DEDY DURYADI SOLIHIN
Department of Biology, Faculty of Mathematic and Natural Sciences, Bogor Agricultural University, Academic Ring Road, Campus IPB Dramaga, Bogor, Indonesia 16680

Published : 40 Documents
Articles

Found 40 Documents
Search

Comparison of DNA Extraction Methods for Microbial Community Analysis in Indonesian Tempe Employing Amplified Ribosomal Intergenic Spacer Analysis SEUMAHU, CECILIA ANNA; SUWANTO, ANTONIUS; RUSMANA, IMAN; SOLIHIN, DEDY DURYADI
HAYATI Journal of Biosciences Vol 19, No 2 (2012): June 2012
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (136.378 KB) | DOI: 10.4308/hjb.19.2.93

Abstract

Tempe fermentation involved complex microbial communities which are only revealed partially through culture dependent methods. Culture-independent methods would be potential to unravel this complex microbial fermentation. Appropriate DNA extraction is an essential tool to obtain reliable data from culture independent method. In this study, we employed two commercial DNA extraction methods to find the best one for microbial community characterization employing amplified ribosomal intergenic spacer analysis (ARISA). Our result showed that PowerFood Microbial DNA Isolation Kit-MOBIO (PFMDIK) is an excellent method for microbial DNA extraction from tempe. It gave high quantity and quality of DNA suitable for PCR amplification of 16S-23S rRNA intergenic spacer to yield a diverse and reproducible ARISA profile.
Nucleus Pearl Coating Process of Freshwater Mussel Anodonta woodiana (Unionidae) RAHAYU, SATA YOSHIDA SRIE; SOLIHIN, DEDY DURYADI; MANALU, WASMEN; AFFANDI, RIDWAN
HAYATI Journal of Biosciences Vol 20, No 1 (2013): March 2013
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (296.431 KB) | DOI: 10.4308/hjb.20.1.24

Abstract

The limiting factor which is a weakness of sea water pearl production are high costs, the risk of major business failures and a long coating time. From the issue of freshwater pearls appear to have prospects of alternative substitution for sea water pearl. This present study aimed to evaluate effect of loads (the number and diameter nucleus) on freshwater pearl coating process and the number and size of the appropriate nucleus diameter, to produce the optimum coating thickness of half-round pearls. The research consists of experimental implantation of 2, 4, and 6 nucleus number per individual mussel was maintained by the method stocked in hapa in bottom waters. Observation method and factorial randomized block design used in the study of the influence of the load to the successfulness of  pearl coating and the pearl layer thickness. The results showed that A. woodiana can be utilized as a producer of freshwater pearls. In addition, the number of optimum nucleus that can be attached to the mussel A. woodiana was 2 grains/individuals with a diameter of 10 mm. Shells implanted with the optimum nucleus diameter and number of pearls produced the highest layer thickness of 17 mm after 9 months cultivation. This result was good enough compared with the layer thickness of sea water pearl production after the same cultivation time.
Functional Group of Spiders in Cultivated Landscape Dominated by Paddy Fields in West Java, Indonesia SUANA, I WAYAN; SOLIHIN, DEDY DURYADI; BUCHORI, DAMAYANTI; MANUWOTO, SJAFRIDA; TRIWIDODO, HERMANU; SCHULZE, CHRISTIAN HANSJOACHIM
HAYATI Journal of Biosciences Vol 16, No 1 (2009): March 2009
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (223.548 KB) | DOI: 10.4308/hjb.16.1.1

