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Utilising Synthetic Biology to Produce Renewable Energy from Indonesia’s Biodiversity: Inspiration from iGEM Competition Kemal, Rahmat Azhari; Rini, Ika Agus; Oktaviani, Indah
Proceeding International Conference on Global Resource Conservation Vol 6, No 1: Proceeding of 6th ICGRC 2015
Publisher : Proceeding International Conference on Global Resource Conservation

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (0.209 KB)

Abstract

The emerging field of synthetic biology focuses on engineering biomolecular systems and cellular capabilities. It can be applied to a wide variety of applications, one of them is renewable energy production. Teams competing in the International Genetically Engineered Machine (iGEM) competition design and assemble biological devices able to do certain purposes such as producing renewable energy. Their ideas can be adapted by using compatible organisms available from Indonesia’s rich biodiversity. Several ideas are highlighted in this review. One of them is the idea of recycling methanol in glycogen that can be used as carbon source for biofuel production. Methanol dehydrogenase from Indonesia’s methylotrophic bacteria can substitute Bacillus methanolycus used in the system. The adapted ideas can serve as starting points for research, production, and implementation of renewable energy in Indonesia.Keywords: Biodiversity; iGEM; Indonesia; renewable energy; synthetic biology
Prospect of Bioremediation Using Synthetic Biology Approach in Indonesia Kemal, Rahmat Azhari; Novianti, Annisa; Rini, Ika A.; Fatmawati, Ruli
Proceeding International Conference on Global Resource Conservation Vol 6, No 1: Proceeding of 6th ICGRC 2015
Publisher : Proceeding International Conference on Global Resource Conservation

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (0.209 KB)

Abstract

Cellular systems can be engineered by synthetic biology approach to make a controllable bioremediation system. Several teams competing in the International Genetically Engineered Machine (iGEM) competition have utilized the potency of synthetic biology for bioremediation. This review highlighted several ideas. One of them is the designing a whole-cell biocatalyst that can degrade PET component in plastic waste. Rice blast (Magnaporthe grisea) produces cutinase, thus its gene encoding cutinase can be used as substitute in the system. Regulation of the application is also discussed. It is hoped that research and implementation of bioremediation using synthetic biology in Indonesia can be developed.Keywords: Biodiversity; bioremediation; iGEM; Indonesia; synthetic biology
Synthetic Biology for Bio-Control: A Mini-Review Kemal, Rahmat Azhari; Islamiah, Paramita W.N.; Lusiany, Tina
Proceeding International Conference on Global Resource Conservation Vol 6, No 1: Proceeding of 6th ICGRC 2015
Publisher : Proceeding International Conference on Global Resource Conservation

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (0.209 KB)

Abstract

Biomolecular systems and cellular capabilities can be engineered by synthetic biology. One of its wide applications is for bio-control. Several teams competing in the International Genetically Engineered Machine (iGEM) competition have utilized the potency of synthetic biology for pest control. Some of their ideas are highlighted in this review. Taking advantages from Indonesia’s rich biodiversity, those ideas can be expanded. Bio-control using E. coli expressing pheromone biosynthesis activating neuropeptide (PBAN) from rice yellow stem borer (Scirpophaga incertulas) can be used to control that pest. The adapted ideas can serve as starting points for research and implementation of bio-control in Indonesia.Keywords: Bio-control, biodiversity, iGEM, Indonesia, synthetic biology
Studi Awal Analisis Molekuler Human Papillomavirus dari Apusan Glans dan Batang Penis Maya Savira; Resty Yuwandari; Yossi Maryanti; Rahmat Azhari Kemal; Donel S
Jurnal Kesehatan Andalas Vol 9, No 4 (2020): Online December 2020
Publisher : Fakultas Kedokteran, Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jka.v9i4.1493

