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Single Nucleotide Polymorphism within the Promoter Region of Cynomolgus Monkey LDLR Gene Achmad - Taher; Dedy Duryadi Solihin; Sulistiyani Sulistiyani; Dewi Apri Astuti; Dondin Sajuthi
Makara Journal of Science Vol 22, No 1 (2018): March
Publisher : Directorate of Research and Community Engagement, Universitas Indonesia

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The cynomolgus monkey (Macaca fascicularis) is one of the most common nonhuman primates used as an animal model in biomedical research related to atherosclerosis. However, little is known about genetic variation in the low density lipoprotein receptor (LDLR) gene, its effect on cholesterol levels, and associated risks of atherosclerosis. Therefore this study aimed to identify genetic polymorphisms, namely single nucleotide polymorphisms (SNPs), within the promoter region of LDLR and their relationship with animal responsiveness to hypercholesterolemia due to an atherogenic diet. In this research, SNPs were studied using DNA isolated from 22 cynomolgus monkeys obtained from a previous study, consisting of two hyporesponders, 19 hyperresponders, and one extreme case. The result showed that two SNPs existed in the promoter region, namely g.−169T>C and g.−265G>A. SNP g.−265G>A showed linkages with extreme responsiveness and can be used as a potential genetic marker for extreme animals. The result of this study has extended our knowledge of polymorphism in the LDLR gene and its use in the selection of cynomolgus monkeys as animal models in research on hypercholesterolemia and atherosclerosis.
Variasi Molekuler Gen Reseptor Melanokortin-4 pada Monyet Ekor Panjang I Gusti Agung Arta Putra; Dondin Sajuthi; Dedy Duryadi Solihin; Raden Roro Dyah Perwitasari
Jurnal Veteriner Vol 11 No 3 (2010)
Publisher : Faculty of Veterinary Medicine, Udayana University and Published in collaboration with the Indonesia Veterinarian Association

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Melanocortin-4 receptor (MC4R) is one of G protein-coupled receptors that plays an important role inregulation of energy homeostasis. MC4R mutations constitute the most common cause of human obesity.The study was conducted in order to investigate the variation of MC4R gene in Macaca fascicularis and itsassociation with obesity as a model of human obesity. Forty eight adult male macaques from Bali (Ubudand Uluwatu), East Java (Alas Purwo and Baluran), and Sumatera island (Palembang) were used in thisresearch. The animals had been anaesthetized using ketamine (10 mg/kg body weight) and xylazine (2mg/kg body weight) before collecting blood samples and phenotypic data (weight, crown rump length. Bloodsamples were used as source of DNA. To determine MC4R variation, coding region of this gene wasamplified and sequenced. The results showed that 20 variations sites were identified and 13 of them werenon-synonymous. Among the non-synonymous mutations, five mutations were only found in obese macaque;two mutations were found both in obese and non-obese macaque; and six mutations were only found in nonobesemacaque .
Variasi Kolesterol Plasma Individual Monyet Ekor Panjang (Macaca fascicularis) sebagai Respons terhadap Diet Aterogenik IPB-1 [INDIVIDUAL PLASMA CHOLESTEROL VARIATION OF CYNOMOLGUS MACAQUE (MACACA FASCICULARIS) IN RESPONSE TO IPB-1 ATHEROGENIC DIET] Achmad Taher; Dedy Duryadi Solihin; Sulistiyani Sulistiyani; Dondin Sajuthi; Dewi Apri Astuti
Jurnal Veteriner Vol 17 No 4 (2016)
Publisher : Faculty of Veterinary Medicine, Udayana University and Published in collaboration with the Indonesia Veterinarian Association

