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All Journal JURNAL SAINS DAN TEKNOLOGI INDONESIA Jurnal Bioteknologi & Biosains Indonesia (JBBI)
purwoko, devit
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Computer Science & IT Education Immunology & microbiology

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Analisis Keragaman Genetik Temulawak (Curcuma xanthorrhiza Roxb.) Menggunakan Penanda Amplified Fragment Length Polymorphism (AFLP) damayanti, dini; tajuddin, teuku; purwoko, devit; zulaeha, siti; suharsono, suharsono
Jurnal Sains dan Teknologi Indonesia Vol. 14 No. 3 (2012)
Publisher : Badan Pengkajian dan Penerapan Teknologi

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (197.369 KB) | DOI: 10.29122/jsti.v14i3.923

Abstract

Curcuma xanthorrhiza Roxb, which is well-known as Java turmeric, has been extensively used in pharmaceutical industries in Indonesia. In spite of this commercial value, the identity of this species is commonly mistaken from other similar orange rhizomes Curcuma. Correct identity of these species is vital in pharmaceutical industries. The objective of the study was to determine genetic diversity of 32 accession Curcuma xanthorrhiza Roxb. Genomic DNA was extracted from leaf using Sodium Dodesyl Sulphate (SDS) modification. Amplified fragment length polymorphism (AFLP) was carried out according to the protocol ofAFLPTM plant mapping kit and the final polymerase chain reaction (PCR) products were separated using The Agilent 2100 Bioanalyzer. The number of fragment produced by 12 pairs primer combination of AFLP ranged from 42 to 60 with an average of 52. Data obtained was analyzed by the NTSys program. From the AFLP amplification on 32 DNA samples, it was proven that the accession of Curcuma xanthorrhiza Roxb. had a high degree of diversity. Based on analysis of AFLP and unweighted pair group with arithme average (UPGMA) it was shown that the accession of Curcuma xanthorrhiza Roxb. could be grouped into two cluster at relative ecludian distance of 0.10 (10%). Cluster I for accession from Palembang, Pacitan and Ciamis 2. Cluster II for accession from Makale, Pontianak, Kulonprogo, Mataram, Boyolali, Salatiga, Sumberejo, Bali, P. Seram, Sentolo, Purworejo, Samas Bantul, Ciamis1, Blora, Semarang, Poso, Kalsesl, Tagari, Merapi Farm, Salakaria, NTB, Menoreh, Karang Anyar, Mangunan, Medan, Toraja, dan Solok.
ANALISIS BIOINFORMATIKA BERBASIS WEB PADA SEKUEN GENOM PARSIAL SAGU (Metroxylon sagu Rottb.) Purwoko, Devit; Cartealy, Imam Civi; Tajuddin, Teuku; Dinarti, Diny; Sudarsono, Sudarsono
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 5 No. 1 (2018): June 2018
Publisher : Balai Bioteknologi, Badan Pengkajian dan Penerapan Teknologi (BPPT)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1161.678 KB) | DOI: 10.29122/jbbi.v5i1.2878

