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Isolation of MA-ACS Gene Family and Expression Study of MA-ACS1 Gene in Musa acuminata Cultivar Pisang Ambon Lumut LISTYA UTAMI KARMAWAN; SONY SUHANDONO; FENNY MARTHA DWIVANY
HAYATI Journal of Biosciences Vol. 16 No. 1 (2009): March 2009
Publisher : Bogor Agricultural University, Indonesia

Musa acuminata cultivar pisang ambon lumut is a native climacteric fruit from Indonesia. Climacteric fruit ripening process is triggered by the gaseous plant hormone ethylene. The rate limiting enzyme involved in ethylene biosynthesis is ACC synthase (ACS) which is encoded by ACS gene family. The objective of this study is to identify MA-ACS gene family in M. acuminata cultivar pisang ambon lumut and to study the MA-ACS1 gene expression. The result showed that there were nine M. acuminata ACS gene family members called MA-ACS1–9. Two of them (MA-ACS1 and MA-ACS2) were assessed using reverse transcriptase PCR (RT-PCR) for gene expression study and it was only MA-ACS1 correlated with fruit ripening. The MA-ACS1 gene fragment has been successfully isolated and characterized and it has three introns, four exons, and one stop codon. It also shows highest homology with MACS1 gene from M. acuminata cultivar Hsian Jien Chiao (GenBank accession number AF056164). Expression analysis of MA-ACS1 using quantitative PCR (qPCR) showed that MA-ACS1 gene expression increased significantly in the third day, reached maximum at the fifth day, and then decreased in the seventh day after harvesting. The qPCR expression analysis result correlated with the result of physical analysis during fruit ripening. Key words: pisang ambon lumut, MA-ACS gene family, gene characterization, gene expression, quantitative PCR (qPCR)

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

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.

Development of Simple-Sequence Repeats Markers from Durian (Durio zibethinus Murr. cultv. Matahari) Genomic Library Panca Jarot Santoso; Adi Pancoro; Sony Suhandono; I Nyoman Pugeg Aryantha
AGRIVITA, Journal of Agricultural Science Vol 39, No 3 (2017): OCTOBER
Publisher : Faculty of Agriculture University of Brawijaya in collaboration with PERAGI

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17503/agrivita.v39i3.1171

Simple sequence repeats have been proved as powerful markers and widely used in molecular breeding to reduce cycles and cost efective. The availability of the marker is, however, very limited in durian. This research aimed to develop SSR markers from durian genomic library. Genomic DNA was isolated from durian shoot leaf, whilst SSR motifs were isolated using membrane-based oligonucleotide enrichment hybridization protocol. Annotation made on the library found 527 unique motifs from 354 durian libraries which form 425 loci. The SSR motifs obtained were generally short repeats which reached 89.6 %, whilst longer repeats were found consisted of compound motifs. Eleven loci were selected as representative for further test to prove their informativity. A number of unique allels were successfully amplified from 17 durian genomes. The analysis showed the polymorphic information content (PIC) values ranged from 0.000 to 0.662 with an average of 0.390. The SSR loci also showed their ability to be used for durian diversity analysis as the evident that the loci could be used as genetic markers for assisting further durian breeding program.

Isolasi dan karakterisasi gen dehydrin dari tebu (Saccharum officinarumL.) yang terlibat dalam respon toleransi cekaman kekeringan (Isolation and characterization of dehydrin gene from sugarcane (Saccharum officinarum L.) involved in drought tolerance response) Hayati MINARSIH; . FANIAR; Tati KRISTANTI; Dian M AMANAH; . SUSTIPRIJATNO; Sony SUHANDONO
E-Journal Menara Perkebunan Vol 86, No 2 (2018): Oktober 2018
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

Nowadays,the development of molecular biology techniques has enabled to engineer drought tolerant sugarcane to accelerate thebreeding program. Dehydrin(DHN)that belong to the group II late embryogenesis abundant (LEA) family is known to havean important role in plant response and adaptation to abiotic stresses (drought, high salinity, cold, heat, etc.). Literature study and bioinformatics analysis reported that DHN1gene on sugarcane showed high homology sequences with sorghum DHN. The expression of DHN1gene on sugarcane var. PSJT 941 treated with various periodof drought stress had been conducted using semi-quantitative reverse transcriptase (RT)-PCR method. The results showed that the expressionlevel of DHN1 geneincreased along withthe increased period of the treatment. The highest expression level of DHN1 gene was resulted from plants that had been subjected to drought for 25 days. Amplification of DHN1gene from plants withthe highest gene expression, resulted an amplicon with a size of 465 bp which representsa full length coding sequence (CDS) of DHN1. Identification using Blast analysis showed that DHN1sequences from sugarcane var. PSJT 941 shared high homology with DHN gene on sugarcane and sorghum. The alignment results also revealed a conserved motif that characterized DHN genes.[Key words: drought stress, dehydrin, DHN1gene, sugarcane]Abstrak Dengan berkembangnya teknik biologi molekuler saat ini, maka perakitan tanaman tebu yang toleran kekeringan lebih diarahkan melalui teknik rekayasa genetika untuk mempercepat program pemuliaan tanaman. Protein dehydrin (DHN) yang termasuk ke dalam kelompok II famili LEA (Late Embryogenesis Abundant)diketahui berperan penting dalam respon dan adaptasi tanaman terhadap cekaman abiotik (kekeringan, salinitas tinggi, suhu dingin, panas, dll). Studi literatur dan analisis bioinformatika menunjukkan bahwa gen DHN1pada tanaman tebu memiliki homologi yang tinggi dengan gen DHNpada sorghum. Analisis ekspresi gen DHN1pada tanaman tebu varietasPSJT 941yang diberi cekaman kekeringan telah dilakukan menggunakan semi-kuantitatifreverse transcriptase (RT)-PCR dan terlihat bahwa ekspresi gen DHN1meningkat secara nyata sejalan dengan semakin lamanya waktu pemberian cekaman. Tingkat ekspresi gen DHN1paling tinggi diperoleh dari tanaman yang mengalami cekaman kekeringan selama 25 hari. Amplifikasi gen DHN1pada tanaman dengan tingkat ekspresi yang paling tinggi menunjukkan pita dengan ukuran 465 bp yang merepresentasikan full coding sequence(CDS) gen DHN1. Identifikasi menggunakan analisis Blast menunjukkan bahwa sekuen gen DHN1dari tanaman tebu varietas PSJT 941yang diperoleh memiliki homologi yang tinggi dengan gen DHNpada tanaman tebu dan sorghum. Hasil penjajaran sekuen protein juga menunjukkan adanya motif lestari yang mencirikan gen DHN. [Kata kunci: cekaman kekeringan, dehydrin, gen DHN1, tebu]

