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All Journal Jurnal Natur Indonesia Majalah Kedokteran Bandung ANNALES BOGORIENSES
Sukma Nuswantara
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Immunology & microbiology Medicine & Pharmacology

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POTENSI GEN ONCOPROTEIN HUMAN PAPILLOMAVIRUS TIPE 16 SEBAGAI KANDIDAT VAKSIN KANKER SERVIKS Taupiqurrohman, Opik; Yusuf, Muhammad; Nuswantara, Sukma; Subroto, Toto
Majalah Kedokteran Bandung Vol 48, No 2 (2016)
Publisher : Faculty of Medicine, Universitas Padjadjaran

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (24.911 KB) | DOI: 10.15395/mkb.v48n2.761

Abstract

Kanker serviks menduduki peringkat dua besar penyebab kematian pada wanita dengan jumlah penderita meningkat setiap tahunnya. Kanker ini banyak diakibatkan oleh infeksi human papillomavirus (HPV) dan tipe prevalensi terbesar di Indonesia adalah tipe HPV 16. Vaksin HPV telah dikembangkan dan diproduksi secara komersial, namun perlu dicari alternatif lain vaksin dengan basis gen penyandi E (early) protein. Gen E6 dan E7 merupakan onkogen penting pada proses terjadinya kanker serviks. Penelitian ini dilaksanakan di Laboratorium Kimia Komputasi dan Bioinformatika, Universitas Padjadjaran, dari bulan Desember 2015 sampai Februari 2016. Pada studi ini, penemuan kandidat vaksin peptida HPV dilakukan dengan pendekatan imunoinformatika. Analisis in silico HPV tipe 16 menunjukkan bahwa gen E7 merupakan sumber kandidat vaksin yang potensial karena tidak homolog dengan genom manusia dan diprediksi memiliki afinitas yang baik terhadap major histocompability complex (MHC). Hasil analisis in silico menunjukkan bahwa kandidat vaksin HPV dari gen E7 adalah peptida YMLDLQPET dan HVDIRTLEDLLMGTL. [MKB. 2016;48(2):84?91]Kata kunci: HPV tipe 16, imunoinformatika, in silico, kanker serviksHuman Papillomavirus Type 16 Oncoprotein Genes as the Candidate of Cervical Cancer VaccineCervical cancer is the second largest cause of death for Indonesian women, with increasing number of cases every year. This cancer is mostly caused by human papillomavirus (HPV) infection, in which HPV 16 is the most prevalent type in Indonesia. Although HPV vaccine has been developed and commercially available, the other alternative of vaccine based on E (early) gene is required. Genes of E6 and E7 are important oncogenes in the development of cervical cancer. This study was conducted at the Laboratory of Computational Chemistry and Bioinformatics, Universitas Padjadjaran, from December 2015 to February 2016. In this study, the candidates of HPV peptide vaccine were discovered using immunoinformatics method. In silico-analysis of HPV type 16, it  was shown gene E7 is not homologous with human genome and it is predicted to have a good affinity with major histocompability complex (MHC). Hence, it was proposed as a potential source of peptide vaccine. It is concluded that he candidates forHPV vaccine from E7 peptides are YMLDLQPET  and HVDIRTLEDLLMGTL. [MKB. 2016;48(2):84?91]Key words: Cervical cancer HPV 16, immunoinformatics, in silico
Efek Sumber Karbon Berbeda terhadap Produksi â-Glukan oleh Saccharomyces Cerevisiae pada Fermentor Air Lift Kusmiati, Kusmiati; Thontowi, Ahmad; Nuswantara, Sukma
Jurnal Natur Indonesia Vol 13, No 2 (2011)
Publisher : Lembaga Penelitian dan Pengabdian kepada Masyarakat Universitas Riau

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (94.458 KB) | DOI: 10.31258/jnat.13.2.138-145

Abstract

The need of â-glucan is increasing in food, medicine and cosmetic industry, because it becomes anticancer,antitumor and antiaging, increases immunosystem, and decreases cholesterol content in blood. The cell walls ofS. cerevisiae contain 80-90% polysaccharides that posses â-glucan. This research was aimed to obtain appropriatecarbon sources to increase the production of â-glucan. The carbon sources used were glucose, glucose commercial,sucrose and molases. The fermentation process was done by using air lift fermentor. The steps of fermentatonincluded regeneration of S. cerevisiae strain, preculture, fermentor preparation and running fermentor for 84hours. Sampling of S. cerevisiae culture was determined the cell growth by optical density (OD) usingspectrophotometer UV/VIS at ë 550 nm. The protein content was determined by Lowry method at ë 755 nm and thetotal glucose was measured by phenol sulphate method at ë 490 nm. The measurement result of cell growthshowed that the high intensity of S. cerevisiae in medium contain molases, but it did not show significant effectwhen compare to other carbon sources. The protein and carbohydrate contain in medium tended to decrease. Theresult of â-glucan on glucose, sucrose, glucose commercial and molases were 933,3, 1100, 1000, and966,7 mg/l. It can be concluded that sucrose and glucose commercial can replace the glucose to produce of â-glucan, because they are cheaper and easier to get. Beside that, molases can be used as an alternative carbonsource because it can produce of â-glucan as well as glucose.
Improvement of Endoglucanase Activity in Penicillium oxalicum ID10-T065 Mutated by Ultra Violet Irradiation and Ethidium Bromide Caniago, Asnany; Mangunwardoyo, Wibowo; Nuswantara, Sukma; Lisdiyanti, Puspita
ANNALES BOGORIENSES Vol 19, No 2 (2015): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (235.811 KB) | DOI: 10.14203/ab.v19i2.236