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Abstract

The effectiveness of atherogenic diet in raising plasma cholesterol level of cynomolgus macaques(Macaca fascicularis) can be predicted for population, but not for individuals.This study aimed to evaluatethe individual plasma cholesterol of cynomolgus macaques in response to IPB-1 atherogenic diet. Theanimals under study were 22 adult malemonkeys from the animal facility of Primate Research CenterBogor Agricultural University (PSSP IPB). All animals were intervened with the IPB-1 atherogenic diet forthree months and individual plasma cholesterol wasevaluated in a monthly basis.The results showedthat the monkeys’ plasma cholesterol had increased significantly (P <0.05) after one month of interventionperiod and the increases were very significantly different (P <0.01) after three months. Individually, increasesin plasma cholesterol varied among animals. Based on these variations, 2 animals were categorised ashypo-response, 18 animals as hyper-response and 2 animals as extreme.This study showed the variationof individual plasma cholesterol of cynomolgus macaques in response tothe IPB-1 atherogenic diet so thatthe animals might be selected based on the their responsiveness.
ANALISIS DNA MITOKONDRIA BADAK SUMATERA DALAM KONSERVASI GENETIK Handayani Handayani; Dedy Duryadi Solihin; Hadi S Alikodra
Proceeding Biology Education Conference: Biology, Science, Enviromental, and Learning Vol 8, No 1 (2011): Prosiding Seminar Nasional VIII Biologi
Publisher : Universitas Sebelas Maret

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ABSTRAK   Populasi badak Sumatera dewasa ini semakin terancam keberadaannya. Hal ini disebabkan oleh beberapa faktor, diantaranya adalah semakin maraknya perburuan liar, rusaknya habitat alamnya yang disebabkan oleh konversi hutan yang cenderung tidak terkendali. Populasi kecil lebih rentan pada penurunan keragaman genetik karena efek inbreeding serta terfiksasinya beberapa alela tertentu dalam populasi sehingga hewan tersebut menjadi monomorf dan mengalami penurunan kemampuan berevolusi atau adaptasinya pada lingkungan yang berubah. Selain itu berkurangnya populasi, faktor lain adalah terjadinya fragmentasi suatu habitat yang akan mendorong putusnya aliran gen (gen flow) dan meningkatnya genetic drift. Keragaman genetik turut menentukan keberhasilan konservasi populasi. Oleh karena itu penelitian keragaman genetik dari populasi Badak Sumatera merupakan langkah penting yang harus dilakukan, dan keberhasilan penelitian ini merupakan langkah  dalam konservasi badak Sumatera. Pengumpulan sampel darah berasal dari SRS (Suaka Rhino Sumatera) TN Way Kambas Lampung. Sample berupa darah dari 2 ekor badak sumatera berjenis kelamin betina (Rosa & Bina) dan 2 ekor badak jantan (Torgamba & Andalas). Isolasi dan purifikasi DNA Total dilakukan menggunakan metode Duryadi. Amplifikasi daerah CO I pada badak Sumatera dilakukan dengan PCR menggunakan pasangan primer RHCOIF dan RHCOIR. Amplifikasi daerah CO I pada badak Sumatera dilakukan dengan menggunakan pasangan primer RHCOIF dan RHCOIR menghasilkan fragmen DNA berukuran 711 bp. Jarak genetik digunakan untuk melihat kedekatan hubungan genetik antar individu badak Sumatera dan spesies badak lain melalui penggunaan analisis perhitungan Pairwie Distance dengan p-distance dapat ditunjukkan matriks perbedaan genetik antara badak Sumatera dan badak outgroup (badak India dan badak Afrika), hasil perhitungan berdasarkan daerah CO I parsial menunjukkan nilai jarak genetik berkisar antara 0.016 sampai 0.147. Jarak genetik pada Bina (♀) terlihat dekat dengan Torgamba (♂) sebesar 0.007. Hubungan kekerabatan CO I menggunakan Neighbor-Joining dengan pengolahan bootstrap 1000 terlihat bahwa badak putih Afrika berbeda kelompok dengan badak Asia. Di dalam kelompok badak Asia terlihat bahwa badak India sama dengan kelompok dengan badak Sumatera (Indonesia). Di dalam badak Sumatera (Indonesia) sendiri terjadi keragaman. Berdasarkan hasil sekuen gen CO I terdapat situs-situs spesifik pada badak Sumatera sebesar adalah 67% hasil tersebut dapat digunakan sebagai data base dalam penelitian-penelitian selanjutnya.   Kata kunci: badak Sumatera, DNA, mitokondria, konservasi
ANALISIS DNA MITOKONDRIA BADAK SUMATERA DALAM KONSERVASI GENETIK Solihin, Dedy Duryadi; S Alikodra, Hadi; Handayani, Handayani
Prosiding Seminar Biologi Vol 8, No 1 (2011): Seminar Nasional VIII Pendidikan Biologi
Publisher : Prodi Pendidikan Biologi FKIP UNS

