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All Journal HAYATI Journal of Biosciences Jurnal Ilmu Pertanian Indonesia Jurnal Primatologi Indonesia Jurnal Sain Veteriner JURNAL PENELITIAN ILMU PENDIDIKAN Jurnal Veteriner Jurnal Usia Dini Microbiology Indonesia Jurnal Pendidikan Anak Seminar Nasional Teknik Kimia Kejuangan Traditional Medicine Journal ZOO INDONESIA The Indonesian Biomedical Journal VISI : Jurnal Ilmiah Pendidik dan Tenaga Kependidikan Pendidikan Non Formal Jurnal Respirologi Indonesia Zoo Indonesia Jurnal Kedokteran Hewan The International Journal of Tropical Veterinary and Biomedical Research
Joko Pamungkas
Fakultas Kedokteran Hewan, Institut Pertanian Bogor
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Decision Sciences, Operations Research & Management Earth & Planetary Sciences Education Engineering Environmental Science Health Professions Immunology & microbiology Medicine & Pharmacology Public Health Social Sciences Veterinary Other

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Identification of Diagnostic Mitochondrial DNA Single Nucleotide Polymorphisms Specific to Sumatran Orangutan (Pongo abelii) Populations Puji Rianti; Dyah Perwitasari-Farajallah; Dondin Sajuthi; Joko Pamungkas; Alexander Nater; Michael Krützen
HAYATI Journal of Biosciences Vol. 22 No. 4 (2015): October 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1662.775 KB) | DOI: 10.4308/hjb.22.4.149

Abstract

The hypervariable region I of mitochondrial DNA has frequently been used to distinguish among populations, in particular in species with strong female philopatry. In such cases, populations are expected to diverge rapidly for hypervariable region I markers because of the smaller effective population size and thus increased genetic drift. This rapid divergence leads to the accumulation of mutations exclusively found in one population, which may serve as diagnostic single nucleotide polymorphisms (SNPs). To date, diagnostic SNPs distinctive to Sumatran orangutan populations have not yet been described. However, given the continuously declining numbers of Sumatran orangutans, this information can be vital for effective conservation measures, especially regarding reintroductions of orangutans in rehabilitation centers. Phylogenetic analyses of 54 samples of Sumatran orangutans from nine sampling sites with good provenance, we found five major clades and a total of 20 haplotypes. We propose a total of 52 diagnostic SNPs that are specific to Sumatran orangutan populations. Data can be used to develop restriction fragment length polymorphism assays to carry out genetic assignments using basic laboratory equipment to assign Sumatran orangutan to their population of origin.
Isolation and Characterization of C-C Chemokine Ligand 7 (CCL7) in Cynomolgus Macaques Sela S. Mariya; Fitriya N. Dewi; Villiandra Villiandra; Yasmina A. Paramastri; Diah Iskandriati; Uus Saepuloh; Eric Hayes; Joko Pamungkas; Dondin Sajuthi
HAYATI Journal of Biosciences Vol. 26 No. 3 (2019): July 2019
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (261.18 KB) | DOI: 10.4308/hjb.26.3.129

Abstract

Cynomolgus macaques (Macaca fascicularis) are an established animal model of asthma, which exhibit different responses to allergen exposure that are clinically relevant. The chemokine ligand gene (CCL7) encodes Monocyte Chemotactic Protein-3, which has an important role in asthma pathogenesis. While CCL7 polymorphism in humans is associated with asthma phenotype, very little is known about CCL7 in nonhuman primate models of respiratory disease. The objective of this study was to isolate and characterize CCL7 gene in cynomolgus macaques of Indonesian origin. In this study, we used sequencing and bioinformatics technique for gene isolation, characterization, and protein 3D structure prediction. We isolated a 2253 base-pair (bp) sequence of CCL7 in cynomolgus macaques, which exhibited 95% similarity in coding sequence to human CCL7. The amino acid sequence was more closely clustered with human CCL7 than with that of rodents. Importantly, the predictive protein structure of CCL7 was similar to that in humans. These similarities in CCL7 suggests the potential of cynomolgus macaque as a translational model to study asthma, particularly in the context of genetics and role of chemokines such as CCL7.
Ekspresi Enzim Rekombinan Reverse Transcriptase (RTRNase H) Simian Betaretrovirus Serotipe-2 Asal Macaca fascicularis Indonesia dalam Sistem Ekspresi Eschericia coli Uus Saepuloh; Diah Iskandriati; Joko Pamungkas; Dondin Sajuthi
Jurnal Ilmu Pertanian Indonesia Vol. 18 No. 1 (2013): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

