Jurnal ILMU DASAR
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Screening of Genomic Library of Soybean Cultivar Lumut by Using Peroxidase Gene from Arabidopsis thaliana as Probe
Get PDFScreening to genomic library of soybean cv. Lumut by using gene encoding for peroxidase (per) from A. thaliana as a probe has an objective isolate the whole gene of per from soybean. The probe was labeled by non-radioisotope alkalin phosphatase. Screening was done by two steps. The first, screening was done to 105 recombinant lambda phages containing genome of soybean cv. Lumut. After southern hybridization, positive signal of plaques were isolated and screened for the second time. After second screening, some recombinant lambda phages containing putatively per genes were isolated. Excision from recombinant lambda phages into recombinant plasmid was successfully done in Escherichia coli strain BM25.8. The plasmid DNAs were isolated from E. coli strain BM25.8 and introduced into E. coli strain DH5α for multiplication. Plasmid DNAs were digested by EcoRI and transferred onto nylon membrane hybond N+. Southern hybridization analysis showed that one clone, L10/R/3/4, contain per gene in the 7.7 kb EcoRI fragment. This fragment is inserted into pSportI.Â
OLS, LASSO dan PLS Pada data Mengandung Multikolinearitas
Get PDFCorrelation between predictor variables (multicollinearity) become a problem in regression analysis. There are some methods to solve the problem and each method has its own complexity. This research aims to explore performance of OLS, LASSO and PLS on data that have correlation between predictor variables. OLS establishes model by minimizing sum square of residual. LASSO minimizes sum square of residual subject to sum of absolute coefficient less than a constant and PLS combine principal component analysis and multiple linear regression. By analyzing simulation and real data using R program, results of this research are that for data with serious multicollinearity (there are high correlations between predictor variables), LASSO tend to have lower bias average than PLS in prediction of response variable. OLS method has the greatest variance of MSEP, that is mostly not consistent in estimating the Mean Square Error Prediction (MSEP). MSEP that is resulted by using PLS is less than that by using LASSO.Â
Kinetics of Complex Reaction of Eugenol Hydrogenation to 2-Methoxy-4-Propylphenol in Pd/Y Catalyst
Get PDFEugenol and isoeugenol hydrogenations using Pt, Pd, Ni as a single or combined metal, that was supported on X and Y zeolite have been carried out. The experiment result showed that in hydrogenation reaction using metal that was supported on zeolite, eugenol is more easily hydrogenated than isoeugenol. Pd metal that was supported on Y zeolite as a catalyst in eugenol hydrogenation is more effective than Ni, Pt or combined metal (Pt,Pd,Ni/X). The highest conversion selectivity of eugenol hydrogenation is in 6% catalyst of Pd (10%)/Y that produced 98.24% of 2-methoxy-4- propylphenol. Kinetic of reaction is very important data that is needed in processing for industry scale, because kinetic can show how fast the starting material is converted into products. In this research, kinetic of the reaction was done by eugenol hydrogenation at 245oC with variation of time using Pd/Y catalyst. The result shows that eugenol hydrogenation is a complex reaction, because the reaction yields not only 2-methoxy-4-propylphenol as a main product, but also cis-isoeugenol and trans-isoeugenol as the side products. The reaction pathway of eugenol hydrogenation in Pd/Y catalyst is a combination of parallel and consecutive pathway and pseudo first order reaction with k = 0.5509
Probit Model on Multivariate Binary Response Using Simulated Maximum Likelihood Estimator
Get PDFIn this paper, we discuss probit model on multivariate binary response. We assume that each of n individuals is observed in T responses. Yit is tth response on ith individual/subject and each response is binary. Each subject has covariate Xi (individual characteristic) and covariate Zijt (characteristic of alternative j). Response on individual ith can be represented by Yi = (Yi1,....,YiT), Yit is tth response on ith individual/subject and each response is multinomial. In order to simplify, we choose one of individual characteristics and alternative characteristics. We use simulated maximum likelihood estimator (SMLE) methods to estimate the parameter based on Geweke-Hajivassiliou-Keane (GHK) simulator. We find the first derivative of likelihood function for multivariate binary probit. Then, we expand to multivariate multinomial response. The first derivative is used in the BHHH (Berndt, Hall, Hall, Hausman) iteration to obtain estimators.Â
Gametogenesis of Nypha Palm Worm Namalycastis rhodochorde (Polychaeta: Nereididae)
Get PDFThe Nypha Palm Worm Namalycastis rhodochorde has been used as bait for fishing in Pontianak. Culturing the worm is one potential effort for its commercialization as well as to overcome the overexploitation of the worm which also brings about the degradation of its natural habitat. Samples of the worm were collected from mangrove forest area in Sungai Kakap, West Kalimantan. Fresh sample of gametes from coelomic fluid were observed carefully under compound microscope to determine phase of gamete development. Oogenesis consisted of three consecutive stages namely immature, submature, and mature with ≤40 μm, 40<x<120 μm, and ≥120 μm in diameter, respectively. The spermatogenesis phases consisted of, spermatogonia, spermatid tetrad and spermatozoa.Â
Generalized AMMI Models for Assessing The Endurance of Soybean to Leaf Pest