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Abstract

ABSTRAK   Populasi badak Sumatera dewasa ini semakin terancam keberadaannya. Hal ini disebabkan oleh beberapa faktor, diantaranya adalah semakin maraknya perburuan liar, rusaknya habitat alamnya yang disebabkan oleh konversi hutan yang cenderung tidak terkendali. Populasi kecil lebih rentan pada penurunan keragaman genetik karena efek inbreeding serta terfiksasinya beberapa alela tertentu dalam populasi sehingga hewan tersebut menjadi monomorf dan mengalami penurunan kemampuan berevolusi atau adaptasinya pada lingkungan yang berubah. Selain itu berkurangnya populasi, faktor lain adalah terjadinya fragmentasi suatu habitat yang akan mendorong putusnya aliran gen (gen flow) dan meningkatnya genetic drift. Keragaman genetik turut menentukan keberhasilan konservasi populasi. Oleh karena itu penelitian keragaman genetik dari populasi Badak Sumatera merupakan langkah penting yang harus dilakukan, dan keberhasilan penelitian ini merupakan langkah  dalam konservasi badak Sumatera. Pengumpulan sampel darah berasal dari SRS (Suaka Rhino Sumatera) TN Way Kambas Lampung. Sample berupa darah dari 2 ekor badak sumatera berjenis kelamin betina (Rosa &amp; Bina) dan 2 ekor badak jantan (Torgamba &amp; Andalas). Isolasi dan purifikasi DNA Total dilakukan menggunakan metode Duryadi. Amplifikasi daerah CO I pada badak Sumatera dilakukan dengan PCR menggunakan pasangan primer RHCOIF dan RHCOIR. Amplifikasi daerah CO I pada badak Sumatera dilakukan dengan menggunakan pasangan primer RHCOIF dan RHCOIR menghasilkan fragmen DNA berukuran 711 bp. Jarak genetik digunakan untuk melihat kedekatan hubungan genetik antar individu badak Sumatera dan spesies badak lain melalui penggunaan analisis perhitungan Pairwie Distance dengan p-distance dapat ditunjukkan matriks perbedaan genetik antara badak Sumatera dan badak outgroup (badak India dan badak Afrika), hasil perhitungan berdasarkan daerah CO I parsial menunjukkan nilai jarak genetik berkisar antara 0.016 sampai 0.147. Jarak genetik pada Bina (?) terlihat dekat dengan Torgamba (?) sebesar 0.007. Hubungan kekerabatan CO I menggunakan Neighbor-Joining dengan pengolahan bootstrap 1000 terlihat bahwa badak putih Afrika berbeda kelompok dengan badak Asia. Di dalam kelompok badak Asia terlihat bahwa badak India sama dengan kelompok dengan badak Sumatera (Indonesia). Di dalam badak Sumatera (Indonesia) sendiri terjadi keragaman. Berdasarkan hasil sekuen gen CO I terdapat situs-situs spesifik pada badak Sumatera sebesar adalah 67% hasil tersebut dapat digunakan sebagai data base dalam penelitian-penelitian selanjutnya.   Kata kunci: badak Sumatera, DNA, mitokondria, konservasi
Keanekaragaman Kumbang Lucanid (Coleoptera:Lucanidae) Pada Berbagai Ketinggian Tempat di Hutan Konsensi Unocal Gunung Salak, Jawa Barat Roni Koneri; Dedy Duryadi Solihin; Damayanti Buchori; Rudi Tarumingkeng
Jurnal Matematika & Sains Vol 15, No 2 (2010)
Publisher : Institut Teknologi Bandung

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Lucanids beetles play a very important role in forest ecosystem and as an crucial element of biodiversity.   The objectives of the research were to study the effects of different altitutdes on the community of lucanids beetles. Beetles collection was conducted by hand collection.  Insect  collections were conducted monthly during 12 months. This result identified 12 species of Lucanids beetles with 1.133 individuals. Altitude was found to have a strong effect on Lucanids beetles community. Redundancy analysis identified that total volume of coarse woody debris in the selected locations was recorded as key environmental factor influencing community structure of lucanids beetles. Based on canonical correspondence analysis, the distribution of the beetles were affected by the volume of coarse woody debris in decay class 2.
Distribution Patterns of the Morphology, Species, and Sex in the Stingray Species Complex of Himantura uarnak, Himantura undulata,and Himantura leopardain Indonesia Irma Shita Arlyza; Dedy Duryadi Solihin; Dedi . Soedharma
Makara Journal of Science Vol 17, No 2 (2013): August
Publisher : Directorate of Research and Community Engagement, Universitas Indonesia

