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Transposon Insertion Phenomenon during Cloning of a Partial Fragment Derived from Metagenomic DNA Isolated from Deep-Sea Water and Sediment of Kawio Island, North Sulawesi Agung, Mochamad Untung Kurnia; Moeis, Maelita Ramdani
Squalen, Buletin Pascapanen dan Bioteknologi Kelautan dan Perikanan Vol 8, No 3 (2013): December 2013
Publisher : Research and Development Center for Marine and Fisheries Product Processing and Biotechnol

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15578/squalen.v8i3.84

Transposon is well-known as mobile element found abundant both in prokaryote and eukaryote genomes. In bacteria, transposon (famous name of a transposable DNA) could jump from chromosome to plasmid and its contrary. One type of transposons in bacteria known as insertion sequence (IS), it does not contain any additional genes except a gene encoding transposase, an enzyme that correlated to transponsition activities. The finding of transposon insertion unfortunately found during cloning of a fragment derived from deep-sea metagenomic DNA in this research. In the initial, this research was aimed to clone and characterize the Ã¡-amylase encoded gene derived from metagenomic DNA isolated from deep-sea water and sediment of Kawio Island, North Sulawesi. Metagenomic DNA has been isolated from deep-sea water and sediment and by using Whole Genome Amplification (WGA) technique, the DNA it could be increased in quantities to 146,31 ng for each 1 ng of metagenomic DNA. A fragment of ~1000 bp in length was obtained by using touchdown PCR method. The presence of a transposon in this DNA fragment is proposed as a hypothesis for losing ~700 bp leaving just 310 bp cloned sequence. Analysis of sequencing result showed a highest similarity between this 310 bp partial fragment with a replication protein (Rep) encoded gene from Pseudomonas putida (Query Coverage: 88%; Max. Identity: 80%, Positive: 86%) and this protein is known to be involved in plasmid replication where transposase encoding genes known usually presence together with this gene (Rep gene) in a bacterial plasmid.

OPTIMASI PROSES UNTUK EKSPRESI GEN ENDOGLUKANASE DARI Bacillus sp. RP1 OLEH Escherichia coli BL21 (DE3)/ egc Victor, Hans; Moeis, Maelita Ramdani
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol 5, No 1 (2018): June 2018
Publisher : Badan Pengkajian dan Penerapan Teknologi (BPPT)

Process Optimization for Endoglucanase Gene Expression Derived from Bacillus sp. RP1 by Escherichia coli BL21 (DE3)/egcABSTRACTCellulases are one of the most used enzymes in industrial processes. In an effort to increase production, industries have developed strategies such as isolating new cellulase producing strains, genetic engineering and process optimization since the last 50 years. One endoglucanase producing strain, Bacillus sp. RP1 was isolated from hot springs. The ribosome binding site and coding sequence of the endoglucanase gene (egc) from Bacillus sp. RP1 was cloned into pGEM-T Easy. The recombinant plasmid was used to transform E. coli BL21 (DE3). Cloning was followed by process optimization. Medium composition was selected using Plackett-Burman design. The medium components tested were rice hull, molasses, ammonium chloride, urea and fishmeal. Rice hull and molasses were found to be the factors most influencing enzyme activity and dry cell weight, respectively. The next step involved Box-Behnken method and response surface methodology to optimize the responses against molasses concentration, rice hull concentration and fermentation time. The concentration intervals used to test were 1%, 5.5% and 10% while the fermentation time used were 24, 36 and 48 hours. The conditions which optimized both enzyme activity and dry cell weight were 7.45% molasses, 6.45% rice hull and 39.52 hours of fermentation.Keywords: Bacillus sp. RP1, E. coli BL21 (DE3), egc, Endoglucanase, optimizationÂ ABSTRAKSelulase adalah salah satu enzim yang banyak dimanfaatkan dalam berbagai industri. Sebagai upaya untuk memenuhi kebutuhan, 50 tahun terakhir dikembangkan beberapa strategi untuk meningkatkan produksi selulase yang mencakup rekayasa genetika dan optimasi proses. Karena itu, dilakukan kloning gen egc dan RBS yang berasal dari Bacillus sp. RP1 yang diisolasi dari sumber air panas ke dalam vektor pGEM-T Easy. E. coli BL21 (DE3) ditransformasikan dengan vektor yang mengandung gen egc tersebut. Setelah kloning, optimasi proses berupa desain medium turut dilakukan untuk mengoptimalkan ekspresi gen egc. Desain medium diawali dengan seleksi komposisi medium menggunakan metode Plackett-Burman. Komponen medium yang diuji adalah kulit beras, molase, amonium klorida, urea dan tepung ikan. Kulit beras dan molase diperoleh sebagai bahan yang paling berpengaruh terhadap aktivitas enzim dan berat kering sel. Tahap selanjutnya melibatkan metode statistik Box-Behnken dan metodologi respons permukaan yang bertujuan mengoptimalkan respons aktivitas enzim dan berat kering sel terhadap konsentrasi molase, konsentrasi kulit beras dan lama fermentasi. Konsentrasi yang diuji adalah 1%, 5,5% dan 10%, sedangkan lama fermentasi yang diuji adalah 24, 36 dan 48 jam. Konsentrasi optimal molase adalah 7,45% dan konsentrasi optimal kulit beras adalah 6,45% dengan lama fermentasi optimal 39,52 jam.Kata Kunci: Bacillus sp. RP1, E. coli BL21 (DE3), egc, Endoglukanase, optimasi

