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Application of Two Molecular Sexing Methods for Indonesian Bird Species: Implication for Captive Breeding Programs in Indonesia
HAYATI Journal of Biosciences , 2012,
Abstract: Visually identifying the sex of a bird can be difficult. It cannot be done in half the world’s species when they are adults, and virtually none can be sexed as chicks. Despite this, the sex of a bird is vital for captive breeding. An increased number of birds are being sexed using DNA amplification techniques. In this approach, the CHD-W and CHD-Z are distinguished by the amplification of an intron present in both genes. PCR products on the gel electrophoresis vary in size revealing one band in males at the CHD-Z, and two bands in females corresponding to both the CHD-W and CHD-Z. Two independent sets of primer (P8/P2 and 2550F/2718R) were used to amplify the CHD gene region from both the Z and W chromosome. One hundred and ten (110) birds were sexed using first pair of primers: (P8/P2). Sexing results indicated that 81.8% were successfully determined, 12.7% failed to be amplified and 5.5% were not perfectly determined because the PCR products showed thick band. The thick band caused misidentified female to male birds. An alternative primer (2550F/2718R) was applied to solve the problem. Two hundreds and twenty-nine birds were sexed and the results showed 100% successfully determined. From this study, it is suggested to use a pair of 2550F and 2718R primers for distinguishing a male from a female bird.
Detection and Host Range Study of Virus Associated with Pepper Yellow Leaf Curl Disease
HAYATI Journal of Biosciences , 2006,
Abstract: High incidence of Pepper yellow leaf curl virus (PepYLCV) was observed in Indonesia since early 2000. Disease incidence in Yogyakarta, Central and West Java reached 100% on Capsicum frutescens, but only 10-35% on C. annuum. As an exception, the disease incidence on C. annuum cv. TM 999 was in the range of 70-100%. The causal agent of the disease, PepYLCV, was detected by polymerase chain reaction. Viral specific DNA fragment of the size ~1600 bp and ~550 bp was amplified from infected plants using two pairs of geminivirus universal primers pAL1v1978/pAL1c715, and pAv494/pAc1048, respectively. The PepYLCV has an intermediate host range including plants belonging to the family of Solanaceae, Leguminosae, and Compositae. The species belonging to the families of Cucurbitaceae, Malvaceae, Chenopodiaceae, and Amaranthaceae were resistant to the virus. Physalis floridana, is very prospective as a propagation host for the geminivirus infecting pepper. Nicotiana spp., cucumber, watermelon, cotton, and Sida sp. could be used as a differential host. Besides, Capsicum frutescens cv. Cakra, tomato, N. benthamiana, N. glutinosa, and Ageratum conyzoides could be used as indicator plants for the geminivirus infecting pepper.
Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequences
HAYATI Journal of Biosciences , 2008,
Abstract: The Mitochondrial DNA (mtDNA) displacement (D)-loop sequences were used to study the genetic diversity and relationship of Indonesian indigenous chickens. A total of 483 individuals belonging to 15 population breeds and 43 individuals belonging to 6 populations of jungle fowl (2 populations of Gallus gallus and 4 populations of Gallus varius) were sampled. The hypervariable I (HVI) segment of the D-loop was PCR amplified and subsequently sequenced. The sequences of the first 397 nucleotides were used for analysis. Sixty nine haplotypes were identified from 54 polymorphic sites with polymorphism between nucleotides 167 and 397 contributing to 94.5% of the sequence variation. Phylogenetic analysis indicates that Indonesian indigenous chickens can be grouped into five distinct clades (clade I, II, IIIc, IIId, and IV) of the previously identified seven clades (clade I, II, IIIa, IIIb, IIIc, IIId, and IV) in Asian indigenous chickens. Fifty haplotypes belong to clade II, seven haplotypes are in clade IV, six are in clade IIId, three are in clade I and one haploype is in clade IIIc. There was no breed-specific clade. Analysis of Molecular Variance (AMOVA) based on partial D-loop sequences of Indonesian chicken indicates that 67.85% of the total sequence variation between haplotypes was present within the population and 32.15% between populations. One of the haplotypes (represented by PLC4) was shared by all populations, suggesting that these populations may share the same maternal ancestor. These results show a high mitochondrial D-loop diversity and indicate multiple maternal origins for Indonesian indigenous chickens.
