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All Journal VALENSI Bionatura Teknotan: Jurnal Industri Teknologi Pertanian Jurnal Natur Indonesia Microbiology Indonesia Majalah Kedokteran Bandung Indonesian Journal of Pharmaceutical Science and Technology LEMMA: Letters Of Mathematics Education Indonesian Journal of Biotechnology QALAMUNA: Jurnal Pendidikan, Sosial, dan Agama Jurnal Biodjati JURNAL PENDIDIKAN JASMANI DAN OLAHRAGA Chimica et Natura Acta Jurnal Moral Kemasyarakatan JURNAL SAINS INDONESIA Jurnal Kimia Terapan Indonesia Jurnal Pendidikan Kimia (JPKim) Indonesian Journal of Chemistry Jurnal PAJAR (Pendidikan dan Pengajaran) Gelanggang Olahraga: Jurnal Pendidikan Jasmani dan Olahraga (JPJO) Molekul: Jurnal Ilmiah Kimia Jurnal Pedagogik Olahraga Journal of Authentic Research on Mathematics Eduacation (JARME) Jurnal PORKES JUMORA: Jurnal Moderasi Olahraga Jurnal Ilmiah Berkala: Sains dan Terapan Kimia Pharmaceutical Sciences and Research (PSR) Rangkiang Mathematics Journal International Journal of Educational Research Excellence (IJERE) Jurnal Sains dan Teknologi Farmasi Indonesia al Kimiya : Jurnal Ilmu Kimia dan Terapan ACTIVE: Journal of Physical Education, Sport, Health and Recreation

Toto Subroto

Department Of Chemistry, Faculty Of Mathematics And Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km 21 Jatinangor, Sumedang, 45363 Jawa Barat, Indonesia

Author-ID : 387376

Agriculture, Biological Sciences & Forestry Arts Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Earth & Planetary Sciences Education Environmental Science Health Professions Immunology & microbiology Languange, Linguistic, Communication & Media Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Public Health Social Sciences Other

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Combination of Genetic Manipulation Improved Saccharomycopsis fibuligera α-Amylase Secretion by Pichia pastoris Shabarni Gaffar; Dessy Natalia; Toto Subroto; Oo Suprijana; Soetijoso Soemitro
Indonesian Journal of Chemistry Vol 19, No 2 (2019)
Publisher : Universitas Gadjah Mada

This study assessed the combinations of genetic manipulation; signal peptide modification, gene dosage increment and co-expression of folding component, to increase Saccharomycopsis fibuligera R64 α-amylase (Sfamy) secretion in Pichia pastoris. Sfamy native signal peptide was replaced with modified signal peptide which contained 15 amino acid of mouse salivary α-amylase signal peptide fused to the pro-region of the signal peptide of Saccharomyces cerevisiae α-mating factor (α-MF). Increase in gene dosage was identified by screening for P. pastoris harboring multicopies of the Sfamy gene. Whereas, co-expression of folding component was done by addition of Protein Disulfide Isomerase (PDI). Expression plasmids harboring Sfamy containing modified signal sequence (pPICZA-MS-Sfamy) was used to transform P. pastoris GS115, and gene dosage increment was screened using zeocin. Effect of PDI co-expression on secretion levels of Sfamy was assessed by constructing the pPIC3.5K-Pdi1 plasmid and introducing into P. pastoris harboring multicopies of MS-Sfamy for expression of Sfamy. Signal peptide modification consequently increased Sfamy secretion by P. pastoris by 3.3-fold compared to native signal peptide. Gene dosage increment had improved Sfamy secretion by 11-fold in P. pastoris [MS-Sfamy] resistant to 2000 μg/mL zeocin, compared to P. pastoris harboring one copy of WT-Sfamy. Hence, PDI co-expression increased the secretion of Sfamy by 2-fold as compared without PDI co-expression. In summary, the combination of genetic manipulation successfully increased Sfamy secretion by 20-fold compared to P. pastoris harboring one copy of WT-Sfamy.

