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All Journal HAYATI Journal of Biosciences Microbiology Indonesia BIOTROPIA - The Southeast Asian Journal of Tropical Biology UNEJ e-Proceeding Indonesian Journal of Chemistry Jurnal Aplikasi Teknologi Pangan
ADI YULANDI
Faculty Of Biotechnology Atma Jaya Catholic University Of Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Education Immunology & microbiology Medicine & Pharmacology Veterinary

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Molecular Dynamic Simulation for Thermal Stability Properties of Endo β-Mannanase Enzyme Yulandi, Adi; Hermosaningtyas, A A; Sutanto, Sheila; Suwanto, Antonius
UNEJ e-Proceeding Indonesian Protein Society (IPS), International Seminar and Workshop 2014
Publisher : UNEJ e-Proceeding

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

Abstract

Endo β-mannanase or mannanase hydrolyse the β-D-1,4 mannopyranoside linkages in β-mannan intomanno-oligosaccharides. Four mannanases, named MAN1, MAN2, MAN3 and MAN4, were isolated from palm kernel meal waste have potential as thermostable mannanases. Series of enzymatic assay to characterize enzyme properties may affect longer time and higher cost. Homology modeling and molecular dynamic simulation are reliable and faster alternative assay to determine enzyme properties by analyzing enzymes’ three-dimensional structure. The structureswere constructed using homology modeling approach using Modeller. Template 2QHA was chosen for having more than 98% sequence similarity with targets. The homology models and template were simulated using molecular dynamics software GROMACS 4.6 for 10 ns production time each at 300 K, 323 K and 353 K. Both targets share the same (β/α)8 TIM barrel folding type similar to template 2QHA The basic analysis of molecular dynamic simulation (root mean square deviation and root mean square fluctuation) showed that both enzymes were thermostable, albeit compared to template 2QHA amino acid residues substitution in samples contribute for different thermostable profile. However, MAN2 was appeared to be more stable at high temperature than other samples. Keywords: endo β-mananase, homology modeling, molecular dynamic simulation
Genotypic Characterization of Rhizopus Spp. Tempeh and Usar: Traditional Inoculum of Tempeh in Indonesia tati barus; Jason Wiranata Sanjaya; Anastasia Tatik Hartanti; Adi Yulandi; Vivitri Dewi Prasasty; David Tandjung
Microbiology Indonesia Vol. 14 No. 3 (2020): September 2020
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1214.939 KB) | DOI: 10.5454/mi.14.3.3

Abstract

Abstract. Soybeans tempeh (tempeh) is processed by fermentation using Rhizopus spp. Tempeh is an important source of protein in Indonesia. The traditional inoculum in fermentation locally is known as Usar which is made from the leaves of Hibiscus tiliaceus. However, Rhizopus information from Usar is still limited. Therefore, this study aims to identify and investigate the genetic diversity of Rhizopus species from Usar and tempeh based on the Internal Transcribed Spacer (ITS) sequence and the Random Amplified Polymorphic DNA (RAPD) markers. Twenty-three Rhizopus strains were isolated from Usar and ten Rhizopus strains were isolated from tempeh. Based on ITS sequences, the isolates were similar to R Rhizopus microsporus (30 isolates) and Rhizopus delemar (3 isolates) with 98-99% similarity. The genetics of R. microsporus and R. delemar are varied and different from the genetics of R. microsporus from tempeh. The growth temperature of R. microsporus varies from 33 to 48°C and R. delemar can grow to a maximum at 33°C. The role of R. microsporus and R. delemar from Usar in determining the quality of tempeh is still limited. Therefore, it needs to be investigated further.
Diversity of Amylase-Producing Bacillus spp. from “Tape” (Fermented Cassava) TATI BARUS; AMANDA KRISTANI; ADI YULANDI
HAYATI Journal of Biosciences Vol. 20 No. 2 (2013): June 2013
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (58.662 KB) | DOI: 10.4308/hjb.20.2.94

Abstract

Fermented cassava or “Tape” is one of traditional Indonesian fermented food. The quality of “Tape” is determined by microorganisms involved during fermentation process. It was reported that Bacillus subtilis determined the quality of cassava “Tape”. The most common way to identify species is by using 16S rRNA gene.  This gene contains conserved regions as unique sequence which is relative among species. It has been widely used as a reliable molecular marker for phylogeny identification. Therefore, the aim of this research was to study diversity of amylase-producing Bacillus spp. from “Tape” based on 16S rRNA gene sequences. Bacillus spp. were isolated from “Tape” from several area in Indonesia i.e. Jakarta, Bandung, Cianjur, Subang, Rangkas Bitung, and Kediri. Amplification of 16S rRNA gene used 63f and 1387r primers. This research showed that based on 16S rRNA gene sequences, twenty-six of amylase-producing Bacillus spp. isolates were divided into four groups. All isolates were identified as species either B. megaterium, B. subtilis, B. amyloliquefaciens, or B. thuringiensis.
Genetic Diversity of Klebsiella spp. Isolated from Tempe based on Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR) TATI BARUS; IVAN HANJAYA; JOANITA SADELI; BIBIANA W LAY; ANTONIUS SUWANTO; ADI YULANDI
HAYATI Journal of Biosciences Vol. 20 No. 4 (2013): December 2013
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (625.021 KB) | DOI: 10.4308/hjb.20.4.171-176