Degradation of Primate Habitat at Tesso Nilo Forest with Special Emphasis on Riau Pale-Thighed Surili (Presbytis siamensis cana)  [PDF]
Jatna Supriatna, Sri Mariati
Journal of Environmental Protection (JEP) , 2014, DOI: 10.4236/jep.2014.512112
Abstract: The habitat of Riau pale-thighed surili (Presbytis siamensis cana) located in Riau province of Sumatra island between Siak in the north and Indragiri rivers in the south, has been seriously degraded in the last a few decades. This swampy peat land forest has been degraded by frequent burning during the dry season. These problems originated because of poor governance on the forest management, and the construction of two access roads by the owners of logging concessions and wood pulp plantations. This forest block consists of Tesso Nilo National Park, Kerumutan protected area, Production Forest areas belong to two companies, and a small recreation Park. It also contains one of the most important mixed peat swamp forests. Here, we tracked changes in forest cover before and after road construction using GIS and remote sensing imagery. Deforestation rates have increased from 1.5% per year before road construction to 9.28% per year after road construction, which means that the area of forest has decreased by an annual average of 8156 ha in Tesso Nillo alone. The habitat of Riau pale-thighed surili decreased almost up to 60% in the last decade after companies started their converting forest for oil palm and acacia and roads were built crisscrossed. If the trend of deforestation continues, further decline of population of habitat of this species is unavoided. Researches should be carried out in more details to understand the status of population of this subspecies before this subspecies disappears in the wild.
Monolayers Langmuir-Blodgett Films of Synthetic Artificial Mimic Molecules That Resemble the Following Tetraether Lipids on Silicon Wafers  [PDF]
Sri Vidawati, Ulrich Rothe
Advances in Biological Chemistry (ABC) , 2015, DOI: 10.4236/abc.2015.54015
Abstract: This study investigated the behavior and molecular organization of synthetic artificial mimic molecules that resemble the following tetraether lipids: di-O-hexadecyl-glycero-3-phosphatidyl-glycerol (DHGPG) and bis-4-dodecylphenyl-12-phosphate. These molecules were analyzed using Langmuir film balance, ellipsometry and atomic force microscopy. The monolayer Langmuir-Blodgett films of DHGPG and bis-4-dodecylphenyl-12-phosphate were stable on the solid surface silicon wafers. The ellipsometry and AFM results showed that monolayers Langmuir-Blodgett films of DHGPG and bis-4-dodecylphenyl-12-phosphate were present, and the thickness of the observed films varied from 1.2 - 5.0 nm.
An Attitude and Character Instructional Development Based on Curriculum 2013 in Elementary School  [PDF]
Badeni Muhamad, Sri Saparahayuningsih
Creative Education (CE) , 2016, DOI: 10.4236/ce.2016.72025
Abstract: The purpose of this research is to identify the weaknesses of the instructional model of attitude and character in the 2013 elementary school curriculum and to develop a conceptual model of attitude and character instruction being able to instill the attitudes and characters contained in the content of social studies subject of elementary schools in the curriculum of 2013. The results of this study showed that 1) scientific learning approach was only able to develop scientific attitudes of students, while sorts of other attitudes were very less embedded into the students’ self. 2) The application of the integrated scientific instructional model was able to instill the values of attitudes and characters contained in the content of social studies to the student.
Analisis D-loop DNA Mitokondria untuk Memposisikan Ayam Hutan Merah dalam Domestikasi Ayam di Indonesia
S. Sulandari,M.S.A. Zein
Media Peternakan , 2009,
Abstract: The current poultry is a domesticated chickens used for both meat and egg production. Pedigree investigation is an important part to understand the process of chicken domestication in Indonesia. Molecular DNA approach using D-loop Mitochondrial DNA marker (hypervariable 1 segment) was used in this analysis. The objective of the study was to construct the pedigree analysis of Indonesian chicken. Four hundreds and eighty four (434) samples belonging to 15 breeds of Indonesian local chicken (Cemani, Kedu, Kedu Putih, Pelung, Sentul, Wareng, Merawang, Kapas, Kate, Arab Silver, Arab Gold, Gaok, Nunukan, Kalosi and Tolaki) and 9 samples of Red jungle fowls (Gallus gallus gallus) were extracted, PCR amplified and subsequently sequenced. Four sequence references from GeneBank, Gallus gallus (NCBI, accession number AB0986688). G. gallus (GenBank accession number AB098668), G. gallus spadiceus (GenBank accession number AB007721), and G. gallus bankiva (GenBank accession number AB007718) were included in this analysis. The sequences of the first 397 nucleotides were used for analysis. The results show that 72 haplotypes were identified from 56 polymorphic sites. Phylogenetic analysis showed that Indonesian chicken have a close relationship with 2 subspecies of Gallus gallus (G. gallus gallus and G. gallus spadiceus). Our results suggest that D-loop region is highly variable in Indonesian chicken with large number of haplotypes.