An Electrochemical Aptasensor for the Detection of HER2 as a Breast Cancer Biomarker Based on Gold Nanoparticles-Aptamer Bioconjugates Yeni Wahyuni Hartati; Sari Syahruni; Shabarni Gaffar; Santhy Wyantuti; Muhammad Yusuf; Toto Subroto
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.67124

Inaccurate diagnoses contributes to the high mortality rate of breast cancer. Human epidermal growth factor receptor 2 (HER2) is overexpressed in breast cancer tumors at around 20–30%. This study aims to develop an electrochemical biosensor for HER2 based on a gold nanoparticle-aptamer bioconjugate (AuNP@HER2 aptamer) and investigate the interaction between DNA aptamer and HER2 using computational methods. The bioconjugate was synthesized using maleimide and polyethylene glycol as a linker. The –NH2 group of cysteamine that modified the gold electrode can form a covalent bond with the bioconjugate maleimide. The interaction of the bioconjugated aptamer with HER2 was measured electrochemically based on the [Fe(CN)6]3−/4− redox system. The limit of detection, the linear range of HER2, precision, and accuracy in this study were 1.52 ng mL–1, 0.01 to 15.0 ng mL–1, 0.1298, and 94.06%, respectively. The structure of the DNA aptamer was modeled using mFold, Assemble2, and Chimera, with the interaction between the DNA aptamer and HER2 explored by NPDock. The modeling of the aptamer with HER2 showed that electrostatic interactions dominated the attractive forces. The resulting interaction pattern can be used as a template to improve the binding energy of the aptamer, thus providing insight into the development of aptamer-based biosensors.

SINTESIS PEPTIDA P251-9 BERGUGUS PELINDUNG DENGAN METODE SINTESIS PEPTIDA FASA PADAT FMOC/TBU MENGGUNAKAN ADITIF OKSIMA Ari Hardianto; Toto Subroto; Unang Supratman
Jurnal Sains dan Terapan Kimia Vol 5, No 2 (2011)
Publisher : Program Studi Kimia, Universitas Lambung Mangkurat

Peptida P25 merupakan epitop yang dapat dengan mudah mengaktivasi sel T penolong. Sel T penolong teraktivasi berperan dalam aktivasi sel B untuk membentuk antibodi. Peptida bahkan protein dapat dibuat dengan metode sintesis peptida fasa padat Fmoc/tBu menggunakan aditif HOBt. Namun sayangnya HOBt memiliki karakter yang mudah meledak. Pada penelitian ini telah berhasil disintesis bagian epitop P25 (peptida P251-9 bergugus pelindung) yang memiliki tingkat kemurnian tinggi dan perolehan 36,4% dengan metode sintesis peptida fasa padat Fmoc/tBu menggunakan aditif oksima pengganti HOBt. Kata kunci: Epitop, P251-9, sintesis peptida fasa padat Fmoc/tBu, oksima.

Studi Mutasi Titik A3243G DNA Mitokondria Penyebab Maternally Inherited Diabetes and Deafness Sriwidodo, Sriwidodo; Suprijana, O; Subroto, Toto; Maksum, Iman Permana
Majalah Ilmu Kefarmasian Vol. 5, No. 3
Publisher : UI Scholars Hub

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

Point mutation of mitochondrial DNA A3243G has been known as a cause of Mater-nally Inherited Diabetes and Deafness (MIDD). Potency of MIDD can be identified from patient phenotype of Non Insulin Dependent Diabetes Mellitus (NIDDM). The objective of this study is acquiring information about MIDD on patient of NIDDM type and obtaining the simple method to detect the point mutation of mtDNA A3243G. 50 NIDDM patients were attained from RSCM Hospital, Jakarta. Information con-cerning family history with NIDDM and existences of deafness, medication, and other complication and manifestation were obtained through interview and ques-tioner. Point mutation of A3243G was determined with the method of PCR Allele’s Specific Amplification (PASA) Mismatch 2 bases and PCR-Restriction Length Poly-morphism (PCR-RFLP) with the HaeIIl restriction enzyme. Detectable Potency MIDD was found by perceiving the patient phenotype and identifying the mutation of heteroplasmic A3243G utilizing the PASA method.

