Bioinformatika: Trend dan Prospek dalam Pengembangan Keilmuan Biologi

PENDAHULUAN Tulisan ini terutama dimaksudkan untuk pengguna awal bioinformatika, termasuk mereka yang selama ini belum mengenal bioinformatika dan tertarik untuk memulainya[1]. Tapi bagi yang selama ini sudah menggeluti bioinformatika secara otodidak melalui internet terutama, cenderung mengalami kesalahan bila tidak memilki dasar-dasar yang kuat terhadap biologi molekuler atau menemui kebuntuan untuk melihat permasalahan biologi yang bisa dipecahkan dengan bioinformatika. Maka dari itu dengan penjelasan agak mendalam tentang prinsip biologi molekuler termasuk bagaimana data biologi molekuler itu didapatkan, diharapkan pembaca makalah ini bisa lebih optimal menggunakan bioinformatika khususnya menunjang pengembangan keilmuan biologi di Tanah Air[2]. [1] Witarto, A.B. Bioinformatika: Mengawinkan teknologi informasi dengan bioteknologi. Trendnya di dunia dan prospeknya di Indonesia. Disampaikan pada Seminar Seminar Teknologi Informasi diselenggarakan oleh MIFTA, Bogor, 9 Januari 2003. Bisa diunduh dari witarto.wordpress.com. [2] Witarto, A.B. Bioinformatics in Indonesia. Disampaikan pada First ASEAN-India Workshop on Bioinformatics di Center for DNA Fingerprinting and Diagnostics, Hyderabad, India, 7-11 November 2005. Bisa diunduh dari witarto.wordpress.co

BIOINFORMATIKA: TREND DAN PROSPEK DALAM PENGEMBANGAN KEILMUAN BIOLOGI

PENDAHULUAN Tulisan ini terutama dimaksudkan untuk pengguna awal bioinformatika, termasuk mereka yang selama ini belum mengenal bioinformatika dan tertarik untuk memulainya[1]. Tapi bagi yang selama ini sudah menggeluti bioinformatika secara otodidak melalui internet terutama, cenderung mengalami kesalahan bila tidak memilki dasar-dasar yang kuat terhadap biologi molekuler atau menemui kebuntuan untuk melihat permasalahan biologi yang bisa dipecahkan dengan bioinformatika. Maka dari itu dengan penjelasan agak mendalam tentang prinsip biologi molekuler termasuk bagaimana data biologi molekuler itu didapatkan, diharapkan pembaca makalah ini bisa lebih optimal menggunakan bioinformatika khususnya menunjang pengembangan keilmuan biologi di Tanah Air[2]. [1] Witarto, A.B. Bioinformatika: Mengawinkan teknologi informasi dengan bioteknologi. Trendnya di dunia dan prospeknya di Indonesia. Disampaikan pada Seminar Seminar Teknologi Informasi diselenggarakan oleh MIFTA, Bogor, 9 Januari 2003. Bisa diunduh dari witarto.wordpress.com. [2] Witarto, A.B. Bioinformatics in Indonesia. Disampaikan pada First ASEAN-India Workshop on Bioinformatics di Center for DNA Fingerprinting and Diagnostics, Hyderabad, India, 7-11 November 2005. Bisa diunduh dari witarto.wordpress.co

BIOINFORMATIKA: TREND DAN PROSPEK DALAM PENGEMBANGAN KEILMUAN BIOLOGI

PENDAHULUAN Tulisan ini terutama dimaksudkan untuk pengguna awal bioinformatika, termasuk mereka yang selama ini belum mengenal bioinformatika dan tertarik untuk memulainya[1]. Tapi bagi yang selama ini sudah menggeluti bioinformatika secara otodidak melalui internet terutama, cenderung mengalami kesalahan bila tidak memilki dasar-dasar yang kuat terhadap biologi molekuler atau menemui kebuntuan untuk melihat permasalahan biologi yang bisa dipecahkan dengan bioinformatika. Maka dari itu dengan penjelasan agak mendalam tentang prinsip biologi molekuler termasuk bagaimana data biologi molekuler itu didapatkan, diharapkan pembaca makalah ini bisa lebih optimal menggunakan bioinformatika khususnya menunjang pengembangan keilmuan biologi di Tanah Air[2]. [1] Witarto, A.B. Bioinformatika: Mengawinkan teknologi informasi dengan bioteknologi. Trendnya di dunia dan prospeknya di Indonesia. Disampaikan pada Seminar Seminar Teknologi Informasi diselenggarakan oleh MIFTA, Bogor, 9 Januari 2003. Bisa diunduh dari witarto.wordpress.com. [2] Witarto, A.B. Bioinformatics in Indonesia. Disampaikan pada First ASEAN-India Workshop on Bioinformatics di Center for DNA Fingerprinting and Diagnostics, Hyderabad, India, 7-11 November 2005. Bisa diunduh dari witarto.wordpress.co

