8 research outputs found
APPLICATION OF PROTEINASE K TO FACILITATE FUNGAL CELL LYSIS IN COMMERCIAL SILICA COLUMN-BASED DNA ISOLATION KIT
No full textEfficient isolation of high-quality genomic DNA is essential for molecular analyses such as PCR and sequencing in Fungal studies. However, the rigid cell walls of mold, composed predominantly of chitin and β-glucans pose significant barrier to standard lysis protocols. This study investigates the integration of Proteinase K into a commercial silica column-based DNA isolation kit to enhance lysis efficiency and DNA recovery from mold cells. Multiple isolates of fungi were subjected to DNA isolation using modified protocol incorporating Proteinase K treatment during the lysis step. The resulting DNA was quantified spectrophotometrically and evaluated for amplifiability via PCR using fungi specific barcoding of Internal Transcribed Spacer (ITS) region, consisting of ITS 5 and ITS 4 primer. The findings demonstrate that the inclusion of Proteinase K along with incubation time significantly improves cell disruption, leading to increased DNA yield and successful PCR amplification of ITS region across all tested isolates. These results underscore the utility of Proteinase K as a robust, cost-effective enzymatic supplement to conventional fungi DNA isolation workflows, especially when working with structurally complex cell wall mold taxa
Probiotic Community of Dage Banyumas: Next Generation Sequencing Approach
No full textTempeh is known as a traditional fermented food that has been popular in Indonesia for hundreds of years. One of the tempeh that is widely consumed in Banyumas regency is Dage, which is made from fermented coconut waste. Currently, there is no information regarding the presence of probiotics in Dage. Therefore, this study aims to detect the diversity of probiotic types in the Dage tempeh microbiome using the Next Generation Sequencing (NGS) approach. The research stages consisted of sampling, enrichment in MRSB and R2A media, DNA extraction, Polymerase Chain Reaction (PCR), Illumina NGS-based sequencing, and bioinformatics analysis using QIIME2 and MEGA XI software. The results showed that the Dage was dominated by bacteria from the genera Lactobacillus, Weisella, and Acetobacter, which are known as a group of probiotics. In addition, bacteria from the genus Bifidobacterium and Enterococcus were also detected. Diversity analysis showed that Dage enriched in R2A medium had higher species diversity than in MRSB medium. However, the presence of the probiotic bacteria group was more abundant in MRSB medium. The dominant amplicons by phylogenetic analysis were identified as Lactobacillus spicheri, Lactobacillus zymae, Lactobacillus crustorum, Companilactobacillus farciminis, Weisella paramesenteroides, and Acetobacter indonesianensis, which previously have several probiotic properties. These results provide novel information regarding the presence of probiotic bacteria in Dage, which can be explored further using a culturable approach
Proses Identifikasi Respon Kekeringan Padi Rojolele, Menthik Wangi, Jatiluhur, Singkarak Berdasarkan Tinggi Tanaman dan Viabilitas Gabah Menggunakan PEG
No full textThe Ability of Secondary Metabolites from Actinomadura sp. as COVID-19 Protease Inhibitor: In Silico Method
No full textThe pandemic of COVID-19 disease in the late of 2019 resulted in the massive screening for drug discovery purpose. However, there is still no reports about the ability of natural products from bacterial group of class Actinobacteria as COVID-19 inhibitor. The aim of this research is to identify the potential ability of natural compounds from Actinomadura sp., the member of class Actinobacteria, against two receptors of COVID-19 protease with PDB ID 6LU7 and 5R7Y. The eleven natural compounds were docked using AutoDock Vina and the interaction between receptor and ligands were analysed using LIGPLOT. The most potential compound was simulated for its interaction stability using Yet Another Scientific Artificial Reality Application (YASARA) dynamics. The result of molecular docking by AutoDock Vina showed that Sagamilactam become the most potential inhibitor for viral protease as it had lower binding affinity (6LU7:-12 and 5R7Y:-10.4) compared to the both of native ligand (6LU7:-11.4 and 5R7Y:-4.6). Furthermore, the interaction of the most potential ligand showed the low number of Root Mean Square Deviation (RMSD) deviation in molecular dynamic simulations. This result validated the docking method that used and indicated that secondary metabolites produced from rare actinobacteria of Actinomadura sp. have promising possibility to inhibit COVID-19 protease
Sertifikat Paten IDS000001765 Proses Identifikasi Respon Kekeringan Padi Rojolele dan Menthik Wangi
No full textThe characterization of Citrus sp. from Parang Island Karimunjawa based on morphological, DNA barcoding and nutritional analysis
No full textThe Citrus sp. from Parang Island Karimunjawa is a wild type of Citrus plant that grow on salt area and
exhibits a high level of vitamin C. Due to its ability, morphological, molecular and nutritional
characterization needs to be carried out to improve its potential. The study was carried out at the
Biotechnology Laboratory and the Integrated Laboratory of Diponegoro University from 2016 to 2017.
