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All Journal JPTK: Jurnal Pendidikan Teknologi dan Kejuruan Neo-Bis INDONESIAN JOURNAL OF APPLIED PHYSICS Jurnal Dinamika Sosial Budaya Jurnal Riset Ekonomi dan Bisnis Menara Perkebunan Indonesian Journal of Clinical Pathology and Medical Laboratory (IJCPML) Jurnal Ilmiah Edunomika (JIE) SOLUSI Jurnal Tanah dan Iklim Jurnal Bingkai Ekonomi (JBE) Jurnal Pengabdian kepada Masyarakat Indonesia (JPKMI) Jurnal Informasi dan Komunikasi Administrasi (JIKAP) Unisia Sustainable Business Journal

Djoko Santoso

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Author-ID : 255068

Religion Agriculture, Biological Sciences & Forestry Arts Humanities Astronomy Biochemistry, Genetics & Molecular Biology Computer Science & IT Decision Sciences, Operations Research & Management Economics, Econometrics & Finance Education Energy Health Professions Industrial & Manufacturing Engineering Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience Nursing Physics Public Health Social Sciences Other

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Penggunaan biostimulan Orgamin untuk efisiensi pemupukan dan peningkatan produktivitas kelapa sawit di dataran tinggi Application of Orgamin biostimulan to enhance fertilizer efficiency and productivity of oil palm grown in highland Happy WIDIASTUTI; Djoko SANTOSO; Soekarno Mismana PUTRA; Memed WIRAMIHARDJA; Aida FARIDA; B. MARAHIMIN MARAHIMIN; K. PANJAITAN PANJAITAN; Jisman SINAGA
E-Journal Menara Perkebunan Vol 81, No 2: Desember 2013
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

AbstractThe extension of oil palm area has been expanded tomarginal land such as the highland regions. However, theproductivity of the oil palm became the main demand for theplanters. Increasing of oil palm productivity can be done byapplication of growth regulators. Growth regulators aresmall molecules in a relatively very small amount that affectthe growth and development of plant. This study wasconducted to asses the efectiveness of plant growth regu-lators (Orgamin and Orgamin plus) in improving fertilizerefficiency and productivity of mature oil palm (TM 7). Theexperiments were conducted at Marjandi oil palm plantationat an altitude of 700 m above sea level in a total area of 16 ha. Six treatments tested were 1). 100% inorganicfertilizer (control), 2). 50% inorganic fertilizer + Orgamin(50K+O), 3). 75% inorganic fertilizer + Orgamin (75K+O),4). 50% inorganic fertilizer + Orgamin plus (50K+OP), 5).75% inorganic fertilizer + Orgamin plus (75K+OP), and 6).100% inorganic fertilizer + Orgamin plus (100K+OP)arranged in a randomized block design (RBD) with threereplications. Orgamin (O) and Orgamin plus (OP) wereapplied in the hole around the oil palm along with inorganicfertilizers. The results showed that application of O and OPimproved the efficiency of inorganic fertilizers by 50% basedon vegetative variables and increased the concentration ofN, P, and K of leaf and soil compared to those of 100%inorganic fertilizer. In addition to the height and leaf numberof plant parameters, the leaf of the plant treated with O andOP showed more greenish compared to those of control.There is an indication that the O application increased thepercentage of female flowers. In addition the application ofOrgamin also produced the highest oil content in oil palmfruit particularly in the treatment of 75% of inorganicfertilizer + orgamin harvested in October compared to thosein March. Moreover, application of OP increased both thetotal weight and weight per bunch of FFB.AbstrakPengembangan kelapa sawit mengharuskan pengguna-an lahan suboptimal seperti daerah dataran tinggi. Produk-tivitas kelapa sawit menjadi tuntutan utama bagi pekebun.Peningkatan produktivitas kelapa sawit di dataran tinggididuga dapat dilakukan dengan aplikasi zat pengatur tumbuh.Zat pengatur tumbuh merupakan molekul “kecil” (small molecules) yang dalam jumlah relatif sangat sedikit mem-pengaruhi pertumbuhan/perkembangan tanaman. Penelitiandilakukan untuk menguji formula zat pengatur tumbuh(Orgamin dan Orgamin plus) dalam meningkatkan efisiensipemupukan dan produktivitas kelapa sawit TM 7. Percobaandilakukan di kebun Marjandi dengan ketinggian 700 dpl padaareal seluas 16 ha. Enam perlakuan yang diuji adalah 1).pupuk anorganik 100% (100K), 2). pupuk anorganik 50% +Orgamin (50K+O), 3). pupuk anorganik 75% + Orgamin(75K+O), 4). pupuk anorganik 50% + Orgamin plus (50K+OP), 5). pupuk anorganik 75% + Orgamin plus (75K+OP),dan 6). pupuk anorganik 100% + Orgamin plus (100K+OP)yang disusun dalam rancangan acak kelompok (RAK)dengan tiga ulangan. Orgamin (O) dan Orgamin plus (OP)diberikan dalam lubang di piringan pokok bersamaan denganpupuk anorganik. Hasil pengamatan menunjukkan bahwapemberian O dan OP dapat meningkatkan efisiensi pemupuk-an anorganik hingga 50% dilihat dari beberapa peubahvegetatif dan menghasilkan kadar N, P, dan K daun dantanah lebih tinggi dibandingkan dengan pemberian pupukanorganik 100%. Selain pada parameter tinggi tanaman danjumlah daun, peningkatan juga terlihat pada tingkatkehijauan daun. Terdapat indikasi bahwa pemberian Orgaminmeningkatkan persentase jumlah bunga betina. PemberianOrgamin juga menghasilkan kadar minyak tertinggi khusus-nya pada pemberian Orgamin + pupuk anorganik 75% padabuah yang dipanen bulan Oktober dibandingkan dengan buahyang dipanen bulan Maret. Baik data bobot per tandanmaupun bobot TBS menunjukkan bahwa pemberian OPdapat meningkatkan kedua peubah tersebut.