Early development of self‐administered COVID‐19 rapid test based on nucleocapsid detection in saliva sample Siti Soidah; Toto Subroto; Sari Syahruni; Fauzian Giansyah; Henry Chandra; Dhiya Salsabila; Bachti Alisjahbana; Nisa Fauziah; Hesti Lina Wiraswati; Leonardus Wiydatmoko; Basti Andriyoko; Anita Yuwita; Muhammad Yusuf
Indonesian Journal of Biotechnology Vol 27, No 3 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.72269

More than 6,000,000 people have died due to the coronavirus (COVID‐19) pandemic. This disease spread quickly due to its highly contagious nature. The SARS‐CoV‐2 virus that causes the disease can be transmitted through saliva droplets secreted by infected people at a distance of less than 1 m. As a result, saliva has been accepted as an alternative specimen for COVID‐19 detection by the Centers for Disease Control and Prevention (CDC). Furthermore, WHO recommended the use of rapid antigen tests based on lateral flow immunoassay when reverse transcription‐polymerase chain reaction (RT‐PCR) is not available. We developed a saliva‐based rapid antigen test by optimizing the antibody concentration and optimum pH for the conjugation of antibody and gold nanoparticles. We found that the best running buffer formulation consisted of 75 mM sodium phosphate buffer, 1% NaCl, 1% Triton X‐100, 0.5% N‐acetyl‐L‐cysteine, and 0.02% sodium azide. The addition of a mucolytic agent in the buffer can reduce the viscosity of saliva, thus improving sensitivity. The rapid test developed detected the lowest concentration of nucleocapsid protein at 0.1 μg/mL. Our study revealed 100% specificity against negative COVID‐19 saliva and no cross‐reaction with avian influenza virus hemagglutinin.

Optimization of Aptamer-Based Electrochemical Biosensor for ATP Detection Using Screen-Printed Carbon Electrode/Gold Nanoparticles (SPCE/AuNP) Rahmaniar Mulyani; Nida Yumna; Iman Permana Maksum; Toto Subroto; Yeni Wahyuni Hartati
Indonesian Journal of Chemistry Vol 22, No 5 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.72820

Electrochemical biosensors are used to detect adenosine triphosphate (ATP) levels, which are involved in a variety of biological processes, such as regulating cellular metabolism and biochemical pathways. Therefore, this research aims to develop an aptamer-based electrochemical biosensor with Screen Printed Carbon Electrode/gold nanoparticles (SPCE/AuNP) and collect data as well as information related to ATP detection. The modification of SPCE with AuNP increased the analyte’s binding sensitivity and biocompatibility. The aptamer was selected based on its excellent bioreceptor characteristics. Furthermore, aptamer–SH (F1) and aptamer-NH2 (F2) were immobilized on the SPCE/AuNP surface, which had been characterized using SEM, EIS, and DPV. Also, the ATP-binding aptamers were electrochemically characterized using the K3[Fe(CN)6] redox system and Differential Pulse Voltammetry (DPV). According to the optimization results using the Box-Behnken experimental design, the ideal conditions obtained from the factors influencing the experiment were the F1 concentration and incubation time of 4 µM and 24 h, respectively, as well as F1/F2/ATP incubation time of 7.5 min. Meanwhile, for the range of 0.1 to 100 µM, the detection (LoD) and quantification (LoQ) limits were 7.43 and 24.78 µM, respectively. Therefore, this aptasensor method can be used to measure ATP levels in real samples.