Jakaria,M.S.A. Zein,S. Sulandari,Subandriyo
Journal of the Indonesian Tropical Animal Agriculture , 2012,
Abstract: The purpose of this research was to study genetic diversity in Indonesian sheep population using microsatellite markers. A total of 18 microsatellite loci have been used for genotyping Indonesian sheep. Total sheep blood 200 samples were extracted from garut sheep of fighting and meat types, purbalingga sheep, batur sheep and jember sheep populations by using a salting out method. Microsatellite loci data were analyzed using POPGENE 3.2 software. Based on this study obtained 180 alleles from 17 microsatellite loci, while average number of alleles was 6.10 alleles (6 to 18 alleles) from five Indonesian sheep populations (garut sheep of fighting type, garut sheep of meat type, purbalingga sheep, batur sheep and jember sheep population). The average of observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.5749 and 0.6896, respectively, while the genetic differentiation for inbreeding among population (FIS), within population (FIT) and average genetic differentiation (FST) were 0.1006, 0.1647 and 0.0712, respectively. Genetic distance and genetic tree showed that Indonesian sheep population was distinct from garut sheep of fighting and meat types, purbalingga sheep, batur sheep and jember sheep population. Based on this results were needed a strategy for conservation and breeding programs in each Indonesian sheep population.
Activity of Oligoresveratrols from Stem Bark of Hopea mengarawan (Dipterocarpaceae) as Hydroxyl Radical Scavenger
HAYATI Journal of Biosciences , 2006,
Abstract: Four oligoresveratrols ranging from dimer to tetramer, isolated from stem bark of Hopea mengarawan (Dipterocarpaceae) plants were tested for their activity as hydroxyl radical scavenger. The activity of these compounds was evaluated against the 2-deoxyribose degradation induced by the hydroxyl radical generated via a Fenton-type reaction. Result showed that balanocarpol, heimiol A, vaticanol G, and vaticanol B had IC50 3.83; 15.44; 2.01; and 4.71 μM, respectively. These results suggest that oligoresveratrols from stem bark of H. mengarawan maybe useful as potential sources of natural antioxidants.
Physical Interactions between Yeast Pichia guilliermondii and Post-Harvest Fruit Pathogen Penicillium expansum
HAYATI Journal of Biosciences , 2008,
Abstract: Attachment of yeast cells or bacteria on fungal hyphae have been observed in various antagonisms between microorganisms. Physical interactions between yeast Pichia guilliermondii and postharvest fruit pathogen Penicillium expansum in culture were studied in detail using light and transmission electron microscope to give better understanding on their mode of antagonism. Both organisms were co-cultured for 24-hr on potato dextrose agar. Light microscopy observations on the co-culture showed that the yeast cells attached firmly on the fungal hyphae. This attachment was inhibited by several substances such as enzymes degrading protein (protease or trypsin), a respiration inhibitor (sodium azide), an acid (hydrochloric acid) or an alkali (sodium hydroxide). Although autoclaved hyphae did not affect the attachment, but boiled enzymes and autoclaved yeast cells totally abolished the attachment. These evidences suggested that the attachment might be an active process mediated by certain protein from live yeast cells. Transmission electron micrographs on the ultrastructure of the co-culture revealed that the hyphae showed abnormalities in their structure and organelles, and a degree of obvious damage. Physical interactions observed in this study could be contributed to the mechanism of antagonism between P. guilliermondii and P. expansum.
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