Abstract

WEB-based bioinformatic analysis on partial genome sequence of Sago (Metroxylon sagu Rottb.)ABSTRACTSago genome sequencing analysis is still very limited. This study is a preliminary study of sago sequence analysis obtained from NGS technology to understand and identify new genetic sequences that have homology to genes in the NCBI database. Sequences were analyzed using Blast2Go to determine the genetic function annotation, putative gene identification was performed on the Arabidopsis database using the BLASTx program with a 10-3 e-value limit on The Arabidopsis Information Resource (TAIR) (http://www.arabidopsis.org/index.jsp). Gene interactions were analyzed using DAVID and GeneMania programs. Based on sequence analysis with Blast2Go, 33 sequences with Blastx hit consisting of: 29 sequences had a high homology. The sago sequences with a similarity of ≥ 90% are glutamate decarboxylase and HT1-like serine threonine kinase with hit number 10. The distribution of interactions between genes from GeneMania analysis is known to be mostly interconnected in the 65.13% protein domain, predicted 19.83%, genes with 14.47% shared expression and the remaining 0.57% had localization together.Keywords: bioinformatics, gene annotation, gene ontology, genome sequence, Metroxylon sagu ABSTRAKKajian analisis sekuen genom sagu hingga saat ini masih amat terbatas. Penelitian ini merupakan riset pendahuluan analisis sekuen sagu yang diperoleh dari teknologi NGS untuk mengetahui dan mengidentifikasi sekuen gen baru yang memiliki homologi dengan gen pada database NCBI. Sekuen dianalisis menggunakan perangkat Blast2Go untuk mengetahui anotasi fungsional gen, identifikasi gen putatif dilakukan terhadap database Arabidopsis menggunakan program BLASTx dengan batas e-value 10-3 pada The Arabidopsis Information Resource (TAIR). Interaksi gen dianalisis menggunakan program DAVID dan GeneMania. Berdasarkan analisis sekuen dengan Blast2Go, diperoleh 33 sekuen dengan Blastx hit yang terdiri atas: 29 sekuen memiliki homologi yang tinggi. Gen dengan rataan kemiripan ≥ 90% adalah glutamate decarboxylase dan serine threonine-kinase HT1-like dengan jumlah hit 10. Persebaran interaksi antar gen hasil analisis GeneMania diketahui sebagian besar saling terkait pada domain protein 65,13%, koneksi yang berhasil diprediksi 19,83%, gen dengan ekspresi bersama 14,47% dan sisanya 0,57% memiliki peranan bersama. Kata Kunci: anotasi gen, bioinformatika, Metroxylon sagu, ontologi gen, sekuen genome 
ANALISIS FILOGENETIK BEBERAPA KLON KARET DENGAN MARKA AFLP (AMPLIFIED FRAGMENT LENGTH POLYMORPHISM) Suparningtyas, Juniza Firdha; Pramudyawardhani, Okky Dwi; Purwoko, Devit; Tajuddin, Teuku
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 5 No. 1 (2018): June 2018
Publisher : Balai Bioteknologi, Badan Pengkajian dan Penerapan Teknologi (BPPT)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (940.1 KB) | DOI: 10.29122/jbbi.v5i1.2544

