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All Journal HAYATI Journal of Biosciences Microbiology Indonesia AGRIVITA, Journal of Agricultural Science Menara Perkebunan
SONY SUHANDONO
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Immunology & microbiology Medicine & Pharmacology

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Journal : Microbiology Indonesia

 1 
Sequence Analysis of Putative potB, potC, and potD Genes from Serratia rubidae SONY SUHANDONO; RASI FITRIA; ERNAWATI ARIFIN GIRI RACHMAN
Microbiology Indonesia Vol. 4 No. 2 (2010): August 2010
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (6698.416 KB) | DOI: 10.5454/mi.4.2.8

Abstract

Amplification of putative potBCD genes from Serratia rubidae was conducted by PCR using a pair of primers FERC and RERC. A fragment with ~1800 bp size was ligated to pGEM-T Easy vector then cloned to competent Escherichia coli DH5α. The recombinant plasmid was sequenced using SP6, T7 and two internal primers, FPC and RPC. A sequence similarity search and analysis was performed with the BLASTN program. The sequence was found to have 83% similarity to potABCD genes from E. coli. Those genes encoded a spermidine-preferential uptake system that consists of four kinds of protein: PotA is a membrane-associated ATPase, PotB and PotC are transmembrane proteins that form channels, and PotD is a periplasmic substrate-binding protein. Alignment analysis showed that the isolated clone consisted of potB (partial), potC (full length) and potD (partial). The sequences for potBCD genes from S. rubidae are not available in the NCBI database. Furthermore, we have submitted this sequence, potBCD from S. rubidae, on GeneBank with Acc. number FJ447342.
Cloning, Expression and Bioinformatic Analysis of Human Papillomavirus Type 52 L1 Capsid Gene from Indonesian Patient SONY SUHANDONO; DEWI AYU KENCANA UNGU; TATI KRISTIANTI; EDHYANA SAHIRATMADJA; HERMAN SUSANTO
Microbiology Indonesia Vol. 8 No. 3 (2014): September 2014
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (328.271 KB) | DOI: 10.5454/mi.8.3.2

Abstract

Human papillomavirus (HPV) type 52 is the most prevalent type for causing cervical cancer in Indonesian population. Cervical cancer becomes the most common cancer suffered by Indonesian women. Prevention of HPV infection can be achieved using HPV virus-like particle (VLP) vaccine derived from L1 major capsid protein.  This study aimed to clone and analyze HPV-52 L1 gene. DNA obtained from biopsy of a cervical cancer patient was amplified using specific primers designed from Asian originated HPV-52 L1 gene available in the GenBank. The isolated HPV-52 L1 gene sequence was submitted to GenBank with accession number [KF225497]. Expression of HPV-52 L1 gene was performed using pRSET/EmGFPEscherichia coli expression vector. We analyzed and compared the HPV-52 L1 gene expressions from recombinant E.coli BL21 (DE3) that had been induced for 3 hours with 1 mM IPTG and without induction. The protein was expressed in insoluble form. We performed the following bioinformatic analyses: construction of phlyogenetic tree, T-cell epitopes prediction and 3D proteins structure modelling. We utilized the following softwares: MEGA5 for phylogenetic tree, IEDBann for MHC prediction, CLC DNA Workbench 6.5 for hydrophobicity analysis and PDB-Viewer Deep for 3D protein structure analysis. The phylogenetic tree which was developed based on [KF225497] sequence showed that it shared a branch with Asian countries (Philippines and Thailand). The deduced amino acid sequences of the predicted epitopes that were consistent in all of the programs were 259GTLGDPVPGDLYIQGS274 and 345KKESTYKNE353. This information may be useful to design diagnostic strategies and vaccine suitable for Indonesian population.
Diversity of Culturable Bacterial in Various Parts of Luwak’s (Paradoxurus hermaprodithus javanica) Gastrointestinal Tract SONY SUHANDONO; HERI SETIADI; TATI KRISTIANTI; ALI BUDHI KUSUMA; ANDINI WARIH WEDARINGTYAS; DEMI TRISTAN DJAJADI; I NYOMAN PUGEG ARYANTHA
Microbiology Indonesia Vol. 10 No. 2 (2016): June 2016
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (622.379 KB) | DOI: 10.5454/mi.10.2.4

Abstract

Luwak coffee is a highly-priced coffee produced exclusively by the palm civet or luwak (Paradoxurus hermaphrodites ssp.). The purpose of this study was to determine the diversity of culturable bacteria in the gastro intestinal tract of luwak. The bacterial isolates were phenotypically characterized by their morphology and molecularly by analysis of their1,500bp 16s rDNA sequence. The results showed that Enterobacter cloacae and Lactobacillus brevis were found all over luwak’s digestive tract. Enterobacter cloacae was the most common species. The most diverse bacterial population was found in small intestine. Seven bacterial generawere successfully identified from the small intestine and colon, compared to only five genera found in the stomach.
Construction and Expression of Single Recombinant Peptide Surfactant for EOR Application CUT NANDA SARI; USMAN USMAN; RIESA KW ROHMAT; LENI HERLINA; KEN SAWITRI SULIANDRI; ONIE KRISTIAWAN; DWIYANTARI DWIYANTARI; TATI KRISTIANTI; SONY SUHANDONO
Microbiology Indonesia Vol. 11 No. 1 (2017): March 2017
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1420.163 KB) | DOI: 10.5454/mi.11.1.5

Abstract

Surfactant is generally synthetic chemical, which is effective and reliable. However, the chemicals usually did not degraded easily in the environment and could cause damage to the environment. The other possible alternative to produce surfactant is using genetic engineering in order to produce peptide based surfactant. In this research, peptide surfactant was produced using a gene construct which was created using overlapped polymerase chain reaction method (OE-PCR). PAGE analysis shows that single surfactant peptide construction can be expressed by induction of IPTG 1 mM and after at least twice sonication. This research proves that both two constructions have been successfully expressed by producing peptide in expected size (approximately 15 kDa).
Co-Authors . FANIAR . SUSTIPRIJATNO Adi Pancoro ANDINI WARIH WEDARINGTYAS CUT NANDA SARI DEMI TRISTAN DJAJADI DEWI AYU KENCANA UNGU Dian M AMANAH DWIYANTARI DWIYANTARI EDHYANA SAHIRATMADJA ERNAWATI ARIFIN GIRI RACHMAN FENNY MARTHA DWIVANY Hayati MINARSIH HERI SETIADI Herman Susanto I Nyoman Pugeg Aryantha KEN SAWITRI SULIANDRI KUSUMA, ALI BUDHI LENI HERLINA LISTYA UTAMI KARMAWAN ONIE KRISTIAWAN Panca Jarot Santoso RASI FITRIA Refiana Lestary Riesa Khairunnisa W.R. RIESA KW ROHMAT syafrizal Tati KRISTANTI TATI KRISTIANTI Usman Usman Usman