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Molecular Phylogenetic: Organism Taxonomy Method Based on Evolution History Dharmayanti, N.L.P Indi
Indonesian Bulletin of Animal and Veterinary Sciences Vol 21, No 1 (2011)
Publisher : Indonesian Animal Sciences Society

Phylogenetic is described as taxonomy classification of anÂ organism based on its evolution history namely its phylogeny and as a part of systematic science that has objective to determine phylogeny of organism according to its characteristic. Phylogenetic analysis from amino acid and protein usually became important area in sequence analysis. Phylogenetic analysis can be used to follow the rapid change of a species such as virus. The phylogenetic evolution tree is a two dimensional of a species graphic that shows relationship among organisms or particularly among their gene sequences. The sequence separation are referred as taxa (singular taxon) that is defined as phylogenetically distinct units on the tree. The tree consists of outer branches or leaves that represents taxa and nodes and branch represent correlation among taxa. When the nucleotide sequence from two different organism are similar, they were inferred to be descended from common ancestor. There were three methods which were used in phylogenetic, namely (1) Maximum parsimony, (2) Distance, and (3) Maximum likehoood. Those methods generally are applied to construct the evolutionary tree or the best tree for determine sequence variation in group. Every method is usually used for different analysis and data. Key words: Phylogenetic, analysis, evolution, nucleotide/protein sequence

Virus Pathogenity of Newcastle Disease in Chicken Hewajuli, Dyah Ayu; Dharmayanti, N.L.P Indi
Indonesian Bulletin of Animal and Veterinary Sciences Vol 21, No 2 (2011)
Publisher : Indonesian Animal Sciences Society

Newcastle disease (ND) is one of the highly infectious diseases in poultry industry. Newcastle disease causes high morbidity and mortality in birds, then it causes significant loss for poultry industry. This disease is caused by Avian paramyxovirus-1, included in the genus of Avulavirus and family of Paramyxoviridae. This virus has six prior proteins and two non structural proteins that evolving its genom. Those proteins are Nucleocapsid protein (N), Phosphoprotein (P), Matrix protein (M), Fusion protein (F), Hemagglutinin-neuraminidase protein (HN) and Large polymerase protein (L) and two non structural proteins iVe and W protein which are produced during the transcriptation process of P gen on editing process. Each of the protein has a specific role that responsible for the virulence of the virus. The previous result showed that HN and F proteins have significant contribution in the virulence and spreading of ND virus in the hosts. Virulence of ND virus primarily is determined by the cleavage site of F protein, but the recent research showed that the cleavage site motiv of F0 protein is not the only factor to determine the virulence of ND virus. Besides F protein, other proteins also contribute patern to the virulence of ND virus. ND virus can infect more than 200 species of birds, but the severity level of the disease varies depending on the host and strain of ND virus. Chicken has the highest pathogenicity index compared to other birds. Generally, the immunity system in chicken against infection of ND virus is similar to the immunity system of other birds. Cell mediated and humoral immunity responses play an important role in overcome ND virus. Key words: Newcastle disease, protein, immunity response

Comparison of sequences of hypervariable region (HVR) subunit S-1 gene of field isolate I-37 infectious bronchitis virus with Connecticut serotype Dharmayanti, N.L.P Indi; Indriani, Risa; ., Darminto
Indonesian Journal of Animal and Veterinary Sciences Vol 8, No 2 (2003)
Publisher : Indonesian Animal Sciences Society

