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Sekuens Gen Protein Kapsid Mayor L1 Human Papilomavirus 16 dari Isolat Klinik Asal Bandung Pradita, Anandayu; Sahiratmadja, Edhyana; Suhandono, Sony; Susanto, Herman
Majalah Kedokteran Bandung Vol 46, No 3 (2014)
Publisher : Faculty of Medicine, Universitas Padjadjaran

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (976.647 KB)

Abstract

Kanker serviks disebabkan oleh infeksi kronik human papillomavirus (HPV) dengan genotipe HPV-16 sebagai HPV tersering yang menginfeksi epitel serviks. Protein penyelubung virus yang disebut kapsid mayor (L1) mempunyai peranan penting dalam menginfeksi epitel serviks. Tujuan penelitian untuk mengisolasi dan menganalisis sekuens gen L1 HPV-16. Pengetahuan mengenai sekuens gen L1 dapat memberikan informasi yang berguna, salah satunya yaitu untuk pengembangan vaksin. Pada studi ini, deoxyribonucleic acid (DNA) virus diekstraksi dari sediaan biopsi pasien kanker serviks yang diambil pada bulan Juni sampai Oktober 2010 di Kebidanan dan Kandungan RS Dr. Hasan Sadikin Bandung. Gen diamplifikasi dengan polymerase chain reaction menggunakan primer spesifik. Infeksi HPV-16 pada jaringan kanker dikonfirmasi dengan menggunakan kit komersial untuk tes genotipe HPV. Fragmen L1 kemudian diklon dan diinsersikan ke dalam pJET1.2/L1-16, kemudian dipotong dengan enzim BamHI dan BgIII untuk kemudian divalidasi dan disekuensing. Hasil sekuensing menunjukkan amplikon gen L1 HPV-16 sebesar 1.595 pasang basa. Analisis dari dua amplikon gen L1 HPV-16 menggunakan software BIOEDIT dan Basic Local Alignment Search Tool menunjukkan kesamaan ho mologi 99% dan 97% dengan sekuens L1 HPV-16 asal Thailand yang terregistrasi pada GenBank. Simpulan, telah dilakukan kloning sekuens gen L1 HPV-16 dari dua isolat klinik Bandung. Hasil kloning HPV-16 pada penelitian ini memberikan informasi tentang variasi sekuens yang perlu dipertimbangkan bagi pengembangan vaksin terutama bagi daerah spesifik seperti penduduk asal Indonesia.Kata kunci: Human papillomavirus, kanker serviks, gen L1 HPV-16 Sequence of Human Papilomavirus 16 Major Capsid L1 Gene from Clinical Isolates in BandungCervical cancer is strongly associated with chronic human papillomavirus (HPV) infection. HPV-16 is the most prevalent genotype infecting cervical epithelium. The major coat protein of viral particle (L1) plays a key role in the infection process. Our study aimed to isolate the HPV-16 L1 gene and analyze its sequence. Samples used were samples collected from the Department of Obstetrics and Gynaecology, Dr. Hasan Sadikin General Hospital, Bandung during the period of June to October 2010. In this study, the HPV-16 L1 sequence was analyzed from the viral deoxyribonucleic acid (DNA) extracted from biopsy sample of cervical cancer patient biopsy samples.The HPV-16 L1 amplification was performed using the polymerase chain reaction with specific primer. The HPV infection in the cervical tissue was confirmed by commercial HPV genotyping test. The L1 fragment was cloned into plasmid and the insert of the recombinant clone pJET1.2/L1-16 was digested using BamHI and BgIII. The amplicon result showed HPV-16 L1 gene with a length of 1.595 base pairs. The sequence analysis of two samples using software BIOEDIT dan Basic Local Alignment Search Tool revealed a high level of sequence similarity to L1 HPV-16 from Thailand (99% and 97%) as registered in GenBank. In conclusion, the L1 HPV-16 gene from Bandung isolates revealed variations from published sequence. Knowledge on L1 gene sequence may give additional information to the development of vaccine. Further study on vaccine development is currently ongoing using this HPV-16 clone that may be specific to Indonesian population. Key words: Cervical cancer, human papillomavirus, L1 HPV-16 DOI: 10.15395/mkb.v46n3.317
TRANSFORMASI MENGGUNAKAN Agrobacterium tumefaciens PADA TUNAS DAUN Kalanchoe mortagei DAN Kalanchoe daigremontiana 1 DAN 2 Suhandono, Sony; Dewanto, Hamami Alfasani
Chimica et Natura Acta Vol 4, No 2 (2016)
Publisher : Departemen Kimia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (355.284 KB) | DOI: 10.24198/cna.v4.n2.10679