Aktivitas ACCase mesokarp kelapa sawit dan kloning fragmen gen penyandi ACCase subunit biotin karboksilase ACCase activity of oil palm mesocarp and cloning of gene fragment encoding biotin carboxylase subunit of ACCase Asmini BUDIANI; Djoko SANTOSO; Hajrial ASWIDINNOOR; Antonius SUWANTO
E-Journal Menara Perkebunan Vol 74, No 1: Juni 2006
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

Summary Genetic engineering to produce high yielding oil palm might be done by over expressing gene encoding key enzyme for oil biosynthesis in the oil palm mesocarp, one of which is ACCase. The objective of this research was to analyze ACCase activity of mesocarp from several developmental stages of fruit and to clone conserved region cDNA of gene encoding biotin carboxylase subunit of ACCase (BC-htACCase) from oil palm mesocarp. Activity of ACCase was analyzed by HPLC. Amplification of cDNA was done by means of reverse transcriptase polymerase chain reaction (RT-PCR) using degenerate heterologous primer on several annealing temperature and MgCl2 concentration. The cDNA fragment of RT-PCR product was cloned, sequenced and analyzed to confirm that the cloned cDNA was conserved region of BC-htACCase. The result showed that ACCase activity increased from the 14 week to the 20 week-old fruit, and then decreased. Using heterologous degenerate primers, cDNA fragments of BC-htACCase conserved region (469 bp) can be specifically amplified at 60 oC annealing temperature with 2 mM MgCl2 concentration.The result of BlastX analysis showed that the sequence of cloned cDNA fragment was highly homologous with the conserved region of BC-htACCase from Glycine max, Arabidopsis thaliana, Nicotiana tabacum, and Brassica napus with 243, 237, 236, 231 bit score, and E. value 2e-63, 1e-61, 2e-61 and 5e-60, respectively. Ringkasan Rekayasa genetika untuk menghasilkan bibit kelapa sawit berdaya hasil tinggi dapat ditempuh dengan meningkatkan ekspresi gen penyandi enzim kunci biosintesis minyak pada kelapa sawit, salah satunya adalah ACCase. Tujuan penelitian ini adalah menguji aktivitas ACCase mesokarp beberapa tahap perkem-bangan buah sawit dan mengklon fragmen cDNA daerah konservatif gen penyandi ACCase heteromerik subunit biotin karbok-silase (BC-htACCase) dari mesokarp buah sawit. Aktivitas ACCase dianalisis dengan HPLC. Amplifikasi cDNA dilakukan dengan teknik RT-PCR menggunakan primer degene-rate heterologus pada berbagai suhu penempelan dan konsentrasi MgCl2. Fragmen cDNA hasil RT-PCR diklon, disekuen dan dianalisis untuk mengkonfirmasi bahwa cDNA terklon adalah daerah konservatif BC-htACCase. Hasil penelitian menunjukkan bahwa aktivitas ACCase meningkat dari buah berumur 14 minggu hingga buah berumur 20 minggu, kemudian menurun kembali Dengan primer degenerate heterologus, fragmen cDNA daerah konservatif BC-htACCase (469 pb) dapat diamplifikasi secara spesifik pada suhu penempelan 60 oC dan konsentrasi MgCl2 2 mM. Hasil analisis BlastX dari sekuen DNA fragmen terklon menunjuk-kan bahwa sekuen tersebut mempunyai homologi tinggi antara lain dengan gen penyandi BC-htACCase dari Glycine max, Arabidopsis thaliana, Nicotiana tabacum dan Brassica napus, masing-masing dengan skor 243, 237, 236, 231 bit, dan E. value 2e-63, 1e-61, 2e-61 dan 5e-60.