Codon Optimization and Chaperone Assisted Solubilization of Recombinant Human Prethrombin-2 Expressed in Escherichia coli SARONOM SILABAN; IMAN PERMANA MAKSUM; SHABARNI GHAFFAR; KHOMAINI HASAN; SUTARYA ENUS; TOTO SUBROTO; SOETIJOSO SOEMITRO
Microbiology Indonesia Vol. 8 No. 4 (2014): December 2014
Publisher : Indonesian Society for microbiology

Prethrombin-2 (PT2) is a thrombin precursor, which plays a role in the conversion of fibrinogen into fibrin during blood clotting process. Previous study reported that the expression of human prothrombin-2 (rhPT2) in Escherichia coli formed inclusion bodies. The aim of this study was to establish a strategy to express a soluble rhPT2 in E. coli. This study was animed to design and codon optimize human prethrombin-2 gene as well as to optimize the expression condition using four strains of E. coli. The codon adaptation index (CAI) of the unoptimized hpt2 gene was 0.336, with 56.8% GC content. After optimization, the CAI of optimized hpt2 became 1.000 with 53.1% GC content. The optimized gene was successfully cloned into pTWIN1 expression vector. Expression analysis indicated that only E. coli ArcticExpress strain could successfully express a soluble recombinant rhPT2 protein, with only part of rhPT2 being expressed in insoluble form. However, the rest of the E. coli strains used in the experiments failed to express the rhPT2 in soluble form. We are deducing that the success in achieving soluble expression was not only due to the availability of chaperonins Cpn60/Cpn10, which played a crucial role in the protein folding in E. coli ArcticExpress strain, but also due to the codon optimization of hpt2 gene.

Heterologous Expression of Î±-Amylase from Saccharomycopsis fibuligera R64 and its Tyr401Trp Mutant in Pichia pastoris RIEZKI AMALIA; WANGSA TIRTA ISMAYA; FERNITA PUSPASARI; KHOMAINI HASAN; TOTO SUBROTO; DESSY NATALIA; SOETIJOSO SOEMITRO
Microbiology Indonesia Vol. 10 No. 1 (2016): March 2016
Publisher : Indonesian Society for microbiology

Î±-Amylase from Saccharomycopsis fibuligera R64 is a non-adsorbing raw-starch degrading enzyme, a unique characteristic. This character is difficult to explain in the absence of its three-dimensional structure. Here we discuss the expression of a-amylase from Saccharomycopsis fibuligera in Pichia pastoris and the effect of site directed mutagenesis on its activity. A model based on the structure of its homologs suggested mutation of codon of Tyr401 into that of a Trp residue. An activity study using whole cells P. pastoris showed similar substrate degradation rates by cells carrying either the native or mutant amylase encoding gene. However, the purified enzyme of the mutant strain showed faster starch hydrolysis.

Cloning, Expression, and Functional Characterization of Autoactivated Human Prethrombin-2 Synthetic Gene by Using Pichia pastoris SMD1168 As a Host TOTO SUBROTO; WULAN PERTIWI; MUHAMMAD FADHILLAH; KHOMAINI HASAN; OGI BUDIANTORO; SUTARYA ENUS; SOETIJOSO SOEMITRO
Microbiology Indonesia Vol. 10 No. 2 (2016): June 2016
Publisher : Indonesian Society for microbiology

Prethrombin-2 is a thrombin precursor that has important role in blood coagulation. It is the smallest precursor which is activated into thrombin by FXa prior to coagulation process. However, as a commercial theurapetic protein in fibrin sealant component, prethrombin-2 must be activated by ecarin before used. Thus, the production process of this protein needs further purification. In order to eliminate ecarin activation step and to increase production efficiency, we designed, cloned and expressed the recombinant autoactivated human prethrombin-2 in Pichia pastoris SMD1168. The variant was designed with 4 mutations, E40A, D47A, G48P, and E52A, following the result of a previous study. The synthetic variant gene was first optimized to conform with P. pastoris codon preference. The optimized synthetic gene was cloned in pD912 plasmid using XhoI and SacII restriction enzymes. The transformed P. pastoris was selected on agar plate supplemented with 1,000 Âµg.mL-1 Zeocin as a selection marker. This study showed that autoactivated prethrombin-2 was succesfully expressed extracellularly by P. pastoris SMD1168. The activity of recombinant autoactivated prethrombin-2 using a chromogenic substrate S-2238 was 0.540 unit/mg. Taken together, these results demonstrated that autoactivated human prethrombin-2 was successfully produced extracellularly in P. pastoris.

