Testing Reliability of Serum Samples as a DNA Source on Captive Breeding Long-tailed Macaques (Macaca fascicularis)

The serum realibility was tested in captive breeding conditions on the long-tailed macaques (Macaca fascicularis). Serum and buffy coat were applied to standard protocol of DNA extration following the amplification of microsatellite DNA locus of D2S1777 by PCR and visualized PCR products by means of PAGE with silver staining.  The amount of genomic DNA extracted from serum was sufficient for genotyping individuals at DNA microsatellite locus of D2S1777 with the allele size is approximately 160 bp.  We show that serum can provide a reliable alternative for obtaining DNA where taking blood using anticoagulant is impracticabl

Determination of Grouper Species of Subfamily Epinephelinae from Raja Ampat (West Papua) Region Using CO1 Gene Sequence

The Raja Ampat Islands, located near the heart of the “Coral Triangle” on Bird's Head Peninsula, West Papua, Indonesia are well known for its outstanding biological diversity and stunning marine and terrestrial habitats. Groupers (family Serranidae) has included as part of the 5 largest families associated with coral reefs on the Bird’s Head region. The grouper identification was generally done on the basis of color patterns and morphological characters, but oftentimes these characters show intraspecific variations or differences in color patterns between juvenile and adult individuals. This study aims to confirm the type of grouper species that were obtained from the sport fishing activities around Raja Ampat Island. Species confirmation from subfamily of Epinephelinae determined by analyzing the number of differences of nucleotides and genetic distance on the sequence of the CO1 gene (Cytochrome oxidase subunit 1). A total of eight fish samples were successfully sequenced and aligned. Those samples consist of eight species belonging to the three genera namely Anyperodon, Epinephelus, and Cephalopolis

Skin Histology and Microtopography of Papuan White Snake (Micropechis ikaheka) in Relation to Their Zoogeographical Distribution

Papuan white snake (Micropechis ikaheka) is endemic to New Guinea (the region of the Papua and Papua New Guinea). Internal histology of skin layer and the microtopography structure on the surface scales of M. ikaheka were the aims of the study. This study also related to zoogeographical of the snake in Papua. Geographical skin color variation of M. ikaheka can be described in three groups, i.e. brown, yellow and black group. The three groups of the snake have specific zoogeography in the mainland of Papua and satellite islands to Papua New Guinea. Paraffin method used in this work showed approximately five layers i.e. oberhautchen, the beta (b)-layer, the mesos layer, the alpha (a)-layer, and the dermis in the snake skin. Although the paraffin method cannot explain the arrangement of pigment cells, however, the dark color on the dermis might contain melanophores that might cause dark color of the snake body. Overlapping scales formed the hinge region were flexible to assist the snakes when they moved across substrate. Scanning electron microscopy (SEM) of the oberhautchen of all of M. ikaheka revealed no microornamentation. However, dorsal and ventral scales showed many follicles on the entire surface of the boundary scales

Karakterisasi Ekson 4 Gen DRD4 pada Ayam Arab Tiara G15 dengan Tingkah Laku Feather Pecking

Feather pecking (FP) is a potentially fatal behavioral disorder in chickens. Various factors, including genetics such as DRD4 gene, affected this behavior. The Arab TIARA G15 chicken is a laying hen breed selected based on FP behavior. However, genetic selection linked to this FP as not yet been conducted. This study aimed to characterize the 4th exon of the DRD4 gene in Arab golden red TIARA G15 chickens and confirm its potential as an FP genetic marker. The study used 30 TIARA G15 chickens that were divided into three groups: high feather pecking (HFP) (n = 10), low feather pecking (LFP) (n = 10), and control (n = 10). The DNA extraction kit extracted total genomic DNA from each blood sample. The 4th exon of the DRD4 gene was amplified using primer pairs MU140-141. Amplicons from samples within a group were pooled in a single tube and sequenced using the Sanger method. The sequencing results were analyzed for nucleotide variation using MEGA6 software. Nucleotide sequences obtained from each group were 642 bp, consisting of partial intron 3 (55 bp), full-length exon 4 (202 bp), and partial 3'UTR (385 bp). None of the three groups of Arab golden red TIARA G15 chickens were found to have any nucleotide variants in the partial intron 3, full-length exon 4, and 3'UTR regions of the DRD4 gene. Consequently, selecting the full-length exon 4 of the DRD4 gene for FP behavior was not feasible.   Keywords: arab chicken, DRD4, feather pecking, golden re

Genetic Structure of Gallus varius Based on Middle-Lower Section of Control Region mtDNA

Gallus varius, an indigenous bird species of Indonesia, demonstrates significant genetic diversity. The genetic diversity assessment in G. varius encompassed both mitochondrial DNA (mtDNA) and nuclear DNA, with the mtDNA analysis primarily centered on domain I of the control region. This study aimed to describe the genetic diversity and structure of G. varius inhabiting Java, Madura, Lombok and Sumbawa based on the middle-lower part of control region mtDNA. Genomic DNA was extracted from the calamus tip of feather, then the middle-lower part of control region was amplified and sequenced using two pairs of primers. In the examined control region, spanning from 944 to 1,008 bp, 13 bp of nucleotide variation was observed, with nucleotide diversity at 0.0021. Between G. varius samples and the reference (NC_007238.1), a total of 7 haplotypes were identified, 5 unique and 2 shared haplotypes, with haplotype diversity at 0.7692. The substantial diversity of haplotypes in this study and two previous study suggests that the genetic diversity of G. varius has remained stable over the past two decades. Additionally, genetic distance data indicate there is multiple G. varius subspecies, and the haplotype network accentuates signs of population differentiation

