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Articles by Rini Widayanti
Total Records ( 8 ) for Rini Widayanti
  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.
  Rony Marsyal Kunda , Niken Satuti Nur Handayani , Hery Wijayanto and Rini Widayanti
  Background and Objective: The DNA barcode can be used as a basis for determining the objectives and direction of development of conservation activities and can clarify differences and kinship relationships between species in the population. This study aimed to determine nucleotides sequences as DNA barcode for investigation of genetic diversity and phylogenetic from cuscuses in Maluku and Papua as well as other biogeography on COX3 gene with sequencing method. Materials and Methods: The genome DNA from 25 samples, extracted according to the Qiamp DNA protocol is the Mini Blood Kit (Qiagen) and is used as a template for COX3 gene amplification using PCR method. Results: Nucleotides alignment of Phalanger members found 23 nucleotides distinguishing and Spilocuscus members found 8 nucleotides distinguishing, which can be used as barcode. The phylogram tree was using Neighbor joining classified cuscus from Maluku and Papua in clade A (Phalanger) and clade B (Spilocuscus), respectively. Clade A and clade B subdivided into clade A1 (Phalanger from Maluku), A2 (Phalanger from Papua) and clade B1 (Spilocuscus from Maluku), B2 (Spilocuscus from Papua). Clade B2 subdivided into one subclade B2' be under cuscus from Halmahera dan Sentani, Jayapura Islands. Conclusion: It was concluded that identification of Spilocuscus and Phalanger members from Maluku, Papua, Halmahera and Sentani could be distinguished by COX3 gene. Spilocuscus maculatus from Halmahera is derived from Papua, it introduced in the colonization of the Austronesian tribes on the Island. S. maculatus from Halmahera and Sentani Islands have one nucleotide distinguish, that is sites position 354 which distinguishes the cuscuses with cuscus from Papua and Maluku.
  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.
  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.
  Faisal Faisal , Muharam Saipulloh , Rini Widayanti , Aris Haryanto and Charles Rangga Tabbu
  To investigate the genetic diversity of the Indonesian Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), the complete Open Reading Frame 5 (ORF5) from 11 clinical samples collected between 2008-2014 was sequenced and phylogenetically analyzed. These sequences were compared with the ORF5 of NA referens viruses (VR2332, MLV and JXA1), lelystad virus and 34 ORF5 sequences North America group from Gen Bank. Sequence analysis revealed that the ORF5 have undergone genetic variation. The ORF5 nucleotide and amino acid identities among 11 Indonesia PRRS viruses ranged from 88.5-100 and 87.5-100%, respectively and all belonged to the North American genotype. The ORF5 sequence of nucleotide and amino acids from the North American prototype virus (VR2332) and derived vaccine virus (MLV) were 97.6-100 and 97.0-100% identical to the various ORF5 Indonesia viruses, respectively. In the phylogenetic analysis, of the Indonesian viruses were clusted into two groups. The ORF5 based sequencing analysis can be used to determine the type of PRRS virus and the presence of genetic diversity of PRRS viruses in Indonesia.
  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.
  Rony Marsyal Kunda , Niken Satuti Nur Handayani , Hery Wijayanto and Rini Widayanti
  Cuscuses is marsupials animal (Phalangeridae) which has limited spread in eastern Indonesia (Sulawesi, Maluku, Papua and Timor islands), Australia and Papua New Guinea. The ex-situ and in-situ conservation of cuscuses under captivating condition is an alternative solution to protect from extinction. This study aimed to determine nucleotide sequences and genetic marker on cyt b gene with sequencing method of each species on two provinces. Whole genome DNA was extracted from 22 samples of cuscuses obtained from different habitats, Maluku (13 individuals) and Papua (8 individuals) according to the protocol of Qiamp DNA Blood Mini Kit (Qiagen) and then it was used as template for amplification of cyt b gene by using PCR method. The PCR product were then purified using column chromatography and were used as template for sequencing reaction. Results sequencing of cyt b gene were analyzed using MEGA program versions 6.0. The PCR product gives results nucleotides of 982 bp according to database GeneBank and sequencing product gives results nucleotides of 771 bp. Nucleotides alignment of Phalanger members was found 24 nucleotides distinguishing and Spilocuscus members was found 11 nucleotides distinguishing, which can be used as genetic marker between Phalanger and Spilocuscus members from Papua and Maluku.
 
 
 
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