Infectious Bronchitis is a contagious and acute respiratory disease in chickens caused by infectious bronchitis virus (IBV).Antigenic differences in IBV are associated with changes in the sequence of the spike glycoprotein (S). The subunit S1 which demonstrates more sequence variability than S-2 have been identified as hypervariable region (HVR-1 and 2). There were several IB virus field isolates included I-37 have been identified in Indonesia by serum neutralization method. However, gene sequence variation in HVR subunit S-1 had not yet been identified. Isolate I-37 was close to the serotype Connecticut 46 (Conn 46). The aim of this study is to identify sequence variation of HVR subunit S-1 gene of isolate I-37 produced by Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) and sequencing. Several procedures were carried out in the study including virus titration, propagation and was concentrated from the allantoic fluid infected with IBV. Then, RNA was extracted for RTPCR. urther the product was sequnced and its homology with IBV references from GenBank was compared by GenMac version 8.0. Result showed that isolate I-37 produced 515 bp of amplification product. Isolate I-37 and Conn 46 are same serotype, yet their HVR subunit S-1 nucleotides and amino acids (protein) differ by 6.9% and 15.6% respectively. It might be concluded that isolate I-37 was variant of Conn 46. Â Key words: Sequences variation, IBV, I-37 field isolate, HVR subunit S-1 gene

Genetic characteristic of protein membran of avian influenza viruses H5N1 subtype Dharmayanti, N.L.P Indi; Hewajuli, D.A; Ratnawati, A; Indriani, R; ., Darminto
Indonesian Journal of Animal and Veterinary Sciences Vol 15, No 3 (2010)
Publisher : Indonesian Animal Sciences Society

In 2006-2008 there were findings about the antigenic drift on AI virus due to vaccination and the AI H5N1 subtype viruses which was similar to H5N1 viruses in human. The findings indicated that the AI viruses continue and undergoing to mutate and try to adapt with their environment.Â The objective of this study was to characterize the mutation of recent AI viruses (2009) on the membran protein namely Hemagglutinin (HA), Neuraminidase (NA) and Matrix 2 (M2). In this study RT-PCR â sequencing methods and genetic analysis for the protein membran of AI viruses were used. Result revealed that there were specific mutation belong to AI 2009 viruses on HA and NA protein such as AI virus mutation in 2008 which was isolated from backyard chicken. The mutations were non synonimous and not caused by immunological pressure. Furthermore, M2 analysis indicated that the viruses were resistant to amantadine. Key Words: Mutation, AI Subtype H5N1 Viruses, Membran Protein

Comparison of sequences of hypervariable region (HVR) subunit S-1 gene of field isolate I-37 infectious bronchitis virus with Connecticut serotype N.L.P Indi Dharmayanti; Risa Indriani; Darminto .
Jurnal Ilmu Ternak dan Veteriner Vol 8, No 2 (2003): JUNE 2003
Publisher : Indonesian Center for Animal Research and Development (ICARD)

Infectious Bronchitis is a contagious and acute respiratory disease in chickens caused by infectious bronchitis virus (IBV).Antigenic differences in IBV are associated with changes in the sequence of the spike glycoprotein (S). The subunit S1 which demonstrates more sequence variability than S-2 have been identified as hypervariable region (HVR-1 and 2). There were several IB virus field isolates included I-37 have been identified in Indonesia by serum neutralization method. However, gene sequence variation in HVR subunit S-1 had not yet been identified. Isolate I-37 was close to the serotype Connecticut 46 (Conn 46). The aim of this study is to identify sequence variation of HVR subunit S-1 gene of isolate I-37 produced by Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) and sequencing. Several procedures were carried out in the study including virus titration, propagation and was concentrated from the allantoic fluid infected with IBV. Then, RNA was extracted for RTPCR. urther the product was sequnced and its homology with IBV references from GenBank was compared by GenMac version 8.0. Result showed that isolate I-37 produced 515 bp of amplification product. Isolate I-37 and Conn 46 are same serotype, yet their HVR subunit S-1 nucleotides and amino acids (protein) differ by 6.9% and 15.6% respectively. It might be concluded that isolate I-37 was variant of Conn 46. Key words: Sequences variation, IBV, I-37 field isolate, HVR subunit S-1 gene

Genetic characteristic of protein membran of avian influenza viruses H5N1 subtype N.L.P Indi Dharmayanti; D.A Hewajuli; A Ratnawati; R Indriani; Darminto .
Jurnal Ilmu Ternak dan Veteriner Vol 15, No 3 (2010): SEPTEMBER 2010
Publisher : Indonesian Center for Animal Research and Development (ICARD)