Abstract

Distribution of spiders in all colonized environments is limited by biotic and abiotic factors requiring adaptations with respect to, for example microhabitat choice and hunting behavior. These two factors were frequently used to group spiders into functional groups. In this study our objectives were to (i) group of genera of spiders into functional group based on their microhabitat specificity, hunting behavior, and daily activity; and (ii) compare the number and composition of functional group of spider at each habitat type and period of paddy growth. The study was conducted at a landscape dominated by paddy fields in Cianjur Watershed for a period of 9 months. Four different habitat types (paddy, vegetable, non-crop, and mixed garden), were sampled using five trapping techniques (pitfall traps, farmcop suction, sweep netting, yellow-pan traps, and sticky traps). The Unweighted Pair-Group Average and the Euclidean Distances were used to generate dendrogram of functional group of spider. We found 14 functional groups of spider at genus level. The number of functional group of spider at four habitat types was differing, but the composition was similar, because all habitats were closed to each other. Habitat structure diversity and disturbance level influenced the number of functional group of spider. Different architecture of vegetation and availability of differ prey during paddy growth, causing the composition of functional group of spider in each period of paddy growth was changed, although its number was unchanged. Key words: spiders, functional group, agricultural landscape, Cianjur Watershed
Kajian Aspek Reproduksi Ikan Lais Ompok hypophthalmus di Sungai Kampar, Kecamatan Langgam, Kabupaten Pelalawan, Provinsi Riau Elvyra, Roza; Solihin, Dedy Duryadi; Affandi, Ridwan; Junior, Zairin
Jurnal Natur Indonesia Vol 12, No 02 (2010)
Publisher : Lembaga Penelitian dan Pengabdian kepada Masyarakat Universitas Riau

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31258/jni.12.02.%p

Abstract

Lais fish of Ompok hypophthalmus is one of high economic fish in Kampar river. It should be protected fromdecreasing of it population estimated due to decreasing of habitat quality and increasing of exploitation. Theobjectives of the research are to study reproduction biology of lais fish as the basic data for conservation. Thisresearch was conducted from January 2007 to January 2008. The results of O. hypophthalmus reproductionaspect show that the smallest female of maturity is 22,9 cm and male is 22,6 cm; the spawning season onSeptember to November; O. hypophthalmus is more appropriate spawning location to oxbow lake that closerelation with tributary; the spawning pattern indicated total spawner fish; the fecundity ranges from 3111 to 11164eggs and the egg diameter ranges 0,41-1,13 mm.
ANALISIS DNA MITOKONDRIA BADAK SUMATERA DALAM KONSERVASI GENETIK Handayani, Handayani; Solihin, Dedy Duryadi; S Alikodra, Hadi
Prosiding Seminar Biologi Vol 8, No 1 (2011): Seminar Nasional VIII Pendidikan Biologi
Publisher : Prodi Pendidikan Biologi FKIP UNS

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (228.595 KB)

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 & 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
Isolation and Characterization of Simian Retrovirus Type D from Macaca fascicularis and M. nemestrina in Indonesia ISKANDRIATI, DIAH; SAEPULOH, UUS; MARIYA, SILMI; GRANT, RICHARD F; SOLIHIN, DEDY DURYADI; SAJUTHI, DONDIN; PAMUNGKAS, JOKO
Microbiology Indonesia Vol 4, No 3 (2010): December 2010
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Simian type D retroviruses (SRVs) are one of the causative agents of simian acquired immunodeficiency syndrome (AIDS) in Asian macaques.  In the past, SRV isolates from macaques had only been identified at the US primate centers, outside the country of origin and after the animals had been introduced into a new environment.  In this study, we report the first isolation, cultivation and molecular characterization of the type D simian retrovirus naturally infecting wild caught macaques in their natural habitats in the country of origin, in this case, Indonesia.  When peripheral blood mononuclear cells (PBMC) from Macaca fascicularis (Mf) and M. nemestrina (Mn) were co-cultured with Raji human B-cell line, syncytia were observed microscopically and confirmed by immunofluoresence assay using antibody to SRV-2.  Immunoblot analysis of purified Mf-ET1006 from cell culture supernatants demonstrated that the viral core and envelope proteins reacted with rabbit anti-SRV.  Sequence analysis of Mf isolates in the viral envelope region revealed high homology to SRV-2 (94-96%). On the other hand, the homologies in the envelope region of Mn isolates were less than 80% to SRV-1, SRV-2, SRV-3 and Mf isolates.   This study suggests that the isolate from Mn may be different from any other published SRV isolates.
Cloning and Expression of Serotype-2 Simian Betaretrovirus Reverse Transcriptase Gene Isolated from Indonesian Cynomolgus Monkey in Escherichia coli SAEPULOH, UUS; ISKANDRIATI, DIAH; HOETAMA, FUNGKEY; MARIYA, SELA SEPTIMA; SOLIHIN, DEDY DURYADI; PAMUNGKAS, JOKO; SAJUTHI, DONDIN
Microbiology Indonesia Vol 7, No 2 (2013): June 2013
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5454/mi.7.2.3

