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All Journal Jurnal Kimia (Journal of Chemistry) Jurnal Ilmu Dasar Indonesian Journal of Pharmaceutical Science and Technology MPI (Media Pharmaceutica Indonesiana) JURNAL BIOLOGI INDONESIA Kinetik: Game Technology, Information System, Computer Network, Computing, Electronics, and Control Indonesian Journal of Chemistry ANNALES BOGORIENSES Indonesian Journal of Electrical Engineering and Computer Science Jurnal Layanan Masyarakat (Journal of Public Service) Berkala Penelitian Hayati Makara Journal of Technology Annales Bogorienses
Ni Nyoman Tri Puspaningsih
Department Of Chemistry, Faculty Of Science And Technology, Airlangga University
Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Control & Systems Engineering Decision Sciences, Operations Research & Management Electrical & Electronics Engineering Energy Engineering Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Mathematics Mechanical Engineering Medicine & Pharmacology Social Sciences Other

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PENGUJIAN IN VITRO XILOOLIGOSAKARIDA SEBAGAI KANDIDAT PREBIOTIK Asnia Zainuddin; Eddy Bagus Wasito; Ni Nyoman Tri Puspaningsih
JURNAL PENELITIAN BIOLOGI BERKALA PENELITIAN HAYATI Vol 14 No 1 (2008): December 2008
Publisher : The East Java Biological Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23869/314

Abstract

The objectives of this study were to fi nd the in-vitro effect of xyloolygosaccharide on the cell count of Lactobacillus casei Shirota strain, to identify the effect of xyloolygosaccharide on the production of lactic, acetic, propionic and butyric acid (short chain fatty acid = SCFA), and to prove the effect of xyloolygosaccharide on the change of pH value.This was a laboratory experimental study using complete randomized design with 4 treatments, i.e, MRS broth media added xyloolygosaccharide with concentrations of 0% (control), 1%, 3%, and 5%, which were then inoculated with Lactobacillus casei Shirota strain and incubated for 6,12, 18, and 24 hours. The Lactobacillus casei Shirota strain cell count was counted using Drop plate. Data obtained were analyzed statistically using two way ANOVA with signifi cance level of 5%. The type and level of organic acids, i.e., lactic, acetic, propionic, and butyric acids (SCFA), formed in incubation time of 12 hours, were measured using gas chromatography and the change of pH value during incubation time was measured using pH paper. Results showed that xyloolygosaccharide addition MRS Broth media provided highly signifi cant interaction effect on the cell count of Lactobacillus casei Shirota strain (p<0.05). The result of gas chromatography showed that the addition of xyloolygosaccharide in MRS Broth media could increase Lactobacillus casei Shirota strain metabolism activity that produced lactic, acetic, propionic, and butyric acid. The reduction of pH value showed that the lowest pH value of 3.8 after the addition of 5% xyloolygosaccharide with incubation time of 24 hours. In conclusion, the addition of xyloolygosaccharide with concentrations of 1%, 3%, and 5% in MRS Broth media with incubation periods of 6, 12, 18, and 24 hours can increase Lactobacillus casei Shirota strain cell count, increase the metabolism activity of Lactobacillus casei Shirota strain, capable in producing SCFA in incubation time of 12 hours, and results in the reduction of pH value.
HIDROLISIS BEBERAPA JENIS XILAN DENGAN ENZIM XILANOLITIK TERMOFILIK REKOMBINAN Ni Nyoman Tri Puspaningsih; Hery Suwito; Sri Sumarsih; Ali Rohman; One Asmarani
JURNAL PENELITIAN BIOLOGI BERKALA PENELITIAN HAYATI Vol 12 No 2 (2007): June 2007
Publisher : The East Java Biological Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23869/353

Abstract

The aims of this research were to know the ability of recombinant xylanolytic enzyme from recombinant E. coli DH5a (pTP510) to hydrolyze several commercial xylan and analysis the reduction sugar product. Recombinant xylanolytic enzyme (exo-xylanase, b-xylosidase and a-L-arabinofuranosidase) could hydrolyzed several commercial xylan (oat-spelt xylan, birchwood, wheat, rye, and arabinan) with xylanolytic activities are: oat-spelt xylan (1.73 U/mL), birchwood (0.92 U/mL), wheat (6.52 U/mL), rye (4.94 U/mL), and arabinan (3.40 U/mL). Xylanolytic enzyme assay use specific substrate p-nitrophenyl-b-D-xylopyranoside (pNP-X) shown xylosidase activity 15.869 U/mL. Hydrolysis product was analyzed by HPLC. The results showed that xylose, arabinose, and xylo-oligosaccharide were produced from birchwood, wheat, rye, and arabinan hydrolysis, although xylose and arabinose were produced from hydrolysis of oat-spelt xylan.
EKSPRESI GEN PENYANDI b-XILOSIDASE DALAM SISTEM pHIS1525/ Bacillus megaterium MS941 Sri Sumarsih; Ni Nyoman Tri Puspaningsih; Sofijan Hadi; Ami Soewandi J.S.
JURNAL PENELITIAN BIOLOGI BERKALA PENELITIAN HAYATI Vol 13 No 2 (2008): June 2008
Publisher : The East Java Biological Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23869/364

