FERA IBRAHIM
Program Studi Ilmu Biomedik Kekhususan Mikrobiologi Fakultas Kedokteran Universitas Indonesia Jl. Salemba Raya Jakarta Pusat Indonesia

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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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (119.131 KB) | DOI: 10.13181/mji.v20i3.447

Abstract

Background: The quantitative assays are important tests in the management of patients with HIV-1/AIDS. The important step in developing the assay is the availability of the standard HIV-1 RNA. For this purpose, we optimized in vitro HIV-1 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 of HIV-1 Gag gene. The PCR product was further cloned into pBluescript II KS. The recombinant plasmid was restricted with EcoRI enzyme. Then, the linearized plasmid was used as template for RNA transcription. RT-PCR and PCR were performed 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. The reaction of the RNA transcription was also successfully performed. The RNA transcripts have been confirmed and showed the accuracy of the transcripts.Conclusion: We successfuly constructed the recombinant plasmid containing a conserved region of HIV-1 Gag gene, and 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
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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (108.411 KB) | DOI: 10.13181/mji.v19i2.387

Abstract

Aim Candida spp. infection commonly occur in immunocompromised patients. Biochemical assay for identification of Candida spp. is time-consuming and shows many undetermined results. Specific detection for antibody, antigen and metabolites of Candida spp. had low sensitivity and specificity. In this study, we developed a rapid diagnostic method, Multiplex-PCR, to identify Candida spp.Methods Five Candida spp. isolates were cultured, identifi ed with germ tube and API® 20 C AUX (BioMerieux® SA) kit. Furthermore, DNA was purified by QIAamp DNA mini (Qiagen®) kit for Multiplex-PCR assay.Results DNA detection limit by Multiplex-PCR assays for C. albicans, C. tropicalis, C. parapsilosis, C. krusei and C. 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 in 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 and specific assay for identification of Candida spp. (Med J Indones 2010; 19:83-7)Keywords: Candida spp., multiplex-PCR
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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (120.308 KB) | DOI: 10.13181/mji.v19i3.397

Abstract

Aim A spesific and rapid diagnosis such as RT-PCR assay is the most needed to minimize transmission of HIV-1 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 voluntary counseling and testing for HIV (VCT) in Rumah Sakit Umum Pemerintah (RSUP) Sanglah, Bali. To get the sensitivity 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 20 serologic test-negative specimens. There was one specimen that was positive in RT-PCR but negative in serologic assay, which might depict a true yield at particular condition when the serologic assay was unable to detect. Five serologic 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 and specificity of 80.8% and 95.0% respectively. (Med J Indones 2010;19:154-7)Key words: AIDS, diagnosis, PoL, sensitivity, specificity
Semi-quantitative dot immunoassay for detection of IgM anti-dengue antibodies in human sera Sjahrurachman, Agus; Ernawati, Betty; Ibrahim, Fera; Mardiastuti, Mardiastuti; Sudiro, Tjahjani M.; Sudarmono, Pratiwi
Medical Journal of Indonesia Vol 9, No 1 (2000): January-March
Publisher : Faculty of Medicine Universitas Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (557.893 KB) | DOI: 10.13181/mji.v9i1.643

Abstract

[no abstract available]
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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1028.215 KB) | DOI: 10.13181/mji.v24i1.1166

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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.
Antibody anti-H5N1 detection in poultry farmers and workers in poultry collection facilities in Indonesia, 2007 Setiawaty, Vivi; Sedyaningsih, Endang R.; Sudiro, Tjahyani M.; van Beest Holle, Mirna Robert D.R.; Pangesti, Krisna N.A.; Ibrahim, Fera
Medical Journal of Indonesia Vol 19, No 2 (2010): May
Publisher : Faculty of Medicine Universitas Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (103.071 KB) | DOI: 10.13181/mji.v19i2.394

Abstract

Aim Between July 2005 and May 2008, Indonesia reported 133 H5N1 confirmed human cases with a case fatality proportion of 81%. Fifty-four percent of cases had a history of direct contact with poultry (chickens). Therefore, it is important to define the detection of antibody of H5N1 among people who have intensive contact with poultry have been exposed to H5N1 viruses.Methods We collected sera from healthy poultry-collecting-facility (PCF) workers in Jakarta and healthy poultry-farmers in Sukabumi which have close contact with poultry. Anti-H5N1 antibodies were tested with modified Haemagglutination Inhibition (HI) assay using A/Ck/Banten/05-1116/05(H5N1) antigen and with Neutralization (NT) assay using A/H5N1/Indo/05/IBCDC-RG virus.Results Among the 216 PCF worker sera and the 495 poultry-farmer sera that we collected, we found that all poultry-farmers were seronegative and one percent of poultry-collecting-facilities workers were seropositive by both HI and 1% by NT assays.Conclusions This study detected asymptomatic H5N1 virus infection among poultry workers in PCFs with intensive contact with various types of different poultry who had different titers of antibody, but no antibodies were detected among poultry farmers. (Med J Indones 2010; 19:124-9)Keywords: Avian infl uenza, farmers, poultry workers, seropositive
Level of Retinol Deposit and Cervical Cancer Utami, Tofan W; Ibrahim, Fera; Purwoto, Gatot; Tiffani, Wely L; Aziz, Muhammad F; Andrijono, Andrijono
Indonesian Journal of Obstetrics and Gynecology Volume. 5, No. 1, January 2017
Publisher : Indonesian Socety of Obstetrics and Gynecology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (131.483 KB) | DOI: 10.32771/inajog.v5i1.465