Komparasi Karakter Morfologi Sapi Madura Sonok dan Madura Pedaging

Madura cattle was selected into three groups by Madura people, there are karapan, sonok, and beef cattle. This selection based on morphological characters and pedigree. The differences of morphological characters in Sonok and beef cattle have not been reported. This research aimed to analyze morphological characters of both types, such as the differences in behaviors. This research was conducted from January-April 2016 at Sumenep and Pamekasan region, Madura Island. Preliminary was conducted with interviews, observation, and literature studies to obtain some characters which will be observed. Eighteen characters were observed in forty-two sonok cattle and fifty beef cattle. Qualitative data was analyzed by frequency analysis and use as input for principal component analysis (PCA) in Minitab 16 Statistical Software. The result shows that all of the observed cattle are divided into two groups. It indicates that sonok and beef cattle have different color around the eye area, the existence of back line, horn direction, and the existence of hump. However, further, observation is needed to find a robust character which can distinguish sonok and beef cattle for sonok selection

Berudu Anura di Sungai Kedurang, Bengkulu Selatan dan Pusat Pendidikan Konservasi Alam Bodogol, Jawa Barat

This paper aims is to identify and to describe morphological characteristic of tadpoles in Kedurang River, South Bengkulu and Cisuren River, PPKA Bodogol. Visual Encounter Survey along the river method was used to collect the sample of tadpoles. Three species were found in both rivers, namely Bufo melanostictus, Limnonectes sp. and Rhacophorus sp

Phylogenetic Study of Madura Cattle Based on Mitochondrial Cyt b and D-loop Sequences

Madura Cattle is one breed of local cattle from Indonesia. Madura cattle are estimated to originate from a crossbreeding between Bos indicus and Bos javanicus. Another presumption is that Madura cattle are the result of a crossbreeding between B. indicus males and mixed B. javanicus or Bos taurus. Tracing the history of Madura cross and another cattle phylogenetic based on maternal lineage can be done by analyzing the variation of the mitochondrial genome (mtDNA). The purpose of this study was to determine the clarity of the origin of Madura cattle based on maternal lineage using mtDNA markers Cyt b and D-loop. This research is expected to provide genetic information and the origin of Madura cattle, so that it can be used to help improve the breeding and conservation program for Madura cattle. The results of the phylogeny tree reconstruction, using the Cyt b and D-loop genes showed that Madura cattle originated from Sampang region (Polagan, Golbung, and Komis) were grouped into two types of maternal origin. Madura cattle clade I are grouped with B. indicus and B. taurus, while Madura cattle clade II are grouped with B. javanicus. A crossbreeding between B. javanicus and B. indicus is estimated to have been carried out since the entry of Hindu culture brought by the India peoples to Indonesia around 1800 years ago. The crossing between B. javanicus and B. indicus was then more intensively carried out at the time of the government's promoting the development of Ongol cattles (B. indicus) in the days of the Dutch East Indies. The length segment of Cyt b that can be amplified is 230 bp and the D-loop segment of varying length, 577 bp for the Madura 41 and 29 samples, and 624 bp for sample 32. 

Exploration and prevalence of gastrointestinal worm in buffalo from West Java, Central Java, East Java and Lombok, Indonesia

The studies of parasites in buffaloes have not been widely explored. The aim of the present study was to explore the prevalence of gastrointestinal worm infection in buffaloes. The fresh faecal samples were collected from 89 buffaloes and observed by a modified McMaster technique. The faecal of buffaloes were collected in Bogor, Demak, East Java, and Lombok. The results of identification on gastrointestinal parasites show that there were one cestode and eight nematode. The total prevalence and infestation of cestodes and nematodes was found highest in Bogor. The prevalence and infestation of differences in geographical conditions were found highest in Bogor. The prevalence of gastrointestinal worm in males were highest than female, whereas for larger was found in females. The prevalence of gastrointestinal worms was found at age 1 year, whereas a larger infestation was found at the age of 1-5 years. The calculation of FEC in Bogor was 840 EPG, in Demak 375 EPG, in East Java 570 EPG and in Lombok 13 EPG. This study informed that there were nine genera of gastrointestinal worm found in Java and five genera in Lombok. Types larvae were found six i.e Strongyloides, Haemonchus, Cooperia, Oesophagostomum, Bunostomum and free living larvae

STUDY ON MORPHOLOGICAL CHARACTERS OF INDONESIAN LITTER FROG (LEPTOBRACHIUM, MEGOPHRYIDAE)

Leptobrachium from Southeast Asian populations previously were recognized as a single speciesLeptobrachium hasseltii Tschudi. Taxonomic reassessment revealed that Leptobrachium consists of somecryptic species due to similarities in their morphological appearance but diverse in molecular characters.Among the Indonesian populations, Leptobrachium was split into seven species (L. hasseltii, L. nigrops,L. waysepuntiense, L. hendricksoni, L. ingeri, L. abbotti, and L. montanum). Specifically, L. hasseltii isseparated into two groups; the Sumatran-Javan and the Bali populations. In this study, we analyzed themorphological data of 100 individuals of Leptobrachium to evaluate their morphological differences.The morphological differences expressed by analysis of variance (ANOVA) and principal componentanalysis (PCA) revealed significant differences between each Leptobrachium and four morphologicalcharacters suitable for species identification (the iris color, color pattern, humeral and femoral gland).The morphological differences also showed that the Bali population probably is undescribed species