5 research outputs found
Identifikasi Bakteri Penghasil Hormon Indole Acetic Acid (IAA) Di Ranu Pani dan Bakteri Pelarut Fosfat Di Ranu Grati Berdasarkan Sekuen Gen 16S rRNA
No full textRINGKASAN Rodiansyah, Achmad. 2019. Identifikasi Bakteri Penghasil Hormon Indole Acetic Acid (IAA) Di Ranu Pani dan Bakteri Pelarut Fosfat Di Ranu Grati menggunakan Sekuen Gen 16S rRNA. Skripsi, Program Studi Biologi, Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Negeri Malang. Pembimbing: (I) Sitoresmi Prabaningtyas, S.Si., M.Si., (II) Dwi Listyorini, M.Si., D.Sc. Kata kunci: Bakteri, Indole Acetic Acid (IAA), Pelarut Fosfat, 16S rRNA Isolat bakteri PIS dari Ranu Pani memiliki potensi menghasilkan hormon Indole Acetic Acid (IAA) tertinggi dan isolat bakteri GPS dari Ranu Grati memiliki potensi untuk melarutkan fosfat tertinggi namun, keduanya belum teridentifikasi. Identifikasi sangat penting untuk konservasi, mempelajari regulasi dan peranannya dalam lingkungan untuk mengatasi masalah lingkungan, kesehatan, pangan dan keperluan industri. Tujuan penelitian ini adalah mengidentifikasi isolat bakteri PIS dan isolat bakteri GPS menggunakan gen 16S rRNA. Hasil penelitian ini dapat digunakan untuk penelitian berikutnya yaitu pengembangan konsorsium bakteri untuk mempercepat pertumbuhan mikroalga sebagai penelitian dasar pengembangan biofuel berbasis mikroalga. Penelitian ini menggunakan pendekatan deskriptif eksploratif yang bertujuan untuk mengidentifikasi serta menganalisis hubungan kekerabatan bakteri yang memiliki potensi menghasilkan hormon IAA tertinggi di Ranu Pani, Kabupaten Lumajang dan bakteri pelarut fosfat tertinggi di Ranu Grati, Kabupaten Pasuruan berdasarkan sekuen 16S rRNA. Prosedur penelitian yang dilakukan adalah pengkulturan isolat bakteri yang kemudian dilanjutkan dengan isolasi genom DNA (gDNA). Hasil isolasi DNA diukur konsentrasi dan kemurniannya kemudian dilanjutkan dengan tahapan amplifikasi menggunakan teknik Polymerase Chain Reaction (PCR). Hasil PCR selanjutnya dicek menggunakan gel elektroforesis untuk melihat gen target. Hasil PCR yang sesuai dengan gen target disekuensing untuk mengetahui urutan basanya. Hasil isolasi gDNA didapatkan bahwa sampel PIS memiliki konsentrasi DNA sebesar 231,5 ng/µL dan sampel GPS sebesar 65,7 ng/µL dengan nilai kemurnian sebesar 1,9 pada kedua sampel. Visualisasi hasil PCR gen 16S rRNA diperoleh gen yang sesuai pada gel elektroforesis 1% yang kemudian disekuensing. Hasil analisis contig pada hasil sekuensing didapatkan bahwa sampel PIS memiliki panjang gen 1431 bp dan sampel GPS memiliki panjang gen 1423 bp. Kedua sekuen hasil contig setelah dilakukan Basic Local Aligment Search Tool (BLAST) merupakan gen 16S rRNA dengan nilai similaritas dan query cover yang tinggi. Hasil rekonstruksi pohon filogenetik dan analisis jarak genetik diperoleh bahwa sampel PIS diduga Bacillus paramycoides (similaritas: 99,9%) dan sampel GPS adalah anggota genus Enterobacter (similaritas: 91,4%) yang berkerabat dekat dengan Enterobacter xiangfangensis. Pendekatan genomik dan pendekskripsian fenotip lebih lanjut perlu dilakukan untuk menentukan spesies yang dapat dipercaya
Screening and Prediction of Potential Compounds from Virgin Olive Oil Acting on Proteins Associated with Cancer Disease
No full textVirgin olive oil contains phenolic compounds that were potential for anti-inflammatory and cancer treatment. Computational biology is a beneficial method to understand how this compound can affect the biological process in humans. This research is conducted by the potential screening of VOO compounds, constructing the pharmacological network and enrichment, and docking simulation. The enrichment result showed that the EGFR, BRAF, MAPK1, CCND1, and MDM2 protein have multiple cancer contributions and related pathways. The docking simulation result showed that the interaction of EGFR-luteolin, BRAF-luteolin, MAPK1-luteolin, CCND1-apigenin, and MDM2-1-hydroxypinoresinol has the highest binding affinity. Further research with the in-vitro method is required to check the reliable mechanisms of each compound to their protein target
Modification of recombinant human epidermal growth factor (rh-EGF) expression vector by site-directed mutagenesis for therapeutic protein production