Molecular identification and phylogenetic analysis of Chlorella isolates from Indonesia using rbcL gene Fauziatul FITRIYAH; Yora FARAMITHA; Dini Astika SARI; Irma KRESNAWATY; Tri PANJI; Djoko SANTOSO
E-Journal Menara Perkebunan Vol 89, No 1 (2021): April, 2021
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v89i1.408

Identifying the newly isolated species is crucial to establishing a reliable algal database with successful commercial applications for different biotechnological applications. Morphological identification does not give sufficient description, especially for tiny unicellular microalgae. The rbcL gene encodes the large unit of ribulose-1, 5-bisphosphate carboxylase /oxygenase (Rubisco) has been widely known for barcoding in plants and developed for microalgae molecular identification. In this study, we examined the local strains of green microalgae from Indonesia using the rbcL partial gene sequence to identify the strains. Green microalgae isolates originated from Yogyakarta, Serayu, Gondol, Ancol, Cilegon, and Teluk Jakarta were cultured in f/2 media and harvested for DNA extraction. The DNA extracted was proceeded to PCR using 1AB_rbcL primer pair to amplify the sequences of rbcL gene with target band located at 582 bp, followed by the sequencing of the PCR product was conducted. Molecular identification of local green microalgae isolates was successfully carried out using primers 1AB_rbcL with a genetic similarity of 99% toward identified species in the NCBI database. Among six isolates, TJ, G, S, C, and A isolates were identified as C. pyrenoidosa. Only CP isolate from Yogyakarta identified as C. sorokiniana. Nannochloropsis gaditana rbcL sequence was selected as an outgroup. The phylogenetic analysis indicated that the five isolates of Chlorella belong to one clade and clearly distinguished from C. sorokiniana isolate from Yogyakarta.

Kloning cDNA lengkap penyandi ACCase subunit biotin carboxylase dari mesokarp kelapa sawit (Elaeis guineensis Jacq.) Cloning of full length cDNA encoding ACCase subunit biotin carboxylase from mesocarp of oil palm (Elaeis guineensis Jacq.) Asmini BUDIANI; Antonius SUWANTO; Hajrial ASWIDINNOO; Djoko SANTOSO; Basil J NIKOLAU
E-Journal Menara Perkebunan Vol 81, No 2: Desember 2013
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

AbstractAcetyl-CoA Carboxylase (ACCase) is considered to beone of the key enzymes in palm oil biosynthesis. Availabilityof genes encoding this enzyme would give some advantagesin the molecular breeding of oil palm. Over expression ofthe genes in the oil palm mesocarp might increase the oilproduction in this tissue. On the other hand, downregulating of ACCase could divert the central metaboliteAcetyl-CoA to other product such as PHB (Polyhydroxy-butyrate), one of the known biodegradable plastic. Thispaper reported the work of cloning of the full length codingsequence of biotin carboxylase (BC), one subunit of theACCase. Based on the DNA sequence of the BC conservedregion that had cloned previously, primers pairs weredesigned to amplify 5’- and 3’- cDNA ends of BC usingRACE-PCR. The RACE products of 5’- and 3’- cDNA endsof BC were cloned into E.coli, and the DNAs weresequenced and analysed. The full cDNA of BC was obtainedby reisolation of the cloned 5’- and 3’- cDNA ends followedby digestion using KpnI, ligation into pGEM-T vector andcloning into E.coli. Colony PCR was carried out to confirmthat the target gene has been cloned. The recombinantplasmid containing full cDNA of BC was then isolated forDNA sequencing. The results showed that the 5’-BC (1367bp), 3’- BC (1032 bp), and the full length cDNA encodingBC (2182 bp) had been successfully cloned, and the DNAsequence had been confirmed as gene encoding ACCasesubunit biotin carboxylase.AbstrakAcetyl-CoA Carboxylase (ACCase) merupakan salahsatu enzim kunci dalam biosintesis minyak sawit. Keter-sediaan gen penyandi enzim ini sangat berguna dalampemuliaan kelapa sawit secara molekuler. Over-ekspresi genpenyandi ACCase pada mesokarp dapat meningkatkan pro-duksi minyak pada jaringan tersebut. Sebaliknya ekspresiACCase dapat ditekan melalui mekanisme down regulation sehingga metabolit central Acetyl-CoA dapat diarahkanuntuk menghasilkan produk lain seperti PHB (polyhydro-xybutyrate), salah satu jenis biodegradable plastik yangtelah banyak dikenal. Penelitian ini bertujuan untukmengklon cDNA lengkap penyandi ACCase subunit biotincarboxylase (BC) dari mesokarp kelapa sawit. Berdasarkansekuen DNA daerah konservatif BC yang telah diklon darimesokarp kelapa sawit pada penelitian sebelumnya, duapasang primer dirancang untuk mengamplifikasi daerahujung 5’- dan 3’- cDNA BC dengan RACE-PCR. Produk5’-RACE dan 3’-RACE diklon dan disekuen. cDNAlengkap penyandi BC diperoleh dengan jalan mengisolasikembali fragmen 5’- dan 3’- cDNA terklon, dilanjutkandengan digesti menggunakan enzim restriksi KpnI, ligasikedua fragmen ke vektor kloning pGEM-T, dan introduksike dalam E. coli. Setelah dilakukan PCR koloni untukmenguji keberhasilan kloning, plasmid rekombinan yangmengandung cDNA lengkap dari BC diisolasi untuk analisissekuen DNA. Dari penelitian ini fragmen cDNA 5’-BC(1367 pb) dan 3’- BC (1032 pb), serta cDNA lengkappenyandi BC berukuran 2182 pb telah diperoleh dan diklondalam E. coli. Analisis sekuen DNA mengkonfirmasi bahwacDNA terklon adalah benar gen penyandi ACCase subunitbiotin carboxylase.