Abstract

Phylogenetic Analysis of Rubber Tree Clones using AFLP (Amplified Fragment Length Polymorphism) MarkerNational rubber productivity is lower than other rubber producing countries in the world. The DNA marker-based plant breeding program is required to increase latex production and other superior characters. Breeding process by identifying genetic diversity can be done using AFLP marker. The aim of this study was to analyze the phylogenetic six rubber clones. Pre-amplification and amplification process were performed using 64 primer pair combinations followed by electrophoresis in 6% polyacrylamide gel. A total of 2806 AFLP fragments have been detected. Phylogenetic tree of six clones showed 60% of genetic similarity, which was consisted of two groups. GT 1 clone in the first group and was separated from other clones in the second group. Sub-group at the phylogenetic peak contained IRR 104 and RRIM 600 clones with genetic similarity of 74%. The information obtained from this study showed the genetic diversity of the six rubber clones. The unique bands were obtained as marker specific which could be used to identify clones.Keywords: AFLP, DNA marker, phylogenetic tree, polymorphism, rubber clones ABSTRAKProduktivitas karet nasional masih lebih rendah dibanding dengan negara-negara penghasil karet lainnya di dunia. Diperlukan program pemuliaan tanaman karet yang berbasis marka DNA untuk meningkatkan produksi lateks serta karakter unggul lainnya. Proses pemuliaan untuk mengidentifikasi keragaman genetik bisa dilakukan dengan marka AFLP. Tujuan studi ini adalah untuk menganalisis filogenetik enam klon karet berdasarkan produktivitasnya. Proses pre-amplifikasi dan amplifikasi dilakukan dengan menggunakan 64 kombinasi pasangan primer yang dilanjutkan dengan analisis hasil elektroforesis pada gel poliakrilamid 6%. Sebanyak 2806 pita AFLP telah dihasilkan. Kekerabatan keenam klon menunjukkan kemiripan genetik sebesar 60%. Pohon filogenetik membentuk dua kelompok, yang memisahkan GT 1 dengan klon-klon lainnya. Sub-kelompok pada puncak filogenetik terdiri dari klon IRR 104 dan RRIM 600 dengan kemiripan genetik sebesar 74%. Informasi yang diperoleh telah menunjukkan keragaman genetik keenam klon karet yang bersifat polimorfis. Diperoleh pita-pita unik dari pasangan primer tertentu yang dapat berperan sebagai marka spesifik dan dapat digunakan untuk mengidentifikasi klon.Kata Kunci: AFLP, klon karet, marka DNA, pohon filogenetik, polimorfisme
PERBANDINGAN TIGA KIT EKSTRAKSI RNA UNTUK ANALISIS TRANSKRIPTOMIKA PADA KELAPA SAWIT (Elaeis guineensis Jacq.) Zulaeha, Siti; Purwoko, Devit; Cartealy, Imam; Tajuddin, Teuku; Karyanti, .; Khairiyah, Hayat
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 6 No. 1 (2019): June 2019
Publisher : Balai Bioteknologi, Badan Pengkajian dan Penerapan Teknologi (BPPT)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (143.283 KB) | DOI: 10.29122/jbbi.v6i1.3372

Abstract

Comparison of Three RNA Extraction Kits for Transcriptome Analysis of Oil Palm (Elaeis guineensis Jacq.) ABSTRACTObtaining high-quality RNA is very important at an early stage of molecular biology research. To isolate RNA, high skill and caution are required in following laboratory procedures because RNA is easily degraded, especially samples from plant tissue culture. One of the parameters used to check the total RNA quality is RIN (RNA Integrity Number). The aim of this study was to obtain RNA extraction methods on oil palm leaves, callus and somatic embryos that were of good quality and high concentrations for transcriptomic analysis. RNA extraction was carried out using Plant RNA PureLink (Ambion), Genezol RNA Extraction (Geneaid) and RibospinTM Plant (Geneall) kit methods. The results showed that oil palm leaf, callus and somatic embryo RNA were successfully extracted using the RibospinTM (Geneall) kit. Based on the total RNA number of more than 4 μg and the RIN value of more than 7, the extracted RNA could be used in RNA sequencing for transcriptomic analysis. Keywords: callus, oil palm, RNA analysis, RNA quality, somatic embryo ABSTRAKMenghasilkan RNA berkualitas tinggi sangatlah penting pada tahap awal penelitian biologi molekuler. Untuk mengisolasi RNA diperlukan keterampilan dan kehati-hatian tinggi dalam mengikuti prosedur di laboratorium karena RNA lebih mudah terdegradasi, khususnya sampel hasil kultur jaringan tanaman. Salah satu parameter yang digunakan pada pengecekan kualitas RNA total adalah RIN (RNA Integrity Number). Penelitian bertujuan mendapatkan metode ekstraksi RNA pada daun, kalus dan embrio somatik kelapa sawit yang berkualitas baik dan memiliki konsentrasi tinggi untuk analisa transkriptomika.  Ekstraksi RNA dilakukan menggunakan metode kit Plant RNA PureLink (Ambion), Genezol RNA Extraction (Geneaid) dan RibospinTM Plant (Geneall). Hasil menunjukkan bahwa RNA daun, kalus dan embrio somatik kelapa sawit telah berhasil diekstraksi dengan menggunakan kit RibospinTM (Geneall). RNA hasil ekstraksi tersebut dapat digunakan untuk sekuensing RNA dengan tujuan analisis transkriptomika, dilihat dari jumlah total RNA yang lebih dari 4 μg dan nilai RIN lebih dari 7. Kata Kunci: analisis RNA, embrio somatic, kalus, kelapa sawit, kualitas RNA 
SKRINING DAN IDENTIFIKASI MIKROBA LIGNINOLITIK PADA PENGOMPOSAN ALAMI TANDAN KOSONG KELAPA SAWIT Rupaedah, Bedah; Purwoko, Devit; Safarrida, Anna; Tajuddin, Teuku; Wahid, Abdul; Sugianto, Mahmud; Sudjai, Imam; Suyono, Agus
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 6 No. 1 (2019): June 2019
Publisher : Balai Bioteknologi, Badan Pengkajian dan Penerapan Teknologi (BPPT)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (713.706 KB) | DOI: 10.29122/jbbi.v6i1.3237

