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All Journal HAYATI Journal of Biosciences Current Biochemistry AGRIVITA, Journal of Agricultural Science Jurnal Ilmiah Kedokteran Wijaya Kusuma Indonesian Journal of Applied Research (IJAR)
Rahadian Pratama
Department Of Biochemistry, Faculty Of Mathematics And Natural Sciences, Bogor Agricultural University (IPB University), Bogor, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Computer Science & IT Earth & Planetary Sciences Education Medicine & Pharmacology Public Health

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 1 
Isolation and Molecular Cloning of Cellulase Gene from Bovine Rumen Bacteria Rahadian Pratama; I Made Artika; Tetty Chaidamsari; Herti Sugiarti; Soekarno Mismana Putra
Current Biochemistry Vol. 1 No. 1 (2014)
Publisher : IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Cellulases are the enzymes that hydrolyze cellulosic biomass and are produced by the microorganisms that grow over cellulosic matters. The objective of this research was to isolate and clone cellulase gene from cellulose-degrading bacteria of bovine rumen. Cellulose-degrading bacteria was isolated from rumen fluid using a selective medium. Total RNA was isolated from selected colony having cellulose degrading activity and was used as a template for cDNA construction using reverse transcriptase polymerase chain reaction (RT-PCR) technique. The resulted cDNA was employed as a template for PCR amplification of cellulase gene using specific primers. The cellulase gene candidate obtained was cloned into the pGEM-T-Easy vector followed by determination of its nucleotide sequence. The sequence was then aligned with sequences of cellulase genes from GenBank. Results showed that a number of isolates of rumen bacteria exhibit cellulase activity and the CR-8 isolate was selected for further analysis. The successful isolation of total RNA from CR-8 was indicated by the presence of two intense bands of ribosomal RNA (23S and 16S). The reverse transcription process was successful and the amplification of cellulase gene using the specific primers F1 and R1 resulted in a DNA fragment of 1900 bp as a candidate of cellulase gene. The fragment was successfully cloned into the pGEM-T-Easy vector, and the resulted recombinant plasmid was successfully introduced into the E. coli cells. Nucleotide sequence analysis suggested that the cloned gene is cellulase gene and shares 99% homology with the endo-1,6-beta-glucanase of T. harzianum.
In Silico Study of Anticancer Activity of Red Betel Leaves Bioactive Compounds against Colon Cancer Marker Proteins Mutmainnah Umar; Mega Safithri; Rahadian Pratama
HAYATI Journal of Biosciences Vol. 30 No. 1 (2023): January 2023
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.30.1.113-121

Abstract

Colon cancer or colorectal cancer is one of the major health problems in the world. Previous research has proven that red betel leaves extract has anticancer activity against breast cancer cells. The study aimed to look at the potential of compounds contained in red betel ethyl acetate fraction as anticancer substances for colon cancer by conducting in silico tests through the docking of three colon cancer biomarker receptors against eight red betel leaves compounds. The parameters of binding affinity energy and inhibition constant used in the molecular docking analysis showed that there are several compounds that have the potential as inhibitors against colon cancer marker proteins to inhibit the development of colorectal cancer and have high bioavalibility as oral drugs. Based on in silico test it is known that the compound N-1,N-9-Bis [E-(2-nitophenyl) methylene] non anedihydrazide has the highest inhibition of human leukotriene A4 hydrolase receptor with binding affinity energy of 11.3160 Kcal/mol. The next compound is 4-({4,6-Bis[3R,5S)-3,5-diamino-1-piperydinyl]-1,3,5-traizin-2-yl}amino) benzenosulfon amide which has the highest inhibition in Chek1 with binding affinity energy of 9.7110 Kcal/mol, and the compound 4-(4-methoxy-phenylamino)-2,3-dihydro-1H-4a, 9-diaza-cyclopenta (b) fluorine-10-carbonitrile has the highest inhibition in the Bcl 2 navitoclax analog receptor with binding affinity energy of 8.4470 Kcal/mol.
In Silico Analysis of Bioactive Compounds in Red Betel Leaves to Glutathion Peroxidase Activity Mutmainnah Agustiawan Umar; Mega Safithri; Rahadian Pratama
Indonesian Journal of Applied Research (IJAR) Vol. 3 No. 3 (2022): Indonesian Journal of Applied Research (IJAR)
Publisher : Universitas Djuanda

