujilestari Sudarmono Purba, Hastuti Handayani S Purnomosidi, Muhammad Abhi Rahayu, Ratih Ratnoglik, Suratno Lulut Rela Febriani Ria Kodariah Rosa, Yulia Rudyanto Sedono Safari, Dodi Salsabila, Korrie Samsuridjal Djauzi Sari Rahmayanti Simon Yosonegoro Liem SJATHA, FITHRIYAH Sudarmo, Fitrahwati Tafroji, Wisnu Teguh Sarry Hartono Thomas Robertus Tjampakasari, Conny Riana Utami, Diah Dwi VIVI SETIAWATY Winarti, Yayah Wresti Indriatmi B. Makes Wulandari, I Gusti Ayu Inten Yeva Rosana Yulia Rosa Saharman YULIANTY MUHAYAR Yusmaniar Yusmaniar Zaenab

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