Analisis Bioinformatika dan Ekspresi Protein Rekombinan Hemagglutinin Domain Globular dari Virus H5N1 Indonesia pada Eschericia coli BL21 (DE3) sebagai Komponen Vaksin Subunit Influenza Muhammad Yusuf; Rima Handiyani; Shinta Kusumawardani; Idar Idar; Umi Baroroh; Toto Subroto
al Kimiya: Jurnal Ilmu Kimia dan Terapan Vol 8, No 2 (2021): al Kimiya: Jurnal Ilmu Kimia dan Terapan
Publisher : Department of Chemistry, Faculty of Science and Technology, UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/ak.v8i2.14138

Flu burung merupakan salah satu penyakit zoonosis yang patut diwaspadai di Indonesia, khususnya galur High Pathogenic Avian Influenza (HPAI) karena dapat mematikan jika menular kepada manusia. Penggunaan vaksin influenza pada unggas, merupakan langkah preventif terhadap evolusi virus yang berbahaya dan juga penyebarannya. Selama ini, Indonesia masih menggunakan seed vaksin impor yang berasal dari luar Indonesia. Namun, karena Indonesia merupakan negara yang berada di garis khatulistiwa, karakteristik virus bisa berbeda dengan virus dari nothern-hemispere maupun southern-hemispere. Mengingat hal tersebut, Indonesia harus mengembangkan vaksin influenza menggunakan galur virus lokal. Berbeda dengan vaksin whole virus, vaksin rekombinan memiliki keunggulan dari sisi kemurnian, kecepatan produksi, dan kesesuaian galur terhadap virus yang beredar saat diperlukan. Penelitian ini bertujuan untuk menganalisis sekuen hemagglutinin (HA) Indonesia dengan strain lainnya serta mengekspresikkan protein HA1 rekombinan pada Escherichia coli BL21 (DE3). Galur yang digunakan pada studi ini berasal dari virus H5N1 (A/Indonesia/05/05), khususnya bagian domain globular dari HA1. Sekuen HA1 bervariasi antara strain Indonesia dengan nothern-hemispere maupun southern-hemispere dan merupakan protein yang terpapar ke luar virus. Gen HA1 disisipkan pada vektor pET-28a, kemudian plasmid diisolasi menggunakan meoe manniatis, setelah itu diekspresikan dengan induksi 1 mM IPTG selama 4 jam. Protein HA1 telah berhasil diekspresikan secara intraseluler dan telah dikonfirmasi pada berat molekul 40 kDa menggunakan SDS-PAGE. Penelitian ini dapat digunakan untuk mengembangkan vaksin subunit yang lebih spesifik terhadap virus yang beredar di lapangan.