No full textRecombinant human epidermal growth factor (rh-EGF) has high value in therapies for h-EGF deficiency-related diseases. The expression of the h-EGF gene was designed by using the pET21b(+) vector and Escherichia coli BL21(DE3) as the expression host. In a previous study, the sequence of a 6xHis tag without any restriction sites was fused to the h-EGF gene, yet it was not possible to obtain a purified and single rh-EGF by this approach. In this study, we modified the rh-EGF expression vector using site-directed mutagenesis (SDM) to remove the sequence of the 6xHis tag. The vector modification was carried out by inserting a stop codon and the EcoRI restriction site, along with deleting the 6xHis tag sequence. The results of PCR showed non-specific bands, while 2-step cycles PCR produced one non-specific band, and 3-step cycles PCR produced two non-specific bands. After purification of the PCR products, the SDM-recombinant plasmids treated for template plasmid-free product were transformed into E. coli DH5a. Even though the transformation efficiency was low, the planned gene mutations including the deletion of the 6xHis tag and insertion of the stop codon and EcoRI restriction site in plasmid pET21b(+) were successfully carried out. When using this modified vector in expression studies, rh-EGF of a similar size to that of the rh-EGF standard and approximately 1 kDa smaller than the rh-EGF-6xHis of the previous study was obtained
Isolation and characterization of α ‐amylase encoding gene in Bacillus amyloliquefaciens PAS
No full textAmylolytic bacteria are a source of amylase, which is an essential enzyme to support microalgae growth in the bioreactor for microalgae culture. In a previous study, the highest bacterial isolate to hydrolyze amylum (namely PAS) was successfully isolated from Ranu Pani, Indonesia, and it was identified as Bacillus amyloliquefaciens. That bacterial isolate (B. amyloliquefaciens PAS) also has been proven to accelerate Chlorella vulgaris growth in the mini bioreactor. This study aims to detect, isolate, and characterize the PAS’s α‐amylase encoding gene. This study was conducted with DNA extraction, amplification of α‐amylase gene with polymerase chain reaction (PCR) method with the specific primers, DNA sequencing, phylogenetic tree construction, and protein modeling. The result showed that α‐amylase was successfully detected in PAS bacterial isolate. The α‐amylase DNA fragment was obtained 1,468 bp and that translated sequence has an identity of about 98.3% compared to the B. amylolyquefaciens α‐amylase 3BH4 in the Protein Data Bank (PDB). The predicted 3D protein model of the PAS’s α‐amylase encoding gene has amino acid variations that predicted affect the protein’s structure in the small region. This research will be useful for further research to produce recombinant α‐amylase
Identification of Potential Bacteria on Several Lakes in East Java, Indonesia Based on 16S rRNA Sequence Analysis
No full textFour bacterial isolates from Ranu Pani and Ranu Grati in east java had been revealed to be potentials to produce IAA (PIS isolate), phosphate solubilizer (GPS isolate), cellulose hydrolysis (PSS isolate) and, amylum hydrolysis (PAS), two dominant bacterial isolates from Rani Pani (PØD isolate) and Ranu Grati (GØD isolate) which were co-cultured with microalgae promoted microalgae growth, yet its taxonomical position has not been clearly known. The aim of this study was to identify those bacterial isolates using 16S rRNA barcode. This research conducted by gDNA isolation, the 16S rRNA sequence was amplified using 27F and 1492R primers. Reconstructed phylogenetic trees and genetic distance analysis showed that the isolate PIS and PSS identified as Bacillus cereus Group closely related to Bacillus paramycoides. PAS isolate identified as Bacillus subtilis Group closely related to Bacillus amyloliquefaciens, GPS isolate identified as novel species in genus Enterobacter, and two dominant isolates (PØD and GØD) identified as Enterobacter cloacae complex closely related to Enterobacter cloacae. The genomic approach and additional phenotypes-examination are required to clarify its taxonomical position