Abstract

Penicillium sp. is known as filamentous fungi that produce complete cellulase. Cellulase. This study aims to improve endoglucanase activity of Penicillium oxalicum ID010-T065 by mutated with ultra violet irradiation (with dose of 0.1 J/cm2, 15 cm), ethidium bromide (10 µg/mL, 1 hour) and combination of both mutagens. The endoglucanase activity of all mutants was higher than that of the wild type (1.03 U/mL). Mutant UVEB-42 exposed to combine mutation showed the highest endoglucanase activity (2.76 U/mL) with a 2.70 fold increase. Mutant EB-45 (1.83 U/mL) exposed to ethidium bromide solution showed a 1.8 fold increase. Mutant UV-13 (1.72 U/mL) exposed to UV irradiation for 3 minutes showed a 1.7 fold increase. All mutants have optimum endoglucanase activity at 50 °C. Mutant UVEB-53 showed the highest thermostability by retaining 86 % of endoglucanase activity at 90 °C. The gene analysis of the endoglucanase I gene showed 3 bases mutated at mutant UV-13 and UVEB-53 that changed proline to serine. Mutant EB-45 showed 4 bases mutated that changed valine to glysine and proline to serine. Two bases mutated at Mutant UVEB-53 changed proline to serine. Bases mutated in eg1 gene could influenced the enhance of enzym activity in mutant.
Enhancement of β-Glucosidase Activity in Penicillium sp. by Random Mutation with Ultraviolet and Ethyl Methyl Sulfonate Syafriana, Vilya; Nuswantara, Sukma; Mangunwardoyo, Wibowo; Lisdiyanti, Puspita
ANNALES BOGORIENSES Vol 18, No 2 (2014): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (450.422 KB) | DOI: 10.1234/98

Abstract

The genus Penicillium has a potential ability to produce β-glucosidase. The aim of the study was to improve the β-glucosidase activity of Penicillium sp. ID10-T065 with physical (Ultraviolet = UV), chemical (Ethyl Methyl Sulfonate = EMS), and combined mutation (UV-EMS). The spores of Penicillium sp. ID10-T065 were exposed into UV irradiation for 3 minutes with dose of 0.1 J/cm2 and 13 cm of distances. Chemical mutation was done by treated spores into 3% of EMS solution for an hour. Combined mutation of UV and EMS were also performed by UV for 3 minutes (0.1 J/cm2, 15 cm) and continued with soaking into 2-3% of EMS solution. The developed mutants were screened, selected and assayed. Comparison of enzyme activities with the wild- type (1.78 U/ml), mutant UV13 (5.53 U/ml) showed a 3.1 fold increase; mutant EM31 (4.26 U/ml) showed a 2.4 fold increase. Meanwhile, mutant UM23 obtained from the multiple exposures showed a decreased activity (1.75 U/ml). Mutant UV13 showed the best enzyme activity to be considered as a potential strain for β-glucosidase producer. This result needs to be further elaborated especially on its genetic stability studies in order for the ascertained as a stable mutant.
Conservation of Major L1 and Variability of Minor L2 Capsid Late Protein Genes in Human Papillomavirus of Indonesia Variants Nuswantara, Sukma; Prana, Titik K; Wulandari, Dwi; Widyowati, Henni; Anzela, Vera; Levy, Dea; Cahyadi, Petrus; Tjandra, Lukas D
ANNALES BOGORIENSES Vol 14, No 2 (2010): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (898.192 KB) | DOI: 10.1234/50

Abstract

Human Papilloma Virus  (HPV) has an out standing feature for its vast intraspecies variability. Of all known 100 types or  more, 15 t ypes of them are classified as high risk  because of their occurrence  in  more than 95% of cervical cancer cases. Among all genes in their genome, E6 and E7 genes are considered oncogenes and have close relevance with their pathogenicity, whilst L1 and L2 ge nes produce capsid proteins that directly interact with their  host  receptors.  Considering  the  importance  of  L1  and  L2  in  host-receptor  relationship,  we  tried  to investigate their molecular variability thereby uncover their specificity as Indonesian variant s. Here we reported about the conservation of L1 minor capsid protein and variability of L2 capsid protein among high-risk types Human Papilloma Virus (HPV). The results indicated that L1 DNA was relatively more conserved than its L2 counterpart Also it was indicated that the middle part of either L1 or L2 CDS‟ showed more DNA variability than those  at  their  upstream  sequences.  It  is  concluded  that  L2  middle  sequences  are  important  factors  for intraspecific variations found in HPV of Indonesian variants.   Keywords: Human Papilloma Virus (HPV), L1 gene, L2 gene, cervical cancer, high risk HPV
Co-Authors Ahmad Thontowi Anzela, Vera Cahyadi, Petrus Caniago, Asnany Dwi Wulandari Kusmiati Kusmiati Levy, Dea Muhammad Yusuf Prana, Titik K PUSPITA LISDIYANTI Taupiqurrohman, Opik Tjandra, Lukas D Toto Subroto WIBOWO MANGUNWARDOYO Widyowati, Henni