Judul: Isolasi Fragmen Gen Penyandi Endoxilanase Streptomyces costaricanus 45I-3 melalui pendekatan PCR
Abstrak: Xilan merupakan polisakarida kedua terbesar di alam setelah selulosa dan mempunyai potensi ekonomi tersendiri terlebih bila telah diuraikan menjadi bahan yang bermanfaat. Penguraian xilan membutuhkan kerja dari kombinasi beberapa enzim dengan endoxilanase (endo-1,4-β-D-xilanase, EC 3.2.1.8) sebagai pendahulu dalam mendegradasi xilan menjadi xilooligosakarida. Salah satu bakteri yang mampu menghasilkan endoxilanase adalah Streptomyces costaricanus 45I-3 koleksi Dr. Ir. Yulin Lestari, Bagian Mikrobiologi Departemen Biologi IPB yang diisolasi dari tanah gambut di Kalimantan. Namun produksi xilanase S. costaricanus 45I-3 secara komersial kurang efisien dan ekonomis disebabkan pertumbuhannya yang lambat bila dibandingkan dengan bakteri pada umumnya. Pendekatan molekuler memungkinkan gen penyandi endoxilanase S. costaricanus 45I-3 diisolasi dan dieskpresikan ke dalam inang yang sesuai untuk mempercepat pertumbuhan dan produksi enzim. Beberapa metode isolasi gen penyandi endoxilanase dari bakteri telah dilaporkan. Salah satu metode isolasi gen penyandi endoxilanase yang tercepat adalah dengan PCR. Penelitian ini bertujuan melakukan isolasi fragmen gen penyandi endoxilanase dari S. costaricanus 45I-3 menggunakan pendekatan PCR yang dilanjutkan dengan penentuan dan analisis urutan DNA. Penelitian ini dilakukan di Laboratorium Bioteknologi Hewan dan Biomedis dan Laboratorium BIORIN (Biotechnology Research Indonesian-The Netherlands), Pusat Penelitian Sumberdaya Hayati dan Bioteknologi (PPSHB) Institut Pertanian Bogor dari bulan Agustus 2008 sampai dengan Mei 2010. Tahapan penelitian yaitu peremajaan isolat S. costaricanus 45I-3, isolasi DNA kromosom, perancangan primer, PCR, ligasi dengan pGEM-T Easy, introduksi ke E. coli DH5α kompeten, isolasi dan verifikasi plasmid rekombinan, pengurutan DNA dan analisis sekuen. Perancangan primer untuk mengamplifikasi gen endoxilanase S. costaricanus 45I- 3 dilakukan berdasarkan data urutan nukleotida gen endoxilanase dari genus Streptomyces yang diperoleh di Gen Bank (http://www.ebi.ac.uk/embl/). Wilayah konservatif dalam gen penyandi endoxilanase Streptomyces dicari melalui penjajaran urutan asam amino maupun nukleotida menggunakan program Clustal W. Primer dirancang menggunakan program Primer3 (http://frodo.wi.mit.edu/cgi-bin/primer3.cgi). Hasil perancangan diperiksa kualitasnya dengan program IDT (http://www.idtdna.com/ SciTools/SciTools.aspx). Rancangan primer diuji spesifitasnya dengan program BLASTn (http://www.ncbi.nlm.nih.gov/BLAST/)....dst
Keyword: Streptomyces costaricanus 45I-3 isolation of endoxylanase gene, design of PCR primer

Judul: Analisis Sekuens Gen Penyandi Enzim Xilanase Ekstraseluler pada Streptomyces costaricanus 45I-3
Abstrak: Streptomyces costaricanus 45I-3 isolated from peat soil is a bacterial strain in the group of actinomycetes. This bacterium is known to produce extracellular xylanase. The objectives of this study were to analyze sequence of gene involved in the synthesis of extracellular xylanase. Complete gene encoding xylanase was isolated from the bacterial genome by Inverse Polymerase Chain Reaction (i-PCR). The resulted gene sequence in a total alignment of 1664 bp amplicons, which consisted of two open reading frame (ORF) with opposite direction. ORF1 consisted of 1029 bp and ORF2 (Partial sequence) consisted of 309 bp. BLASTX analysis showed ORF1 homology with xylanase of bacterium enrichment culture clone Xyl8B8 (GenBank accession No. AFH35005.1) that had 95% identity and 99% similarity. ORF2 homolog with glyoxalase bacterium enrichment culture clone Xyl8B8 (GenBank accession No. AFH35007.1) that had 95% identity and 98% similarity. Upstream of the ORF1 sequence was found Ribosome Binding Site (RBS) 7 bp from the start codon and putative promotor sequence at 100 bp (-35) and 77 bp (-10) from the start codon. Analysis of protein sequence deduced from ORF1 showed that there were 2 domains, i.e Glyco_hydrolase 11 (GH11) and Carbohydrate Binding Type 2 (CBM2). Active sites found on the 130 amino acid on GH11 domain. Visualization of 3 dimension structure showed that 1664 bp fragment had 19 area.
Keyword: 

Judul: Tinjauan Matematis pada Model Makroskopik dan Mikroskopik Arus Lalu-lintas
Abstrak: Traffic flow phenomenon can be described through mathematical model such as continuous dynamic model with an ordinary differential equation so that it can be solved with integral factors. In this paper three simple models of traffic flow are discussed, i.e, two macroscopic and one microscopic models. Macroscopic model formulates dynamics of the traffic flow that occurs on a large number of vehicles on a road. While the microscopic model explains drivers’ behavior in their interaction with other vehicles ahead, i.e, car-following model. This paper shows the existence of ordinary differential equation found in the traffic flow model and indicates some different representations in the context of the same model. It also reviews a simple model of traffic flow along a single link, which leads to some unexpected results, i.e, it can express the solution model in term of link outflows as well as trip time. In the microscopic model, simulation is done to illustrate the behavior of the drivers with a sensitivity coefficient as a benchmark parameter.
Keyword: