HAYATI Journal of Biosciences
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Modeling the Wintering Habitat Distribution of Oriental Honey Buzzards in West Java Indonesia with Satellite Tracking Data Using Logistic Regression
Get PDFOriental honey buzzards (OHBs, Pernis ptilorhynchus) are one of migratory raptor from Japan to Indonesia which is widely recognized as indicator species reflecting the conditions of their habitat. Since 2003, OHBs have been satellite-tracked in their wintering grounds in Indonesia. Less information available on wintering areas in the west Java, which hampers the OHB conservation efforts. This paper proposes a new approach for predicting the probability models of the wintering habitat distribution of OHBs with the presence data derived from satellite tracking using logistic regression analysis coupled with RAMAS GIS. This spatial model was locally constructed from the data concerning Talaga Bodas and its surrounding areas and extrapolated for the entire West Java region. The best predicted probability model successfully characterized the distribution of the OHB wintering habitat using slope (25–40%), elevation (0–300 m and >1,000 m), and land cover (forest, paddy field, and water body). The extrapolation model generated potential areas of the wintering habitat distribution covering an area of 3013.13 km2 (8.11% of West Java). These areas were predominantly located outside the protected areas (94.04%). The modeling approach proposed herein may be used to study other migratory species that are tracked using satellite or other navigation technologies
Cross Species use of Human Microarray Genotyping Technology for Bornean Orangutan (Pongo pygmaeus) SNP Discovery
Get PDFPrevious genetic studies of orangutans (Pongo spp.) have relied mainly upon mitochondrial DNA or microsatellite short tandem repeats (STR) for genomic genotyping analysis. Scientists have yet to take advantage of the genetic closeness of the great apes to humans for genomic analysis by using advanced techniques available for human genotyping. To genotype orangutans at Tanjung Puting National Park, we developed a novel combination of a methyl-based magnetic enrichment capture of genomic fecal DNA with genotyping on a human targeted single nucleotide polymorphism (SNP) microarray, and compared this to additional microsatellite (STR) micro-capillary genotyping. We successfully isolated 125 known human genomic SNP loci (0.08% of those targeted) which hybridized orangutan DNA on the human targeted Illumina Infinium QC array. We estimated genetic diversity and relatedness (r) using three estimators for a total of 32 (21 female and 9 male) wild orangutans at the Camp Leakey study site. Average TrioML relatedness within the sample, estimated from our combo SNP/STR dataset, was at a range consistent with half and first cousins (r = .082). All sampled males and females had relatives within the study site indicating we have verified a local, closely related community of wild orangutans at Camp Leakey
Carotenoid Assessments and Antioxidant Activities from Flower Petals
Get PDFThe objectives of this study were to evaluate carotenoid pigment profile and the antioxidant activity from 14 commonly grown flowers in Thailand. The result found that orange marigold showed the highest total carotenoid content at as 2,209±75.58 µg/g, followed by deep yellow chrysanthemum at 551.27±47.72 µg/g (P<0.01). The next lower total carotenoid content group was found in yellow silk cotton, yellow trumpetbush, yellow marigold and yellow golden shower with total carotenoid content of 447.42±27.56, 429.46±28.34, 409.85±34.58 and 363.88±12.74 µg/g, respectively. The highest antioxidant activities against DPPH and ABTS radicles were found from orange marigold, which were 32.34±2.16 and 50.08±0.87%, respectively. Deep yellow chrysanthemum, yellow silk cotton, yellow trumpetbush, yellow marigold and yellow golden shower also showed significantly higher antioxidant activities than other flowers (P<0.01). Total carotenoid contents well correlated with antioxidant activities against DPPH and ABTS radicals (r = 0.6924 and r = 0.8270, respectively) at P<0.01. TLC result elucidated that orange marigold, yellow silk cotton and yellow golden shower were a good source of β-carotene, while deep yellow chrysanthemum and yellow marigold were a good source of lutein and/or zeaxanthin. The result indicated that flower petals would be useful as natural carotenoid source and provide antioxidants for food industry
Characteristics and Activity of Anti Qourum Sensing Bacillus spp. Isolated from Penaeus vannamei Shrimp Ponds
