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All Journal HAYATI Journal of Biosciences Microbiology Indonesia Media Penelitian dan Pengembangan Kesehatan Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Jurnal Biotek Medisiana Indonesia Medical Journal of Indonesia Sari Pediatri Paediatrica Indonesiana Indonesian Journal of Obstetrics and Gynecology (Majalah Obstetri dan Ginekologi Indonesia) The Indonesian Journal of Infectious Diseases Eksakta : Berkala Ilmiah Bidang MIPA Journal of the Indonesian Medical Association : Majalah Kedokteran Indonesia Makara Journal of Science Journal of Clinical Microbiology and Infectious Diseases Jurnal Kefarmasian Indonesia
Fera Ibrahim
Departemen Mikrobiologi Fakultas Kedokteran Universitas Indonesia/KSM Mikrobiologi Klinik RSUPN Dr Cipto Mangunkusumo, Jakarta, Indonesia
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 Earth & Planetary Sciences Education Energy Engineering Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Mathematics Mechanical Engineering Medicine & Pharmacology Neuroscience Public Health

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The H5N1 influenza virus in Indonesia has caused more than 100 people died due to the virus infections.  Cases in humans were mostly due to the virus spread from the infected birds. This study characterized molecularly the H5N1 virus from birds around the H5N1 infection cases in humans in Indonesia. Result from this study revealed that in several cases, waterfowl species could become the source of H5N1 infections in human. We found that the one of six viruses used in this study probably was a fi NI LUH PUTU INDI DHARMAYANTI; FERA IBRAHIM; . DARMINTO; AMIN SOEBANDRIO
HAYATI Journal of Biosciences Vol. 18 No. 2 (2011): June 2011
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.18.2.82

Abstract

The H5N1 influenza virus in Indonesia has caused more than 100 people died due to the virus infections.  Cases in humans were mostly due to the virus spread from the infected birds. This study characterized molecularly the H5N1 virus from birds around the H5N1 infection cases in humans in Indonesia. Result from this study revealed that in several cases, waterfowl species could become the source of H5N1 infections in human. We found that the one of six viruses used in this study probably was a first antigenic shift virus in Indonesia. This study shows that the AI viruses isolated from birds around humans infected by H5N1 virus has specific characteristics namely the presence of several amino acid substitutions especially on the M1 and M2 proteins. The substitutions are similar in most of H5N1 human cases in Indonesia.
Development of a SYBR Green real-time PCR-based assay system for detection of Neisseria gonorrhoeae Andi Yasmon; Rela Febriani; Louisa Ivana Utami; Fithriyah Fithriyah; Yeva Rosana; Fera Ibrahim; Pratiwi Sudarmono
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 54, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19106/JMedSci005401202201

Abstract

Diagnosis of Neisseria gonorrhoeae infection is needed for patient therapy and for reducing this bacterial transmission in the population. The culture method is a gold standard method for N. gonorrhoeae detection, however it has low sensitivity. Among molecular methods with high sensitivity and specificity, SYBR Green real-time PCR is the potential method for N. gonorrhoeae detection. In this study, we developed an SYBR Green real-time PCR-based system assay for N. gonorrhoeae detection. Several PCR conditions were optimized and analyzed including primer annealing temperature, DNA template volume, the limit of detection (LoD), cross-reaction with others (bacteria, viruses, fungus, protozoa), and quality assurance. The results showed that the annealing temperature and DNA template volume were 60oC and 5 µL, respectively. The LoD was 29 DNA copies corresponding to 3 bacterial cells per reaction. No cross-reaction was detected for other bacteria, viruses, fungus and protozoa. The external quality assurances enrolled in 2019 and 2021 showed 100% concordance. The preliminary testing for clinical samples was also 100% concordance. In conclusion, the SYBR Green real-time PCR-based system assay developed in this study is promising for application in clinical laboratories.
Amantadine Resistant of Indonesian H5N1 Subtype Influenza Viruses During 2003-2008 NI LUH PUTU INDI DHARMAYANTI; FERA IBRAHIM; AMIN SOEBANDRIO
Microbiology Indonesia Vol. 4 No. 1 (2010): April 2010
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1101.851 KB) | DOI: 10.5454/mi.4.1.3