Abstract

The aim of this research was to express the β-xylosidase gene in the pHIS1525/ Bacillus megaterium MS941 system. The xyl gene was amplified from pTP510 and cloned into pHIS1525 in E. coli DH10β. The recombinant plasmid was transformed into B. megaterium MS941 by protoplast transformation. Transformants were selected by growing the recombinant B. megaterium MS941 on solid LB medium containing tetracycline (10 μg/ ml). The expression of β-xylosidase was assayed using 0.2% methylumbelliferyl-β-D-xyloside (MUX) and the proteins were analyzed by SDS-PAGE method. The β-xilosidase activity was determined toward p-nitrophenyl-β-Dxylopyranoside (pNPX) as a substrate and p-nitrofenol releasing was measured by UV/Vis spectrophotometer at λ = 405 nm. This research showed that recombinant B. megaterium MS941 expressed the β-xylosidase gene (xyl) and secreted it into the culture medium. The SDS-PAGE analysis of extracellular protein (culture medium) showed a 60,0 kD protein band. The recombinant Bacillus megaterium MS941 expressed and secreted the β-xilosidase into culture medium 5 hours after adding 5% xylose. The b-xylosidase activity was 0.441 unit/ml toward pNPX as a substrate.
ANALISIS 6 DNA REKOMBINAN DENGAN ENZIM EcoR1 Ni Nyoman Tri Puspaningsih; Akhmaloka; Afaf Baktir; Ami Soewandi J.S.; Y. Sriwulan M.
JURNAL PENELITIAN BIOLOGI BERKALA PENELITIAN HAYATI Vol 3 No 1 (1997): June 1997
Publisher : The East Java Biological Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23869/490

Abstract

Amylase enzyme from Endomycopsis fibuligera capable to hidrolize starch into glucose. Insertion of amylase gene from Endomycopsis fibuligera into yeast (Saccharomyces cereviceae) will be able to increase the function of yeast (S.cereviceae) to digest more cheaper substrate, like starch. Before cloning in yeast, recombinant DNA will be made and analyzed in Escherichia coli strain DH5a. The result showed that the sixth transformant consist recombinant DNA that were sensitive to tetracycline medium. Analysis by EcoR1 digestion showed that the size of insertion fragment into Ycp 50 vector are around 0.3 untill 16 kb.
ISOLASI KARAKTERISASI DAN UJI EKSPRESI GEN ALP1 DI Escherichia coli DH5a Ni Nyoman Tri Puspaningsih; Akhmaloka; Sofyan Hadi; Y. Sri Wulan Manuhara; Bambang Irawan
JURNAL PENELITIAN BIOLOGI BERKALA PENELITIAN HAYATI Vol 4 No 2 (1999): June 1999
Publisher : The East Java Biological Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23869/517

Abstract

Amylase gene (ALP1) insertion in YCp 50 cloning vector was detected by Direct Screening PCR. Result of Direct Screening PCR showed one transformants which assumed have amylase gene insert. Characterization of the recombinant DNA by Stu1 and EcoR1 restriction enzymes indicated nucleotide sequence of insert gene. Digestion by BamHI, Cla1, and EcoRV restriction enzymes showed only one band that assumed size of insert gene is about 1500 bp. Gene expression showed that amylase enzyme activity by using Somogyi-Nelson method was 88.0265 Unit. This activity was 10% higher than transformant control (Escherichia coli DH5a which content YCp50).
XGBoost and Network Analysis for Prediction of Proteins Affecting Insulin based on Protein Protein Interactions Mohammad Hamim Zajuli Al Faroby; Mohammad Isa Irawan; Ni Nyoman Tri Puspaningsih
Kinetik: Game Technology, Information System, Computer Network, Computing, Electronics, and Control Vol. 5, No. 4, November 2020
Publisher : Universitas Muhammadiyah Malang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22219/kinetik.v5i4.1076