Abstract

In this study, we isolated the simian betaretrovirus serotype-2 (SRV-2) reverse transcriptase (RT) gene from infected Indonesian cynomolgus monkey (Macaca fascicularis). The gene was then cloned in Escherichia coli expression system. The SRV-2 RT gene is located between nucleotides 3284-4925 in the polyprotein (Pol) region encodes 547 amino acids. Analysis of expression using SDS-PAGE and western blot techniques showed a specific band of 64.9 kDa, indicating SRV-2 RT recombinant enzyme. Purification of SRV-2 RT recombinant enzyme produced 312 μg mL-1 protein with 7.1 U μL-1 enzyme activities. Application of this recombinant enzyme in reverse transcription-PCR (RT-PCR) of β-globin and β-actin genes produced DNA fragments of 206 and 350 bp, indicating amplification of β-globin and β-actin genes, respectively. Therefore, the expressed SRV-2 RT enzyme was proven to be functional, although the activity was low.
Kajian Penanda Genetik Gen Cytochrome B Pada Tarsius sp. =Study of Genetic Marker on Cytochrome B Gene of Tarsius sp. Widayanti, Rini; Solihin, Dedy Duryadi; Sajuthi, Dondin; Perwitasari, RR. Dyah
Jurnal Sain Veteriner Vol 24, No 1 (2006)
Publisher : Fakultas Kedokteran Hewan

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (71.575 KB)

Abstract

Tarsius merupakan salah satu satwa endemik Indonesia yang keberadaannya mulai memprihatinkan. Konservasi sebagai salah satu cara untuk pelestarian satwa ini akan lebih terarah dan berhasil guna apabila karakteristik dan keragaman sumber genetiknya diketahui dengan pasti. Tujuan dari penelitian ini adalah mengkaji penanda genetik spesifik gen cyt b pada Tarsius sp. Pengurutan hasil PCR menggunakan primer H 15149 pada gen cyt b didapatkan urutan basa sebesar 276 pb (menyandi 92 asam amino. Fragmen cyt b hash! pengurutan disejajarkan berganda dengan primata lain dari data Genbank dengan bantuan perangkat lunak Genetyx-Win versi 3.0 dan Clustal W, kemudian dianalisis dengan menggunakan program MEGA versi 3.1. Dari hasil analisis diperoleh 14 situs asam amino yang berbeda. Tarsius dianae memiliki 12 situs asam amino (asam amino ke 2, 6, 9, 22, 23, 29, 39, 41, 42, 45, 55 dan 85), T. spectrum memiliki 7 situs asam amino (asam amino ke 2, 6, 9, 41, 45, 55 dan 85) dan T bancanus memiliki 2 situs asam amino ( ke 23 dan 45) yang dapat digunakan sebagai penanda genetik. Lima asam amino unik ditemukan pada T dianae, yaitu pada situs asam amino ke 6 (valina), ke 22 (alanina), ke 29 (alanina), ke 39 (serina) dan ke 42 (valina). Jarak genetik berdasar nukleotida cyt b yang dihitung menggunakan model 2 parameter Kimura ditemukan nilai paling kecil sebesar 0,7%, nilai paling besar 22,3% dan rata-rata 13,1%. Filogram menggunakan metode neighbor joining berdasar hasil urutan nukleotida dan asam amino cyt b tersebut dapat dijadikan pembeda masing-masing spesies Tarsius.
Keragaman Fenotipik dan Pendugaan Jarak Genetik pada Ayam Lokal dan Ayam Broiler Menggunakan Analisis Morfologi (PHENOTYPIC VARIATION AND ESTIMATION GENETIC DISTANCE BETWEEN LOCAL CHICKEN AND BROILER CHICKEN USING MORPHOLOGICAL ANALYSIS) Mariandayani, Harini Nurcahya; Solihin, Dedy Duryadi; Sulandari, Sri; Sumantri, Cece
Jurnal Veteriner Vol 14, No 4 (2013)
Publisher : Jurnal Veteriner

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (71.575 KB)