Abstract

The M2 protein of 146 avian influenza (AI) viruses data available in public database (NCBI), including 20 AI isolates used in this study, were sequenced at the M2 protein to find out the probability of mutation and the increase of resistance to amantadine after more than 5 years of their circulation in Indonesia. The results showed that during 2003-2008, around 62.58% (92/147) AI viruses in Indonesia have showed resistance to amantadine and 10 of them have dual mutations at V27A and S31N.
The Genetic Drift of Indonesian Avian Influenza A H5N1 Viruses During 2003-2008 NI LUH PUTU INDI DHARMAYANTI; GINA SAMAAN; FERA IBRAHIM; RISA INDRIANI; . DARMINTO; AMIN SOEBANDRIO
Microbiology Indonesia Vol. 5 No. 2 (2011): June 2011
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (6822.343 KB) | DOI: 10.5454/mi.5.2.4

Abstract

The avian influenza A H5N1 outbreaks started in 2003 and Indonesia introduced a vaccination campaign in 2004 to control the disease. In 2007, anecdotal reports about reduced vaccine effectiveness were received from commercial farmers. This paper describes the evolution of viruses in Indonesia up till 2008 and focus on viruses from vaccinating farms reporting vaccine failure were compared to viruses isolated from outbreak areas with no vaccination program. Result of the study revealed that viruses from vaccinated chickens had more extensive mutation at the HA molecule compared to chicken and other avian species without vaccination. Substitutions occurred at the HA gene level as well as at NA, M1 and NS1 genes. Viruses isolated and characterized form 2008 vaccinated flocks had substitutions that were unique and different with the old viruses. The recommendation arising from this study to the avian influenza disease control program in Indonesia is that continuous monitoring of genetic character of viruses and the vaccine seed strain should be updated periodically and matched with the virus circulated in the field.
Five Unique Amino Acid Residues of Hemagglutinin (HA) Proteins of Swine Influenza A (H1N1) Detected in 2009 in Jakarta, Indonesia ANDI YASMON; YULIANTY MUHAYAR; VIVI SETIAWATY; BETI ERNAWATI DEWI; BUDIMAN BELA; FERA IBRAHIM
Microbiology Indonesia Vol. 6 No. 2 (2012): June 2012
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (669.535 KB) | DOI: 10.5454/mi.6.2.3

Abstract

Nine HA genes of influenza A (H1N1) viruses originating from swine which were detected in 2009 in Jakarta, Indonesia, were characterized in this study. Nasopharyngeal and/or pharyngeal samples were extracted to obtain viral RNA genomes. Amplification of the HA segment was performed by using the reverse transcription-polymerase chain reaction (RT-PCR), and followed by nested PCR in cases of RT-PCR negative. DNA sequencing was performed by using eight overlapping primers. All the Jakarta strains were closely related to vaccine strain A/California/07/2009. Nine amino acid changes were found in the Jakarta strains, and 5 (P100S, S220T, G239D, R240Q, and I338V) of those were unique to all Jakarta strains with respect to strain A/California/07/2009 used to produce vaccine. An I338V substitution was detected in a cleavage site of HA and no amino acid changes were detected in potential sites for N-linked glycosylation. For seven sites (positions 131, 158, 160, 183, 187, 222, and 227) playing an important role in viral attachment to host receptor, none of the expected amino acid changes was detected; however, a S220T substitution close to amino acid 222 was found in all the Jakarta strains. All amino acid changes potentially affect the pathogenicity of the viruses and the efficacy of strain A/California/07/2009 in neutralizing the Jakarta strains.
Konstruksi Plasmid Pengekspresi Antigen Gag dan Protein Penghantar VP22 untuk Pengembangan Vaksin HIV-1 Melinda Remelia; Budiman Bela; Silvia Tri Widyaningtyas; Fera Ibrahim
Media Penelitian dan Pengembangan Kesehatan Vol 31 No 2 (2021)
Publisher : Sekretariat Badan Penelitian dan Pengembangan Kesehatan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22435/mpk.v31i2.3046