Abstract

Protein Interaction Analysis (PPI) can be used to identify proteins that have a supporting function on the main protein, especially in the synthesis process. Insulin is synthesized by proteins that have the same molecular function covering different but mutually supportive roles. To identify this function, the translation of Gene Ontology (GO) gives certain characteristics to each protein. This study purpose to predict proteins that interact with insulin using the centrality method as a feature extractor and extreme gradient boosting as a classification algorithm. Characteristics using the centralized method produces  features as a central function of protein. Classification results are measured using measurements, precision, recall and ROC scores. Optimizing the model by finding the right parameters produces an accuracy of  and a ROC score of . The prediction model produced by XGBoost has capabilities above the average of other machine learning methods.
SCREENING OF THERMOPHYLIC MICROORGANISM FROM IJEN CRATER BANYUWANGI AS PHYTASE ENZYME PRODUCER Aline Puspita Kusumadjaja; Tutuk Budiati; Ni Nyoman Tri Puspaningsih; Sajidan Sajidan
Indonesian Journal of Chemistry Vol 9, No 3 (2009)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (156.814 KB) | DOI: 10.22146/ijc.21518

Abstract

Phytase is enzyme which hydrolysis phytic acid to anorganic phosphate and myo-inositol pentakis-, tetrakis-, tris-, bis-, and monophosphate. The use of phytase in feed industry can overcome environment and nutrition problems which were arisen from unmetabolism phytic acid or its salt by poultry, swine and fish. The feed industry needs a thermostable enzyme due to the need of high temperature in pelleting process, i.e. 81 °C. By using thermostabile phytase, the pelleting process will not affect the enzyme activity. Thermostabile phytase can be isolated from microorganism live in hot spring water or volcano crater. In this study, the screening of thermophylic microorganism having thermostabile phytase activity in Ijen Crater, Banyuwangi, has been done. From this process, it was obtained 33 isolates that produce phytase enzyme. Isolate was code by AP-17 yields highest phytase activity, that is 0.0296 U/mL, so this isolate was choosen for further study. The activity of crude phytase enzyme was measured based on the amount of anorganic phosphate that was produced in enzymatic reaction using UV-VIS spectrophotometer at 392 nm. Based on morphology test to identify the gram type of microorganism, isolate AP-17 has a bacill cell type and identified as positive gram bacteria. This isolate was assumed as Bacillus type.
Construction of pY-Af Vector for Expression of Thermostable α-L-Arabinofuranosidase in Saccharomyces cerevisiae I Nengah Wirajana; Ni Nyoman Tri Puspaningsih; Eddy Bagus Wasito; Soekry Erfan Kusuma; Tetsuya Kimura; Kazuo Sakka
ANNALES BOGORIENSES Vol 14, No 2 (2010): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (822.516 KB) | DOI: 10.14203/ann.bogor.2010.v14.n2.15-20

Abstract

In this research,  construction  of expression  vector  for thermostable α -L-arabinofuranosidase  in Saccharomyces cerevisiae was conducted. BJ1824 was conducted The  Escherichia coli/S. cerevisiae  shuttle vector, pYES2 was  used  as  parental  vector  in  construction.  The  abfA  gene  encoding  α-L- arabinofuranosidase  from Geobacillus  thermoleovorans  IT-08  was  amplified  by  PCR,  in  which  the  plasmid  pTP510 was  used  as  a template. The amplification product was treated with  SacI and XhoI and then subcloned to the pYES2 vector, which was previously digested with  SacI and  XhoI. The recombinant plasmid was designated as pY-Af and propagated  first  in  E.  coli  Top 10,  and  then  transformed  into  S.  cerevisiae  BJ1824.  For  α- Larabinofuranosidase (AbfA) production, the yeast transformants were grown in YNBG selective medium and YPG rich medium, using galactose as an inducer. The AbfA activity was assayed by measuring the amount of p-nitrophenol (pNP) released  from  p-nitrophenyl-α-L-arabinofuranoside  (pNPA) substrate at pH 6.0 and 70 C  for  30  min.  The  recombinant  AbfA  activity  was  detected  in  either  of  culture  medium  (0.98%),  cellassociated (14.17%) and intracellular (84.85%) when recombinant yeast was grown in YPG rich medium.Key words: α-L-arabinofuranosidase; Saccharomyces cerevisiae; expression vector
The Synergy of Recombinant Xylanolytic Enzyme on Xylan Hydrolysis Asmarani, One; Wardojo, Bambang Prajogo Eko; Puspaningsih, Ni Nyoman Tri
Makara Journal of Technology Vol. 15, No. 1
Publisher : UI Scholars Hub