COMPARISON OF GENES EXPRESSION; MIRNA 146 A, MIR-103, MIR-423-3P, MIR-21, MIR-16 IN CELL LINES HEP-G2 SERIES 1886 AND PLC5

Objective: Detection of hepatocellular cancer cells(HCC) in vitro has reached the smallest level, that is miRNA(micro RNA) in particular miRNA146A. This study was conducted from February to May2013 at the Department of Molecular Biology, Dharmais Cancer Hospital. The purpose of this study was to compare the value of Cq and expression ofmicroRNA(miRNA/mir) on Hep-G2 and PLC5.Methods: In vitro study were performed in Hep-G2 series 1886 and PLC5. The study used on 33 samples consisting of 5 groups of mir (miRNA146A, miR-423-3p, miR-103, miR-21and miR-16) in Hep-G2 and 5 groups of mirinPLC5 with 3 times repetition, 1 NTC and 2 spike.Results: MiRNA146 A expressionin Hep-G2against mir-423-3p, mir-103, mir-21, mir-16resulted in values as follows in consecutive order: (0.05), (0.03), (0.01), and (0.55). The highest expression was: miRNA146 Aagainst mir-16 and the smallest expression miRNA146 Aagainst mir-21in Hep-G2. MiRNA146 A expressionincell linesPLC5against mir-423-3p, mir-103, mir-21, mir-16resulted in values as follows: (0.01), (0.00), (0.00), and(0.02). The highest expression: miRNA146 A against mir-16, and the smallest expression: miRNA146 Aagainstmir-103 and mir-21 in PLC5.Conclusion: MiRNA 146 A, mir-423-3p, mir-103, mir-21, and mir-16 were expressed in Hep-G2 series 1886 and PLC5. The highest gene expression in miRNA146 A against mir-16 was found inHep-G2 andPLC5. The lowest gene expression in miRNA 146 A against mir-103 andmir-16 was found in PLC5.Keyword: Cell lines Hep-G2, miRNA 146 A, mir-423-3p, mir-103, mir-21, mir-16, PLC5

Effect of Photoperiodicity on Co2 Fixation by Chlorella Vulgaris Buitenzorg in Bubble Column Photobioreactor for Food Supplement Production

To reduce the level of CO2 content in air, effort on converting CO2 to useful products is required. One of thealternatives includes CO2 fixation to produce biomass using Chlorella vulgaris Buitenzorg. Chlorella vulgarisBuitenzorg is applied for production of food supplement. Chlorella vulgaris Buitenzorg is also easy to handle due to itssuperior adaptation. Currently, Chlorella vulgaris Buitenzorg has been analyzed by some experts for its cellularcomposition, its ability to produce high quality biomass and the content of essential nutrition. A series of experimentswas conducted by culturing Chlorella vulgaris Buitenzorg using Beneck medium in bubbling column photobioreactor.The main variation in this experiment was photoperiodicity, where growth of Chlorella vulgaris Buitenzorg wasexamined during photoperiodicity condition. The difference between CO2 gas concentration of inlet and outlet of thereactor during operational period, was compared to the same experiment under continuous illumination. Underphotoperiodicity of 8 and 9 h/d, the culture cell densities (N) were approximately 40 % higher than under continuousillumination. Final biomass density of Chlorella vulgaris Buitenzorg at 9 h/d illumination was 1.43 g/dm3, around 46%higher than under continuous illumination. Specific carbon dioxide transfer rate (qCO2) in photoperiodicity was 50-80%higher than under continuous illumination. These experiments showed that photoperiodicity affects the growth ofChlorella vulgaris Buitenzorg The specific growth rate (μ) by photoperiodicity was higher than that by continuousilumination while the growth period was two times longer. Based on the experiments, it can be concluded thatphotoperiodicity might save light energy consumption. The prediction of kinetic model under continuous illuminationas well as under photoperiodicity illumination showed that Haldane model became the fitted kinetic model

Efektivitas Probiotik Lactobacillus plantarum 2C12 dan Lactobacillus acidophilus 2B4 Sebagai Pencegah Diare pada Tikus Percobaan