Abstract

Pria juga dapat mengalami keganasan akibat infeksi Human Papillomavirus (HPV) serta bertindak sebagai reservoir virus. Metode skrining HPV pada wanita telah terstandardisasi, namun belum ada standar metode skrining pada pria di Indonesia. Beberapa studi pada populasi pria di luar negeri menunjukkan potensi sampling pada daerah genitalia eksterna untuk skrining HPV. Tujuan: mengoptimasi metode skrining HPV secara molekuler pada pria. Metode: Responden adalah partner seksual wanita pansien kanker serviks di RSUD Arifin Achmad Provinsi Riau. Apusan dari glans dan batang penis diambil menggunakan nylon-flocked swab yang kemudian dimasukkan ke dalam 350µl viral transport medium terpisah. DNA diisolasi dari sampel yang kemudian dianalisis untuk mendeteksi gen human β-globin dan HPV. Hasil: Optimasi awal menunjukkan gen β-globin dapat terdeteksi dari hasil ekstraksi dengan kit Zeesan Viral RNA Extraction. Pita HPV hasil PCR dengan primer MY09 dan MY11 dapat muncul namun masih tipis. Simpulan: Studi awal ini menunjukkan bahwa apusan glans dan batang penis dapat digunakan untuk deteksi HPV secara molekuler pada pria, namun proses pengambilan sampel, ekstraksi DNA, dan PCR masih perlu dioptimasi.Kata kunci: apusan, glans, HPV, penis
IL-10 Promoter Polymorphism Distribution among HBsAg-Reactive and HBsAg-Nonreactive Blood Donors Rahmat Azhari Kemal; Arfianti Arfianti; Reni Oktora; Bebe Gani; Fauzia Andrini Djojosugito; Winarto Winarto
Majalah Kedokteran Bandung Vol 52, No 1 (2020)
Publisher : Faculty of Medicine, Universitas Padjadjaran

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (694.508 KB) | DOI: 10.15395/mkb.v52n1.1812

Abstract

Hepatitis B surface antigen (HBsAg) serves as a serological marker for Hepatitis B virus (HBV) infection. People with HBV asymptomatic infection might readily donate blood due to the lack of clinical manifestations. Host immunity contributes to susceptibility and progression of infection. A polymorphism in IL-10 gene promoter, rs1800896, might contribute to host immunity. This study was conducted on May 2019 – January 2020 in Faculty of Medicine, University of Riau on  70 blood samples from donors  in the Indonesian Red Cross Pekanbaru. Out of these samples, 35 were reactive for HBsAg and 35 donors were nonreactive. Genotyping of rs1800896 was conducted using Amplification Refractory Mutation System (ARMS-PCR). In total, The distribution of AA (74.3%), AG (24.3%), and GG (1.4%) genotypes revealed in this study seemed to be similar to genotype distribution among East and South-East Asian populations. While no significant difference was observed on age mean and gender distribution, a significant difference was identified in  genotype distribution between HBsAg status (p-value 0.028) with the percentage of AA genotype was higher among HBsAg-nonreactive donors (85.7%) compared to reactive donors (62.9%). More studies should be conducted to characterize HBsAg-reactive blood donors, including the donor characteristics and the viral genotypes. Such studies should contribute to hepatitis B management in Indonesia. Distribusi Polimorfisme Promoter IL-10 pada Donor Darah dengan HBsAg Reaktif dan Nonreaktif di Pekanbaru Hepatitis B surface antigen (HBsAg) merupakan penanda serologis infeksi virus hepatitis B (HBV). Individu dengan infeksi HBV asimptomatik dapat melakukan donasi darah karena tidak adanya gejala klinis. Imunitas inang berkontribusi pada kerentanan dan perkembangan infeksi. Polimorfisme pada promoter gen IL-10, rs1800896, dapat berkontribusi pada imunitas inang. Penelitian dilakukan pada bulan Mei 2019 – Januari 2020 di Fakultas Kedokteran Universitas Riau. Sampel diambil adalah 70 darah donor dari Palang Merah Indonesia Pekanbaru, 35 sampel reaktif HBsAg dan 35 sampel nonreaktif. Genotipe rs1800896 dilihat berdasarkan Amplification Refractory Mutation System (ARMS-PCR). Pada populasi studi ini, distribusi genotipe AA (74.3%), AG (24.3%), dan GG (1.4%) sesuai populasi Asia Timur dan Tenggara. Walaupun tidak terdapat perbedaan pada rerata umur dan distribusi jenis kelamin, penelitian ini menemukan perbedaan signifikan pada distribusi genotipe antar kelompok status HBsAg (p-value 0.028), yaitu persentase genotipe AA lebih tinggi pada kelompok donor dengan HBsAg nonreaktif (85.7%) dibandingkan kelompok reaktif (62.9%). Studi lebih lanjut perlu dilakukan untuk karakterisasi donor darah dengan HBsAg reaktif, termasuk gneotipe donor dan virus. Informasi tersebut diharapkan dapat bermanfaat pada manajemen hepatitis B di Indonesia.
Identifikasi gen kariogenik glukosiltransferase Streptococcus mutans pada pasien karies gigiIdentification of Streptococcus mutans cariogenic gene glucosyltransferase (gtf) in dental caries patients Rita Endriani; Fajri Marindra Siregar; Elita Rafni; Rahmat Kemal Azhari; Jefrizal Jefrizal
Jurnal Kedokteran Gigi Universitas Padjadjaran Vol 33, No 1 (2021): April 2021
Publisher : Fakultas Kedokteran Gigi Universitas Padjadjaran