OPTIMASI PROSES UNTUK EKSPRESI GEN ENDOGLUKANASE DARI Bacillus sp. RP1 OLEH Escherichia coli BL21 (DE3)/ egc Victor, Hans; Moeis, Maelita Ramdani
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 5 No. 1 (2018): June 2018
Publisher : Balai Bioteknologi, Badan Pengkajian dan Penerapan Teknologi (BPPT)

Process Optimization for Endoglucanase Gene Expression Derived from Bacillus sp. RP1 by Escherichia coli BL21 (DE3)/egcABSTRACTCellulases are one of the most used enzymes in industrial processes. In an effort to increase production, industries have developed strategies such as isolating new cellulase producing strains, genetic engineering and process optimization since the last 50 years. One endoglucanase producing strain, Bacillus sp. RP1 was isolated from hot springs. The ribosome binding site and coding sequence of the endoglucanase gene (egc) from Bacillus sp. RP1 was cloned into pGEM-T Easy. The recombinant plasmid was used to transform E. coli BL21 (DE3). Cloning was followed by process optimization. Medium composition was selected using Plackett-Burman design. The medium components tested were rice hull, molasses, ammonium chloride, urea and fishmeal. Rice hull and molasses were found to be the factors most influencing enzyme activity and dry cell weight, respectively. The next step involved Box-Behnken method and response surface methodology to optimize the responses against molasses concentration, rice hull concentration and fermentation time. The concentration intervals used to test were 1%, 5.5% and 10% while the fermentation time used were 24, 36 and 48 hours. The conditions which optimized both enzyme activity and dry cell weight were 7.45% molasses, 6.45% rice hull and 39.52 hours of fermentation.Keywords: Bacillus sp. RP1, E. coli BL21 (DE3), egc, Endoglucanase, optimizationÃ‚Â ABSTRAKSelulase adalah salah satu enzim yang banyak dimanfaatkan dalam berbagai industri. Sebagai upaya untuk memenuhi kebutuhan, 50 tahun terakhir dikembangkan beberapa strategi untuk meningkatkan produksi selulase yang mencakup rekayasa genetika dan optimasi proses. Karena itu, dilakukan kloning gen egc dan RBS yang berasal dari Bacillus sp. RP1 yang diisolasi dari sumber air panas ke dalam vektor pGEM-T Easy. E. coli BL21 (DE3) ditransformasikan dengan vektor yang mengandung gen egc tersebut. Setelah kloning, optimasi proses berupa desain medium turut dilakukan untuk mengoptimalkan ekspresi gen egc. Desain medium diawali dengan seleksi komposisi medium menggunakan metode Plackett-Burman. Komponen medium yang diuji adalah kulit beras, molase, amonium klorida, urea dan tepung ikan. Kulit beras dan molase diperoleh sebagai bahan yang paling berpengaruh terhadap aktivitas enzim dan berat kering sel. Tahap selanjutnya melibatkan metode statistik Box-Behnken dan metodologi respons permukaan yang bertujuan mengoptimalkan respons aktivitas enzim dan berat kering sel terhadap konsentrasi molase, konsentrasi kulit beras dan lama fermentasi. Konsentrasi yang diuji adalah 1%, 5,5% dan 10%, sedangkan lama fermentasi yang diuji adalah 24, 36 dan 48 jam. Konsentrasi optimal molase adalah 7,45% dan konsentrasi optimal kulit beras adalah 6,45% dengan lama fermentasi optimal 39,52 jam.Kata Kunci: Bacillus sp. RP1, E. coli BL21 (DE3), egc, Endoglukanase, optimasi