Deteksi dan analisis sekuen gen inhibitor proteinase pada beberapa klon kakao harapan tahan penggerek buah kakao dari Sulawesi Selatan Detection and sequence analysis of proteinase inhibitor gene in cacao clones putatively cacao pod borer-tolerant from South Sulawesi Abdul Mollah S. JAYA; Hajrial ASWIDINNOOR; Djoko SANTOSO
E-Journal Menara Perkebunan Vol 72, No 1: Juni 2004
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

Summary Cacao is socially and economically an important commodity for Indonesia, in which the cacao plantations have been challenged with a threatening pest, cacao pod borer (CPB). This research aimed to identify and clone PIN (proteinase inhibitor), a gene carrying resistance of plant to some chewing pests like CPB. The methodology included several experiments. Detection of PIN in cacao was done by PCR using PIN-specific heterologous primers and cacao genomic DNA as templates. Cloning vector pGEM-T was utilized to clone the PCR products. Sequence analysis was conducted with BlastX and Blast Special programs from NCBI. Alignment analysis to determine genetic similarity was performed with ClustalW from EBI. Thirteen of the 18 clones tested were detected to have PIN homologs. Two DNA fragments from cacao clones putatively tolerant to CPB, MJ-1 and LW-1, were sequenced. One of them, MJ-1 was cloned. Sequence analyses of the fragments of both cacao clones, indicated that they have PIN homologs and a very closed genetic relation with 96% level of similarity. Ringkasan Kakao adalah komoditas yang secara sosial maupun ekonomi penting bagi Indonesia, dimana perkebunan kakao menghadapi masalah serius hamapenggerek buah kakao (PBK). Penelitian ini bertujuan mengidentifikasi dan mengklon PIN (inhibitor proteinase), gen yang membawa sifat ketahanan tanaman terhadap hama ulat seperti PBK. Metodologinya terdiri dari beberapa percobaan. Deteksi PIN di dalam kakao dikerjakan dengan PCR menggunakan primer heterologous yang spesifik terhadap PIN dan DNA genomik kakao sebagai templetnya. Vektor kloning pGEM-T digunakan untuk mengklon produk PCR. Analisis sekuen dilakukan dengan program BlastX dan Blast spesial dari NCBI. Analisis penjajaran (alignment) untuk menentukan kemiripan genetik menggunakan program ClustalW dari EBI. Tiga belas dari 18 klon kakao yang diuji menunjukkan adanya homolog PIN. Dua DNA fragmen dari klon harapan tahan, MJ-1 dan LW-1, telah ditentukan sekuen nukleotidanya. Satu diantara-nya, MJ-1 berhasil diklon. Analisis sekuen kedua klon tersebut menunjukkan identitas sebagai homolog PIN dan keduanya memiliki kemiripan genetik yang tinggi.

