Journal of Microbiology Indonesia
http://repository.ipb.ac.id/handle/123456789/29134
2024-03-29T01:56:07ZPerpustakaan Gen: Bagaimana Mengonstruksinya?
http://repository.ipb.ac.id/handle/123456789/54549
Perpustakaan Gen: Bagaimana Mengonstruksinya?
Wahyudi, Aris Tri
Many methods can be used to construct genomic DNA library in the cosmid vector. In this system, large fragments of genomic DNA generated by randomly digestion are ligated to the cosmid vector to form concatemers that can be packaged into bacteriophage λ tparticles. These particles serve as vehicles by which the recombinant DNA molecules are efficiently introduced into bacteria. The method for constructing libraries of bacterial genomic DNA in cosmid is to clone genomic fragments of appropriate size (30-45 Kb) obtained by partial digestion with Sau3AI that recognize a 4-bp sequence compat- ible with that of the vector. The partially digested DNA is cloned into the BamHI site of pJRD215 cosmid vector. The recombinant cosmids are subsequently packaged into bakteriphage 1 and infected into the E. coli NM554 as a host strain. Screening of the E. coli harboring recombinant cosmids containing gene(s) of interest is usually performed by colony hybridization.
2001-01-01T00:00:00ZPembentukan Magnetosom pada Bakteri (Magnetosome Formation in Bacteria)
http://repository.ipb.ac.id/handle/123456789/54548
Pembentukan Magnetosom pada Bakteri (Magnetosome Formation in Bacteria)
Wahyudi, Aris Tri
Magnetic bacteria orient and navigate along geomagnetic field lines and are widely distributed in freshwater and marine habitat. The ability of these bacteria to respond to magnetic fields is based on the presence of intracellular magnetosome, i.e. membrane-bound magnetic particle of either magnetite (Fe3O4,) or greigite (Fe3S4). The magnetosome formation is achieved by tightly controlled processes which involves the accumulation of iron and deposition of the mineral particles at a specific location in the cell. Biomineralization of magnetosome may involve intricate processes, but the exact mechanisms is still poorly understood. This review focuses on the current knowledge about biochemical, physiological as well as molecular biological aspects of the biomineralization process of magnetic bacteria, especially in the magnetosome formation.
2004-01-01T00:00:00ZConstruction of Genomic Library of Magnetospirillnm magneticum AMB-I and Screening of Genes Involved in Magnetosome Synthesis
http://repository.ipb.ac.id/handle/123456789/54547
Construction of Genomic Library of Magnetospirillnm magneticum AMB-I and Screening of Genes Involved in Magnetosome Synthesis
Wahyudi, Aris Tri
Magnetospirillum magneticum AMB-1 is a fresh-water magnetic bacterium capable of synthesizing membrane- bound magnetic particle. called magnetosome, under microaerobic conditions. To screen and isolate genes involved in magnetosome synthesis, genomic library of M. magneticum AMB-1 was constructed using pJRD2l5 as a cosmid vector. The genomic DNA of AMB-1 was partially digested with Saµ3AI and ligated into BamHI digestion of pJRD215. The ligated DNA was packaged into bacteriophage λ particle and subsequently infected into Escherichia coli NM554 as a host strain. A thousand and five colonies of NM554 library carrying the recombinant cosmids were obtained that grew on luria agar supplemented with kanamycin (25 µg ml-1) and streptomycin (50 µg ml-1). Screening of the library by colony hybridization revealed that the library carried all DNA sequences or genes involved in magnetosome synthesis used as probes. The average of the genome size inserted in the library was approximately 10-40 kb. These large fragments would facilitate complementation analysis of genes involved in magnetosorne synthesis in this forming magnetic bacterium.
2005-01-01T00:00:00ZCloning of Genomic DNA Fragment Involve in Acid-Aluminium Tolerance in Bradyrhizobium japonicum 38 Through Transposom Mutagenesis
http://repository.ipb.ac.id/handle/123456789/54546
Cloning of Genomic DNA Fragment Involve in Acid-Aluminium Tolerance in Bradyrhizobium japonicum 38 Through Transposom Mutagenesis
Astuti, Rika Indri; Wahyudi, Aris Tri; Mubarik, Nisa Rachmania
An acid-aluminium sensitive mutant of Bradyrhizobium japonicum 38. designated as AAS38, was generated by mini-Tn5 transposon mutagenesis. The experiment was carried out to identify acid-aluminium tolerance gene (AAT) in B. japonicum. Transposon delivery was carried out through conjugation between Escherichia coli S17-I (λ pir) carrying pUTmini-Tn5Kml and acid-Al tolerant B. japonicum with different of mating time. Frequency of transconjugation was in the range of 10-7 -10-6. A mutant AAS38 was not able to grow on the Ayanaba medium (pH 4.5) containing 50 µM aluminium. However, this mutant formed root nodule of soybean and Siratro plants indicating the gene involved in acid-Al tolerance was not related with nodulation. A 0.8 kb of the genomic DNA fragment flanking the transposon involved in acid-aluminium tolerance was successfully isolated by inverse polymerase chain reaction (Inverse PCR) from AAS38 genome. This fragment was subsequently cloned into pGEM-T Easy (~3 kb) to yield a recombinant plasmid, designated as pGEMT-38 (~3.8 kb), and sequenced. DNA sequence analysis revealed that the genomic DNA fragment had high homology to inner membrane protein from Salmonella typhimurium (80% identity and 86% similarity, E-value= 8xe-62 predicted function as efflux transporter.
2006-01-01T00:00:00Z