Abstract

Cocor bebek adalah tumbuhan sukulen yang mampu memproduksi tunas adventif (reproduksi vegetatif) pada tepian daunnya. Kemampuan reproduksi vegetatif ini menghasilkan tanaman yang sama dalam waktu yang singkat, sehingga memungkinkan untuk dijadikan sebagai bioreaktor protein rekombinan. Transformasi dilakukan menggunakan Agrobacterium tumefaciens pada tunas daun cocor bebek dari spesies Kalanchoe mortagei dan Kalanchoe daigremontiana. Optimasi dilakukan mencakup: galur A. tumefaciens, kerapatan optis dari kultur A. Tumefaciens, konsentrasi acetosyringone, teknik ko-kultivasi, pH medium dan komposisi medium ko-kultivasi. Hasil optimasi transformasi secara transien menunjukan bahwa perbedaan galur A. tumefaciens, kerapatan optis, konsentrasi acetosyringone menghasilkan ekspresi transien yang relatif sama secara kualitatif. Berdasarkan uji GUS teknik ko-kultivasi dengan infiltrasi vakum dan pH medium 5,5 menghasilkan ekspresi transien lebih baik dibandingkan dengan perendaman dan pH medium 7,0. Medium ko-kultivasi M9 menghasilkan ekspresi transien yang lebih baik dibandingkan dengan medium ½MS0. Tunas daun K. daigremontiana 2 menunjukan ekspresi transien yang lebih baik dibandingkan K. mortagei dan K. daigremontiana 1.
Construction of Binary Vector With Wound Inducible Promoter for Hbsag Expression: Development of Plant-Based Edible Hepatitis B Vaccine from Indonesian Isolate Supraba, Apsari; Utari, Putri Dwi; Zainuddin, Ima M.; Rachman, Ernawati A.Giri; Suhandono, Sony; Estiati, Amy
ANNALES BOGORIENSES Vol 11, No 1 (2007): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.1234/22

Abstract

Hepatitis B is a serious infectious disease In the third world countries including Indonesia . Vaccination is  the most effective way to prevent the spread of the disease;  therefore the demand for HBV vaccine is high.  In order to produce more vaccine at lower cost, transgenic plant can be chosen to express the vaccine with the above criteria. Several researches were successfully producing transgenic plants expressing HBsAg that formed virus-like particles and  induced  immune response  in  human.  However. HBsAg expression  in  transgenic plant needs to be  improved especially on gene  expression control system. Here, we describe the construction of HBsAg .  structural gene under the control of wound  inducible promoter, MeEFl promoter from  manihot esculenta Crantz. The HBsAg gene was amplified using PCR from HBV genome isolated from an  Indonesian patient. The gene was subsequently fused with VSPaS signal peptide, which targeted the reticulum endoplasm of plant cell . The construct was cloned into binary expression vector for Agrobacterium plant Transformation  in  near future.Keywords: HBsAg. VSPaS signal peptide and MeEFI promoter
THE CONCEPTUAL CHANGE ASSESSMENT BASED ON ESSAY QUESTIONS IN CASE STUDY OF DNA/RNA AND INTRON TOPICS Suhandono, Sony; Widodo, Ari; Kristianti, Tati
Jurnal Penelitian Pendidikan IPA Vol 4, No 1 (2019): Juni 2019
Publisher : Perkumpulan Pendidik IPA Indonesia (PPII)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jppipa.v4n1.p31-37

Abstract

Most of the study on conceptual change was analysed using multiple-choice, true/false and true/false-reason type of questions. However, these questions are unable to reveal the variation in understanding of the university students. In this study, we developed a new conceptual change assessment based on essay questions. Here, student responses on DNA and intron term are presented as case studies in order to show the application of this assessment. The assessment is able to classify the various degree of understanding in university students such as construction, revision, complementation, static and disorientation. Our findings in university students studying DNA term showed that of 70 university students, 34% (construction), 36% (revision), 21% (complementation), 4% (static) and 5% (disorientation). On intron term finds construction (4%), revision (14%), static (44%) and disorientation (38%). Overall analysis using various categories of understanding reveals that DNA term is easier to understand by the university students than the intron term. This assessment is useful to evaluate the conceptual change level of university students in the class. Therefore, the assessment might also be useful to evaluate various teaching strategies and other topics.Keywords: conceptual change, essay, assessment, DNA, Intron
KONSTRUKSI DAN EKSPRESI REKOMBINAN TUNGGAL PEPTIDA SURFAKTAN (SINGLE SUPEL CONSTRUCTION) UNTUK APLIKASI EOR (Construction and Expression of Single Recombinant Peptide Surfactant for Eor Application) Sari, Cut Nanda; Pasarai, Usman; Rohmat, Riesa K. W; Herlina, Leni; Suliandari, Ken Sawitri; Kristiawan, Onie; Dwiyantari, Dwiyantari; Kristianti, Tati; Suhandono, Sony
Lembaran Publikasi Minyak dan Gas Bumi Vol 50, No 3 (2016)
Publisher : Lembaran Publikasi Minyak dan Gas Bumi

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Surfaktan yang digunakan pada aplikasi peningkatan perolehan minyak tahap lanjut pada umumnya merupakan hasil sintesis kimia. Hasil sintesis ini bersifat cepat dan efektif namun secara kuantitas sangat kecil, sehingga bila dibutuhkan dalam jumlah banyak akan membutuhkan banyak biaya untuk memproduksinya. Alternatif lain yang bisa digunakan untuk menghasilkan surfaktan adalah dengan rekayasa genetika melalui produksi rekombinan dalam mikroorganisme seperti bakteri untuk menghasilkan surfaktan berbasis peptida. Teknologi ini relatif murah dan simpel untuk dilakukan yaitu dengan manipulasi ekspresi sel inang agar menghasilkan peptida surfaktan yang dikonstruk kedalam vektor ekspresi berbasis bakteri. Pada penelitian ini dilakukan konstruksi peptida surfaktan dengan menggunakan metode overlaped reaksi berantai polimerase untuk menghasilkan surfaktan peptida sebagai peptida tunggal. Hasil analisis SDS PAGE (Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis) menunjukkan konstruksi peptida surfaktan tunggal dapat diekspresikan dengan cara diinduksi IPTG 1 mM dan dilakukan pemecahan sel untuk mendapatkan protein yang diproduksi diperiplasma. Penelitian ini membuktikan bahwa kedua konstruk berhasil diekspresikan dengan menghasilkan peptida pada ukuran yang sesuai.  Surfactant that is used in enhanced oil recovery applications is generally synthetic chemical result. This synthetic result is quick and effective but very small in quantity, so if the demand in great amount, the more expensive cost needed. The other possible alternative to produce surfactant is by genetic engineering through recombinant production in micro organism such as bacteria to produce peptide based surfactant. This technology is relatively cheap and simple to be implemented, that is by manipulating bacterial based main cell expression. In this research, construction of peptide surfactant using overlapped polymerase chain reaction method to generate surfactant peptide as single peptide. Analysis result of SDS poly acrilamid gel electrophoresis shows that single surfactant peptide construction can be expressed by induction of IPTG 1 mM and also cell cracking to obtain protein which is produced by diperiplasma. This research proves that both two constructions have been successfully expressed by producing peptide in suitable size.
CONSTRUCTION AND EXPRESSION
OF QUARTET RECOMBINANT PEPTIDE SURFACTANT FOR EOR APPLICATION Sari, Cut Nanda; Usman, Usman; Lestary, Refiana; Khairunnisa W.R., Riesa; Herlina, Leni; Syafrizal, Syafrizal; Kristianti, Tati; Suhandono, Sony
Scientific Contributions Oil and Gas Vol 39, No 3 (2016)
Publisher : Scientific Contributions Oil and Gas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29017/SCOG.50.3.98

Abstract

The main drawback of the SUPEL peptide surfactant product which has been developed for EOR application is it isunstable at a high temperature. This research is aimed at generating the prototype of peptide surfactant construction in recombinant by stringing up 4 SUPEL linier sequences. Quartet recombinant technology can produce the peptide surfactant characterized as reversible biosurfactant, which is active at high temperature but inactive at low temperature. Multiple SUPEL Construction (MSC) that was developed in this research is using synthetic DNA and producing SUPEL in 4 sequences that can flip at normal temperature and can open when heated. SDS PAGE analysis results show that MSC construction can be expressed by inducting IPTG and cell harvested at 90°C. This research proves that construction and expression of the SUPEL quartet has been achieved by producing the peptide at an ideal size.
Analysis of Microsatellite Allele That potential as Resistance Marker of Giant Gouramy (Osphronemus gouramy Lac.) to Aeromonas hydrophila Kusumawardhani, Meirina Kartika; Kusumawaty, Diah; Suhandono, Sony
Aquacultura Indonesiana Vol 15, No 1 (2014): Volume 15 Issue 1 Year 2014
Publisher : Indonesian Aquaculture Society (MAI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (157.124 KB) | DOI: 10.21534/ai.v15i1.30