In 2006-2008 there were findings about the antigenic drift on AI virus due to vaccination and the AI H5N1 subtype viruses which was similar to H5N1 viruses in human. The findings indicated that the AI viruses continue and undergoing to mutate and try to adapt with their environment. The objective of this study was to characterize the mutation of recent AI viruses (2009) on the membran protein namely Hemagglutinin (HA), Neuraminidase (NA) and Matrix 2 (M2). In this study RT-PCR – sequencing methods and genetic analysis for the protein membran of AI viruses were used. Result revealed that there were specific mutation belong to AI 2009 viruses on HA and NA protein such as AI virus mutation in 2008 which was isolated from backyard chicken. The mutations were non synonimous and not caused by immunological pressure. Furthermore, M2 analysis indicated that the viruses were resistant to amantadine. Key Words: Mutation, AI Subtype H5N1 Viruses, Membran Protein

Virus Pathogenity of Newcastle Disease in Chicken Dyah Ayu Hewajuli; N.L.P Indi Dharmayanti
WARTAZOA, Indonesian Bulletin of Animal and Veterinary Sciences Vol 21, No 2 (2011): JUNE 2011
Publisher : Indonesian Center for Animal Research and Development

Newcastle disease (ND) is one of the highly infectious diseases in poultry industry. Newcastle disease causes high morbidity and mortality in birds, then it causes significant loss for poultry industry. This disease is caused by Avian paramyxovirus-1, included in the genus of Avulavirus and family of Paramyxoviridae. This virus has six prior proteins and two non structural proteins that evolving its genom. Those proteins are Nucleocapsid protein (N), Phosphoprotein (P), Matrix protein (M), Fusion protein (F), Hemagglutinin-neuraminidase protein (HN) and Large polymerase protein (L) and two non structural proteins iVe and W protein which are produced during the transcriptation process of P gen on editing process. Each of the protein has a specific role that responsible for the virulence of the virus. The previous result showed that HN and F proteins have significant contribution in the virulence and spreading of ND virus in the hosts. Virulence of ND virus primarily is determined by the cleavage site of F protein, but the recent research showed that the cleavage site motiv of F0 protein is not the only factor to determine the virulence of ND virus. Besides F protein, other proteins also contribute patern to the virulence of ND virus. ND virus can infect more than 200 species of birds, but the severity level of the disease varies depending on the host and strain of ND virus. Chicken has the highest pathogenicity index compared to other birds. Generally, the immunity system in chicken against infection of ND virus is similar to the immunity system of other birds. Cell mediated and humoral immunity responses play an important role in overcome ND virus. Key words: Newcastle disease, protein, immunity response

Molecular Phylogenetic: Organism Taxonomy Method Based on Evolution History N.L.P Indi Dharmayanti
WARTAZOA, Indonesian Bulletin of Animal and Veterinary Sciences Vol 21, No 1 (2011): MARCH 2011
Publisher : Indonesian Center for Animal Research and Development

Phylogenetic is described as taxonomy classification of an organism based on its evolution history namely its phylogeny and as a part of systematic science that has objective to determine phylogeny of organism according to its characteristic. Phylogenetic analysis from amino acid and protein usually became important area in sequence analysis. Phylogenetic analysis can be used to follow the rapid change of a species such as virus. The phylogenetic evolution tree is a two dimensional of a species graphic that shows relationship among organisms or particularly among their gene sequences. The sequence separation are referred as taxa (singular taxon) that is defined as phylogenetically distinct units on the tree. The tree consists of outer branches or leaves that represents taxa and nodes and branch represent correlation among taxa. When the nucleotide sequence from two different organism are similar, they were inferred to be descended from common ancestor. There were three methods which were used in phylogenetic, namely (1) Maximum parsimony, (2) Distance, and (3) Maximum likehoood. Those methods generally are applied to construct the evolutionary tree or the best tree for determine sequence variation in group. Every method is usually used for different analysis and data. Key words: Phylogenetic, analysis, evolution, nucleotide/protein sequence

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