Get PDFCertain strains of V. parahaemolyticus carry a gene that encodes a toxin that causes Acute hepatopancreatic necrosis disease (AHPND) in P. vannamei. AHPND attacks shrimp post larvae within 20-30 days after stocking causing up to 100% mortality. The expression of these virulent genes is controlled by the quorum sensing system. This system is inhibited by an anti-quorum sensing (AQS) mechanism. Several Bacillus strains have AQS mechanism by producing AHL-Lactonase enzyme. Therefore, this study aimed to obtain Bacillus spp. having AQS activity for controlling AHPND. The study was conducted from isolation and selection of Bacillus isolates, as well as determination of AQS activity. From 22 samples consisting of shrimp intestines, water and pond sediment samples, a total of 151 isolates of Bacillus spp. were isolated. The screening test for AQS activity obtained 11 isolates that showed AQS activity on Cromobacterium violaceum. Determination of violacein pigment in liquid cultures of C. violaceum showed the index value of the pigment formation was between 0.025-0.166 and 0.026-0.567 at 24-hour and between 48-hour incubations, respectively. The quantitative analysis of violacein production showed that there were six isolates of Bacillus could inhibit the pigment production more than 75%. The isolates were identified as Bacillus cereus (four isolates), Bacillus thuringiensis (one isolate), and Bacillus velezensis (one isolate), respectively. The molecular analysis had confirmed that the isolates have aiiA genes encoding AHL-lactonase enzyme. These Bacillus isolates have potential application for controlling AHNPD disease
Application of Proteomics to Identify Fertility Markers in Angus Bull Sperm
Get PDFThe goal of the study was to ascertain sperm proteins as fertility markers by identifying sperm proteins in Angus bull sperm using proteomics and validate the markers through comparative sperm biology between Angus and Holstein bulls for which there is reliable fertility data available. We aimed to determine proteins differentially expressed in sperm from Angus bulls with different fertility phenotypes. Two-dimensional differential gel electrophoresis with mass-spectrometry, functional gene clusters, canonical pathways and protein networks, using integrated discovery bioinformatics software and ingenuity pathway analysis were used to identify and analyze sperm proteome. We identified 80 proteins that were differentially expressed in sperm of our experimental population. Using computational biology approaches we demonstrated involvement of structural proteins such as outer dense fiber of sperm tails 2 and enzymes including kinases, and phosphatases having functions in essential pathways in glycolysis/gluconeogenesis and free scavenging. The results are significant because analyzed proteins in Angus sperm are determinants of fertility, gene-environment interactions, as well as potential biomarkers for animal breeding
Isolation, Selection and Identification of Polyaromatic Hydrocarbons (PAHs) Degrading Bacteria from Heavy Oil Waste (HOW)-Contaminated Soil
Get PDFThe heavy oil waste (HOW) containing polyaromatic hydrocarbon (PAHs) is a persistent organic pollutants (POPs) that difficult to degrade. The new PAH degrading consortium was investigated from HOW contaminated soil in North Sumatera of Indonesia. The isolation, selection and identification of polyaromatic hydrocarbon degrading bacteria from soil contaminated by HOW was conducted to solve a bioremediation process. The isolation microbes from soil contaminated by HOW was performed using a minimum ONR7a media and followed on marine agar media for purification purposes. From the performed isolation results, 11 isolates were able to degrade PAHs compounds, such as phenanthrene, dibenzothiophene, or fluorene compounds. They grew at pH range of 4.8-8.2 and performed on emulsification activity in paraffin from 0.150-0.662. Three of them showed the best performance on HOW biodegradation capability and then successfully selected and identified as Salipiger sp., Bacillus altitudinis, and Ochrobactrum anthropi. using 16S rDNA. The HOW biodegradation as TPH-degradation were 38.66%, 59.60%, and 47.16%, respectively. Those isolated bacteria could potentially be as bioremediation agents to develop on bioremediation process for soils contaminated by HOW
Integration Stability of sHBsAg-Multi Expression Cassettes in Pichia pastoris GS115 during Methanol Induction
Get PDFHepatitis B is the major health problem worldwide including in Indonesia. Vaccination is the best prevention strategy for the disease. For the purpose of vaccine development and to decrease drug import, production of Hepatitis B Virus (HBV) small surface antigen (sHBsAg) from Indonesian HBV subtype is needed. The recombinant protein production can be conducted by integrating multi expression cassettes of sHBsAg gene in Pichia pastoris chromosome using gene replacement method. Such integration method turns out to allow loss of foreign gene from chromosome by excisional recombination-mediated looping out. This research was aimed to determine integration stability of four copies of sHBsAg expression cassette in P. pastoris GS115 chromosome inducted with 2% methanol in FM22 medium. The methanol induction was conducted twice at 63-h and 75-h. Integration stability determination was conducted qualitatively using PCR and quantitatively using qPCR absolute quantification. A band of 208 bp with similar intensity was observed after amplification of genomic DNA. All samples generated the same Ct value of around 22 with four copies of sHBsAg gene per genome. The result from this experiment shows that integration of four copies of sHBsAg expression cassette in P. pastoris GS115 chromosome is stable during methanol induction