Abstract

This aim of the research was to study the morphological characteristic and estimating genetic distancebetween local chicken and broiler chicken with discriminant and canonical analysis. This research washeld in Faculty of Animal Husbandry, Bogor Agricultural University, using 25 sentul chickens,  25  kampongchickens, 25 kedu chickens , 25  pelung chickens and 25 broiler chickens. The variable as the length ofshank, beak length, back length, chest depth and chest width were measured in this study. The collecteddata were analyzed by using SAS  and SPSS package program. Kampung chickens were mixed with sentulchickens (17.60 %) and kedu chickens (17,70 %). Kedu, kampong,  and  sentul chickens have a relativelyclose genetic distance   compared the genetic distance to pelung chickens with the kampung, sentul, andkedu chickens. Fenogram tree show that there were three separate groups of chickens at the age of eightweeks i.e. : (1) pelung chickens (2), kedu, kampong, and sentul chickens, (3) broiler chickens.  Fenogram treealso shows two separate groups : (1) pelung chickens (2) kedu, kampong, and Sentul chickens (at the age of28 weeks chicken).  The crossbreed between kedu and sentul chickens, also have a relatively close geneticdistance. The phenotypic size of  chickens giving a strong influence on the distinction variable of chickengroups were body length and chest circumference.
ANALISIS DNA MITOKONDRIA BADAK SUMATERA DALAM KONSERVASI GENETIK Handayani, Handayani; Solihin, Dedy Duryadi; S Alikodra, Hadi
Prosiding Seminar Biologi Vol 8, No 1 (2011): Seminar Nasional VIII Pendidikan Biologi
Publisher : Prodi Pendidikan Biologi FKIP UNS

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (228.595 KB)

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 & 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
Co-Authors Abdul Rahman Singkam Achmad Machmud Thohari Agus Nuryanto Agus Wahyana Anggara, Agus Wahyana ANI MARDIASTUTI Ani Suryani ANTONIUS SUWANTO ARIEF BOEDIONO Bahiyah, nFN Cece Sumantri CECILIA ANNA SEUMAHU CHRISTIAN HANSJOACHIM SCHULZE DAMAYANTI BUCHORI Dedy Dur Heny Suseno2 Wahyu Prihatini1 Prihatini DEWI APRI ASTUTI Dewi Malia Prawiradilaga, Dewi Malia DIAH ISKANDRIATI Dodi Nandika DONDIN SAJUTHI Endrawati, Yuni Cahya Epa Paujiah, Epa EVY AYU ARIDA Fahma Wijayanti Fahri Fahrudin, Fahri FUNGKEY HOETAMA Hadi S Alikodra HADI SUKADI ALIKODRA Handayani Handayani Hari Prayogo Harini Nurcahya Mariandayani Heny Suseno HERMANU TRIWIDODO I WAYAN SUANA Ibnu Maryanto Iman Rusmana Irzaman Irzaman Jarulis Jarulis Jito Sugardjito Joko Pamungkas Jusmaldi, . Jusmaldi, Jusmaldi Khustina, Yenny Chusna Lilik Budi Prasetyo M F Rahardjo M. F. Rahardjo, M. F. Mulyani, Yuli Wahyu Tri Mustafa Sabri NASTITI KUSUMORINI NEVIATY PUTRI ZAMANI Niken Subekti Niken TM Pratiwi Rahardjo, MF RICHARD F GRANT Ridwan Affandi Rini Widayanti Robba Fahrisy Darus, Robba Fahrisy Roza Elvyra RR. Dyah Perwitasari Rudhy Gustiano SAEPULOH, UUS Safrida Safrida Saroyo Saroyo SATA YOSHIDA SRIE RAHAYU SELA SEPTIMA MARIYA SILMI MARIYA SJAFRIDA MANUWOTO Sri Catur Setyawatiningsih Sri Ningsih SRI SULANDARI Sri Supraptini Mansjoer Subyakto Subyakto Suharsono Suharsono SULISTIYANI SULISTIYANI Taher, Achmad Tarumingkeng, Rudy C Tedjo Sukmono Tri Haryoko, Tri UUS SAEPULOH Wahyu Prihatini Wasmen Manalu Watanabe, Kunio Zairin Junior