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Abstract

Reverse transcriptase (RT) enzyme is a key tool in molecular biology for the synthesis of complementary DNA (cDNA) from messenger RNA (mRNA). Combining RT activity with PCR amplification has been a gold standard as the first step in cloning the coding region of any gene of interest. Evidently, RTs have been critical in advancing molecular biology, genetics and medicine to their current stage. In this study, we were developing the RTDRNase H recombinant enzyme isolated from serotype-2 simian betaretrovirus-2 (SRV-2) infected Indonesian Macaca fascicularis using Escherichia coli expression system. The study was conducted using RT SRV-2 gene expression using E. coli expression system, proteins purification, and application to RT PCR technique. The SDS PAGE expression analysis showed a specific band size of 32.7 kDa assumed as RT protein enzyme. Application of RT SRV-2 enzyme generated to the RT PCR technique of β-globin CDV and SRV-2 env gene target showed that the RT SRV-2 enzyme was capable to reverse transcribed mRNA into cDNA as indicated by the presence of specific DNA band compared with commercial RT enzymes. This RT SRV-2 enzyme showed its activity similar to that of commercial one, although the activity was lower.
Antibodi Simian Aids Retrovirus (SRV) pada Kera Ekor Panjang (Macaca fascicularis) asal Indonesia Joko Pamungkas; Bambang Joeniman; Robin Watanabe; LaRene Kuller; Ann Schmidt; Margaret E Thouless; William R Morton
Jurnal Ilmu Pertanian Indonesia Vol. 1 No. 1 (1991): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

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Abstract

In 1986, Institut Pertanian Bogor
Tarsier an endemic primate species to the Indonesian island of Sulawesi. It is important to find information on the type of habitat, use of nesting trees, natural food consumed and distribution of tarsier in Central Sulawesi and Gorontalo.  The study was implemented from June to August 2009 at five locations.  Data collected consisted of habitat, nests or sleeping trees, type of vegetation, and natural food sources of tarsier.  Observations of tarsiers activities were started at 04.00-07.00 cont Walberto Sinaga; Wirdateti .; Entang Iskandar; Joko Pamungkas
Jurnal Primatologi Indonesia Vol. 6 No. 2 (2009)
Publisher : Pusat Studi Satwa Primata LPPM-IPB

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Abstract

Tarsier an endemic primate species to the Indonesian island of Sulawesi. It is important to find information on the type of habitat, use of nesting trees, natural food consumed and distribution of tarsier in Central Sulawesi and Gorontalo.  The study was implemented from June to August 2009 at five locations.  Data collected consisted of habitat, nests or sleeping trees, type of vegetation, and natural food sources of tarsier.  Observations of tarsiers activities were started at 04.00-07.00 continued from 07.30-10.00 and at 16.00, every day for a period of three months.  Distribution of tarsier was estimated by capturing the tarsier using a net of six, nine and 12 meters.  This study showed that tarsier inhabits secondary forests, and crop fields belonging to local inhabitants. Vegetation used as sleeping trees or nests were bamboo (Bambuseae sp.), beringin (Ficus sp.), alang-alang (Imperata cylindrica), waru (Hibiscus tiliaceus), enau (Arenga pinnata), and liana (Liana sp.).  In addition, tarsier also nested in stony crevices, holes in the ground wood. The distribution of tarsier encompases secondary forest, estates, agricultural land, fields, and brushes. Natural food consumed by tarsier were insects 81.2%, reptiles 12.5% and young birds 1.3%. Mature tarsier consumed 12.76 g/individual/day of edible dry matter or about 12% by body weight and used 69.09 kkal/kg of energy.  These numbers are considered sufficient to satisfy their needs for reproduction.Key words: Tarsius sp., habitat, feed, Central Sulawesi, Gorontalo.
Karakteristik Morfometri, Fisiologi, Hematologi dan Kimia Darah Owa Jawa (Hylobates moloch) di Penangkaran Pusat Studi Satwa Primata–IPB Permana wati; Y. Fitrianis; Lila .; Y. Paramastri; I Nengah Budiarsa; Joko Pamungkas
Jurnal Primatologi Indonesia Vol. 6 No. 1 (2009)
Publisher : Pusat Studi Satwa Primata LPPM-IPB