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Abstract The assessment of the morphology and stingray species distribution of the Himantura uarnak species complex covers eight sampling sites in western and eastern Indonesia as many as 113 individuals. The observation of the reticulate pattern was accomplished by directly checking the dorsal side of the stingrays, and growth observations also carried out. The distribution patterns were analyzed using the principal component analysis (PCA), while the growth patterns were evaluated using correlation analyses. The reticulation patterns of the H. uarnak species complex were highly variable, and the distribution patterns based on the morphological parameters, species, and sex produced four groups. The distribution of the length frequency of H. undulata and H. uarnak showed a range of different sizes. The body length of the female in the western region is relatively longer than the male, while in the eastern region the female revealed a range in relative size showing that the male was longer than the female. The length-weight relationships of the stingrays were negative allometric, indicating a b-value of less than 3. The b-values of both the male and female H. undulata were 1.5860 and 0.4380, respectively; while the male and female H. uarnak were 0.2956 and 0.4376, respectively. Abstrak Pola Distribusi dari Morfologi, Spesies dan Jenis Kelamin pada Kompleks Spesies Ikan Pari Himantura uarnak, Himantura undulata dan Himantura leoparda di Indonesia. Penilaian terhadap morfologi dan distribusi spesies dari ikan pari kompleks spesies H. uarnak meliputi delapan lokasi pengambilan sampel di barat dan timur Indonesia sebanyak 113 individu. Identifikasi spesimen mengikuti kunci family Dasyatidae, untuk genus Himantura. Pengamatan pola retikulasi dilakukan dengan pengecekan langsung pada punggung ikan pari dan observasi pertumbuhan juga dilakukan. Pola distribusi ikan pari dianalisis dengan principal component analysis (PCA), sedangkan pola pertumbuhan menggunakan analisis korelasi. Pola retikulasi kompleks spesies H. uarnak sangat bervariasi. Pola distribusi berdasarkan parameter morfologi, spesies dan jenis kelamin ikan pari menghasilkan empat kelompok. Distribusi panjang frekuensi H. undulata dan H. uarnak menunjukkan berbagai ukuran yang berbeda. Panjang tubuh dari betina di wilayah barat relatif lebih panjang dari jenis kelamin jantan, sedangkan wilayah timur menunjukkan bahwa ukuran tubuh dari jenis kelamin jantan relatif lebih panjang dari betina. Hubungan panjang-berat ikan pari menunjukkan alometrik negatif dengan nilai b kurang dari 3. Nilai b pada masing-masing jantan dan betina dari H. undulata adalah 1,5860 dan 0,4380, sedangkan masing-masing jantan dan betina H. uarnak adalah 0,2956 dan 0,4376. Keywords: distribution pattern, Himantura uarnak species complex, morphology, reticulation, stingray
Identification of Gene Resistance to Avian Influenza Virus (Mx Gene) among Wild Waterbirds Dewi Elfidasari; Dedy Duryadi Solihin; Retno Damayanti Soejoedono; Sri Murtini
Makara Journal of Science Vol 17, No 1 (2013): April
Publisher : Directorate of Research and Community Engagement, Universitas Indonesia

