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All Journal HAYATI Journal of Biosciences ILMU KELAUTAN: Indonesian Journal of Marine Sciences Jurnal Ilmu Ternak Sosiohumaniora Jurnal Ilmiah Aplikasi Isotop Radiasi Microbiology Indonesia AL KAUNIYAH Jurnal Biologi dan Pembelajarannya (JBP) Jurnal Sosioteknologi Journal of Mathematical and Fundamental Sciences Jurnal Riset Kimia JURNAL BIOLOGI INDONESIA Mimbar Agribisnis: Jurnal Pemikiran Masyarakat Ilmiah Berwawasan Agribisnis Jurnal Penelitian Pendidikan IPA (JPPIPA) Jurnal Agribisnis Terpadu Journal of Management - Small and Medium Enterprises (SME's) Makara Journal of Science
PINGKAN ADITIAWATI
Microbial Biotechnology Research Group, School of Life Sciences and Technology Institut Teknologi Bandung, Jl. Ganesha 10 Bandung, Jawa Barat 40132, Indonesia
Agriculture, Biological Sciences & Forestry Arts Humanities Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Engineering Health Professions Immunology & microbiology Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics Social Sciences Veterinary

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The Effect of Mutation at Thr 295 of Saccharomyces cerevisiae eRF1 on Suppression of Nonsense Codons and eRF1 Structure PRIMA ENDANG SUSILOWATI; PINGKAN ADITIAWATI; FIDA MADAYANTI; . AKHMALOKA
Microbiology Indonesia Vol. 2 No. 1 (2008): April 2008
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (223.554 KB) | DOI: 10.5454/mi.2.1.3

Abstract

The termination of translation in Saccharomyces cerevisiae is controlled by two interacting polypeptide chain release factors, eRF1, and eRF3. Two regions in eRF1, at position 281-305 and 411-415, were proposed to be involved on the interaction to eRF3. In this study we have constructed and characterized eRF1 mutants at position 295 from threonine to alanine and serine residues resulting in eRF1(T295A) and eRF1(T295S) respectively. The mutations did not affect the viability or temperature sensitivity of the cells. The stop codons readthrough of the mutants were analyzed in vivo using PGK-stop codon-LACZ gene fusion and the results showed that thesuppression of the mutants was increased in all of the codon terminations. The suppression of the UAG codon was the high for both mutants, with a 7-fold increased for eRF1(T295A) and a 9 fold increase for eRF1(T295S). The suppressor activity of eRF1(T295S) was higher compared to that of eRF1(T295A), suggesting that the accuracy of translational termination in eRF1(T295S) was lower than that of eRF1(T295A). Computer modeling analysis using Swiss-Prot and Amber version 9.0 programs revealed that the overall structure of eRF1 mutants has no significant difference with the wild type. However, substitution of threonine to serine on eRF1(T295S) triggered a secondary structure change on the other motif of the C-terminal domain of eRF1. This observation did not occur for on eRF1(T295A). This suggests that the high stop codon suppression on eRF1(T295S) is probably due to the slight modification of the structure of the C terminal motif.
Cell Lysis Method Affects Assessment of Microbial Diversity Based on Ribotyping Analysis HENI YOHANDINI; FIDA MADAYANTI; PINGKAN ADITIAWATI; . AKHMALOKA
Microbiology Indonesia Vol. 2 No. 1 (2008): April 2008
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (593.051 KB) | DOI: 10.5454/mi.2.1.6

Abstract

The microbial community in Kawah Hujan, Kamojang, West Java, Indonesia, was analyzed using 16S-rRNA-gene-sequencing combining with denaturing-gradient-gel electrophoresis (DGGE) technique. Two different cell lysis methods, enzymatic-based, and physical treatment-based DNA extraction, were used to isolate chromosomal DNA for 16S rDNA gene-fragment amplification. The DGGE profiles showed some differences in banding pattern that were obtained from both cell lysis methods. The DNA sequence analysis of the individual DGGE bands revealed that most of the band sequences obtained by physical treatment were close to 16S rRNA gene fragments from the bacterial domain, while most of band sequences performed by enzymatic method had high homology with 16S rRNA gene fragments from archaeal domain. Further analysis of the sequences from both methods performed by comparisons with the Ribosomal Database Project showed that some of DGGE sequences from Kawah Hujan consisted unique 16S rDNA sequences.
16S Ribosomal RNA-Based Analysis of Thermophilic Bacteria in Gedongsongo Hot Spring AGUSTINA LULUSTYANINGATI NURUL AMININ1; FIDA MADAYANTI; PINGKAN ADITIAWATI; . AKHMALOKA
Microbiology Indonesia Vol. 1 No. 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (444.526 KB) | DOI: 10.5454/mi.1.1.9