Face Shape Variation Among Sundanese People from Western Java, Indonesia WOLLY CANDRAMILA; SONY HERU SUMARSONO; BAMBANG SURYOBROTO; MAELITA RAMDANI MOEIS
HAYATI Journal of Biosciences Vol. 22 No. 1 (2015): January 2015
Publisher : Bogor Agricultural University, Indonesia

The face is an important visual stimulus in daily life and each face identifies a particular person. The bone structure of the skull along with various soft tissues and coloration influence perception of the face. Facial averageness, and bilateral symmetry are the two most commonly used criterion of facial attractiveness, yet, both may be perceived differently based on hormonal status of the person observed. Facial perceptions may also differ according to cultural norms. In this research, we examined variations in face-shape among Sundanese male and female adults aged 18 to 40. We applied geometric-morphometric methods to analyze the landmark-based morphological variations in the frontal and lateral views of subjects’ faces. We identified five types of female frontal face views and four of male. We also identified five types each of female and male lateral face views. The trichion, gonion and gnathion were three most variable landmarks among the face views in our study, and highly determined the shape of the individuals’ faces. Multiple face type variation may refer to many categories of attractive faces since there is no exactly perfect category in the assessment of facial attractiveness by the viewers. Therefore, we believe that the configuration of facial features cannot constitute the sole visual criterion of facial attractiveness.

OPTIMASI PROSES UNTUK EKSPRESI GEN ENDOGLUKANASE DARI Bacillus sp. RP1 OLEH Escherichia coli BL21 (DE3)/ egc Hans Victor; Maelita Ramdani Moeis
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 5 No. 1 (2018): June 2018
Publisher : Balai Bioteknologi, Badan Pengkajian dan Penerapan Teknologi (BPPT)

Process Optimization for Endoglucanase Gene Expression Derived from Bacillus sp. RP1 by Escherichia coli BL21 (DE3)/egcABSTRACTCellulases are one of the most used enzymes in industrial processes. In an effort to increase production, industries have developed strategies such as isolating new cellulase producing strains, genetic engineering and process optimization since the last 50 years. One endoglucanase producing strain, Bacillus sp. RP1 was isolated from hot springs. The ribosome binding site and coding sequence of the endoglucanase gene (egc) from Bacillus sp. RP1 was cloned into pGEM-T Easy. The recombinant plasmid was used to transform E. coli BL21 (DE3). Cloning was followed by process optimization. Medium composition was selected using Plackett-Burman design. The medium components tested were rice hull, molasses, ammonium chloride, urea and fishmeal. Rice hull and molasses were found to be the factors most influencing enzyme activity and dry cell weight, respectively. The next step involved Box-Behnken method and response surface methodology to optimize the responses against molasses concentration, rice hull concentration and fermentation time. The concentration intervals used to test were 1%, 5.5% and 10% while the fermentation time used were 24, 36 and 48 hours. The conditions which optimized both enzyme activity and dry cell weight were 7.45% molasses, 6.45% rice hull and 39.52 hours of fermentation.Keywords: Bacillus sp. RP1, E. coli BL21 (DE3), egc, Endoglucanase, optimizationÂ ABSTRAKSelulase adalah salah satu enzim yang banyak dimanfaatkan dalam berbagai industri. Sebagai upaya untuk memenuhi kebutuhan, 50 tahun terakhir dikembangkan beberapa strategi untuk meningkatkan produksi selulase yang mencakup rekayasa genetika dan optimasi proses. Karena itu, dilakukan kloning gen egc dan RBS yang berasal dari Bacillus sp. RP1 yang diisolasi dari sumber air panas ke dalam vektor pGEM-T Easy. E. coli BL21 (DE3) ditransformasikan dengan vektor yang mengandung gen egc tersebut. Setelah kloning, optimasi proses berupa desain medium turut dilakukan untuk mengoptimalkan ekspresi gen egc. Desain medium diawali dengan seleksi komposisi medium menggunakan metode Plackett-Burman. Komponen medium yang diuji adalah kulit beras, molase, amonium klorida, urea dan tepung ikan. Kulit beras dan molase diperoleh sebagai bahan yang paling berpengaruh terhadap aktivitas enzim dan berat kering sel. Tahap selanjutnya melibatkan metode statistik Box-Behnken dan metodologi respons permukaan yang bertujuan mengoptimalkan respons aktivitas enzim dan berat kering sel terhadap konsentrasi molase, konsentrasi kulit beras dan lama fermentasi. Konsentrasi yang diuji adalah 1%, 5,5% dan 10%, sedangkan lama fermentasi yang diuji adalah 24, 36 dan 48 jam. Konsentrasi optimal molase adalah 7,45% dan konsentrasi optimal kulit beras adalah 6,45% dengan lama fermentasi optimal 39,52 jam.Kata Kunci: Bacillus sp. RP1, E. coli BL21 (DE3), egc, Endoglukanase, optimasi