The effects of seaweed fertilizer on the growth and productivity of upland rice, maize and oil palm grown in green house Pengaruh pupuk rumput laut terhadap pertumbuhan dan produktivitas padi gogo, jagung dan kelapa sawit di rumah kaca Djoko SANTOSO; Tetty CHAIDAMSARI; . SYAFARUDDIN; Dedi Soleh EFFENDI
E-Journal Menara Perkebunan Vol 79, No 2: Desember 2011
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

AbstrakSebagai negara kepulauan di daerah tropis, Indonesiakaya akan sumberdaya alam untuk swasembada pangan.Berjuta-juta hektar lahan di Indonesia ditanami tanamanperkebunan, tanaman tahunan yang memiliki masa juvenilyang relatif lama, terutama tanaman kelapa sawit dan karet.Sementara itu, upaya untuk meningkatkan produksi panganterkendala oleh terbatasnya lahan subur. Penelitian yangmengeksplorasi bioregulator alami mampu meningkatkanproduktivitas tanaman, menemukan bahwa Sargasum sp.,rumput laut tipe liar yang di sepanjang pantai beberapawilayah Indonesia, menunjukkan kemampuannya meningkat-kan pertumbuhan dan produktivitas tanaman seperti padi,jagung, tomat dan pertumbuhan kelapa sawit tanpapenambahan pupuk kimia. Percobaan pada padi gogovarietas Batutegi yang ditanam di rumah kaca, menunjuk-kan bahwa bioregulator alami tersebut meningkatkanproduktivitasnya 50% lebih tinggi daripada kontrolnya.Percobaan menggunakan jagung var. Arjuna, tanaman yangtelah diperlakukan dengan bioregulator tersebut mem-produksi dua hingga tiga tongkol, sementara pada tanamankontrol hanya satu tongkol. Percobaan pada tanamankelapa sawit di rumahkaca memperlihatkan bahwa bio-regulator tersebut menginduksi pertumbuhan vegetatifnyasecara signifikan, lebih baik daripada kontrol dengan atautanpa pupuk kimia. Intercropping tanaman kelapa sawitTBM dengan tanaman pangan seperti padi gogo ataujagung, diharapkan lebih menguntungkan bagi usahaperkebunan.AbstractBeing a tropical archipelago, Indonesia is rich withnatural resources enabling more production for food.Millions hectares of Indonesian lands is now planted withestate crops, perennial crops with relatively lengthenjuvenile phase mainly oil palm and rubber. Meanwhile,attempts to increase national food production have beenlimited by availability of fertile lands. Our researchexploring natural bioregulator capable of improving cropproductivity, found that Sargasum sp., a wild sea weedgrown mostly along the coast line in Indonesia, indicated itsability to improve the growth and productivity of crops likerice, maize, tomato and oil palm even though with nochemical fertilizers added. The experiment on upland rice oflocal variety Batutegi planted in greenhouse, demonstratedthe natural bioregulator has increased the rice productivityby at least 50% over the control. The experiment usingmaize var. Arjuna, the bioregulator treated plants has madetwo to three corncobs instead of only one corncob on thecontrol plants. The experiment on the oil palm grown in thenursery showed that the bioregulator has significantlyinduced vegetative growth better than the control with orwithout chemical fertilizers. Intercropping the food crops,rice or maize in the juvenile phase of the oil palmplantations, should be beneficial to the productivity of theplantation.

Keragaman sekuen DNA fragmen gen penyandi ACCase subunit BCCP dari tiga tipe kelapa sawit Variability of DNA sequence of gene fragment encoding BCCP subunit of ACCase from three types of oil palm Asmini BUDIANI; Djoko SANTOSO; A.R. PURBA PURBA
E-Journal Menara Perkebunan Vol 75, No 1: Juni 2007
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