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The Mx gene is an antiviral gene used to determine the resistance or the susceptibility to different types of viruses, including the Avian Influenza (AI) virus subtype H5N1. The AI virus subtype H5N1 infection in chickens causes Mx gene polymorphism. The Mx+ gene shows resistant to the AI virus subtype H5N1, whereas the Mx- gene shows signs of susceptible. The objective of this research was to detect the Mx gene in wild aquatic birds using the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method with the primer pairs F2 and NE-R2/R and the RsaI restriction enzyme. DNA samples were obtained from eight species of wild waterbirds with positive and negative exposure to the AI virus subtype H5N1. DNA amplification results showed that the Mx gene in wild aquatic birds is found in a 100 bp fragment, which is the same as the Mx gene found in chickens. However, unlike chickens, the Mx gene in wild aquatic birds did not show any polymorphism. This study proves that Mx- based resistance to AI virus subtype H5N1 in different in wild birds than in chickens. Keywords: Mx gene, wild waterbirds, exposure, AI virus subtype H5N1, resistance Keywords: Mx gene, wild waterbirds, exposure, AI virus subtype H5N1, resistance
Serosurveillance of Avian Influenza Virus Subtype H5N1 with Haemagglutination-Inhibition on Wild Aquatic Birds in Pulau Dua Serang Natural Reserves, Banten Province Dewi Elfidasari; Dedy Duryadi Solihin; Retno Damayanti Soejoedono; Sri Murtini; Yus Rusila Noor
Makara Journal of Science Vol 15, No 2 (2011): November
Publisher : Directorate of Research and Community Engagement, Universitas Indonesia

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Further detailed research is required to obtain deeper information on the role of wild birds on the distribution of Avian influenza in Asia. A research has been carried out on February&ndash;June 2007 focused on blood sampling (serosurveillance) of wild birds in Pulau Dua Nature Reserves (CAPD), Serang, Banten. The research is aimed to investigate the infection of AI virus sub-tye H5N1 on the studied wild birds. The blood samples were taken from studied aquatic birds, followed by HI (haemagglutination-inhibition) test. A total of 183 samples represent 7 water bird species were taken i.e Cattle egret Bubulcus ibis, Javan pond-heron Ardeola speciosa, Little egret Egretta garzetta, Intermediate egret Egretta intermedia, Black-crowned night heron Nycticorax nycticorax, Great egret Casmerodius albus and Grey heron Ardea cinerea. The result revealed that 41 (23.27%) samples showed the present of AIV antibodies serotype H5N1 which is identified as positive. Data showed 5 positive-test species, including B. ibis (29.27%), E. garzetta (29.27%), E. intermedia (4.88%), Ardeola speciosa (7.32%), and N. nycticorax (29.27%). A total of 41.46% were infected adult individual, whereas 58.54% were juveniles.
Genetic Diversity and The Relationship Between The Indonesian Mangosteen (Garcinia Mangostana) and The Related Species Using Isozyme Markers Sinaga, Soaloon; Sobir, Sobir; Poerwanto, Roedhy; Aswidinnoor, Hajrial; Duryadi, Dedy
Jurnal Natur Indonesia Vol 13, No 1 (2010)
Publisher : Lembaga Penelitian dan Pengabdian kepada Masyarakat Universitas Riau

