Improvement of HER2I655V TARMS-PCR Performance by DNA Quality Analysis
Bugi Ratno Budiarto, Azamris, and Desriani
Annales Bogorienses Vol. 21 (2): 52-62.
Reliable TARMS-PCR is a prerequisite in constructing a solid conclusion in genetic diagnostics. The validity of data generated by this molecular technique in most cases is hampered by a false positive result. In attempt to develop a TARMS-PCR for HER2I655V genotyping with no interfering of bias we used DNase I to eliminate DNA contaminant resided in PCR reagent. TARMS-PCR with no enzymatic pretreatment on PCR master mix kit produced a false positive result on HER2I655V TARMS-PCR using as recombinant plasmids system model proven by the presence of multiple PCR products in Non-Template Control (NTC). A dose of 0.1 U of the enzyme could eliminate this DNA contaminant effectively, although this pretreatment altered the specificity of HER2I655V TARMS-PCR genotyping on certain genotype. Combination of touchdown TARMS-PCR with another allelespecific primer recovered specificity of detection on this model system. Interestingly, this optimized HER2I655V TARMS-PCR can only be used for genotyping the clinical samples if only further optimization was done using genomic DNA as template.
Keywords: TARMS-PCR, HER2I655V, DNase I, Polymorphism
Disusun oleh: Ludya AB/Pustakawan
Optimization of Substrate and Starter Cell Concentrations for Dibenzothiopene Biodegradation by Indigeneous Marine Bacteria Mauricauda olearia LBF-1- 0009, Alcanivorax xenomutants LBF-1-0018, and Stakelama pacifica LBF-1- 0031
Elvi Yetti, Ahmad Thontowi, and Yopi
Annales Bogorienses Vol. 21, No. 2: 38-44
Dibenzothiophene (DBT) and its derivatives are widely used-model of organic sulfur compounds for the biodegradation process of petroleum oil. The abilities of microorganisms to degrade pollutants are significantly influenced by various factors such as microbial species, nutrients and environmental parameters. In this research, we conducted a follow-up study to determine the optimum conditions of two parameters affecting DBT biodegradation, namely substrate and starter cell concentrations. Three indigenous marine bacteria isolated from Indonesia’s sea environments potentially degrading DBT were examined. The isolates are belong to Mauricauda olearia strain CL-SS4 (99%), Alcanivorax xenomutants strain JC109 (99%), and Stakelama pacifica strain JLT832 (99%). The optimum DBT concentrations act as the growth substrate for all three isolates was 100 ppm, while the optimum cell concentrations for starter inocula was 20 of OD600 nm conversion units.
Keywords: optimization, substrate concentration, starter cell concentration, dibenzothiophene biodegradation, marine bacteria
Disusun oleh: Ludya AB/Pustakawan
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