SummaryHeteromeric acetyl-CoA carboxylase (ht-ACCase) is one of key enzymes in palm oilbiosynthesis. Isolation and characterization ofthe gene is an important step in metabolicengineering to increase palm oil content andquality. The objective of this research was toisolate DNA fragment of gene encoding biotincarboxyl carrier protein (BCCP) subunit of ht-ACCase from three different oil palm types(Simalungun, Hibrida and Backcross) andinvestigate the variation of its DNA sequence.Total RNA was isolated from the mesocarp ofoil palm. DNA fragment encoding BCCP wasamplified by means of Reverse TranscriptasePolymerase Chain Reaction (RT-PCR) usingspecific primers with total RNA as a template.The products of RT-PCR were then purifiedfrom the gel, cloned and sequenced. The DNAsequences were analyzed for their homologiesto BCCP gene using BlastN and aligned todetect the sequence variability using ClustalWprogram from BioEdit. The results show thatone of the two RT-PCR products at about 300bp was highly homologous with the geneencoding BCCP from Glycine max, Brassicanapus and Arabidopsis thaliana. Nucleotidesequences of that BCCP fragments from thethree types of oil palm displayed some degreesof variability. Further investigation is neededto analyze the variability of the DNA sequencesof the full-length gene in relation with oilcontent or other characterRingkasanAsetil-CoA karboksilase heteromerik (ht-ACCase) merupakan salah satu enzim kuncidalam biosintesis minyak sawit. Isolasi dankarakterisasi gen tersebut merupakan langkahpenting dalam upaya rekayasa metabolismeuntuk peningkatan rendemen dan kualitasminyak sawit. Penelitian ini bertujuan untukmengisolasi fragmen DNA penyandi subunitbiotin carboxyl carrier protein (BCCP) dari ht-ACCase dari tiga tipe kelapa sawit yang ber-beda (Simalungun, Hibrida dan Backcross)dan mempelajari keragaman susunan nukleo-tidanya. RNA total diisolasi dari mesokarpbuah sawit. Fragmen gen penyandi BCCPdiamplifikasi dengan Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) meng-gunakan primer spesifik dan templat RNA total.Fragmen hasil RT-PCR dimurnikan dari gel,diklon kemudian disekuen. Sekuen DNA yangdiperoleh dianalisis homologinya dengan genBCCP menggunakan BlastN dan disejajarkanuntuk mengetahui keragamannya mengguna-kan program ClustalW dari BioEdit. Hasilnyamenunjukkan bahwa satu dari dua fragmenhasil RT-PCR yang berukuran sekitar 300 pbmemiliki homologi yang tinggi denganfragmen gen penyandi BCCP dari Glycine max,Brassica napus dan Arabidopsis thaliana.Urutan nukleotida fragmen BCCP dari ketigatipe kelapa sawit menunjukkan keragaman.Perlu analisis lebih lanjut mengenai keragamansekuen DNA dari gen lengkapnya dan dikajihubungannya dengan akumulasi minyak ataukarakter lain

Kloning gen penyandi β-1,6-glukanase kapang secara cepat dengan teknik RT-PCR menggunakan primer spesifik Rapid cloning for gene encoding fungal β-1,6-glucanase by means of RT-PCR using specific primers Asmini BUDIANI; Riza A. PUTRANTO; Hayati MINARSIH; Niyyah FITRANTI; Djoko SANTOSO
E-Journal Menara Perkebunan Vol 77, No 1: Juni 2009
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

AbstractProduction of bioethanol from biomass ofagricultural waste has been hindered with a highproduction cost because enzymes needed for theprocess has to be imported with relatively a highprice. Genetic engineering using its encodinggenes is able to produce those enzymes withlower cost. In this report we described a researchaimed to clone gene encoding β-1,6-glucanasefrom Trichoderma harzianum with a relativelyrapid and inexpensive method, by means of RT-PCR using gene specific primers. The primerswere designed based on the DNA sequence of thetarget gene from the same species of organismused in this research. RT-PCR using that primersresulted in DNA fragment with sizescorresponding to the predicted size of full lengthgene encoding β-1,6-glucanase, about 1300 bp.After a sequential experiments of cloning usingpGEM-T Easy vector, DNA sequencing andBlastN - BlastX analyses of the sequences, it wasproven that the isolated DNA was full length geneof β-1,6-glucanase. This was implied from thepercentage of Identity and E-value which were96% and 0.0 (< e-04) respectivety.AbstrakProduksi bioetanol dari biomassa limbahpertanian, terkendala oleh tingginya biayaproduksi karena enzim yang diperlukan untukproses tersebut masih harus diimpor denganharga yang relatif mahal. Melalui rekayasagenetika menggunakan gen-gen penyandinya,enzim-enzim tersebut dapat diproduksi denganbiaya yang lebih murah. Penelitian ini bertujuanuntuk mengklon gen penyandi β-1,6-glukanasedari Trichoderma harzianum secara cepat danekonomis, dengan RT-PCR menggunakan primerspesifik. Primer tersebut dirancang berdasarkansekuen DNA dari gen target asal spesiesorganisme yang sama dengan yang digunakandalam penelitian. RT-PCR dengan primertersebut menghasilkan fragmen DNA yangukurannya sesuai dengan gen lengkap penyandiβ-1,6-glukanase, yaitu sekitar 1300 bp. Setelahsecara berurutan diklon menggunakan vektorpGEM-T Easy, sekuensing urutan DNA dananalisis BlastN maupun BlastX dari sekuen yangdiperoleh, terbukti bahwa fragmen DNA tersebutadalah gen lengkap penyandi β-1,6-glukanase.Hal ini ditunjukkan oleh Nilai Kesamaan(Identity) dan E-Value yang masing-masingmencapai 96% dan 0.0.