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Abstract

Indonesia was known to have high diversity of mangosteens (Garcinia mangostana) and the related species. Inorder to elucidate the genetics variability of the diversity, thirty three accessions were examined by using isozymeanalysis. The genetic diversity and relationships among several mangosteens and other Garcinia sp wereestablished by using four isozymes. The level of polymorphism as revealed by isoenzyme was 88%. Althoughmangosteen is believed to reproduce exclusively through apomixis, our result show that considerable geneticdiversity exists within G. mangostana and between other Garcinia species. Based on 27 bands there were 5-42%dissimilarity level among mangosteen accessions, while the other species has 75% dissimilarity. The dendrogramis built based on isozyme marker analysis to separate clusters of mangosteen and other Garcinia sp. The datashowed that G. mangostana is a close relative of G. malaccensis, G. porrecta, G. celebica, and G. hombroniana. Theconcurrence analysis on isozyme analysis result showed the very good fit of Rolf correlation value (0.914). Thisresult indicated that isozymes could group G.mangostana and the related species.
Co-Authors Abdul Rahman Singkam Abdul Rahman Singkam Achmad - Taher ACHMAD FARAJALLAH Achmad Machmud Achmad Machmud Thohari Achmad Taher Achmad Taher Achmad, Taher Agus Nuryanto Agus Wahyana Anggara Agus Wahyana Anggara Agus Wahyana Anggara, Agus Wahyana Alam Putra Persada Ani Mardiastuti Ani Mardiastuti Ani Suryani Antonius Suwanto dan Meity S. Sinaga . Budi Tjahjono Andi Khaeruni R Any Aryani Ardi Kapahang Arief Boediono Arzyana Sunkar Bahiyah Bahiyah Bambang Purwantara Cece Sumantri CECILIA ANNA SEUMAHU CHRISTIAN HANSJOACHIM SCHULZE D.D. Sastraatmadja DAMAYANTI BUCHORI Dedi . Soedharma Dedi Soedharma DEWI APRI ASTUTI Dewi Elfidasari Dewi Malia Prawiradilaga Dewi Malia Prawiradilaga, Dewi Malia Diah Iskandriati DIAH ISKANDRIATI DIETMAR BLOHM Dodi Nandika Dondin Sajuthi Dwi Astuti Dwi ASTUTI Dwi Sendi Priyono DYAH PERWITASARI -FARAJALLAH Epa Paujiah Epa Paujiah Evy Ayu Arida EVY AYU ARIDA Fahma Wijayanti FAHRI FAHRUDIN FUNGKEY HOETAMA Gita Kusuma Rahayu Hadi Allikodra Hadi S Alikodra Hadi S Alikodra HADI SUKADI ALIKODRA HAJRIAL ASWIDINNOOR Handayani Handayani Hari Prayogo Hari Prayogo Harini Nurcahya Mariandayani Heddy Julistiono HEDDY JULISTIONO Hermanu Triwidodo I Gusti Agung Arta Putra I WAYAN SUANA Ibnu Maryanto Iman Rusmana Irma Shita Arlyza Irzaman, Irzaman Isdradjad Setyobudiandi Ismayati Afifah Jamhari Jamhari Jarulis Jarulis Jarulis Jarulis Jarulis Jarulis Jarulis Jarulis Jito Jito Jito Sugardjito Joko Pamungkas Jusmaldi Jusmaldi Jusmaldi Jusmaldi Jusmaldi Jusmaldi Kadarwan Soewardi Khustina, Yenny Chusna Khustina, Yenny Chusna Kunio Watanabe Lia Aseptin Murdini Lilik Budi Lilik Budi Prasetyo Lilik Budi Prasetyo Lucia Johana Lambey M F Rahardjo M. F. Rahardjo M. Zairin Junior MARIA BINTANG MF Rahardjo Muhammad Nur Findra Mustafa Sabri Nastiti Kusumorini NEVIATY PUTRI ZAMANI NIKEN SUBEKTI Niken TM Pratiwi Nurlisa Butet, Nurlisa Prasetyo Prasetyo Priyono, Siti N. Retno Damayanti Soejoedono RICHARD F GRANT Ridwan Affandi Ridwan Affandi Ridwan Affandi Ridwan Affandi Ridwan Affandi Ridwan Affandi Ridwan Affandi Ridwan Affandi Rini Widayanti Robba Fahrisy Darus ROEDHY POERWANTO Roedy Poerwanto Roedy Poerwanto Roni Koneri Ronny Rachman Noor Roza Elvyra Roza Elvyra Rudhy Gustiano Rudhy Gustiano Rudhy Gustiano Rudhy Gustiano Rudi Afnan Rudi Tarumingkeng Rudy C Tarumingkeng Safrida Safrida Saroyo Saroyo SATA YOSHIDA SRIE RAHAYU SATRIYAS ILYAS SELA SEPTIMA MARIYA SILMI MARIYA Siti N. Priyono SJAFRIDA MANUWOTO Soaloon Sinaga Soaloon Sinaga Sobir Sobir Sobir Sobir Sobir Sobir Solihin Solihin Sri Catur Setyawatiningsih Sri Catur Setyawatiningsih sri murtini . SRI NINGSIH Sri Sulandari Sri Supraptini Mansjoer Subyakto Subyakto Sugardjito Sugardjito Suharsono Suharsono Sulistiyani Sulistiyani SULISTIYANI SULISTIYANI SULISTIYANI SULISTIYANI Sulistiyani, Sulistiyani Surjono Surjokusumo Syaiful Anwar Syamsul Bachry Tedjo Sukmono Thohari Thohari Tike Sartika Tri Haryoko Tri Haryoko, Tri UUS SAEPULOH UUS SAEPULOH Wasmen Manalu Yuli Wahyu Tri Mulyani YULIN LESTARI Yuni Cahya Endrawati Yus Rusila Noor Yusnarti Yus