Get PDFAMMI(Additive Main Effect Multiplicative Interaction)model for interactions in two-way table provide the major mean for studying stability and adaptability through genotype × environment interaction (GEI), which modeled by full interaction model. Eligibility of AMMI (Additive Main Effect Multiplicative Interaction) model depends on that assumption of normally independent distributed error with a constant variance. In the study of genotypes’ resistance, disease and pest (insect) incidence on a plant for example, the appropriateness of AMMI model is being doubtful. We can handle it by introducing multiplicative terms for interaction in wider class of modeling, Generalized Linear Models. Its called Generalized AMMI model. An algorithm of iterative alternating generalized regression of row and column estimates its parameters. GAMMI log-link model will be applied to the Poisson data distribution. GAMMI log-link models give us good information of the interaction by its log-odd ratio.Â
Analysis of DNA Fragment Obtained from Groupers (Epinephelus fuscoguttatus) Challenged by Vibrio alginolyticus
Get PDFThe objective of this study was to analyse the size of DNA fragment from both resistant and susceptible groupers (Epinephelus fuscoguttatus) after infection by Vibrio alginolyticus. This study was conducted by two steps, firstly, determination of Lethal Concentration (LC50) of Vibrio alginolyticus to obtain fish which resistant and susceptible against Vibrio alginolyticus infection. Secondly, analysis of DNA fragment from both resistant and susceptible fish against Vibrio alginolyticus infection by PCR-RAPD method. In order to analyse the fragment of DNA from the fish, DNA was extracted and the concentration was counted using Kit. Sixteen primers were used, which six primers (RAPD 1-6) were from RAPD Kit, other primers were OPA-14, -A, -B, -C, and -D, YNZ 22, UBC-122, -158, -456, and -457. The results demonstrated that the concentration of bacteria that caused 50 % of fish mortality (LC50)was 7.4 × 105 CFU/L. Based on this concentration, the number of fish which were resistant and susceptible against Vibrio alginolyticus infection were obtained. For the DNA fragment analysis, the concentration of DNA after extraction ranges from 448 μg/ml to 3320 μg/ml with the purity ranges from 86-95 %. From 16 primers used for PCR-RAPD, only 6 primers showed DNA fragments in the gel electrophoresis. Those primers are OPA-14, YNZ 22, UBC-122, -158, -456, and -457. The number of DNA fragments was higher in the group of resistant fish (average 6.4 fragments) than in the group of susceptible fish (average 4.9 fragments). Fifty seven percent (57%) from resistant fish showed specific DNA fragments with size 2.0 kb, indicate that these fragment sizes have a potential role to be used as a marker for obtaining the resistant fish against bacterial infection.Â
Performance of Multimode-Fiber Coupler with Different Coupler Parameter for Displacement Sensor
Get PDFThree multimode-fiber couplers with different coupling ratios, excess losses and directivities are used to sense adisplacement. The fiber coupler is handmade from 1 mm diameter plastic optical fiber. The light source is 632.8nm He-Ne Laser. OPT 101 (Burr Brown) detector is used to detect the change in power output due to theobject’s displacement. The opted displacement’s resolution is 5 μm. The experiment shows that multimode-ficecoupler with 0.25 ratio, 1.37 dB excess loss, and 25 dB directivity gives the highest performance, which has 4mm dynamic range, 1 mm linear range, and 55.4 μW/mm sensitivity. Higher performance can be reached ifmultimode-fiber coupler with the highest coupling ratio and the lowest excess loss is opted
Visualization of Iris Data Using Principal Component Analysis and Kernel Principal Component Analysis
Get PDFPrincipal component analysis (PCA) is a method used to reduce dimentionality of the dataset. However, the use of PCA failed to carry out the problem of non-linear and non-separable data. To overcome this problem such data is more appropriate to use PCA method with the kernel function, which is known as the kernel PCA (KPCA). In this paper, Iris dataset visualized with PCA and KPCA, that contains are the length and the width of sepal and petal.Â
Capability Increasing of Some Antibiotics for Eliminate Liberibacter asiaticus Bacteria to Find the Free-CVPD Citrus Seedling
Get PDFCitrus Vein Phloem Degeneration (CVPD, is considered to be one of the most serious diseases of citrus, having been responsible for the loss of tens millions trees. It is caused by phloem-limited bacteria, Liberibacter asiaticus which are transmitted by citrus psyllids. The bacteria could be found in the budwood as the matter for producing seedling. The use of free-pathogen seedling for citrus plantation was the one of the disease control mechanism. Founding the way to eliminate CVPD bacteria from budwood to produce the free-pathogen seedling was the goal of this research. The study was also compared to the previously research. The research used budwood from L. asiaticus infected-Siem and healthy-Japansche Citroen (JC) which were detected by PCR (polymerase chain reaction). Before grafting, budwoods was soaked in penicillin, kanamycine, tetracyclin, and choramphenicol with concentration 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 ppm and time of soaking was 25 – 30, 40 – 45, and 55 – 60 minutes. The detection of L. asiaticus in the leaves of seedlings was done by PCR. The research showed that (1) penicillin from 400 ppm to 1000 ppm and tetracyclin from 300 ppm to 1000 ppm with time of soaking 25 – 30, 40 – 45, and 55 – 60 minutes, could eliminate the CVPD bacteria from budwood; (2) kanamycine could not eliminate the CVPD bacteria and causes phytotoxis in budwood; (3) choramphenicol could not eliminate the CVPD bacteria. The penicillin and tetracyclin results different with previously research, but kanamycine and choramphenicol not different with previously research. The information from this research supports that some antibiotics could eliminate the bacteria from budwood for producing the free-CVPD seedlings.Â