Abstract

Denaturing gradient gel electrophoresis was used to identify the bacterial community at the Gedongsongo (WGS-2) hot spring. The bacterial samples were obtained from both culture dependent and independent strategies. Partial 16S rRNA genes were amplified by a set of primers to produce at around 400 bp fragments, including the highly variable V9 region of the 16S rRNA genes. The DGGE profiles showed that there were a few distinct bands, namely G1-G3, and G8-G12, which represent the predominant bacteria in natural habitat and the medium.Further analysis of these bands showed that most of them, except for G7, have a high homology to the 16S rRNA gene sequences of Thermus sp. As for G7, the highest homology was shown to unculturable bacteria. In addition to the distinct bands in DGGE, there were other three thin bands, namely G4, G5, and G6, which possibly represent non dominant microorganisms in the natural habitat, but could grow on GS-A medium. Further analysis of these bands showed that G6 has 80% similarity to the 16S rRNA of Burkholderia sp., while G4 and G5 have a high homology to each other but only contained 10-15% homology to the sequences of 16S rRNA from unculturable microorganisms. The phylogenetic analyses of the last organisms showed that there was branching from Burkholderia. From all the data obtained it was suggested that the WGS-2 hot spring was predominantly occupied by the genus Thermus. In addition, there were a few novel microorganisms found in the hot spring.
Strategi Pengembangan Usahatani Kopi Arabika (Kasus pada Petani Kopi Di Desa Suntenjaya Kecamatan Lembang Kabupaten Bandung Barat, Provinsi Jawa Barat) Akhmad Zakaria; Pingkan Aditiawati; Mia Rosmiati
Jurnal Sosioteknologi Vol. 16 No. 3 (2017)
Publisher : Fakultas Seni Rupa dan Desain ITB

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/sostek.itbj.2017.16.3.7

Abstract

Coffee is an important export commodity for Indonesia, which is able to contribute a sizeable foreign exchange. West Bandung Regency is a regency in West Java province which have significant potential for the development of Arabica coffee commodity. Suntenjaya village, Lembang district is one of the Arabica coffee-producing areas in West Bandung regency. However, there are some obstacles in the development of arabica coffee farming including land resources utilization, harvest and post-harvest, quality and institutional aspects. Therefore, it is necessary to formulate business development strategies that can be applied arabica coffee farmers. Data and information needed were primary data and secondary data. Data were analyzed using SWOT analysis and QSPM. The study concluded that in order to help farmers in developing a business, there are several strategies a priority that can be conducted, that is  develop the processing of product, improve technical skills of farming to increase product quality, empowerment of farmer to further improve the business, increasing access to capital, optimize of farming business land, optimizing production capacity and maintain marketing network. Keywords: arabica coffee, SWOT analysis, coffee farming, the development strategy
The Use of Biofiltration Technology and 3-dimensional Cubical Bamboo Shelters for Nursery Phase Productivity Improvement of Giant Freshwater Prawns Gede Suantika; Pingkan Aditiawati; Malendra Rusni; Rifki R. Arief; Osman R. Turendro
Journal of Mathematical and Fundamental Sciences Vol. 44 No. 2 (2012)
Publisher : Institute for Research and Community Services (LPPM) ITB