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.30997/ijar.v3i3.227

Abstract

Glutathione peroxidase (GPx) is one of the antioxidants that acts as a protector of organisms from oxidative stress. Several compounds in certain plants have been shown to increase GPx activity. Red betel leaves are known to contain antioxidant compounds that have the potential to increase GPx activity. This study aims to see the potential of red betel compound as an activator of the enzyme glutathione peroxidase. As many as 44 red betel leaves active compounds which were tested by in silico method started with receptor and ligand preparation, followed by grid box determination, then proceeded to virtual screening and molecular docking. The virtual screening stage eliminated 7 compounds and in Lipinski test stage there were 2 compounds that were eliminated, also the AdmetSAR test eliminated 21 sompunds, so that there were 14 compounds continued to the file preparation stage, molecular docking and analysis of ligand-receptor interactions. The parameters of affinity energy and percentage of binding site similarity (%BSS) used in the molecular docking analysis showed that there are several compounds that have the potential as antioxidant compounds by increasing the performance of the glutathione peroxidase enzyme, the best compound identified is guanidine tartrate with an affinity energy of -4.8 Kcal/mol and BSS percentage of 62.5%, this compound is also considered safe to be consumed based on its physicochemical and toxicity test.
Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study Siska Nurfajri; Fifi Gus Dwiyanti; Rahadian Pratama; Muhammad Majiidu; Iskandar Z. Siregar
AGRIVITA Journal of Agricultural Science Vol 45, No 3 (2023)
Publisher : Faculty of Agriculture University of Brawijaya in collaboration with PERAGI

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17503/agrivita.v41i0.3930

Abstract

Balsa (Ochroma pyramidale) is fast-growing forest plant species introduced to Indonesia with limited genetic information. Genetic information can be obtained through molecular assessment which is now feasible due to sequencing technology development. This is supported by the third-generation sequencer technology, which has been developed using long-read sequencing technology. MinION Oxford Nanopore Technology is one of the long-read sequence-based sequencers with a real-time process and portable. This study aims to generate genomic data and analyze the phylogenetic relationship of balsa (O. pyramidale) based on long-read sequences with MinION Oxford Nanopore Technologies. Balsa long-read sequencing generated a partial chloroplast genome (cpDNA) sequence of 155,430 bp, which can be used for further DNA barcode-based phylogenetic analysis from the chloroplast genome. Phylogenetic analysis showed that the balsa species (O. pyramidale) was genetically grouped in one clade with other O. pyramidale species in phylogeny analysis based on rbcL, matK, and a combination of rbcL and matK genes indicated that those genes were a suitable marker for phylogenetic analysis in balsa species (O. pyramidale).
In Vitro Study of Red Betel Leaves as Lymphocyte Cell Proliferator and Colorectal Cancer Cytotoxic Agent in Widr Cells Pratama, Rahadian; Safithri, Mega; Umar, Mutmainnah Agustiawan; Tarman, Kustiariyah
Indonesian Journal of Applied Research (IJAR) Vol. 5 No. 3 (2024): Indonesian Journal of Applied Research (IJAR)
Publisher : Universitas Djuanda