Abstract

The endogenous HIV-1 vaccine based on Gag protein is expected to stimulate the immune response of CD8+ T cells (cytotoxic). The Gag protein that has been produced by the E.coli prokaryote system is an exogenous antigen. The fusion of VP22 protein is expected to deliver Gag antigen into the cytoplasm of cell, observed by eGFP markers. Sequences of VP22 (114 pb), GagHIV-1 (1506 pb), and eGFP (733 pb) were inserted into the pQE80L, respectively. The recombinant protein was expressed in the E.coli system and purified by the Ni-NTA method. Antigen delivery fused with VP22 and eGFP was observed with fluorescence and confocal microscopy. The recombinant plasmid constructs of protein expression eGFP, VP22-eGFP, GagHIV-1-eGFP, VP22-GagHIV-1-eGFP were verified by DNA sequencing according to the reference. The recombinant plasmid constructs of Gag HIV-1-eGFP and VP22-GagHIV-1-eGFP still need to be optimized so they can be expressed in the E.coli system. The recombinant protein VP22-eGFP (27.02 kDa) was succesfully obtained and fluorescent green (entered) into the cytoplasm and nucleus of vero cells. In addition to the HIV-1 vaccine, this recombinant plasmids pQE80L-eGFP and pQE80L-VP22-eGFP also have the potential to be used as tools in the development of endogenous vaccines for another viruses/microbes. Abstrak Vaksin endogen HIV-1 berbasis protein Gag diharapkan dapat menstimulus respons imun sel T CD8+ (sitotoksik). Protein Gag yang telah diproduksi dengan sistem prokariota E.coli merupakan antigen yang bersifat eksogen. Fusi protein VP22 diharapkan mampumenghantarkan antigen Gag masuk ke sitoplasma sel, diamati dengan marker eGFP. Sekuens VP22 (114 pb), GagHIV1 (1506 pb), dan eGFP (733 pb) telah diinsersikan pada vektor pQE80L. Protein rekombinan diekspresikan pada sistem E.coli dan dipurifikasi dengan metode Ni-NTA. Penghantaran antigen yang difusikan dengan VP22 dan marker eGFP diamati dengan mikroskop fluoresens dan konfokal. Konstruksi plasmid rekombinan pengekspresi protein eGFP, VP22-eGFP, GagHIV1-eGFP, dan VP22-GagHIV1-eGFP telah diverifikasi dengan sekuensing DNA sesuai dengan sekuen referensi. Plasmid rekombinan pengekspresi GagHIV1-eGFP dan VP22-GagHIV1-eGFP masih perlu dioptimasi agar dapat diekspresikan di sistem E.coli. Protein rekombinan VP22-eGFP (27,02 kDa) telah berhasil diperoleh serta berpendar fluoresens hijau (masuk) ke sitoplasma dan nukleus sel vero. Selain vaksin HIV-1, plasmid rekombinan pQE80L-eGFP dan pQE80L-VP22-eGFP juga berpotensi dapat digunakan sebagai ‘tools’ dalam pengembangan vaksin endogen dari virus atau mikroba lainnya.
Perbedaan Sekuens Asam Amino Epitop Sel B dan Sel T pada Protein Hemaglutinin (H) Antara Virus Campak Liar dan Virus Vaksin di Indonesia Made Setiawan; Agus Sjahrurachman; Fera Ibrahim; Agus Suwandono
Sari Pediatri Vol 10, No 3 (2008)
Publisher : Badan Penerbit Ikatan Dokter Anak Indonesia (BP-IDAI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14238/sp10.3.2008.190-5

