Dedy Duryadi Solihin

Genetic characterization of the Aceh cattle using phenotypic, mitochondrial DNA of D-loop region and microsatellite DNA analyses.

The present study reports the phenotypic variation of body weight and body size, the genetic variation of D-loop of mtDNA and microsatellite DNA allele in Aceh cattle in Indonesia within the frame of the design of a conservation programme for this indigenous species. Aceh cattle differ from Bali, Madura, Java-Ongole and Pesisir cattle, but its ancestry relates it closest to Pesisir, thus adding more information to its entry from the Indian sub-continent.

Single Nucleotide Polymorphism within the Promoter Region of Cynomolgus Monkey LDLR Gene

The cynomolgus monkey (Macaca fascicularis) is one of the most common nonhuman primate s used as an animal model in biomedical research relat ed to atherosclerosis. However, little is known about genetic variation in the low density lipoprotein receptor (LDLR) gene , its effect on cholesterol levels , and associated risk s of atherosclerosis. The refore this study aimed to identify genetic polymorphisms , namely single nucleotide polymorphism s (SNP s ) , within the promoter region of LDLR and their relation ship with animal responsiveness to hypercholesterolemia due to an atherogenic diet. In this research, SNPs were studied using DNA isolated from 22 cynomolgus monkeys obtained from a previous study, consisting of two hyporesponders, 19 hyperresponders, and one extreme case . The result showed that two SNP s existed in the promoter region , namely g.−169T>C and g.−265G>A. SNP g.−265G>A showed linkages with extreme responsive ness and can be used as a potential genetic marker for extreme animals. The result of this study has extended our knowledge of polymorphism in the LDLR gene and its use in the selection of cynomolgus monkeys as animal models in research on hypercholesterolemia and atherosclerosis.

Variasi Kolesterol Plasma Individual Monyet Ekor Panjang (Macaca fascicularis) sebagai Respons terhadap Diet Aterogenik IPB-1 [INDIVIDUAL PLASMA CHOLESTEROL VARIATION OF CYNOMOLGUS MACAQUE (MACACA FASCICULARIS) IN RESPONSE TO IPB-1 ATHEROGENIC DIET]

The effectiveness of atherogenic diet in raising plasma cholesterol level of cynomolgus macaques(Macaca fascicularis) can be predicted for population, but not for individuals.This study aimed to evaluatethe individual plasma cholesterol of cynomolgus macaques in response to IPB-1 atherogenic diet. Theanimals under study were 22 adult malemonkeys from the animal facility of Primate Research CenterBogor Agricultural University (PSSP IPB). All animals were intervened with the IPB-1 atherogenic diet forthree months and individual plasma cholesterol wasevaluated in a monthly basis.The results showedthat the monkeys’ plasma cholesterol had increased significantly (P <0.05) after one month of interventionperiod and the increases were very significantly different (P <0.01) after three months. Individually, increasesin plasma cholesterol varied among animals. Based on these variations, 2 animals were categorised ashypo-response, 18 animals as hyper-response and 2 animals as extreme.This study showed the variationof individual plasma cholesterol of cynomolgus macaques in response tothe IPB-1 atherogenic diet so thatthe animals might be selected based on the their responsiveness.

Culturable and unculturable actinomycetes associated with the sponge Neofibularia from Bira Island, Indonesia

Aims: The diversity of the actinomycete community associated with Neofibularia sp. from Bira Island, Indonesia, has been largely unstudied. This study was undertaken to address the paucity of information in this respect. Methodology and results: Culturable actinomycetes were isolated and cultured on HV medium. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) targeting the metagenomic 16S rRNA was used to analyse the structure of the actinomycete community. Five culturable actinomycetes that were isolated belonged to the genus Streptomyces. They showed various degrees of similarity to the reference strains Streptomyces sampsonii (9799%), Streptomyces resistomycificus (97-99%), Streptomyces gougerotii (97-99%), Streptomyces erringtonii (97-99%), and Streptomyces albus (97-99%). The culturable actinomycetes isolates also showed differences in morphological characteristics as compared with the reference strains. The metagenomic analysis suggested that the actinomycete community was dominated by rare actinomycetes. Eight DGGE DNA bands that were obtained had sequences that showed similarities to Ferrithrix thermotolerans (88-94%), Lamia majanohamensis (87-92%), Aciditerrimonas ferrireducens (87-92%), and Thermobispora bispora (85-92%), while 4 bands had sequences similar to Propionibacterium acnes (97-100%) and another band matched sequences belonging to an uncultured bacterium clone (86-87%). The actinomycetes detected by the metagenomic approach were assigned identities that were mostly under 97.5% as compared with reference strains available in Genbank. Conclusion, significance and impact of study: Observations from both culture and DGGE analysis give a better understanding of the diversity and community structure of actinomycetes associated with Neofibularia sp. The culturable actinomycetes were Streptomyces spp., while rare actinomycetes were dominant when the metagenomic approach was adopted. Several of these actinomycetes showed identities below 97% when matched to reference strains, indicating possible novel species associated with the sponge Neofibularia.