Abstract

Tempe is an Indonesian fermented food prepared by fermenting dehulled cooked soybeans with Rhizopus oligosporus. Many types of bacteria are also involved during tempe fermentation, and one of these is Klebsiella spp.  Some isolates of K.  pneumoniae produces vitamin B12 in tempe but it has also been classified as an opportunistic pathogen. For this reason Klebsiella spp. in tempe is important to be studied. The aim of this study was to investigate the genetic diversity of Klebsiella spp. from tempe employing ERIC-PCR method. Sixty-one isolates of Klebsiella have been isolated from sixteen tempe producers  in Bogor, Jakarta, Malang, Tengerang, Bandung and Cianjur. 63F and 1387R primers were used to amplify 16S rDNA sequences, and 1R and 1F primers were used for ERIC analysis. The results of this research showed that sixty-one strains of Klebsiella were clustered into 17 groups. Based on ERIC-PCR analysis, isolates of Klebsiella could be grouped into different profiles which some of these groups consisted of isolates with identical ERIC-PCR profiles. Several identical ERIC-PCR profiles were found in tempe from the same producer. There was no correlation observed between genetic similarity  among isolates with the origin of tempe.
Molecular Dynamic Simulation for Thermal Stability Properties of Endo β-Mannanase Enzyme Adi Yulandi; A A Hermosaningtyas; Sheila Sutanto; Antonius Suwanto
UNEJ e-Proceeding Indonesian Protein Society (IPS), International Seminar and Workshop 2014
Publisher : UPT Penerbitan Universitas Jember

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

Abstract

Endo β-mannanase or mannanase hydrolyse the β-D-1,4 mannopyranoside linkages in β-mannan intomanno-oligosaccharides. Four mannanases, named MAN1, MAN2, MAN3 and MAN4, were isolated from palm kernel meal waste have potential as thermostable mannanases. Series of enzymatic assay to characterize enzyme properties may affect longer time and higher cost. Homology modeling and molecular dynamic simulation are reliable and faster alternative assay to determine enzyme properties by analyzing enzymes’ three-dimensional structure. The structureswere constructed using homology modeling approach using Modeller. Template 2QHA was chosen for having more than 98% sequence similarity with targets. The homology models and template were simulated using molecular dynamics software GROMACS 4.6 for 10 ns production time each at 300 K, 323 K and 353 K. Both targets share the same (β/α)8 TIM barrel folding type similar to template 2QHA The basic analysis of molecular dynamic simulation (root mean square deviation and root mean square fluctuation) showed that both enzymes were thermostable, albeit compared to template 2QHA amino acid residues substitution in samples contribute for different thermostable profile. However, MAN2 was appeared to be more stable at high temperature than other samples. Keywords: endo β-mananase, homology modeling, molecular dynamic simulation
AN SNP MARKER POTENTIALLY LINKED TO SOMATIC EMBRYOGENESIS OF OIL PALM (Elaeis guineensis) Irang Wahyunanto; Diana E Waturangi; Nurita Toruan-Mathius; Adi Yulandi
BIOTROPIA - The Southeast Asian Journal of Tropical Biology Vol. 24 No. 2 (2017)
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11598/btb.2017.24.2.678

Abstract

Oil palm (Elaeis guineensis) is one of the most important oil-bearing crop in the world. This crop can be vegetatively propagated only using tissue culture technique. Oil palm tissue culture technique has low efficiency, with callogenesis and embryogenesis stages as the limiting factors. Genetic factor has a major role in determining the success rate of these two stages. The use of molecular markers which represent the rate of embryogenesis or callogenesis has the potential to improve the efficiency of oil palm tissue culture process. In this study, SNP mining was conducted on embryogenesis transcriptome data, oil palm cDNA database, oil palm genome database, and oil palm SNPs marker database in NCBI.  The objective of this study was  to obtain SNP marker which represents the embryogenesis potential, to be further used in marker assisted selection of oil palm ortets. One SNP (EMB6) showed significant association with embryogenesis rate. This SNP was found in one of Auxin Response Factor (ARF) family gene. Nucleotide replacement from Adenine to Guanine changed the 307th amino acid from Isoleucine to Methionine. Oil palms with Adenine homozygote (A/A) pattern on the EMB6 showed 8-fold higher chance to produce significantly higher embryogenesis rate than Adenine-Guanine heterozygote (A/G).
Profil Bakteri Asam Laktat dan Evaluasi Sensori dari Tempe Bungkus Daun Jati yang Disuplementasi dengan Daun Kelor Stella Magdalena; Yogiara Yogiara; Adi Yulandi
Jurnal Aplikasi Teknologi Pangan Vol 10, No 1 (2021): February 2021
Publisher : Faculty of Animal and Agricultural Sciences, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17728/jatp.7330