Co-Authors Abdul Alim Kahari, Abdul Alim Abu Bakar M.I. Syihab Agus Gumilar Alifa I. Nabila Amiruddin, Mohd. Hasril Anita Yuwita Anneke Noviyanti Aprillia, Mutiara Sukma Ari Hardianto Bachti Alisjahbana Basti Andriyoko Bisri Musthofa Budiantoro, Ogi D Agus Yusuf Wildan Dani Permana Debby M Sumanti Defi Supriyati, Ayu DESSY NATALIA DESSY NATALIA DESSY NATALIA Dewi Astriany Dhiya Salsabila Dian Budiana, Dian Diana P Rahmawati Didi Suryadi DWI RAHMAWATI Eddy, Diana Rakhmawaty Effendi, Syulastri EKO YULIANTO Elazmanawati Lembong Fadhilah, Muhammad Naufal Fadhlillah, Muhammad Fadillah, Lukky Farihandiandra, Yusron Fathurrohman, Muhammad Andi Fatin, Nuri Nuraini Fauzian Giansyah Febriani Aji Kusuma, Sherlynda FERNITA PUSPASARI Firdaus, Muhammad Lutfi Gifa Nur Arofah Gumelar, Abih Gumilar, Agus Hafizatunnisa, Hafizatunnisa Hambali, Burhan Hamdiyanti, Meti Henry Chandra Hesti Lina Wiraswati Idar Idar Idar Idar Idar Idar Idar, Idar IMAN PERMANA MAKSUM Iman Permana Maksum Iman Permana Maksum Iman Permana Maksum Iman Permana Maksum Iman Permana Maksum Iman Permana Maksum Iman Permana Maksum Iman Permana Maksum Iman Permana Maksum IMAN PERMANA MAKSUM Kharimah, Nurul Ikhsan KHOMAINI HASAN Kusumawardhani, Shinta Laelasari Laelasari Laelasari, Laelasari Leonardus Wiydatmoko Lesmana, Gianjar Mony, Siti Rasnawati Muchamad Subali Noto Muhammad Fadhil Z, Rusdi Noor Rosa (p:43-50) Muhammad Fadhlillah Muhammad Hilman Daniswara Muhammad Yusuf Muhammad Yusuf Muhammad Yusuf Murniaty Simorangkir Murniaty Simorangkir Naufal D, Kevin Nida Yumna Nisa Fauziah Noviyanti, Anneke Nurfairuz, Hasna Siti Nurmalasari, Ratna Nurul Ikhsan Karimah O Suprijana O Suprijana O Suprijana, O OGI BUDIANTORO Ogi Budiantoro Oo Suprijana Opik Taupiqurrohman Opik Taupiqurrohman Pertiwi, Wulan Praja, Ena Suhena Purba Upay Rahmaniar Mulyani Rahmat, Alit Riezki Amalia Rima Handiyani Rizky Rosjanuardi Rodiana, Ivta Safri Ishmayana Safri Ishmayana Safri Ishmayana Safrl Ismayana Sahroni, Sahroni Santhy Wyantuti Sari Agung, Syennie Sari Syahruni Sari Syahruni SARONOM SILABAN Saronom Silaban Saronom Silaban Saronom Silaban Shabarni Gaffar Shabarni Gaffar Shabarni Gaffar Shabarni Gaffar Shabarni Gaffar Shabarni Gaffar Shabarni Gaffar -, Shabarni Gaffar SHABARNI GHAFFAR Shinta Kusumawardani Siti Soidah Siti Umayah, Siti Soetijoso Soemitro Soetijoso Soemitro Soetijoso Soemitro Soetijoso Soemitro Soetijoso Soemitro Soetijoso Soemitro SOETIJOSO SOEMITRO Sofyan Multazam N Aji Sriwidodo Sriwidodo Sriwidodo Sriwidodo, Sriwidodo Sriwidodo, . Sukma Nuswantara Sukma Nuswantara Sukma Nuswantara Sunan M. Alpiansyah Sutarya Enus Sutarya Enus Sutarya Enus SUTARYA ENUS Syani, Mamay Syfa Nurfadilah Taupiqurrohman, Opik Taupiqurrohman, Opik Tika Pradnjaparamita, Tika Tonah Triana N Meirina Umi Baroroh Unang Supratman Upay, Purba wahyu widayat WANGSA TIRTA ISMAYA Windy Aulia Putri Wulan Pertiwi Yani Suryani Yeni W Hartati Yeni Wahyuni Hartati Zakiyyah, Salma Nur

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