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.30997/ijar.v5i3.522

Abstract

Colorectal cancer remains a leading cause of mortality worldwide and is closely linked to the immune system, particularly lymphocytes. This study evaluated the ethyl acetate fraction of red betel (Piper crocatum Ruiz & Pav) leaf ethanol extract for its anticancer activity against WiDr colon cancer cells and its effect on lymphocyte cell proliferation. Using MTT assays, the fraction showed significant WiDr cell inhibition (98.18% ± 1.21% at 500 ppm) and enhanced lymphocyte viability (143.3% ± 19.46% at 20 ppm). These results suggest the ethyl acetate fraction serves both as an effective anticancer agent against WiDr cells and as a promoter of lymphocyte proliferation, offering potential for dual therapeutic application.
Metagenomic Analysis of Intestinal Microbiota Derived from Stool Samples of Third-Trimester Pregnant Women Mudyawati Kamaruddin; Miftahul Khairiyah Zamzam; Rahadian Pratama; AbdurRahman Shakhr Nur; Cut Muthiadin; Christine Sembiring; Nurhidayat Triananinsi; Nurisyah Nurisyah; Ratnasari Dewi; Fatmawati Fatmawati; Erniawati Erniawati; Jusni Jusni; Basmiati Basmiati
Jurnal Ilmiah Kedokteran Wijaya Kusuma Vol 14, No 1 (2025): EDISI MARET 2025
Publisher : Universitas Wijaya Kusuma Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.30742/jikw.v14i1.4173

Abstract

Background: The human gut microbiota plays a unique role in metabolism, immunity, and nutrient absorption.  Various studies on the gut microbiota have identified a link between changes in bacterial abundance in the gut known as dysbiosis (imbalance) and the pathogenesis of certain disorders. It is known that an imbalance in the ratio of the phyla Firmicutes and Bacteroidetes has been associated with various chronic diseases, including inflammatory bowel disease and metabolic disorders. The Firmicutes/Bacteroidetes (F/B) ratio is a measure used to assess gut microbiota composition, which is believed to play a significant role in intestinal health and metabolism. Studies suggest that a higher F/B ratio is often associated with obesity and other metabolic conditions. Objective: This study aims to carry out metagenomic analysis of third-trimester pregnant women's faecal samples to predict degenerative diseases using third-generation whole genome sequencing, namely PromethION nanopore technology.  Method: Nanopore Technology: DNA sequencing of faecal samples from pregnant women in the third trimester was performed using the Oxford Nanopore Technology (ONT) device based on the Ligation Sequencing gDNA - Native Barcoding Kit 24 V14 and following its guidelines. Result: Based on the quality and quantity of total DNA reads from 20 stool samples from pregnant women, only 4 samples were continued for analysis (1A, 2A, 3A and 4A). The results of the abundance of intestinal microbiota based on the most abundant phylum are Proteobacteria, Bacteriodetes, and Firmicutes. Conclusion: Meanwhile, based on species abundance, it shows that Prevotella copri (phylum Bacteriodetes) is abundant in samples 2A, 3A and 4A, while in sample 1A the most abundant species is Succinivirio dextrinosolvens (phylum Proteobacteria). Bacteroidetes are a group of Gram-negative bacteria that are often found to increase in individuals with type 2 diabetes and obesity
Co-Authors AbdurRahman Shakhr Nur Basmiati Basmiati Christine Sembiring Cut Muthiadin Erniawati Erniawati Fatmawati Fatmawati Fifi Gus Dwiyanti Herti Sugiarti Herti Sugiarti, Herti I MADE ARTIKA Iskandar Z. Siregar Jusni Jusni Kustiariyah Tarman Mega Safithri Miftahul Khairiyah Zamzam Mudyawati Kamaruddin Muhammad Majiidu Mutmainnah Agustiawan Umar Mutmainnah Umar Nurhidayat Triananinsi Nurisyah Nurisyah Ratnasari Dewi Siska Nurfajri Soekarno Mismana Putra Soekarno Mismana Putra, Soekarno Mismana Tetty Chaidamsari Tetty Chaidamsari, Tetty Umar, Mutmainnah Agustiawan