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/itbj.sci.2012.44.2.3

Abstract

This experiment was aimed at finding out the effects of usingnitrifying bacteria and Chlorella sp. and the application of a differing number of 3-dimensional cubical bamboo shelters for enhancing the growth performance of Giant Freshwater Prawns (Macrobrachium rosenbergii de Man) during the nursery phase in an indoor system. During 28 days of culture, treatment II (application of 4 shelters ~40% culture volume occupation) resulted in better prawn growth and culture performance compared to control (no shelter application) (p<0,05). At the end of the experiment, treatment II showed the highest biomass, specific growth rate, mean body weight and length of prawns with (1.96+0.05) g.cage-1, 8.24% BW.day-1, (2.18+0,89) g and (6.50+0.91) cm, respectively. However, these results were not significantly different compared to treatment I (application of 2 shelters ~20% culture volume occupation). The survival rate after treatment I and II (treatment I=90%, and treatment II=92%) was significantly higher compared to control (78%). During the experiment the increase of the concentration of ammonium and nitrate was controlled by the addition of nitrifying bacteria and microalgae, which can keep the microbial loop between ammonium reduction by bacteria and nitrate uptake by microalgae in balance. The addition of nitrifying bacteria and microalgae, and the availability of 40% bamboo shelter occupation in the culture can improve prawn culture productivity.
Effect of Stimulants on Biogenic Methane Formation and Dynamics of Bacterial Population Pingkan Aditiawati; Agus Pujobroto; Indra Rudiansyah; Harry Rahmadi
Journal of Mathematical and Fundamental Sciences Vol. 45 No. 3 (2013)
Publisher : Institute for Research and Community Services (LPPM) ITB

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/j.math.fund.sci.2013.45.3.6

Abstract

Coal bed methane (CBM) is a renewable energy source produced through thermogenic and biogenic activity during the coal formation process. The aim of this research was to stimulate biogenic methane formation using simple carbon as stimulant. The microcosm set-up was done using subbituminous coal at 37°C in an anaerobic chamber. Stimulation with Na-acetate, methanol, formic acid, and no additions, respectively, was carried out for 54 days; observation took place on day 2, 15, 24, 45, and54. The results of all treatments showed differences in the initial pH of the basal medium: 7.76 (Na-acetate), 6.69 (methanol), 4.06 (formic acid), and 8.95 (no stimultant), respectively. Addition of Na-acetate resulted in the highest methane formation rate (5.034 mmol/g coal on day 24 of incubation), followed by methanol (4.377 mmol/g on day 24 of incubation), formic acid (2.520 mmol/g on day 22 of incubation), and no addition (1.2 mmol/g on day 15 of incubation). Using denatured gradient gel electrophoresis (DGGE) it was observed that the microbial population dynamics of the microcosm depended on the stimulant. A decrease of bands indicated that the addition of Na-acetate and methanol had caused a decrease of bacterial diversity during the stimulation process compared to the control treatment (without stimulant).
Isolation of Asphaltene-Degrading Bacteria from Sludge Oil Aditiawati, Pingkan; Kamarisima,
Makara Journal of Science Vol. 19, No. 1
Publisher : UI Scholars Hub

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Abstract

Sludge oil contains 30%–50% hydrocarbon fractions that comprise saturated fractions, aromatics, resins, and asphaltene. Asphaltene fraction is the most persistent fraction. In this research, the indigenous bacteria that can degrade asphaltene fractions from a sludge oil sample from Balikpapan that was isolated using BHMS medium (Bushnell-Hass Mineral Salt) with 0.01% (w/v) yeast extract, 2% (w/v) asphaltene extract, and 2% (w/v) sludge oil. The ability of the four isolates to degrade asphaltene fractions was conducted by the biodegradation asphaltene fractions test using liquid cultures in a BHMS medium with 0.01% (w/v) yeast extract and 2% (w/v) asphaltene extract as a carbon source. The parameters measured during the process of biodegradation of asphaltene fractions include the quantification of Total Petroleum Hydrocarbon (g), log total number of bacteria (CFU/ml), and pH. There are four bacteria (isolates 1, 2, 3, and 4) that have been characterized to degrade asphaltic fraction and have been identified as Bacillus sp. Lysinibacillus fusiformes, Acinetobacter sp., and Mycobacterium sp., respectively. The results showed that the highest ability to degrade asphaltene fractions is that of Bacillus sp. (isolate 1) and Lysinibacillus fusiformes (Isolate 2), with biodegradation percentages of asphaltene fractions being 50% and 55%, respectively, and growth rate at the exponential phase is 7.17x107 CFU/mL.days and 4.21x107 CFU/mL.days, respectively.
Sequential Isolation of Saturated, Aromatic, Resinic, and Asphaltic Fractions Degrading Bacteria from Oil Contaminated Soil in South Sumatera Munawar, Munawar; Aditiawati, Pingkan; Astuti, Dea Indriani
Makara Journal of Science Vol. 16, No. 1
Publisher : UI Scholars Hub

