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Articles by Suhendra Pakpahan
Total Records ( 6 ) for Suhendra Pakpahan
  Suhendra Pakpahan , Wayan Tunas Artama , Rini Widayanti and I. Gede Suparta
  Background: Hutan Sumatera goat (Sumatran serow) is one of wildlife that is quite similar to the domesticatic goats and have never been investigated at the molecular level. Indonesian society believes that Hutan Sumatera goat belongs to the group of the genus Capra, therefore, this animal is called a wild goat or forest goat. Hutan Sumatera goat has been categorized as an endangered species in the IUCN as red list. Materials and Methods: The genomic DNA of Sumatran serow and Indonesian goat were isolated by gSYNC DNA Mini Kit (Geneaid) and cytochrome b gene was amplified using PCR method with a pair of primer. Cytochrome b gene region was amplified completely from all samples with a length 1140 bp. Results: Alignment results show that there are many nucleotide differences between Hutan Sumatera goat and Indonesian domestic goats. Translation nucleotide results indicate that there are 11 different amino acids between Hutan Sumatera goat and domestic goats except with JAW (12 amino acids) and GS (10 amino acids). The percentage of A+T and G+C on Hutan Sumatera goat is 56.4 and 43.6%, whereas the Indonesian domestic goat is 58.6 and 41.4%. Using the restriction enzyme BamHI results in differences fragments between Hutan Sumatera goats and domestic goats. In the Cyt b gene Hutan Sumatera goat was cut on site 561 bp to produce two DNA bands, while in the domestic goat there is no cutting of DNA fragments at the site. Conclusion: The genetic distance between Hutan Sumatera goats ranged from 0.001-0.004, while the Hutan Sumatera goat to domestic goat ranged from 0.001-0.118. Based on a phylogenetic tree analysis, Hutan Sumatera goat form a group with genus Capricornis. This suggests that goat Hutan Sumatera goat is a part of the genus Capricornis.
  Suhendra Pakpahan , Rini Widayanti , Wayan Tunas Artama and I. Gede Suparta Budisatria
  Background: The coat color is important for the production of wool, for heat tolerance in hot climates, cultural value and for the identification of the breed. Goat has very important roles in the agricultural economies of Indonesia. The goat is not only to produce meat, milk, wool and compost, but also for cultural and religious events. Batak tribe in North Sumatra has a unique tradition of customary celebration by using goat. Goat that has completely white coat should be used, so that the white coat has economic value much higher than other colors. Materials and Methods: This study used blood from each individual. Four subpopulations of domestic goat breeds in Indonesia, namely Samosir goat, Kacang goat, Gembrong goat and Peranakan Etawah goat. The agouti signaling protein (ASIP) gene fragments amplified and sequenced. The length of the ASIP gene amplification products was 610 bp for every individual and analyzed to detect variations on every Indonesian local goat. Results: From all samples of Indonesian goats, there is only one difference on Samosir goat 1 c.158 G-T. This polymorphism only foundin Samosir goat 1 while the other Indonesian local goats and other organisms were the similar. This variation would change to the order of amino acids in goat Samosir 1. Conclusion: There is no variation in the ASIP fragment of Indonesian goats that can be used to investigate the relationship between exon 4 of ASIP and coat color expression of Indonesia local goats. The exon 4 of the ASIP cannot be made target to investigate different coat color in some Indonesian goat breeds.
  Suhendra Pakpahan , Wayan Tunas Artama , Rini Widayanti and I. Gede Suparta
  Indonesia has several breeds of goats as the source of genetic. This study aimed to characterize genetic of Indonesian goats. The phylogenetic relationship among and genetic variability within eight native Indonesian goats were analyzed using mtDNA D-loop region sequences. The results show that the length of complete sequences mtDNA D-loop in Indonesian goats are1212 bp. There are 68 polymorphic sites and 21 different haplotypes. Haplotype diversity and nucleotide diversity based on mtDNA D-loop in eight breeds of Indonesian goats are 0.5000-1.000 and 0.248-1.1595%, respectively. The value of genetic distance between groups of native Indonesian goats ranged from 0-0.011. Indonesia goat genetic distance value against wild goat Capra aegagrus (AB004082) is in the range 0.0038-0.045 while against Capra falconeri (AB044306) is 0.087-0.095. The results indicate that the genetic diversity of Indonesian goats is not abundant. Indonesian goats originated from one maternal. Maternal origin of Indonesian goats based on mtDNA D-loop is lineage B.