An Optimization Model for Environmental Ergonomics Assessment in Bioproduction of Food SMEs
Get PDFEnvironmental ergonomics in bioproduction of food Small Medium-sized Enterprises (SMEs) become a concern and need to be optimized. An optimization model was developed using a Genetic Algorithm (GA). The weight of an Artificial Neural Network Model was used as a fitness function for GA. The research objectives were: 1) To design an environmental ergonomic assessment system for bioproduction of Food SMEs, 2) To develop an optimization model for environmental ergonomic assessment using a Genetic Algorithm. GA is utilized to search optimal set points of environmental ergonomics based on the predicted fitness values. Each chromosome of GA represents the environmental ergonomics value. The parameters were heart rate, bioproduction temperature, distribution of bioproduction relative humidity and light intensity. The target of the optimization model was the bioproduction temperature set points. The research result indicated the model generated optimum values of environmental ergonomics parameter in bioproduction of food SMEs. The parameters could be used to provide standard workplace environment for the sustainability of food SMEs
The Genetic Structure of Nilaparvata lugens (Stal.) in Java Populations
Get PDFThe brown planthopper Nilaparvata lugens (Stal.) causes hopperburn in the rice field. The wing macropterous adults of this insect have capability for long distance flight. We aimed to analyze the genetic structure of six N. lugens populations in Java inferred from the combined COI-COII mitochondrial and ten loci of microsatellites markers. This study found low levels of nucleotides and high levels of haplotype diversity of the planthopper. The demographic test might indicate the genetic bottleneck history of N. lugens population in Java. The genetic diversity analyzed by using microsatellite markers also showed high levels of heterozygosity (Ho>He) that indicated an isolated-breaking effect in the six populations in Java. Moreover, we found a homogenous genetic structure of N. lugens based on pairwise fixation indices (Fst) analyzes that appears to be maintained by high levels of gene flow and showed no correlation between genetic and geographical distance. Importantly, these studies also support accurate information of widely distributed and genetically intermixed among N. lugens across Asia populations. Thus, our results support the theory of long-distance migration among N. lugenspopulations. The genetic structure information of N. lugens in Java could support regional management, such as the new controlling strategies based on forecasting systems
Photosynthetic Rate of Lettuce Cultivated on Floating Raft Hydroponic with Controlled Nutrient Solution
Get PDFLettuce becomes the main ingredient of salad as one of the healthy foods. The lettuce cultivation in tropical areas is often performed in highland. To reduce soil erosion and pesticide contamination, the cultivation of lettuce plants in high open land needs to be reduced. The lettuce cultivation in hydroponic system at tropical lowland requires cooling. The root zone cooling requires enormous electrical energy. However, it can be solved by controlling the temperature based on the automatically. Therefore, it has been developed control and monitoring system for the root zone on floating raft hydroponic system. This study aimed to evaluate the photosynthetic rate of lettuce cultivated in floating raft hydroponic system whose nutrient solution was controlled by the developed control and monitoring system. Statistical analysis was performed to draw the conclusions about photosynthetic variance of lettuce on two hydroponic systems, namely controlled and uncontrolled system. Furthermore, this paper presents an artificial neural network (ANN) model to estimate the photosynthetic rate of lettuce cultivated in the hydroponic systems. The ANN model was comprised of eight input (nutrient temperature, EC, pH, DO, and ORP, air temperature, air humidity, and photon flux density of photosynthetic) and one output (photosynthetic rate). It was noted that the ANN model predicted accurately the photosynthetic rate of lettuce leaves whose R2 was 0.87 for plants cultivated in floating raft hydroponic system whose nutrient solution was controlled by control and monitoring system. The ANN was useful for identifying the photosynthetic rate of lettuce cultivated in floating raft hydroponic systems on tropical lowland