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Abstract

The aim of this study was to provide information on morphometrical, physiological, hematological and blood chemical values data of Javan Silvery Gibbon (Hylobates moloch). These data were collected from one family in captive breeding at the Primate Research Center of Bogor Agricultural University. The family consisted of one adult male, and female, including their  three offspring (2 females and 1 male). There was no previous publication reference available for Hylobates moloch.  In comparison to other different species within the same genus of Hylobates, there were difference in hematologic and serum biochemical values between Hylobates moloch and Hylobates lar. Keywords: morphological, physiological, hematological, blood-chemical values, Hylobates moloch.
Tingkah Laku Owa Jawa (Hylobates moloch) di Fasilitas Penangkaran Pusat Studi Satwa Primata, Institut Pertanian Bogor Septiantina Dyah Riendriasari; Entang Iskandar; Jansen Manansang; Joko Pamungkas
Jurnal Primatologi Indonesia Vol. 6 No. 1 (2009)
Publisher : Pusat Studi Satwa Primata LPPM-IPB

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Abstract

The Javan Gibbon is a primate species endemic to Java, Indonesia and considered as an endangered species (IUCN 2008). The Primate Research Center of Bogor Agricultural University (PRC-IPB) in cooperation with Taman Safari Indonesia have established an ex situ breeding facility for the Javan Gibbon to support conservation program. The breeding was started in 2003, and up to recently, the pair of Javan Gibbons ( 15 and 7 years old) has had three offspring, and still occupy one common cage. Assessment of the Javan Gibbon’s behavior in captivity especially to the family with five individuals was conducted using focal animal sampling to provide basic behavioral data.  Moving was the greatest frequency (45.70%) of each individual compared to other behaviors, while resting was the greatest duration that occurred to the parents, and playing was the greatest duration (18.02%) to the offspring respectively.    Keywords : behavior, javan gibbon, endangered, captive breeding
Analisis DNA Mikrosatelit untuk Identifikasi Paternitas pada Beruk (Macaca nemestrina) di Penangkaran Pusat Studi Satwa Primata IPB Novita Anggraeni; Ellis Dwi Ayuningsih; Dyah Perwitasari Farajallah; Joko Pamungkas
Jurnal Primatologi Indonesia Vol. 6 No. 2 (2009)
Publisher : Pusat Studi Satwa Primata LPPM-IPB

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Abstract

The increase of population number of pigtailed macaque in Bogor Agricultural University captive breeding facility, was the reason to conduct the research of paternity using microsatellite DNA analysis. Paternity data will be used for determination of Macaca nemestrina colony management. Based on the paternity analysis results showed that in the Koral A, male (No. 6742) is a breeder for offspring (100%), these male is sub-ordinate in that group. Meanwhile, in the Koral B, male (No. 6180) is a breeder for the siblings in that group (92%) this is dominant male, and another male (No. 6747) is 8% of breeder for the existing siblings. On the other hands, the heterozigosity analysis showed that there were ten allele had been detected in locus D1S548, seven alleles in locus D5S820, and six alleles in locus D2S1777 and D3S1768. The amplicon of locus D1SS548, D3S1768, D5S820, D12S1777 are 180-232 bp, 150-178, 189-217, 153-174, respectivelly. The heterozygosis per locus (h) was 0,5168 for D3S1768, D12S1777 and 0,5934 for D1S548. And the average Heterozigosis per all loci       detected was 0.5399.Key words: microsatellite DNA, paternity, beruk, Macaca nemestrina
Konsumsi Pakan Asal Hewan pada Kukang (Nycticebus coucang) di Fasilitas Penangkaran, Pusat Studi Satwa Primata (PSSP) IPB Walberto Sinaga; Dewi Apri Astuti; Entang Iskandar; Wirdateti .; Joko Pamungkas
Jurnal Primatologi Indonesia Vol. 7 No. 2 (2010)
Publisher : Pusat Studi Satwa Primata LPPM-IPB