  Aris Haryanto , Vera Wati , Suhendra Pakpahan and Nastiti Wijayanti
  Newcastle disease is an infectious disease in poultry caused by the Newcastle Disease Virus (NDV) which belongs to the family Paramyxoviridae. The NDV can infect various species of birds, both domestic and wild birds with highly morbidity and mortality. Based on the pathotype, NDV can be classified into velogenic (high), mesogenic (moderate) and lentogenic (low) pathotypes, however, clinical symptoms appear on infected birds are often similar that it is difficult to distinguish. In this study, molecular pathotyping of NDV has been done to ten virus isolates that isolated from various type of chicken which naturally infected by NDV using a combination method of RT-PCR and RFLP. It was then compared with quantification of Mean Death Time (MDT) value and DNA sequencing which is commonly method used for NDV pathotyping. The aim of this study was to develop a rapid, precise and efficient method for NDV pathotyping by combination method of RT-PCR amplification and RFLP using HinfI restriction enzyme. The results of NDV pathotyping showed that combination of RT-PCR amplification and RFLP using HinfI enzyme can be used well to differentiate the pathotype of virulent NDV versus avirulent NDV rapidly, accurately and efficiently. A total of ten NDV samples isolated from naturally NDV infected chickens showed that three samples are avirulent NDV, while seven other samples are virulent NDV. In compared with other pathotyping methods, namely MDT quantification and DNA sequencing, the molecular NDV pathotyping by RT-PCR and RFLP methods showed similar conclusion and consistent with highly compatibility.
  Suhendra Pakpahan , Wayan Tunas Artama , Rini Widayanti and I. Gede Suparta
  Phylogenetic relationships and genetic variation among 9 Indonesian goat breeds were analyzed using cytochrome b gene sequences. The genomic DNA was isolated by gSYNC DNA Mini Kit (Geneaid) and amplified cytochrome b gene using PCR method with a pair of primer. Complete sequences of Cyt b genes of Indonesian goats is 1140 bp contained 19 variable sites and 8 haplotypes between Indonesian goats and C. hircus (D84201), when compared to C. aegagrus and C. falconeri, there are 59 variable sites. Phylogenetic analysis of haplotype in the combination with the goats from GenBank showed that Indonesian goats are grouped with C. aegagrus. Indonesian goat breeds have 4 amino acid units, which are different with C. hircus, at site 17, 191, 215 and 341th amino acids. The genetic distance score between Indonesian goat populations ranged from 0 to 0.007, while if compared to C. aegagrus ranged from 0.002 to 0.006 and to the C. falconeri ranged from 0.039 to 0.045. The relationship between subpopulation of Indonesian goats are very close. Indonesian goats have a closer genetic relationship with wild goat C. aegagrus than to C. falconeri.
  Rini Widayanti , Agustianti , Tito Suprayogi , Rony Marsyal Kunda and Suhendra Pakpahan
  Cuscuses is marsupials animal (Phalangeridae), which has limited spread in Eastern Indonesia (Sulawesi, Maluku, Papua and Timor islands), Australia and Papua New Guinea. This study, the phylogenetic relationship of cuscuses from Papua and Maluku based on mitochondrial sequences of NADH dehydrogenase subunit 1 gene was investigated. Whole genome DNA was extracted from 22 tissue biopsy samples from Maluku (13 individuals) and Papua (9 individuals) according to the protocol of Qiamp DNA Blood Mini Kit (Qiagen) and then it was used as template for amplification of ND1 gene by using PCR method. The PCR product gives result nucleotides of 1152 bp and sequencing product gives result nucleotides of 956 bp of the ND1 gene for phylogenetic analysis. The genetic distance between Phalanger and Spilocuscus, 14.2% was found higher than the genetic distance between cuscus from Papua and Maluku 7.8%. The genetic distance within Phalanger was 3.7% and genetic distance within Spilocuscus was 1.3%. The genetic distance within Phalanger from Papua and Maluku was 1.3% and the average genetic distance within Spilocuscus from Papua and Maluku was 1.3%. The phylogram tree using Neighbor Joining classified cuscus from Papua and Maluku in clade A (Phalanger) and clade B (Spilocuscus), respectively. Clade A and B were further subdivided into clade A1 (Phalanger from Papua), A2 (Phalanger from Maluku) and clade B1 (Spilocuscus from Papua), B2 (Spilocuscus from Maluku). Spilocuscus genera members from Ternate and Sentani islands was found five nucleotides distinguishing compared to Spilocuscus from Papua and Maluku. It was concluded that identification of Spilocuscus and Phalanger members from Maluku, Papua, Ternate and Sentani could be distinguished by mitochondrial DNA sequencing of the ND1 gene.
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