Abstract

Screening and Identification of Ligninolytic Microbes in the Natural Decomposition of Oil Palm Empty Fruit Bunch  ABSTRACTOPEFB (oil palm empty fruit bunch)could potentially be utilized as organic fertilizer or animal feed through composting. Information on microorganisms that play important roles in the natural decomposition of OPEFB is to date not much known yet. This research was aimed to obtain and, subsequently, to molecularly identify lignin-degrading microbial isolates responsible for naturally decomposing OPEFB in the Oil Plant Plantation and Palm Oil Refinery Plant, PTPN VIII Cikasungka, Bogor. Screening for active lignin-degrading isolates was carried out on 17 naturally decomposing OPEFB samples. A total of 19 isolates of fungi and 80 isolates of bacteria were obtained. Ligninolytic activity was measured by Sundman and Nase testing methods. Ligninolytic activity was found on 13 fungal isolates and 15 bacterial isolates. The active isolates were subsequently identified molecularly based on ITS sequence in the ribosome DNA area for fungi and in 16S rRNA genes for bacteria. The results showed that the lignin-degrading microorganisms obtained consisted of 5 bacterial isolates from the genus Bacillus and 3 fungal isolates from the genus Rhizopus and Aspergillus. Keywords: composting, lignin, microbes, OPEFB, 16S rRNA ABSTRAKTKKS (tandan kosong kelapa sawit) berpotensi dimanfaatkan sebagai pupuk organik atau pakan ternak dengan cara pengomposan. Informasi mikroba yang berperan dalam pengomposan alami TKKS hingga saat ini belum banyak diketahui. Penelitian ini bertujuan mendapatkan isolat mikroba pendegradasi lignin dalam pengomposan alami TKKS asal Perkebunan dan Pabrik Pemerasan Kelapa Sawit, PTPN VIII Cikasungka, Bogor, serta mengidentifikasi mikroba tersebut secara molekuler. Skrining mikroba aktif pendegradasi lignin dilakukan terhadap 17 sampel TKKS yang sudah lapuk secara alami. Sebanyak 19 isolat jamur dan 80 isolat bakteri telah dihasilkan. Aktivitas ligninolitik diukur dengan metode pengujian Sundman dan Nase. Isolat jamur yang memiliki aktivitas ligninolitik sebanyak 13 isolat, sedangkan bakteri sebanyak 15 isolat. Isolat-isolat aktif tersebut selanjutnya diidentifikasi secara molekuler berdasarkan pada sekuen ITS di daerah DNA ribosom untuk jamur dan menggunakan gen 16S rRNA untuk bakteri. Hasil menunjukkan bahwa 5 isolat bakteri yang memiliki kemampuan mendegradasi lignin berasal dari genus Bacillus, sedangkan 3 isolat jamur pendegradasi lignin berasal dari genus Rhizopus dan Aspergillus Kata Kunci: lignin, mikroba, pengomposan, TKKS, 16S rRNA 
PROLIFERATION OF OIL PALM (Elaeis guineensis Jacq.) EMBRYOGENIC CALLUS WITH REPEATED SUBCULTURES IN LIQUID MEDIUM Karyanti, Karyanti; Tajuddin, Teuku; Khairiyah, Hayat; Purwoko, Devit; Sukarnih, Tati; Rahmadara, Gemilang; Hanifah, Nurul Fitri; Rudiyana, Yayan; Kitagawa, Sayuri; Mira, Farida Rosana; Saga, Hirohisa
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 8 No. 1 (2021): June 2021
Publisher : Balai Bioteknologi, Badan Pengkajian dan Penerapan Teknologi (BPPT)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (977.075 KB) | DOI: 10.29122/jbbi.v8i1.4715