Abstract

Latar belakang. Protein H virus campak sangat penting agar virus dapat menginfeksi sel pejamu. Selain itu, protein H dapat merangsang antibodi spesifik yang dapat menetralisasi virus campak, sehingga virus tidak dapat menginfeksi sel. Bila ada perbedaan sekuens asam amino epitop sel B dan sel T pada protein H antara virus campak liar dan virus vaksin campak, maka vaksin tidak dapat merangsang terbentuknya antibodi protektif.Tujuan. Mengetahui perbedaan sekuens asam amino epitop sel B dan sel T pada protein H antara virus campak liar (G2, G3, dan D9) dan virus vaksin CAM-70, Schwarz dan Edmonston-wt.Metode. Ekstraksi dan amplifikasi gen dilakukan di laboratorium menggunakan teknologi biologi molekuler dan analisis gen dan protein dilakukan menggunakan teknologi bioinformatika.Hasil. Ditemukan perbedaan sekuens asam amino epitop sel T pada protein H antara virus campak liar dan virus Edmonstone-wt, sedangkan antara virus campak liar dan virus vaksin (CAM-70 dan vaksin Schwarz) tidak ditemukan perbedaan. Ditemukan perbedaan sekuens asam amino pada epitop sel B protein H antara virus campak liar dan virus vaksin (CAM-70 dan Schwarz, sedangkan antara CAM-70 dan Schwarz tidak ditemukan perbedaan.Kesimpulan. Tidak ada perbedaan sekuens asam amino epitop sel T antara virus campak liar dan virus vaksin (Schwarz dan CAM-70). Perbedaan ditemukan pada epitop sel B antara virus campak liar dan virus vaksin (CAM-70 dan Schwarz).
Difference of hemaglutinins between wild-type and vaccine measles virus in Indonesia Made Setiawan; Agus Sjahrurachman; Fera Ibrahim; Agus Suwandono
Paediatrica Indonesiana Vol 48 No 1 (2008): January 2008
Publisher : Indonesian Pediatric Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (465.242 KB) | DOI: 10.14238/pi48.1.2008.42-8

Abstract

Background Hemaglutinin (H) protein of measles virus is veryimportant in the process of host cell infection. H protein is alsoable to induce specific antibodies which can neutralize measlesvirus and block the cell infection.Objective This study aimed to explore the nucleotide and aminoacid sequence differences between wild-type measles virus (G2,G3 and D9) with CAM-70, Schwarz and Edmonston-wt vaccinevirus.Methods The exctration and amplification of the gene wereconducted in the laboratory using biomolecular technology. Thegene and protein analysis were conducted using the bioinformatictechnology.Results The results showed that the differences in nucleotidesequences were highest between wild-type virus and CAM-70vaccine virus (76-77 nucleotides), followed by Schwarz (61-64nucleotides) and Edmonston (60-63 nucleotides). The differencesin amino acid sequences were highest between wild-type virusand CAM-70 (24-29 residues), followed by Schwarz (13-20residues) and Edmonston (12-19 residues).Conclusion The Indonesian wild-type measles virus was geneticallycloser to Schwarz vaccine virus than CAM-70 vaccine virus,hence the neutralizing antibodies generated by Schwarz vaccinewere more specific against Indonesian wild-type virus comparedto CAM-70 vaccine.
Differences of nucleotide and amino acid sequences of nucleoprotein (N) gene between wild-type measles virus and vaccine virus in Indonesia Made Setiawan; Agus Sjahrurachman; Fera Ibrahim; Agus Suwandono
Paediatrica Indonesiana Vol 48 No 2 (2008): March 2008
Publisher : Indonesian Pediatric Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (447.334 KB) | DOI: 10.14238/pi48.2.2008.81-7

Abstract

Background Measles virus is a member of genus morbiliviruswhich belongs to family paramyxovirus with negative, single-strand RNA genome. RNA is packed by nucleocapsid (N) protein.The N protein is very important for RNA replication andtranslation. Abnormality in N protein will induce abnormality invirus replication.Objective This study aimed to explore the differences ofnucleotide sequence of N gene and amino acid sequences of Nprotein between wild-type measles virus (G2, G3 and D9) andvaccine virus (CAM-70, Schwarz and Edmonston-wt)Methods The exctraction and amplification of the gene wereconducted in the laboratory using biomolecular technology. Thegene and protein analysis were conducted using the bioinformatictechnology.Results The results showed that more differences were foundbetween nucleotide sequences of N gene of wild-type measlesvirus against CAM-70 vaccine virus (77 – 79 nucleotides)compared against Schwarz and Edmonston-wt vaccine virus (71-74 nucleotides). Likewise, more differences were also observedbetween amino acid sequences of N protein of wild-type measlesvirus against CAM-70 vaccine virus (18-24 residues) comparedagainst Schwarz and Edmonston-wt vaccine virus (17-23 residues).
Critical site differences of fusion protein between wildtype and vaccine measles virus strains in Indonesia Made Setiawan; Agus Sjahrurachman; Fera Ibrahim; Agus Suwandono
Paediatrica Indonesiana Vol 51 No 3 (2011): May 2011
Publisher : Indonesian Pediatric Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (248.395 KB) | DOI: 10.14238/pi51.3.2011.123-7