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Abstract

Abstrak. Sebagai salah satu upaya konservasi, Pusat Studi Satwa Primata, Institut Pertanian Bogor (PSSP IPB) menangkarkan kukang (Nyticebus coucang) di luar habitat aslinya (eks-situ). Penelitian ini bertujuan untuk mendapatkan data konsumsi pakan asal hewan pada kukang dewasa selama satu tahun di Penangkaran PSSP IPB. Hewan yang diamati berada dalam enam kandang dengan ukuran yang sama, serta umur yang hampir seragam, masing-masing kandang berisi 2 atau 1 ekor kukang dewasa dengan jumlah keseluruhan sepuluh ekor.  kukang berasal dari Pulau Sumatera, dan sudah beradaptasi di penangkaran selama tiga tahun.  Jenis pakan yang diberikan berasal hewan, berupa jangkrik (Gryllus mitratus), ulat hongkong (Tenebrio molitor), ulat sutra (Bombyx mori), cicak (Cosymbotus platyurus) dan kadal rumput (Takydromus sexlineatus). Penelitian perilaku makan kukang dilakukan dengan menggunakan metode One Zero Sampling. Komposisi gizi pakan percobaan dianalisis dengan metode proksimat. Hasil penelitian menunjukkan persentase rerata kesukaan makan  jenis hewan pada semua kukang, dari yang paling disukai hingga yang kurang disukai (rendah) adalah ulat sutra (Bombyx mori) dengan nilai (100%), jangkrik (91,6%), cicak (60%), kadal rumput (59%), dan pakan asal hewan yang kurang disukai adalah ulat hongkong (2,2%). Total konsumsi bahan kering pakan serangga sebanyak 284,11 g/kandang/hari atau sekitar 84,94% dan energi sebanyak 5626,79 kkal/kg.Abstract. As one of the conservation efforts, the Primate Research Center (PRC) of Bogor Agricultural University  has been developing ex-situ captive breeding of coucangs (Nyticebus coucang) since 2005. This study aims to obtain data on the consumption of feed of animal origin by adults coucang during one year at PRC breeding facility. Animals were housed in six cages of the same size, while age was almost similiar. Each cage consists of 2 or 1 coucang with a total of ten animals. The animals originated from the island of Sumatra, and were adapted to captivity for three years. The type of feeds of animal origin were crickets (Gryllus mitratus), caterpillars (Tenebrio Molitor), silkworms (Bombyx mori), lizards (Cosymbotus platyurus) and grass lizards (Takydromus sexlineatus). Feeding behavior was carried out by using One Zero Sampling method. Nutritional composition of the experimental feeds were analyzed by proximate method. The results showed the average percentage of favorite by the coucang from most preferred to least preferred (low) were silkworms (Bombyx mori) with a value of (100%), crickets (91.6%), lizards (60%), grass lizards (59%), while feeds of animal origin which were less favored were hongkong worms (2,2%). Total consumption of dry feed of all insects given, amounted to 284.11 g/cage/day or approximately 84.94% with a high energy level of 5626.79 kcal/kg.Key words: feed consumption, animal origin, N.coucang, captive breeding, nutrient
Aplikasi Metode Perhitungan Hydraulic Flow Unit (HFU) dalam Penentuan Persebaran Permeabilitas pada Model Reservoir Statis Joko Pamungkas; Bambang Bintarto; Farah S Normaysti
Prosiding Seminar Nasional Teknik Kimia "Kejuangan" 2017: PROSIDING SNTKK
Publisher : Seminar Nasional Teknik Kimia Kejuangan