The aim of this study was to evaluate the effectiveness of probiotics Lactobacillus plantarum 2C12 and Lactobacillus acidophilus 2B4 to prevent diarrhea caused by enteropathogenic Escherichia coli (EPEC). Albino rats (Rattus norvegicus) were daily orally administered by 108 cfu/ml of both probiotics without or simultaneously infected with EPEC (106 cfu/ml) for 7 days. Negative control was not infected by probiotic and EPEC while positive control was challenged with EPEC alone. After 1, 2 and 3 weeks, total of lactic acid bacteria (LAB) and E. coli of mucosa of cecum and cecum content were evaluated.  It was observed that rats administered by L. plantarum 2C12 and L. acidophilus 2B4 and challenged with EPEC had better performances when compared with the positive control for daily weight gain, feed consumption, feed efficiency rate. Diarrhea was determined by total of E. coli on cecum and watery fecal. Both probiotics could increase 1 log10 cfu/cm2 of total LAB on mucosa of cecum and also 1 log10 cfu/g of cecum content. Both probiotics also could reduce 1-3 log10 cfu/cm2 population of E.coli on mucosa of cecum and 1 log10 cfu/g of cecum content. L. plantarum 2C12 and L. acidophilus 2B4 were effective as probiotics against EPEC on rats

MIR-423-3P USED AS REFERENCE GENE FOR MIRNA 146 A IN CELL LINES HEP-G2

Objective: We explored the stable reference genes for miRNA 146 A by RT-PCR in the cell lines Hep-G2 that were treated chlorogenic acid. We must do a series of tests in order to get a reference genes. Based on the literature there are 7 candidates recommended reference genes; mir-423-3p, 423-5p, 191, 103, 21, 16, and let-7a. We conducted using four candidates reference gene; mir-423-3p, 103, 16, and 21. Methods: In vitro study was performed in Hep-G2 cells. The samples were divided into control group and experiment group treated with 727μM chlorogenic acid. Samples were analyzed at 0, 2, 8, 18, and 24 hours after being treated with chlorogenic acid. Total RNA was isolated from Hep-G2 with RNA extraction kit (miRCURYTM RNA Isolation Kit-Cell and plant Exiqon, Code Number 300110) and reverse transcribed to cDNA with Primerscript RT Reagent Kit (miRCURY LNATM Universal RT microRNA PCR, Polyadenylation and cDNA synthesis kit Exiqon, Code Number 203300). The primers for miRNA 146 A were Code Number 204688 from Exiqon (forward and reverse), and quantitative real time reverse transcription polymerase chain reaction was performed using SYBR Master Mix with Code Number 203450 (Exicon). MiRNA profiling was performed in four pairs of mir, consist of; mir-423-3p, 103, 21, and mir-16. By using the mean expression value of all expressed mir, we identified the most stable candidate reference genes for subsequent validation with normfinder software. Results: Data from RT-PCR were analyzed using Normfinder software. We found out that mir expression with good stablity is mir-103 and the best combination from two genes are mir-103 and mir-423-3p. Finally mir-423-3p is found more stable than mir-16, 21, and 103. Conclusion: We conclude the stable reference genes for miRNA 146 A treated with chlorogenic acid is mir-423-3p

PENGEMBANGAN MATERIAL NANO BERBASIS PROTEIN DAN PEPTIDA

Protein adalah rantai asam amino yang melipat dalam bentuk tertentu yang menentukan fungsinya. Bentuk pendek dari protein disebut peptida. Protein yang berukuran nano-meter, di alam telah menjalankan fungslnya dalam berbagai aktivitas dengan sangat efisien dan akurat. Upaya untuk memanfaatkan protein dan peptida sebagai material nano dengan plikasl yang kadang sangat berbeda dengan kegunaan asalnya, adalah salah satu topik utama dalam bidang nano-bloteknologl. Usaha pertama yang harus dllakukan adalah produksi protein dengan teknologi DNA rekombinan untuk mendapatkan kuantitas yang mencukupi bagi aplikasi tersebut. Selanjutnya dengan rekayasa protein, karakter/kualitas protein tersebut disesuaikan dengan kondisi aplikasi yang diperlukan. Perbedaan antara bioteknologi dan nano-bioteknologi, tidak sekedar pada ukuran, karena obyek bioteknologi memang sudah berskala nano-meter. Tetapi dalam nana-bioteknologi, penekanannya adalah proses rekayasa untuk menghasllkan produk yang artifisial dan fungsional. Dalam makalah ini, dijelaskan bagaimana teknik-teknik yang digunakan dalam nana-bioteknologi protein, contoh-contoh pengembangan produk protein/peptida dengan nanobioteknologi oleh orang Indonesia khususnya dan beberapa hasll penelitian penulis dalam perancangan peptida.</p