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Molecular Genetic Analysis of sup45 Paromomycin Hypersensitive Mutants In Saccharomyces cerevisiae Rukman Hertadi; Hadi Sutedjo; Akhmaloka Akhmaloka
Jurnal Matematika & Sains Vol 6, No 2 (2001)
Publisher : Institut Teknologi Bandung

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Translation termination in Saccharomyces cerevisiae is mediated by eRF-1 and eRF-3 protein encoded by SUP45 and SUP35 gene respectively. To probe more detail concerning the mechanism of translation termination in this organisms, the structure-function of the eRF-1 protein was studied by analyzing of sup45 mutants. In this study, we used three paramomycin hyper sensitive mutants, namely sup45-23, sup45-24 and sup45-38. Phenotypic characterization and quantitation of allosuppresor level showed that the mutants were allele specific mutants. Cloning and sequencing of the sup45 genes from these mutants showed that the sup45-23 exhibited Met48ATG â Ile48Ala and Gly431GGT â Gly431GGA mutation. While sup45-24 and sup45-38 exhibited single silent mutation, Gly431GGT â Gly431GGA . The structure-function analysis of sup45 gene of these mutant suggested that phenotypic mutants were not only due to the alteration of amino acid of eRF-1 protein in the cells.

Isolasi dan Karakterisasi Mutan sup45 Saccharomyces cerevisiae Sensitif Temperatur Akhmaloka Akhmaloka; R. Hertadi; Senam Senam; P. E. Susilowati; M. Sindumarta; H. Sutedjo
Jurnal Matematika & Sains Vol 9, No 2 (2004)
Publisher : Institut Teknologi Bandung

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One of the approachs to understand the structure-function of the gene is by studying its mutants. A few of sup45 ts mutants was isolated from Saccharomyces cerevisiae strain BSC483/1a induced by EMS. The concentration EMS of 1.5% (v/v) was found to be the most effective concentration on this study. Eight of sup45 ts mutants were selected from 515 allosupressor mutants. All of the mutants showed lower growth rate and maximum growth compared to that of the wild type. In addition of allosuppression phenotype, six of the mutant showed temperature sensitive and the other two exhibited temperature and paromomycine sensitive. Quantitation of an allosuppression phenotype using plasmid-borned gene fusion, PGK-termination codon-LACZ, showed that the mutants have a variation level of allosuppression. Temperature sensitivity analysis of the mutants showed that one, three, and one mutants were unviable at 32, 34, and 37OC, respectively. Further analysis on two of the mutants showed that the allosuppression level increased by increasing temperature growth. All the data suggested that the mutants were allelic specific mutants.

Ribotyping Identification of Thermophilic Bacterium from Papandayan Crater Akhmaloka, Akhmaloka; Suharto, A.; Nurbaiti, S.; Tika, I. N.; Warganegara, F. M.
Journal of Engineering and Technological Sciences Vol 38, No 1 (2006)
Publisher : ITB Journal Publisher, LPPM ITB

A few thermophilic bacteria were isolated from a hot spring located in Papandayan Crater, Garut. One of the organisms showed a well growth at temperature of up to 80 oC. Chromosomal DNA from the organism was isolated and used to amplify 16S rRNA gene fragment. The gene was amplified by a set of universal primers (27F and 1492R) resulting in a 1.5 kb DNA fragment. The gene was cloned and sequenced. The phylogenetic tree, homological analysis, and detailed comparison of the sequences showed that 16S rRNA gene sequence of the Papandayan isolate is unique compared to other known strains, however the sequence had closest similarities with Bacillus caldolyticus and Bacillus caldotenax.

Bioethanol Production from Sugarcane Bagasse Using Neurospora intermedia in an Airlift Bioreactor Restiawaty, Elvi; Gani, Kindi Pyta; Dewi, Arinta; Arina, Linea Alfa; Kurniawati, Katarina Ika; Budhi, Yogi Wibisono; Akhmaloka, Akhmaloka
International Journal of Renewable Energy Development Vol 9, No 2 (2020): July 2020
Publisher : Center of Biomass & Renewable Energy, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ijred.9.2.247-253

Bagasse as solid waste in sugarcane industry can be utilized as one of the potential raw materials in the bioprocess industry. This research aims to investigate the conversion of bagasse to bioethanol using simultaneous saccharification and fermentation in an airlift bioreactor. Neurospora intermedia was used as a biological agent that carried out the saccharification and fermentation of sugarcane bagasse simultaneously for bioethanol production. Cell morphology of N. intermedia in the form of pellet was required to provide free movement in the axial flow of airlift bioreactor. The medium pH strongly affects the morphological shape of N. intermedia. Therefore, the formation of good pellets of inoculum was observed under acidic conditions, i.e. pH 3.0 â€“ 3.5. The effect of the initial concentration of nutrient on the inoculum growth was also investigated. Inoculums cultured in potato dextrose broth (PDB) medium with a half the strength of the common nutrient concentration of PDB qualitatively indicated good growth in terms of the size and density of cells. The inoculums with good morphological form were fed into the airlift bioreactor, which already contained a liquid medium with initial pH of 3.5 and also contained pre-treated bagasse. In experiments using the airlift bioreactor, the pre-treated bagasse was added to various nutrient concentrations of the PDB infusion medium. The highest bioethanol production from bagasse was monitored in the medium culture of half strength PDB infusion. The yield of bioethanol obtained from total sugarcane bagasse and PDB in an air lift bioreactor achieved approximately 40%, which has an infusion medium with a half-strength PDB and initial pH of 3.0.Â