Abstract

The availability of high-quality seeds is now a necessity. This is due to a government program to replace oil palm trees in smallholder plantations with high quality seeds. An efficient protocol to produce a large number of embryos is needed. To increase the number of embryogenic callus production, the callus proliferation experiment was carried out through suspension culture. This study aimed to examine the proliferation ability of embryogenic callus from three different oil palm clones, in several repeated subcultures. Liquid MS media added with 1 ppm 2.4-D and 0.1 ppm NAA were used. Embryogenic callus was weighed by 0.1 - 0.2 g, transferred into the liquid media, shaking at 60-80 rpm and 27 ºC for 8 weeks without light. Continues subcultures were repeated up to 7 times. The results showed that the growth rate of embryogenic callus increased in the third and fourth subcultures and then decreased in subsequent subcultures. It also revealed that the entire embryogenic callus from the first subculture up to seventh subculture still has the ability to regenerate into new plants. These results indicate that oil palm embryogenic callus can be proliferated by suspension culture with a limit up to the fourth subculture. Ketersediaan benih kelapa sawit berkualitas saat ini merupakan kebutuhan karena adanya program pemerintah untuk menggantikan tanaman sawit di kebun-kebun petani. Salah satu cara vegetatif yang dapat dilakukan adalah meningkatkan jumlah kalus embriogenik yang dihasilkan melalui pengembangan kultur suspensi. Penelitian ini bertujuan mengkaji kemampuan proliferasi kalus embriogenik dari tiga klon kelapa sawit, pada beberapa kali subkultur yang berulang. Media cair MS dengan penambahan 1 ppm 2,4-D dan 0,1 ppm NAA digunakan untuk memperbanyak 0,1–0,2 g kalus embriogenik, dikocok pada 60-80 rpm dan suhu 27 ºC tanpa cahaya selama 8 minggu. Subkultur berulang dilakukan hingga 7 kali. Hasil percobaan menunjukkan bahwa kemampuan proliferasi kalus dipengaruhi oleh genotip tanaman induk. Rata-rata kalus embriogenik dapat meningkat pada subkultur ke-3 dan ke-4 dan semakin menurun pada subkultur selanjutnya. Kalus embriogenik hasil proliferasi subkultur pertama hingga ke-7 dapat tumbuh menjadi calon tanaman baru. Hasil ini menunjukkan bahwa kalus embriogenik kelapa sawit dapat diperbanyak dengan kultur suspensi pada batas sampai subkultur ke-4.
Co-Authors Abd. Rasyid Syamsuri AGUS SUYONO Anna Safarrida, Anna Bedah Rupaedah, Bedah Cartealy, Imam Cartealy, Imam Civi damayanti, dini Diny Dinarti Farida Rosana Mira, Farida Rosana Hanifah, Nurul Fitri Karyanti Karyanti, Karyanti Karyanti, . Khairiyah, Hayat Kitagawa, Sayuri Mahmud Sugianto, Mahmud Pramudyawardhani, Okky Dwi Rahmadara, Gemilang Rudiyana, Yayan Saga, Hirohisa Siti Zulaeha, Siti Sudarsono Sudjai, Imam Suharsono Suharsono Suparningtyas, Juniza Firdha Tati Sukarnih, Tati Teuku Tajuddin