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

Abstract

Microbial xylanases or xylanolytic enzyme have received considerable attention over the last years owing to a multitude of possible applications. These enzymes have potential in the biodegradation of lignocellulosic biomass to fuels, chemicals, fruit juice, animal feed and in improving rumen digestion. More recently, the use of xylanases as bleaching agent in the pulp and paper industry has been suggested to replace of some of the chemicals presently used for this purpose. Such applications could have an important positive impact on the environment. The purpose of this research was determining the synergy of 3 recombinant xylanolytic enzymes (β-xylosidase, exo-xylanase and α-Larabinofuranosidase) from recombinant Eschericia coli BL21 (DE-star) in xylan hydrolysis by analysis the reduction sugar product. Purified of recombinant xylanolytic enzyme β-xylosidase (Xyl), exo-xylanase (Exo-Xyl) and α-Larabinofuranosidase (Abfa) with Ni-NTA resin. Seven samples of enzyme (each and enzyme mixture) used to hydrolyze xylan substrate (oat-spelt xylan). Analysis of hydrolysis product was done by HPLC. The xylanolytic activities of this enzyme before and after purification were 0,91 and 9,94 U/mL (Exo-Xyl); 1,65 and 14,2 U/mL (Xyl); 0,65 and 5,6 U/mL (Abfa). The xylosidase activity were 2,37 and 14,3 U/mL (Xyl); 1,49 and 10,5 U/mL (Exo-Xyl); 2,54 and 18,6 U/mL (Abfa). The highest hydrolysis product of xylan (xylose) shown in enzyme mixture of exoxylanase and β-xylosidase was 1,084 mg/mL.
Design and Cloning of Gene Encoding SLPI C-Terminal Domain in Escherichia coli TOP10 Evi Umayah Ulfa; Ni Nyoman Tri Puspaningsih
Indonesian Journal of Pharmaceutical Science and Technology Vol 9, No. 3, 2022
Publisher : Indonesian Journal of Pharmaceutical Science and Technology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24198/ijpst.v9i3.36918

Abstract

Elevated levels of neutrophil elastase in CPOD (Chronic Obstructive Pulmonary Disease) airways are regarded as the main trigger of lung destruction and inflammation. SLPI (Secretory leukocyte protease inhibitor), an inhibitor protease, represents an attractive candidate for treatment in chronic lung diseases due to proteases excess. The antiprotease active site of SLPI has been located on the C-terminal domain. This study aimed to design and clone the gene encoding the C-terminal domain of SLPI (SLPIc). The gene encoding SLPIc was optimized and predicted solubility using OptimumGene™ and SoDoPe software. The nucleotide sequence of the optimized SLPIc was synthesized, inserted into the pGEX 4T-2 vector commercially by Genscript, and transformed into the Escherichia coli TOP10. The pGEX 4T-2 vector contains a glutathione S transferase (GST) gene located before the MCS to generate a recombinant protein for fusion with GST. For purification purposes, the His-tag synthesized together with SLPIc. The optimized SLPIc nucleotide sequence gave a CAI value of 0.81, GC content 52.31, and a CFD of 2%. The solubility probability of SLPI fused with GST increased from 0.124 to 0.4656. Confirmation of the transformant using restriction and sequencing analysis showed that the gene encoding of SLPI domain C-terminal optimized in the pGEX 4T-2 plasmid was successfully transformed into E. coli TOP10 as novelty of this study. The optimized SLPIc gene in pGEX 4T-2 has a high probability of being expressed in E. coli based on in-silico analysis.
Co-Authors A. A. Istri Ratnawati A.A. Ketut Agung Cahyawan W AFAF BAKTIR Ahmad Thontowi Akhmaloka Akhmaloka Akhmaloka Alfa Akustia Widati Ali Rohman Aline Puspita Kusumadjaja Aline Puspita Kusumadjaja Ami Soewandi J.S. Ami Soewandi J.S. Antonius Suwanto Asnia Zainuddin Badi'ah, Hanim Istatik Bambang Irawan Budi Prasetyo, Antonius Deby Vinolia Dinda Khoirul Ummah Eddy Bagus Wasito Evi Umayah Ulfa Fatiha Khairunnisa Ganden Supriyanto H.M. Soekry Erfan Kusuma Hadi, Sofjan Hadi, Sofjan Handoko Darmokoesoemo Hartati Hartati Hery Suwito Hwei Voon, Lee I Nengah Wirajana Imam Mukhlash Indrajati Kohar Kazuo Sakka Kimura, Tetsuya Kimura, Tetsuya Kusuma, Soekry Erfan Kusuma, Soekry Erfan Leon Janssen Maemonah, Maemonah Maggy T Suhartono Mario Mario Miratul Khasanah Mochamad Zakki Fahmi Mohammad Hamim Zajuli Al Faroby Mohammad Isa Irawan Mohammad Jamhuri Nasronudin Nasronudin Ni'mahtuzahroh, Ni'mahtuzahroh One Asmarani One Asmarani, One Purkan Purkan, Purkan Purwaningsih, Aning Qurrota A’yuni Sajidan Sajidan Sajidan Sakka, Kazuo Sakka, Kazuo Soediatmoko Soediman Soekry Erfan Kusuma Sofijan Hadi Sofyan Hadi Sri Sumarsih Tetsuya Kimura Tokok Adiarto Tutuk Budiati Tutuk Budiati Wardojo, Bambang Prajogo Eko Wuryanti Handayani Y. Sri Wulan Manuhara Y. Sriwulan M. Yanuardi Raharjo, Yanuardi