Nucleotide sequence of cryIA gene cloned from Btk isolate of Bacillus thuringiensis and comparison with cryIA(c) gene from B. thuringiensis subsp. kenyae Sekuen nukleotida gen cryIA dari B.thuringiensis isolat Btk dibandingkan dengan gen crylA(c) dari B. thuringiensis subsp. Kenyae Asmini BUDIANI; Djoko SANTOSO
E-Journal Menara Perkebunan Vol 68, No 1: Juni 2000
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

Ringkasan Perakitan tanaman perkebunan yang toleran terhadap serangga hama dapat ditempuh melalui rekayasa genetika menggunakan gen cry. Gen cryIA merupakan gen cry yang paling banyak dipelajari di antara gen cry lainnya. Berdasarkan homology sekuen dan spesifisitas protein yang disandinya terhadap serangga sasaran, gen ini telah diklasifikasikan menjadi 10 subklas. Tulisan ini melaporkan hasil sekuensing (ragmen gen cryIA penyandi domain toksin yang diisolasi dengan teknik PCR dari Bacillus thuringiensis isolat Btk dan diklon menggunakan vektor pGEMT. Untuk menentukan sekuen gen cryIA yang berukuran sekitar 2 kb tersebut, dilakukan konstruksi satu seri mutan terdelesi searah dari ujung 5' menggunakan kit Erase-a-Base-System. Tiga DNA gen cryIA mutan dengan tingkat delesi yang sesuai dan satu nonmutan dipilih untuk sekuensing DNAnya. Sekuensing dilakukan dari satu arah menggunakan primer universal SP6 pada alat ABI 377A automatic DNA sequencer. Sekuen lengkap dari gen cryIA diperoleh dengan cara menggabungkan sekuen ketiga mutan dengan sekuen dari gen cryIA nonmutan secara manual. Untuk konfirmasi sekuen ujung 3', dilakukan sekuensing dari arah lainnya menggunakan primer universal T7. Sekuen lengkap dari fragmen tersebut mengandung 2021 nukleotida dan menyandi protein dengan 673 asam amino. Dibandingkan dengan sekuen gen crylA(c) dari B. thuringiensis subsp. kenyae, terlihat adanya sepuluh mutasi titik masing-masing pada nukleotida ke 444, 477, 1089, 1092, 1098, 1242, 1566, 1869, 1906 dan 1961. Tujuh mutasi titik pada nukleotida ke 444, 477, 1089, 1092, 1242, 1566, dan 1869 tidak merubah asam amino, sedangkan tiga mutasi lainnya mengakibatkan perubahan asam amino, yaitu pada nukleotida ke 1098 (kodon ke 366, yang menyebabkan perubahan dari Phe menjadi Leu), nukleotida ke 1906 (kodon ke 636, yang mengubah Val menjadi Leu) dan pada nukleotida ke 1961(kodon ke 654, yang mengubah Cys menjadi Tyr).Summary Estate crops tolerant to pests can be development through genetic engineering using cry gene. CryIA is the best studied among cry genes. Based on the sequence homology and specificity of their encoded proteins to the, targeted insect, these genes have been classified into 10 subclasses. This paper reports sequencing of cryIA gene fragment en-coding toxin domain isolated from Btk isolates of Bacillus thuringiensis using PCR technique and cloned with pGEM-T vector. To determine the full sequence of the 2-kb gene fragment, a series of mutants uni-directionally deleted at the 5'-end were constructed. Mutation was done using Erase-a Base-System kit. Three DNA mutants with appropriate degree of deletion and the un-mutated DNA were chosen for sequencing. Sequencing was conducted from one direction with SP6 universal primer using the ABI 377A automatic DNA sequencer. The full sequence of cryIA fragment was assembled manually using the sequences of DNA mutants and the non-mutant cryIA fragment. To confirm the sequence of the 3'-end, sequencing from the other direction was performed using the T7 universal primer.The completed sequence of the fragment contains 2021 nucleotides encoding a protein of 673 amino acids. Compares to the sequence of cryIA(c) from B. thuringiensis subsp. kenyae, it was shown that there were ten point mutations (nucleotides of 444, 477, 1089, 1092, 1098, 1242, 1566, 1869, 1906 and 1961), sevent of them (nucleotides of 444, 477, 1089, 1092, 1242, 1566 and 1869) were identified as silent mutations, while the other three substituted the amino acids, which are at the nucleotide 1089 (codon 366, substitution of Leu for Phe), nucleotide 1906 (codon 636, substitution of Leu for Val), and nucleotide 1961 (codon 654, substitution of Tyr for Cys).