The characterization was based on the morphplogical appearence of the tree, its fuits, and leaves. Its
DNA barcoding consists of 18S ribosomal RNA and the ITS region on the plants is dispersed along the
coastal ends and the centre of the island. Furthermore, the nutritional characterization consists of an
edible fruit part, a high vitamin C level and protein content. The research showed that the Citrus sp. on
the coastal ends and at the center of Parang Island Karimunjawa exhibits a close relation with the C.
hystrix and members of Papeda clade. However, the morphology of the Citrus is quite different from the
common C. hystrix in Indonesia. The nutritional content also shows that the Vitamin C content is higher
than that of the C. hystrix by almost four times. The features of the Citrus sp. in Parang Island
Karimunjawa have potential and showed possibility to improve its superiority in industrial applications
and breeding programs
PENANAMAN MANGROVE SEBAGAI UPAYA REHABILITASI EKOSISTEM MANGROVE DAN PEMBERDAYAAN MASYARAKAT DESA MOJO, KECAMATAN ULUJAMI, KABUPATEN PEMALANG, JAWA TENGAH
No full textDesa Mojo merupakan kawasan pesisir pantai utara Jawa yang dilalui oleh Daerah Aliran Sungai (DAS) Comal dan terdapat ekosistem mangrove yang tiap tahunnya mengalami penurunan luas hutan mangrove dengan penyebab tertinggi adalah abrasi. Oleh karenanya, perlu dilakukan upaya rehabilitasi hutan mangrove melalui penanaman mangrove kembali. Kegiatan ini dilakukan sebagai upaya pengembalian fungsi ekologis dan ekonomis ekosistem mangrove. Kegiatan dilakukan dengan tahapan perencanaan dan koordinasi, penanaman mangrove, monitoring dan evaluasi. Perencanaan dan koordinasi dilakukan dengan observasi dan diskusi mendalam bersama Kelompok Tani Hutan (KTH) Lestari sebagai kelompok masyarakat yang berfokus pada kelestarian hutan mangrove. Penentuan lokasi dan waktu pelaksanaan dilaksanakan pada tahap ini. Penanaman mangrove dilaksanakan dengan metode partisipatif yang melibatkan anggota KTH Lestari, dosen, dan mahasiswa Universitas Jenderal Soedirman. Bibit mangrove yang ditanam adalah spesies Rhizopora mucronata atau dikenal dengan bakau. Pasca satu bulan penanaman dilakukan monitoring sebagai langkah pemantauan keberhasilan bibit pasca tanam yang dapat bertahan hidup. Berdasarkan hasil monitoring, perlu dilakukan perawatan dan penyulaman mangrove dikarenakan tingkat keberhasilan bibit mangrove yang rendah
Keragaman Morfologi Bakteri Nitrifikasi Asal Kompos Kotoran Domba pada Peternakan Domba dengan Sistem Bedding
No full textThe application of compost bedding system on sheep farm is a technology to minimize the negative impact of sheep manure waste toward environment. The microorganisms which inhabit the compost bedding, especially nitrifying bacteria are expected to have significant role in odor emission reduction which become environmental problem around the sheep farm. This study aims to analyze the abundance and diversity of nitrifying bacteria of compost bedding obtained from sheep farm which have important role in reducing odor emission of ammonia. The 12 days, 1 and 1,5 months old of compost bedding samples were obtained from sheepfold, while 3 and 4 months old of compost samples were obtained from compost pile. Furthermore, nitrifying bacteria were isolated from compost samples by pour plate method using specific media for Nitrosomonas and Nitrobacter. The results indicated that compost bedding samples with different composting time duration displayed different abundance and diversity of nitrifying bacteria. The current study was successfully isolated 39 and 47 nitrifying bacterial isolates using specific media for Nitrobacter and Nitrosomonas, respectively. The highest diversity of nitrifying bacteria was gained from 12 days old compost bedding sample. Nitrifying bacterial isolates from compost bedding samples have significant role in odor emission declining as well as manure composting at sheep farm. The obtained bacterial isolates are also potentially to develop as bio-activator for compost bedding