Identification of single nucleotide polymorphisms on the D-loop region of mtDNA in Sundanese population Wolly Candramila; Sony Heru Sumarsono; Bambang Suryobroto; Maelita Ramdani Moeis
Tropical Genetics Vol. 1 No. 1 (2021)
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (884.282 KB)

Identification of sequence polymorphism on the D-loop region of mtDNA has been done for various purposes, including health and medical treatment. In this research, single nucleotide polymorphisms were identified in the D-loop region of mtDNA of the Sundanese population in western Java. A total of 118 unrelated and healthy Sundanese probands were collected from closed-traditional kampung adat and open communities distributed in 14 cities and regencies in western Java. DNA amplification and direct sequencing of the D-loop region were proceeded using primers L15990 and H409. Multi-alignment was conducted not only intrapopulation but also with D-loop sequence data stored in GenBank for comparison. In this research, we categorized high-frequency SNPs as less effective for identification in population studies because of their presence in other populations outside Indonesia. Meanwhile, lower-frequency SNPs showed typical variants of Sundanese haplotypes. On the other hand, rare or low-frequency SNPs should be re-examined in larger size of samples to have a better understanding of risk factors for many diseases.

Marine Bacteria Producing L-Asparaginase with Low Glutaminase and Urease Co-Activity from Pangandaran East Coast Indonesia Pertiwi, Wulan; Namira, Azmy Jasmine; Moeis, Maelita Ramdani; Muharram, Luthfia Hastiani; Hernahadini, Nelis
Squalen, Buletin Pascapanen dan Bioteknologi Kelautan dan Perikanan Vol 20, No 1 (2025): May 2025
Publisher : :Agency for Marine and Fisheries Research and Human Resources, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15578/squalen.908

acterial L-asparaginase is a therapeutic enzyme widely used in the treatment of Acute Lymphoblastic Leukemia (ALL). Although L-asparaginase is prominent in treating ALL, its use is limited due to its side effects caused by its dual substrate specificity towards both asparagine and glutamine. This study aimed to isolate and identify marine bacteria from the East Coast of Pangandaran capable of producing L-asparaginase with low glutaminase and urease co-activities. A semi-quantitative approach was employed, involving the isolation and screening of seawater bacteria using Zobell Marine media supplemented with L-asparagine, glutamine or urea and phenol red as a pH indicator to determine the enzymatic activity. Molecular identification was performed by amplifying and sequencing the 16S rRNA gene, followed by phylogenetic analysis using the neighbor-joining method with 1,000 bootstrap replicates. The results indicated that the bacterial isolate designated PT3 exhibited a high enzymatic index of 4.2 for L-asparaginase, surpassing that of the positive control (E. coli), which had an index of 1.4. Sequence analysis revealed that PT3 shared 99.58% identity with Marinobacterium georgiense strain NBRC 102606, an earlier synonym of Marinobacterium iners. Therefore, PT3 was identified as a strain of Marinobacterium iners, with potential as a novel source of L-asparaginase and displayed significant L-asparaginase activity with minimal co-activity of glutaminase and urease, highlighting its potential as a safer alternative for therapeutic enzyme development.

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