Isolation and Identification of Chitinolytic Bacteria as Biocontrol Agent of Pathogenic Fungi on Gold Silkworm Cocoon Cricula trifenestrata

Aims: Cricula trifenestrata is one of natural insects which has not been domesticated yet, thus called as the wild silkworm. C. trifenestrata is known as a silk producer which has high economic and market value. However, the fungi attack on C. trifenestrata cocoon decreased quality and quantity of silk yarn. Chitinolytic bacteria have a high potential as biological control against pathogenic fungi. This research aimed to isolate, select, characterize, and identify chitinolytic bacteria as pathogenic fungi growth inhibitors on C. trifenestrata cocoon. Methodology and results: Chitinolytic bacteria was isolated from the uninfected and infected cocoon while fungi was isolated from the uninfected cocoon. Inhibition test was conducted by Fokkema method and chitinase activity was measured by Spindler method. A total of 36 chitinolytic bacteria and 10 suspected pathogenic fungi isolates have been isolated. Fungal pathogenicity test showed that isolate CSAJ.2 was suspected as fungal pathogen. In vitro inhibition test indicated that chitinolytic bacteria isolate BSEP.3 could inhibit the growth of pathogenic fungi CSAJ.2 with percentage of inhibition 50%. Isolate BSEP.3 showed highest chitinase activity (5.11 U/mL) at the 15 th h. It able to inhibit the growth of pathogenic fungi with percentage of inhibition of 47.5% and 46.25%, respectively. Conclusion, significance and impact of study: Identification of bacteria targeted on 16S rRNA gene showed that isolate BSEP.3 had 98% identity with Bacillus amyloliquefaciens B5 while identification of fungi using ITS region of the rDNA showed that isolate CSAJ.2 had 100% identity with Trichoderma virens TV242. Chitinase crude extract was effective to be used as a biological control agent of T. virens CSAJ.2.

Mercury depuration effectiveness on green mussel (Perna viridis L.) and blood cockle (Anadara granosa L.) from Jakarta Bay using ozone, chitosan and hydrodynamic technique

Depuration has been used to eliminate microorganism and toxic chemical contaminants in bivalve. However, scientific research still needs to discover the effectiveness of depuration. This research aimed at assessing the best depuration effectiveness in decreasing mercury (Hg) concentration level in two species of bivalves, green mussel (Perna viridis L.) and blood cockle (Anadara granosa L.). The depuration treatments applied 1.5 ppm ozon, 0.5 ppm chitosan, hydrodynamic technique (1.3 m/s), combination between hydrodynamic-ozon, hydrodynamic-chitosan and ozon-chitosan. The experiment were conducted in mini aquaria for 60 minutes. Mercury concentration was measured in 10 g dry weight of green mussel (4.05±0.020 ppm) and blood cockle (3.27 ± 0.666 ppm). The result showed that mercury depuration were highly effective by combination of ozone-chitosan in green mussel (96.51%) and 1.5 ppm ozone in blood cockle (87.06%).

Population genetic structure of the tropical eel Anguilla bicolor in Indonesian waters based on microsatellite markers

Abstract. The short-finned eel Anguilla bicolor is known to be subdivided in two distinct subspecies (i.e. A. bicolor bicolor and A. bicolor pacifica), each subspecies being geographically distributed in allopatry. The present survey intends to describe genetic differentiation, population structure, molecular variance and phylogeny of both subspecies of A. bicolor in Indonesian waters. The genotypes of seven microsatellite locus and sequences of the entire cytochrome b were analyzed on 180 specimens collected in 10 representative locations, where one of the two subspecies spend their freshwater life. The results showed high heterozygosity (0.767 < He < 0.891). Significant deviation from Hardy-Weinberg equilibrium were essentially detected on AjTR04 and Aro63 loci. No diagnostic microsatellite loci was observed between the subspecies which shared most of their alleles. Genetic Reynolds distances computed for each population ranged between 0.029 and 0.073 among A. bicolor pacifica populations, between 0.045 and 0.149 among A. bicolor bicolor populations and between 0.042 and 0.114 among populations of different subspecies. Both the mitochondrial and the microsatellite markers confirm the subdivision into two subspecies while microsatellite loci suggest a moderate differentiation between subspecies.