Ribotyping Identification of Thermophilic Bacterium from Papandayan Crater Akhmaloka Akhmaloka; A. Suharto; S. Nurbaiti; I. N. Tika; F. M. Warganegara
Journal of Engineering and Technological Sciences Vol. 38 No. 1 (2006)
Publisher : Institute for Research and Community Services, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/itbj.eng.sci.2006.38.1.1

A few thermophilic bacteria were isolated from a hot spring located in Papandayan Crater, Garut. One of the organisms showed a well growth at temperature of up to 80 oC. Chromosomal DNA from the organism was isolated and used to amplify 16S rRNA gene fragment. The gene was amplified by a set of universal primers (27F and 1492R) resulting in a 1.5 kb DNA fragment. The gene was cloned and sequenced. The phylogenetic tree, homological analysis, and detailed comparison of the sequences showed that 16S rRNA gene sequence of the Papandayan isolate is unique compared to other known strains, however the sequence had closest similarities with Bacillus caldolyticus and Bacillus caldotenax.

STUDI BIOINFORMASI URUTAN ASAM AMINO DAN STRUKTUR 3D PROTEIN ALDOLASE KELAS II (AldII) DARI Uncultured Acidilobus sp. Nishia Waya Meray; Suharti Suharti; Akhmaloka Akhmaloka
Jurnal Kimia Riset Vol. 6 No. 2 (2021): Desember
Publisher : Universitas Airlangga, Campus C Mulyorejo, Surabaya, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jkr.v6i2.31097

Pada penelitian sebelumnya fragmen gen 1,9 kb telah berhasil diisolasi dari Kawah Domas, Jawa Barat melalui pendekatan metagenom. Fragmen tersebut diketahui mengandung daerah Open Reading Frame (ORF) utuh dari gen pengkode aldolase kelas II dari uncultured Acidilobus sp. yang kemudian disebut sebagai aldII. Fragmen gen aldII tersebut berhasil diekspresikan menjadi protein termostabil aldolase kelas II yang kemudian disebut sebagai AldII. Penelitian ini bertujuan untuk melakukan studi bioinformasi terhadap protein AldII tersebut. Protein AldII kemudian diketahui memiliki massa molekul ~21,2 kDa dengan rumus molekul C940H1539N261O281S8. Total residu bermuatan negatif (Asp + Glu) sebanyak 22 residu, sedangkan total residu bermuatan positif (Arg + Lys) adalah 18 residu. Nilai pI teoritis AldII sebesar 5,86. Hasil perhitungan indeks kestabilan protein ini adalah 36,61 dan diklasifikasikan sebagai protein yang stabil. Lewat penjajaran dengan homologi terdekat, ditemukan daerah lestari yang dapat menunjukan residu yang mungkin berperan dalam pengikatan logam dan sisi aktif. Prediksi struktur 3D dilakukan secara ab initio, menunjukan adanya 6 struktur β-sheet dan 6 struktur α-heliks. Dengan demikian dapat disimpulkan bahwa protein AldII dari uncultured Acidilobus sp. diduga memiliki aktivitas enzimatik.

ANALISIS 6 DNA REKOMBINAN DENGAN ENZIM EcoR1 Ni Nyoman Tri Puspaningsih; Akhmaloka; Afaf Baktir; Ami Soewandi J.S.; Y. Sriwulan M.
JURNAL PENELITIAN BIOLOGI BERKALA PENELITIAN HAYATI Vol 3 No 1 (1997): June 1997
Publisher : The East Java Biological Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23869/490

Amylase enzyme from Endomycopsis fibuligera capable to hidrolize starch into glucose. Insertion of amylase gene from Endomycopsis fibuligera into yeast (Saccharomyces cereviceae) will be able to increase the function of yeast (S.cereviceae) to digest more cheaper substrate, like starch. Before cloning in yeast, recombinant DNA will be made and analyzed in Escherichia coli strain DH5a. The result showed that the sixth transformant consist recombinant DNA that were sensitive to tetracycline medium. Analysis by EcoR1 digestion showed that the size of insertion fragment into Ycp 50 vector are around 0.3 untill 16 kb.

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