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Abstract

Sequential isolation has been conducted to obtain isolates of saturated, aromatic, resin, and asphaltene fractions degrading bacteria from oil contaminated sites. Five soil samples were collected from South Sumatera. These bacterial isolates were obtained using soil extract medium enriched with oil recovery or remaining-oil recovery degradated (ROD) as sole carbon and energy sources according to the isolation stage as the isolation medium. ROD at the end of every isolation stage analyzed oil fractions by use of the SARA analysis method. Six isolates of bacteria have been selected, one isolate was fraction saturates degrading bacteria that are Mycobacterium sp. T1H2D4-7 at degradation rate 0.0199 mgs/h with density 8.4x106 cfu/g from stage I. The isolate T2H1D2-4, identified as Pseudomonas sp. was fraction aromatics degrading bacteria at accelerate 0.0141 mgs/h with density 5.1x106 cfu/g are obtained at stage II. Two isolates namely Micrococcus sp. T3H2D4-2 and Pseudomonas sp. T1H1D5-5 were fraction resins degrading bacteria by accelerate 0.0088 mgs/h at density 5.6x106 cfu/g and 0.0089 mgs/h at density 5.7x106 cfu/g are obtained at stage III. Isolation of stage IV has been obtained two isolates Pseudomonas sp. T4H1D3-1and Pseudomonas sp. T4H3D5-4 were fraction asphaltenes degrading bacteria by accelerate 0.0057 mgs/h at density 5.6x106 cfu/g and accelerate 0.0058 mgs/h at density 5.7x106 cfu/g.
Antibacterial compounds derived from marine Streptomyces aureofaciens A3 through in-silico molecular docking Srikandace, Yoice; Syani, Ira Rhabbiyatun; Wahhaab, Aisha; Kamarisima, Kamarisima; Putri, Sastia Prama; Aditiawati, Pingkan
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 29, No 3 (2024): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.29.3.403-413

Abstract

Streptomyces aureofaciens widely produces the antibiotic tetracycline and many other compounds during fermentation. The compounds have yet to be known for their antibacterial potential. This work aims to determine new antibiotics or other possible antibacterial compounds produced by marine S.aureofaceiens A3 through an in silico molecular docking method. The ethyl acetate (EA) extracts from fermented marine S. aureofaciens A3 in ISP4 medium enriched with seawater components showed strong antibacterial activity.  The antibacterial activity of EA extracts during 6-12 days of fermentation was carried out by the Kirby-Bauer method and the compounds of EA extracts were analyzed by GC/MS. Compounds identified by GC/MS were ligands for an in silico molecular docking study against four target proteins (DNA gyrase, topoisomerase IV, PBP 1a, and DHFR) of pathogenic bacteria. The drug-likeness of selected chemicals as antibacterial agents was assessed using Lipinski's Rule of Five. The results showed the prospective compounds as a narrow-spectrum antibacterial, including 3,5-di-tert-Butyl-4-hydroxyphenylpropionic acid against PBP 1a and Benzenepropanoic acid, and 3,5-bis (1,1-dimethyl ethyl)-4-hydroxy-, methyl esters against DHFR. Substances with broad-spectrum antibacterial activity, such as 3-Acetylphenanthrene and 3-(p-Ethoxyphenyl)-5-(O-tolyloxymethyl)-2-oxazolidone, against multitarget DNA gyrase B and DHFR, 7,9-Di-tert-butyl-1-oxaspiro (4,5) Deca-6,9-diene-2,8-dione against PBP1a and DHFR, and isobenzofuro [5,6-b] benzofuran-8-carboxylic acid, 1,3-dihydro-7,10-dimethoxy-9-methyl-1-oxo-, methyl ester against DNA gyrase B, PBP 1a, and DHFR. On the 12th day of fermentation, two compounds were identified: isobenzofuro[5,6-b] benzofuran-8-carboxylic acid, 1,3-dihydro-7,10-dimethoxy-9-methyl-1-oxo-, methyl ester, and 3-(p-Ethoxyphenyl)-5-(O-tolyl oxy methyl)-2-oxazolidone.  This is the first report that these two compounds, known as potential drugs like antibiotics through in silico molecular docking, were first produced by Streptomyces species.
Pengembangan Minuman Probiotik dari Buah Kawista (Feronia limonia) dengan Bakteri Asam Laktat Indigenous herawati, elysabet; aditiawati, pingkan
Jurnal Biologi dan Pembelajarannya (JB&P) Vol 2 No 1 (2015): Jurnal Biologi dan Pembelajarannya
Publisher : Universitas Nusantara PGRI Kediri