Abstract

Tempe bungkus daun jati merupakan produk pangan fermentasi tradisional Indonesia yang kaya protein, serat, dan vitamin yang sangat popular di Kabupaten Blora, Jawa Tengah. Penelitian ini bertujuan mengetahui pengaruh penambahan daun kelor pada tahapan perendaman dan peragian dalam proses produksi tempe terhadap profil bakteri asam laktat (BAL) dan tingkat kesukaan. Daun kelor segar dan serbuk disuplementasikan dengan variasi konsentrasi pada proses produksi tempe kacang kedelai. Hasil penelitian menunjukkan bahwa daun kelor tidak menghambat aktivitas pertumbuhan dari kapang Rhizopus. Penambahan serbuk daun kelor sebanyak 1x dan 2x (b/b) dari total jumlah ragi pada proses peragian menghasilkan tekstur tempe yang kompak. Semakin tinggi konsentrasi air perasan daun kelor dalam proses perendaman, jumlah total bakteri asam laktat menurun hingga 103 CFU/g. Profil BAL dari tempe bungkus daun jati dengan ataupun tanpa suplementasi daun jati mengandung BAL dari genus Weissella. Tempe bungkus daun jati dengan suplementasi 1x (b/b) serbuk daun kelor sangat berpotensi untuk disosialisasikan sebagai pangan fungsional kepada masyarakat.Lactic Acid Bacteria Profile and Sensory Evaluation of Teak Leaf-Wrapped Tempeh Supplemented with Moringa LeavesAbstractTempeh wrapped in teak leaves is a traditional Indonesian fermented food product that is rich in protein, fiber, and vitamins which is very popular in Kabupaten Blora, Central Java. This study aimed to investigate the effect of Moringa leaves addition in the soaking and fermentation stages of tempeh production towards the profile of lactic acid bacteria (LAB) and the level of respondent acceptance. Fresh and powdered leaf was supplemented in various doses to soybean tempeh production. As results, Moringa leaves did not inhibit the growth of Rhizopus. The addition of Moringa leaf powder as much as 1x and 2x (w/w) of the total amount of yeast in the fermentation process produced a compact tempeh texture. The higher the concentration of Moringa leaf juice in the soaking process reduced total number of lactic acid bacteria to 103 CFU/g. LAB profile of teak leaf-wrapped tempeh with or without teak leaf powder supplementation contained LAB that belongs to the genus Weissella. Teak leaf-wrapped tempeh supplemented by 1x (w/w) Moringa leaf powder has a potential value to be socialized as functional food to the community.
Computational Evaluation of Intermolecular Interaction in Poly(Styrene-Maleic Acid)-Water Complexes Using Density Functional Theory Daru Seto Bagus Anugrah; Laura Virdy Darmalim; Permono Adi Putro; Liana Dewi Nuratikah; Nurwarrohman Andre Sasongko; Parsaoran Siahaan; Adi Yulandi
Indonesian Journal of Chemistry Vol 21, No 6 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.67961

Abstract

The high application of Poly(styrene-maleic acid) (PSMA) in an aqueous environment, such as biomedical purposes, makes the interaction between PSMA and water molecules interesting to be investigated. This study evaluated the conformation, the hydrogen bond network, and the stabilities of all the possible intermolecular interactions between PSMA with water (PSMA−(H2O)n, n = 1–5). All calculations were executed using the density functional theory (DFT) method at B3LYP functional and the 6–311G** basis set. The energy interaction of PSMA–(H2O)5 complex was –56.66 kcal/mol, which is classified as high hydrogen bond interaction. The Highest Occupied Molecular Orbital (HOMO) – Lowest Unoccupied Molecular Orbital (LUMO) energy gap decreased with the rise in the number of H2O molecules, representing a more reactive complex. The strongest hydrogen bonding in PSMA–(H2O)5 wasformed through the interaction on O72···O17–H49 with stabilizing energy of 50.32 kcal/mol, that analyzed by natural bond orbital (NBO) theory. The quantum theory atoms in molecules (QTAIM) analysis showed that the hydrogen bonding (EHB) value on O72···O17–H49 was –14.95 kcal/mol. All computational data revealed that PSMA had moderate to high interaction with water molecules that indicated the water molecules were easily transported and kept in the PSMA matrix.
Co-Authors A A Hermosaningtyas A A Hermosaningtyas, A A AMANDA KRISTANI Anastasia Tatik Hartanti Antonius Suwanto dan Meity S. Sinaga . Budi Tjahjono Andi Khaeruni R Anugrah, Daru Seto Bagus BIBIANA W LAY David Tandjung Diana E Waturangi Irang Wahyunanto IVAN HANJAYA Jason Wiranata Sanjaya JOANITA SADELI Laura Virdy Darmalim Liana Dewi Nuratikah NURITA TORUAN-MATHIUS Nurwarrohman Andre Sasongko Parsaoran Siahaan Permono Adi Putro Sheila Sutanto Sheila Sutanto, Sheila Stella Magdalena Tati Barus Vivitri Dewi Prasasty Yogiara Yogiara