Kloning dan karakterisasi gen penyandi inhibitor proteinase dari kulit buah kakao Cloning and characterization of gene encoding proteinase inhibitor of cacao pod wall Mayta Novaliza ISDA; Musliar KASIM; . MANSYURDIN; Tetty CHAIDAMSARI; Djoko SANTOSO
E-Journal Menara Perkebunan Vol 76, No 2: Desember 2008
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

Summary Attempts to increase cocoa production in Indonesia have been hinderred by attack of CPB (Conopomorpha cramerella). There has been no effective measures to control this pest leading to development of cacao planting materials which resistant to the pod borer. One of genes functioning in plant defense system against insect pests such as catepilar is Proteinase Inhibitor (PIN). This research aimed to isolate and characterize TcPIN gene of cacao pod wall. A clone of TcPIN was isolated with RT-PCR technique using total RNA of cacao pod wall and DNA primer designed based on the sequence Trypsin Inhibitor of cocoa bean accessible online. BlastX analysis of the sequence of the cDNA clone demonstrated that the ± 600 bp gene cloned with pGEM-T was PIN gene as indicated by highly homologous to Trypsin Inhibitor of Theobroma microcarpum resulted in 248 Score bits and E value 1 e-64. Two sequence alligment with the putative 21 kDa PIN of cacao seed indicated a moderately high homology. Contrasting these two sequences however found some non identical amino acids implying some variations. Ringkasan Usaha peningkatan produksi kakao di Indonesia terkendala antara lain oleh adanya serangan hama PBK (Conopomorpha cramerella). Untuk menanggulangi serangan PBK tersebut perlu adanya satu cara pengendalian yang efektif dan efisien, sehingga dapat mendorong usaha pengembangan bahan tanam yang tahan PBK. Salah satu gen membawa sifat ketahanan tanaman terhadap hama ulat adalah Proteinase Inhibitor (PIN). Penelitian ini bertujuan untuk mengisolasi dan mengkarakterisasi gen TcPIN dari kulit buah kakao. Klon cDNA TcPIN diisolasi dari kulit buah kakao dengan teknik RT-PCR meng-gunakan RNA total kulit buah kakao dan primer DNA yang dirancang atas dasar sekuen Inhibitor Tripsin biji kakao yang diakses lewat internet. Hasil analisis BlastX dari sekuen klon cDNA menunjukkan bahwa gen berukuran ± 600 pb yang telah diklon dengan pGEM-T tersebut adalah PIN karena memiliki homologi yang tinggi terhadap 21 kDa trypsin inhibitor dari Theobroma microcarpum yang meng-hasilkan Skor 248 bits dengan Nilai E 1e-64. Penjajaran dua sekuen dengan PIN putatif 21 kDa yang berasal dari biji kakao menunjuk-kan tingkat homologi yang tinggi, dengan perbedaan nyata sehingga dapat terlihat bahwa keduanya tidak identik.

Co-Authors . Mansyurdin . SAMANHUDI . SYAFARUDDIN A. H. SARAGIH SARAGIH A.R. PURBA PURBA Abdul Mollah S. JAYA Agus Laesanpura Agustina A. HANDAYAN Ahmad Isyabul Izzi Aida Farida Ajeng Nuzulia H Antonius Suwanto Anwar, Aswaldi Aprih Santoso Asmini Budiani Auzar SYARIEF B. MARAHIMIN MARAHIMIN Bambang S PURWOKO Bambang Wahyudiyono Basil J NIKOLAU Budi Sulistijo Candra Auromiqo Christantius Dwiatmadja Deden Dewantara ERIS DEDI SOLEH EFFENDI Dini Astika SARI Efendi, Darda F NURILMALA Fauziatul FITRIYAH GALUH WENING PERMATASARI Hajrial ASWIDINNOO HAJRIAL ASWIDINNOOR Hanny Hafiar HAPPY WIDIASTUTI Happy Widiastuti Hayati MINARSIH Hayati Minarsih I GEDE PUTU WIGENA Imron Riyadi Indarto Indarto Indarto Irma KRESNAWATY Isnu Irwantoro Jayawarsa, A.A. Ketut Jisman SINAGA K. PANJAITAN PANJAITAN M. A. GHONI GHONI Mayta Novaliza Isda Memed WIRAMIHARDJA Muhammad Jusuf Muhammad Munir Musliar Kasim Niyyah FITRANTI Niyyah FITRANTY Oktaviany Ferry TRIASTANTO Patni Ninghardjanti Pratama, Azka Dhiya R.D.B LEFROY Rita Hayati Riza A PUTRANTO Riza A. PUTRANTO Roedhy Poerwanto Roesalia Anggraenie SATRIYAS ILYAS Soekarno Mismana Putra Suharyanto Sukarti Moeljopawiro Tetty CHAIDAMSARI Tri Panji Umi Rochayati VS Ariyanto Wyati Saddewisasi Yatini Y Yora FARAMITHA Yuli Budiati Yuniarti Anis Pramukawati

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