Abstract

Background Measles virus can cause high morbidity and mortality in infants and children. Fusion glycoprotein (F protein) found in the viral envelope is important for the host cell infection mechanism. F protein is immunogenic and may cause specific immune responses in the host. High variability is found in the F protein gene of vaccine viral strains compared to 'Wild type strains. This amino add sequence variability may result in a less specific immune response against other strains, possibly rendering thevaccine to be less effective.Objective To detennine the amino add sequence differences in critical sites of F protein in Mld type and vaccine measles virus strains in Indonesia.Methods We compared amino acid sequences of three genotypes of Mld type measles virus (02, 03 and D9) to those of the vaccine strains, CAM􀀸 70, Schwarz, and Edmonston􀀸wt type measles virus.Resul ts Analysis showed that there were differences at Fl􀀸F2 cleavage site, B cell epitopes, and H protein binding site between the CAM􀀸70 vaccine viral strains and Mld type strains. Schwarz vaccine strain differed from the wild type strains at the H protein binding site. A 03 wild type strain potential glycosylation site was also different from all other strains studied.Conclusion There were differences in the critical sites of F protein between Mld type strains and the CAM􀀸70 and Schwarz vaccine strains. 
Co-Authors . Andriansjah . DARMINTO . DARMINTO Ade P.R. Simaremare Agus Sjahrurachman Agus Sjahrurachman Agus Sjahrurachman Agus Sjahrurachman Agus Suwandono Agus Suwandono Agus Suwandono Agus Syahrurachman Akrom, Akrom Amin Soebandrio Andi Yasmon Andrijono Andrijono Andrijono Andrijono Anna, Shoffiana Noor Ardiana Kusumaningrum Ariyani Kiranasari Aroem Naroeni Aroem Naroeni Atna Permana Beti Ernawati Dewi Betty Ernawati Budiman Bela Cliff Clarence Haliman Conny R Tjampakasari Dimas Seto Prasetyo Elisna Syahruddin Endang R. Sedyaningsih Fithriyah Fithriyah Fithriyah Fithriyah Gatot Purwoto GINA SAMAAN Hartiyowidi Yuliawuri Herna Herna Herna, Herna Iin Maemunah Ketut Tuti Parwati Krisna N.A. Pangesti Lola Febriana Dewi Louisa Ivana Utami Made Setiawan Made Setiawan Made Setiawan Mardiastuti H Wahid Mardiastuti Mardiastuti Melinda Remelia Mirna Robert D.R. van Beest Holle Muhammad F Aziz Muhammad F Aziz Mursinah Mursinah Mursinah Mursinah Mursinah, Mursinah NI LUH PUTU INDI DHARMAYANTI NI LUH PUTU INDI DHARMAYANTI Ni Luh Putu Indi Dharmayanti Ni Made Adi Tarini Ni Nengah Dwi Fatmawati Pratiwi Pujilestari Sudarmono Rela Febriani RISA INDRIANI Samsuridjal Djauzi Silvia Tri Widyaningtyas Simon Yosonegoro Liem Subangkit Subangkit T Mirawati Sudiro Tiffani, Wely L Tjahjani M. Sudiro Tjahyani M. Sudiro Tofan W Utami Tofan W Utami VIVI SETIAWATY Vivi Setiawaty Wely L Tiffani Yeva Rosana Yulia Rosa Saharman YULIANTY MUHAYAR Yuliar Budi Hartanto Yuyun Soedarmono