Abstract

Giant gouramy is one of economical important freshwater fish. However, the production of the fish was declined because of a Motile Aeromonas Septicemia (MAS) disease. Giant gouramy with MAS disease caused an ulcer on their skin, and the worst case infection may cause death. The symptoms is vary widely depends on fish resistance to the disease. The aim of this study is to analyze microsatellite alleles that potential as a resistance marker against Aeromonas hydrophila. In previous studies, eleven microsatellite loci were isolated from giant gouramy genome. These loci were tested on DNA from resistant and susceptible giant gouramy that had been treated with Aeromonas hydrophila. Resistant giant gouramy was the gouramy that survived at least 50 days post-infection and ssusceptible giant gouramy was the gouramy that died before 50 days post- infection. Three of eleven microsatellite loci were found with unique alleles that appeared only in resistant giant gouramy and potential as resistance marker, which is the 342 bp allele at GE 1.9 locus with (GCA)10 (ACA) 6 motif, the 262 bp allele at GE 2.4 locus with (GCA) 6 (GGA)10 motif, and the 244 bp allele at GE 1.4 locus with (GCT) 9 (TA) 6 motif. All three loci were used to scan 48 giant gouramy broodstock from Tasikmalaya, Singaparna, and Sukabumi. Amplification of the microsatellite loci was performed by PCR with M13 tail sequence in forward primer and fluorescence dye. Successfully amplified alleles were analyzed with GeneAlEx 6.5 software. As a result, fragment 262 bp and 244 bp that contained in 43.75% of 48 gouramy broodstock predicted have a potency as resistance marker to Aeromonas hydrophila. For further study, microsatellite motifs have to be screened in gouramy progeny, because microsatellites are inhereted in Mendelian traits.
Segmentasi Citra Digital Objek Hasil Pengamatan In Situ Localization Gen gfp pada Tanaman Transforman Atqiya, Firas; Ihsani, Nisa; Sholahuddin, Muhammad Rizqi; Dwivany, Fenny Martha; Suhandono, Sony
Jurnal Pendidikan Multimedia (Edsence) Volume 1 No 2 (Desember 2019)
Publisher : Universitas Pendidikan Indonesia (UPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17509/edsence.v1i2.21575

Abstract

Penelitian berbasis biomolekuler membutuhkan beragam penggunaan perangkat lunak pengolah data. Salah satunya yaitu kebutuhan perangkat lunak yang mampu mengolah data citra digital pada proses segmentasi warna. Dalam penelitian biomolekuler, segmentasi warna dapat digunakan untuk menganalisis pendaran warna hijau sebagai hasil ekspresi gen gfp. Gen pelapor ini banyak digunakan dalam proses rekayasa genetik tumbuhan maupun hewan yaitu: memonitor ekspresi gen, in situ localization, biosensor, physiological indicators, dan studi interaksi protein. Sinar UV pada panjang gelombang eksitasi 450-490 nm dapat diserap dan diemisikan oleh molekul protein GFP sebagai warna hijau. Adanya pendaran hijau tersebut diharapkan hanya muncul sebagai penanda terekspresinya gen gfp. Namun demikian, pada sampel tumbuhan terkandung senyawa metabolit sekunder yang dapat menyerap dan mengemisikan sinar UV sebagai warna hijau. Adanya warna hijau selain hasil ekspresi gen gfp ini tentunya dapat menyebabkan hasil analisis in situ localization menjadi bias. Oleh karena itu, diperlukan teknik pengolahan citra digital yang mampu memilah warna hijau hasil ekspresi gen gfp dan warna hijau dari emisi senyawa metabolit tumbuhan. Tujuan  penelitian  ini  adalah untuk memisahkan objek hasil ekspresi gen gfp pada citra digital jagung transforman dengan warna hijau yang diemisikan oleh senyawa metabolit sekunder jagung menggunakan pengolahan citra digital. Proses yang digunakan adalah color filtering, thresholding, dan Canny edge detection. Hasil penelitian yang diperoleh berupa citra yang mengandung citra objek hasil ekspresi gen gfp yang telah tersegmentasi pada sayatan melintang akar jagung transforman.
THE CONCEPTUAL CHANGE ASSESSMENT BASED ON ESSAY QUESTIONS IN CASE STUDY OF DNA/RNA AND INTRON TOPICS Kristianti, Tati; Widodo, Ari; Suhandono, Sony
Jurnal Penelitian Pendidikan IPA Vol 4, No 1 (2019): Juni 2019
Publisher : Perkumpulan Pendidik IPA Indonesia (PPII)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jppipa.v4n1.p31-37