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

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. Â 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 Luwakâ€™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

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 luwakâ€™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

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).

CONSTRUCTION AND EXPRESSION?OF QUARTET RECOMBINANT PEPTIDE SURFACTANT FOR EOR APPLICATION Cut Nanda Sari; Usman; Refiana Lestary; Riesa Khairunnisa W.R.; Leni Herlina; Syafrizal; Tati Kristianti; Sony Suhandono
Scientific Contributions Oil and Gas Vol. 39 No. 3 (2016): SCOG
Publisher : Testing Center for Oil and Gas LEMIGAS

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29017/scog.39.3.271

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 90C. This research proves that construction and expression of the SUPEL quartet has been achieved by producing the peptide at an ideal size.

Isolasi dan karakterisasi gen dehydrin dari tebu (Saccharum officinarumL.) yang terlibat dalam respon toleransi cekaman kekeringan (Isolation and characterization of dehydrin gene from sugarcane (Saccharum officinarum L.) involved in drought tolerance response) Hayati MINARSIH; . FANIAR; Tati KRISTANTI; Dian M AMANAH; . SUSTIPRIJATNO; Sony SUHANDONO
Menara Perkebunan Vol. 86 No. 2 (2018): 86 (2), 2018
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v86i2.300

Nowadays,the development of molecular biology techniques has enabled to engineer drought tolerant sugarcane to accelerate thebreeding program. Dehydrin(DHN)that belong to the group II late embryogenesis abundant (LEA) family is known to havean important role in plant response and adaptation to abiotic stresses (drought, high salinity, cold, heat, etc.). Literature study and bioinformatics analysis reported that DHN1gene on sugarcane showed high homology sequences with sorghum DHN. The expression of DHN1gene on sugarcane var. PSJT 941 treated with various periodof drought stress had been conducted using semi-quantitative reverse transcriptase (RT)-PCR method. The results showed that the expressionlevel of DHN1 geneincreased along withthe increased period of the treatment. The highest expression level of DHN1 gene was resulted from plants that had been subjected to drought for 25 days. Amplification of DHN1gene from plants withthe highest gene expression, resulted an amplicon with a size of 465 bp which representsa full length coding sequence (CDS) of DHN1. Identification using Blast analysis showed that DHN1sequences from sugarcane var. PSJT 941 shared high homology with DHN gene on sugarcane and sorghum. The alignment results also revealed a conserved motif that characterized DHN genes.[Key words: drought stress, dehydrin, DHN1gene, sugarcane]Abstrak Dengan berkembangnya teknik biologi molekuler saat ini, maka perakitan tanaman tebu yang toleran kekeringan lebih diarahkan melalui teknik rekayasa genetika untuk mempercepat program pemuliaan tanaman. Protein dehydrin (DHN) yang termasuk ke dalam kelompok II famili LEA (Late Embryogenesis Abundant)diketahui berperan penting dalam respon dan adaptasi tanaman terhadap cekaman abiotik (kekeringan, salinitas tinggi, suhu dingin, panas, dll). Studi literatur dan analisis bioinformatika menunjukkan bahwa gen DHN1pada tanaman tebu memiliki homologi yang tinggi dengan gen DHNpada sorghum. Analisis ekspresi gen DHN1pada tanaman tebu varietasPSJT 941yang diberi cekaman kekeringan telah dilakukan menggunakan semi-kuantitatifreverse transcriptase (RT)-PCR dan terlihat bahwa ekspresi gen DHN1meningkat secara nyata sejalan dengan semakin lamanya waktu pemberian cekaman. Tingkat ekspresi gen DHN1paling tinggi diperoleh dari tanaman yang mengalami cekaman kekeringan selama 25 hari. Amplifikasi gen DHN1pada tanaman dengan tingkat ekspresi yang paling tinggi menunjukkan pita dengan ukuran 465 bp yang merepresentasikan full coding sequence(CDS) gen DHN1. Identifikasi menggunakan analisis Blast menunjukkan bahwa sekuen gen DHN1dari tanaman tebu varietas PSJT 941yang diperoleh memiliki homologi yang tinggi dengan gen DHNpada tanaman tebu dan sorghum. Hasil penjajaran sekuen protein juga menunjukkan adanya motif lestari yang mencirikan gen DHN. [Kata kunci: cekaman kekeringan, dehydrin, gen DHN1, tebu]

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