Abstract

Objective: To analyze level of retinol deposit sufficiency in the natural history of cervical cancer. Methods: Serum retinol level was measured by ELISA from peripheral blood of subjects with normal cervix, cleared and persistent high risk human papilloma virus (HR-HPV) subclinical infection, and cervical cancer who fulfilled the inclusion and exclusion criteria. The study was held in Dr. Cipto Mangunkusumo and Fatmawati Hospital, Jakarta, within 2 years (August 2013- 2015). Blood was taken twice, consisting of post-8-hour fasting blood and 2 hours after 6000 IU retinyl palmitate oral administration. Results: Of 47 total samples, sufficient level of retinol deposit in normal cervix, cleared and persistent HR-HPV subclinical infection, and cervical cancer group was 85.0% (reference), 75.0% (OR 1.89), 33.3% (OR 11.33), and 75% (OR 1.89); respectively. Statistically, there was no significant difference from sufficiency level of retinol deposit between normal cervix and clearance HR-HPV subclinical infection (p=0.628), normal cervix and persistent HR-HPV subclinical infection (p=0.078), normal cervix and cervical cancer (p=0.433), cervical cancer and clearance HR-HPV subclinical infection (p=1.000), cervical cancer and persistent HR-HPV subclinical infection (p=0.430), persistent and clearance HR-HPV subclinical infection group (p=0.740). Conclusion: This study proves that normal cervix group has the highest level of retinol deposit sufficiency; however, it cannot be stated that cervical cancer group has less sufficiency level. Persistent HR-HPV subclinical infection group has the lowest level of retinol deposit (OR 11.33). There is no association between sufficient level of retinol deposit and clearance of HR-HPV. [Indones J Obstet Gynecol 2017; 5-1: 46-54] Keywords: cervical cancer, HR-HPV clearance, retinol deposit
Level of Retinol Deposit and Cervical Cancer Utami, Tofan W; Ibrahim, Fera; Purwoto, Gatot; Tiffani, Wely L; Aziz, Muhammad F; Andrijono, Andrijono
Indonesian Journal of Obstetrics and Gynecology Volume. 5, No. 1, January 2017
Publisher : Indonesian Socety of Obstetrics and Gynecology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (131.483 KB) | DOI: 10.32771/inajog.v5i1.465

Abstract

Objective: To analyze level of retinol deposit sufficiency in the natural history of cervical cancer. Methods: Serum retinol level was measured by ELISA from peripheral blood of subjects with normal cervix, cleared and persistent high risk human papilloma virus (HR-HPV) subclinical infection, and cervical cancer who fulfilled the inclusion and exclusion criteria. The study was held in Dr. Cipto Mangunkusumo and Fatmawati Hospital, Jakarta, within 2 years (August 2013- 2015). Blood was taken twice, consisting of post-8-hour fasting blood and 2 hours after 6000 IU retinyl palmitate oral administration. Results: Of 47 total samples, sufficient level of retinol deposit in normal cervix, cleared and persistent HR-HPV subclinical infection, and cervical cancer group was 85.0% (reference), 75.0% (OR 1.89), 33.3% (OR 11.33), and 75% (OR 1.89); respectively. Statistically, there was no significant difference from sufficiency level of retinol deposit between normal cervix and clearance HR-HPV subclinical infection (p=0.628), normal cervix and persistent HR-HPV subclinical infection (p=0.078), normal cervix and cervical cancer (p=0.433), cervical cancer and clearance HR-HPV subclinical infection (p=1.000), cervical cancer and persistent HR-HPV subclinical infection (p=0.430), persistent and clearance HR-HPV subclinical infection group (p=0.740). Conclusion: This study proves that normal cervix group has the highest level of retinol deposit sufficiency; however, it cannot be stated that cervical cancer group has less sufficiency level. Persistent HR-HPV subclinical infection group has the lowest level of retinol deposit (OR 11.33). There is no association between sufficient level of retinol deposit and clearance of HR-HPV. [Indones J Obstet Gynecol 2017; 5-1: 46-54] Keywords: cervical cancer, HR-HPV clearance, retinol deposit