Abstract

Most of the study on conceptual change was analysed using multiple-choice, true/false and true/false-reason type of questions. However, these questions are unable to reveal the variation in understanding of the university students. In this study, we developed a new conceptual change assessment based on essay questions. Here, student responses on DNA and intron term are presented as case studies in order to show the application of this assessment. The assessment is able to classify the various degree of understanding in university students such as construction, revision, complementation, static and disorientation. Our findings in university students studying DNA term showed that of 70 university students, 34% (construction), 36% (revision), 21% (complementation), 4% (static) and 5% (disorientation). On intron term finds construction (4%), revision (14%), static (44%) and disorientation (38%). Overall analysis using various categories of understanding reveals that DNA term is easier to understand by the university students than the intron term. This assessment is useful to evaluate the conceptual change level of university students in the class. Therefore, the assessment might also be useful to evaluate various teaching strategies and other topics.Keywords: conceptual change, essay, assessment, DNA, Intron
KONSTRUKSI DAN EKSPRESI REKOMBINAN TUNGGAL PEPTIDA SURFAKTAN (SINGLE SUPEL CONSTRUCTION) UNTUK APLIKASI EOR (Construction and Expression of Single Recombinant Peptide Surfactant for Eor Application) Sari, Cut Nanda; Pasarai, Usman; Rohmat, Riesa K. W; Herlina, Leni; Suliandari, Ken Sawitri; Kristiawan, Onie; Dwiyantari, Dwiyantari; Kristianti, Tati; Suhandono, Sony
Lembaran publikasi minyak dan gas bumi Vol 50, No 3 (2016)
Publisher : PPPTMGB "LEMIGAS"

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1105.582 KB) | DOI: 10.29017/LPMGB.50.3.3

Abstract

Surfaktan yang digunakan pada aplikasi peningkatan perolehan minyak tahap lanjut pada umumnya merupakan hasil sintesis kimia. Hasil sintesis ini bersifat cepat dan efektif namun secara kuantitas sangat kecil, sehingga bila dibutuhkan dalam jumlah banyak akan membutuhkan banyak biaya untuk memproduksinya. Alternatif lain yang bisa digunakan untuk menghasilkan surfaktan adalah dengan rekayasa genetika melalui produksi rekombinan dalam mikroorganisme seperti bakteri untuk menghasilkan surfaktan berbasis peptida. Teknologi ini relatif murah dan simpel untuk dilakukan yaitu dengan manipulasi ekspresi sel inang agar menghasilkan peptida surfaktan yang dikonstruk kedalam vektor ekspresi berbasis bakteri. Pada penelitian ini dilakukan konstruksi peptida surfaktan dengan menggunakan metode overlaped reaksi berantai polimerase untuk menghasilkan surfaktan peptida sebagai peptida tunggal. Hasil analisis SDS PAGE (Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis) menunjukkan konstruksi peptida surfaktan tunggal dapat diekspresikan dengan cara diinduksi IPTG 1 mM dan dilakukan pemecahan sel untuk mendapatkan protein yang diproduksi diperiplasma. Penelitian ini membuktikan bahwa kedua konstruk berhasil diekspresikan dengan menghasilkan peptida pada ukuran yang sesuai. Surfactant that is used in enhanced oil recovery applications is generally synthetic chemical result. This synthetic result is quick and effective but very small in quantity, so if the demand in great amount, the more expensive cost needed. The other possible alternative to produce surfactant is by genetic engineering through recombinant production in micro organism such as bacteria to produce peptide based surfactant. This technology is relatively cheap and simple to be implemented, that is by manipulating bacterial based main cell expression. In this research, construction of peptide surfactant using overlapped polymerase chain reaction method to generate surfactant peptide as single peptide. Analysis result of SDS poly acrilamid gel electrophoresis shows that single surfactant peptide construction can be expressed by induction of IPTG 1 mM and also cell cracking to obtain protein which is produced by diperiplasma. This research proves that both two constructions have been successfully expressed by producing peptide in suitable size.