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29407/jbp.v2i1.329

Abstract

Kawista (Feronia limonia) merupakan tanaman suku jeruk-jerukan (Rutaceae) berpotensi sebagai tanaman obat. Menurut penelitian yang pernah dilaksanakan, buah kawista baru diolah menjadi sirup, dodol, selai dan madumongso. Semakin meningkatnya perhatian terhadap pengaruh makanan dan minuman terhadap kesehatan, memicu berkembangnya produk kesehatan dengan pemanfaatan bahan alami. Berdasarkan manfaat buah kawista, penelitian bertujuan untuk mengembangkan produk sirup buah kawista sebagai minuman probiotik dengan pemanfaatan bakteri indigenous genus Lactobacillus yang diisolasi dari buah kawista. Pembuatan minuman probiotik kawista diawali dengan pembuatan sirup dengan metode maserasi. Bakteri  indigenous diisiolasi dari kulit luar, kulit dalam dan sirup buah kawista dengan teknik pengenceran bertingkat. Isolasi dilakukan pada media NA yang dimodifikasi dengan sirup kawista. Sebanyak 35 isolat bakteri yang didapat diseleksi dengan pemindahan ke media MRS. Dilakukan uji metode difusi sumur untuk mengetahui aktivitas antimikroba isolat terhadap bakteri patogen pencernaan yakni Bacillus subtilis, Escherichia coli dan Staphylococcus aureus. Diamati zona bening yang terbentuk pada 3 bakteri uji sehingga didapatkan 3 isolat bakteri terpilih dengan diameter zona 15,5 mm; 17 mm dan 30,5 mm. Isolat terpilih didentifikasi dengan metode  perwarnaan gram sehingga diketahui jenis bakteri adalah gram positif. Identifikasi molekuler dilakukan oleh Macrogen-Korea. Dari hasil sekuensing didapatkan spesies Lactobacillus paracasei strain FT179 sebagai isolat fermentasi. Dilakukan pembuatan kurva baku dan kurva tumbuh untuk mengetahui pertumbuhan optimal sebagai acuan pembuatan starter. Waktu pertumbuhan optimum Lactobacillus paracasei didapatkan pada jam ke 12.
Co-Authors . AKHMALOKA Agus Pujobroto Agustina L.N. Aminin Akhmad Zakaria Anthoni Agustien Crhisterra Ellen Kusumaningrum Dadang Sumardi Dadang Sumardi Dadang Sumardi Dea Indriani Astuti Dea Indriani Astuti Dea Indriani Astuti Dwiwahju Sasongko Dwiwahju Sasongko Fatimah, Anisah Nur Felicia Irene Saputra FIDA MADAYANTI Gede Suantika Gede Suantika Harry Rahmadi Heni Yohandini Herawati, Elysabet Indra Rudiansyah Indriani, Dea Indriani, Dea Irawan Sugoro Irawan Sugoro Irawan Sugoro Kamarisima Kamarisima Kamarisima, Kamarisima, Kamarisima Kusnadi Kusumawardhani, Meirina Kartika Liliasari Magdalena Lenny Situmorang Malendra Rusni Markhamah, Nadya Julia Megga Ratnasari Pikoli Mia Rosmiati Mia Rosmiati Mia Rosmiati Munawar . Munawar Munawar Novi Mulyawati, Novi Nurhajati, Jetty Osman R. Turendro PRIMA ENDANG SUSILOWATI Putri, Sastia Prama Rifki R. Arief Rosmiati, Mia Sandra Hermanto Sastia Prama Putri SONY SUHANDONO Srikandace, Yoice Syani, Ira Rhabbiyatun Togar M Simatupang Trisna Amelia Udin, Linar Z. Ulya Alviredieta Wahhaab, Aisha