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Abstract

AbstractPermeability in petrophysical analysis is one of the physical properties of rocks that determination productivity, reservoir in place, and fluid distribution in the reservoir. In this study, calculation for permeability distribution using the equation of crossplot between porosity and permeability from routine coredidn’t representative for S Field. Hydraulic Flow Unit (HFU) methodused to gave more representative distribution of permeability in static model.The method of calculated HFU on the S Field is divided into several methods such as : calculated HFU of routine core data (HFU Core), calculated HFU of routine core data and added with permeability and porosity from well test (HFU Core + Perm. Well test), calculatedHFU of routine core data and combined with oil rate from well test (HFU Core + Qo test), and calculatedHFU of routine core data and combined with cumulative oil production from each well (HFU Core + Np). Permeability distribution from HFU Method gave higher values of permeability for S Field than from single transformation (crossplot). The effect of calculated permeability distribution in static reservoir model with HFU method can be seen from oil in place. HFU Core + Np have better permeability distribution than other calculations. It can be seen from a comparison of oil in place (reserves of oil in the reservoir) between the calculation HFU Core + Np with single transformation (crossplot). Oil in place in the static model from the calculation with HFU Core + Npis 58.57 MMSTB while the oil in place with crossplotpermeability and porosity of routine core data is 46.88 MMSTB.
Co-Authors - Sudarmanto Ad Dieni Maulana Rizka Alexander Nater Amir Syamsudin Ann Schmidt Aris Tri Wahyudi Azhari Purbatrapsila Bambang Bintarto Bambang Joeniman Budiman Bela CHAIRIN N MAROEF DEWI APRI ASTUTI Dewi, Fitriya Nur Annisa DIAH ISKANDRIATI Diah Iskandriati DIAH ISKANDRIATI Diah Iskandriati Diah Iskandriati Diah Iskandriati Diah Iskandriati Dondin Sajuthi DYAH PERWITASARI -FARAJALLAH Ellis Dwi Ayuningsih Ellis Dwi Ayuningsih Entang Iskandar Eric Hayes Eric Hayes ERLIN LISTIYANINGSIH ESTHER ARIFIN Faisal Faisal Farah S Normaysti Febrita Cipta Putranti FUNGKEY HOETAMA Gede Eko Darmono I NENGAH BUDIARSA I Nengah Budiarsa Ika Budi Maryatun IMELDA WINOTO Indyah Wahyuni Jansen Manansang JONATHAN STURGIS KEVIN RANDALL PORTER LaRene Kuller Lila . Lilik Prayitno Margaret E Thouless Marlefzena Marlefzena Martha Christianti MARYATI SURYA Michael Krützen Mohamad Sadikin MOSES AFFANDI Nangoy, Meis Ni Luh Putu Ika Mayasari Novita Anggraeni Nur Hayati Nuri Andarwulan PATRICK J BLAIR Permana wati PERMANAWATI PERMANAWATI Puji Rianti Purbatrapsila Azhari Puspo Edi Giriwono R. Suryo Saputra R.P Agus Lelana Rachmitasari Noviana RATNA TAN RICHARD F GRANT Robin Watanabe Safriyanto Dako Sela S Mariya Sela S. Mariya Sela Septima Mariya SELA SEPTIMA MARIYA Septiantina Dyah Riendriasari SILMI MARIYA Silmi Mariya Silvia Triwidyaningtyas Sofia Hartati sri murtini . SUSANA WIDJAJA TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN Tiltje Andretha Ransaleh UUS SAEPULOH Uus Saepuloh UUS SAEPULOH Uus Saepuloh Uus Saepuloh Uus Saepuloh Villiandra Villiandra Villiandra Villiandra Villiandra Villiandra VINCENTIUS ARCA TESTAMENTI Wahid Yulianto Walberto Sinaga Wenty Dwi Febriani William R Morton Wirdateti . Y. Fitrianis Y. Paramastri Yasmina A Pramastri Yasmina A. Paramastri Yasmina Arditi Pramastri YASMINA PARAMASTRI