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24198/jkg.v33i1.30397

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Pendahuluan: Streptococcus mutans (S. mutans) merupakan bakteri yang mempunyai glukosiltransferase surface (GTFs) yang berperan pada proses  perlekatan dan virulensi bakteri pada permukaan gigi. Enzim GTFs terdiri atas  tiga jenis enzim GTFs yaitu GTFB, GTFC dan GTFD dan masing-masing enzim ini dikode oleh gen gtfB, gtfC dan gtfD yang juga berperan sebagai prekursor dalam adhesi seluler plak gigi yang dapat menyebabkan karies gigi. Tujuan penelitian adalah mengidentifikasi gen gtfC dan gtfD S. mutans  pada pasien karies gigi. Metode: Penelitian dilakukan dengan consecutive sampling. Sampel penelitian diambil dari kerokan jaringan karies gigi, diisolasi, dikultur, dan diidentifikasi di laboratorium Mikrobiologi dan Sentral FK UNRI. Identifikasi S. mutans dan gen kariogenik gtfC dan gtfD menggunakan metode Polymerase Chain Reaction (PCR). Data ditampilkan dalam bentuk tabel distribusi frekuensi dan dinyatakan dalam persentase Hasil: Dari 60 kerokan jaringan karies  didapatkan  S. mutans sebanyak 10 isolat, sedangkan gen gtfC dan gen gtfD didapatkan masing-masing 4 (40%) isolat. Simpulan: Gen kariogenik teridentifikasi gen gtfC dan gtfD pada isolat S. mutans dari pasien karies gigi sebanyak 40%.Kata kunci: gtfC, gtfD, kariogenik glukosiltransferase Streptococcus mutans. ABSTRACTIntroduction: Streptococcus mutans (S. mutans) is a bacterium with a glucosyltransferase (Gtfs) surface, which plays a role in the attachment process and bacteria virulence on the tooth surface. The Gtfs enzyme consists of three types of Gtfs enzymes, namely GtfB, GtfC, and GtfD. These enzymes are encoded by the GtfB, GtfC, and GtfD genes, which also act as precursors in the cellular adhesion of dental plaque that can cause dental caries. This study was aimed to identify the GtfC and GtfD of S. mutans in dental caries patients. Methods: This study was conducted with consecutive sampling. Research samples were taken from dental caries tissue scrapings, isolated, cultured, and identified in the Microbiology and Central Laboratory of the Faculty of Medicine University of Riau. Identification of S. mutans and GtfC and GtfD cariogenic genes using the Polymerase Chain Reaction (PCR) method. The data was displayed in the form of a frequency distribution table and expressed as a percentage. Results: From 60 caries tissue scrapings, ten isolates were obtained, while the GtfC gene and GtfD gene were obtained 4 (40%) isolates each. Conclusion: Forty percents of S. mutans isolates from dental caries patients were identified as the GtfC and GtfD cariogenic genes.Keywords: GtfC, GtfD, cariogenic, Streptococcus mutans glucosyltransferase.
Pemberdayaan Remaja sebagai Penyuluh Deteksi Dini Kanker Serviks di Kabupaten Siak Arfianti Arfianti; Rahmat Azhari Kemal
ETHOS (Jurnal Penelitian dan Pengabdian) Vol 9 No.1 (Januari, 2021) Ethos: Jurnal Penelitian dan Pengabdian kepada Masyarakat (Sains & Teknol
Publisher : Universitas Islam Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29313/ethos.v9i1.6159

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Abstract. Cervical cancer is the fourth most common cancer in women and one of the leading causes of mortality from cancer. Early-stage cervical cancer is generally asymptomatic, therefore early detection is very important to reduce the number of patients with advanced stage of cervical cancer. Promotive and preventive efforts based on community empowerment are the best strategy to reduce the prevalence of advanced cervical cancer in Indonesia. To increase public awareness about the importance of early detection of cervical cancer requires the involvement of government, private sector and the community. Adolescents have great potential to play an active role as counselors in cervical cancer screening program. The purpose of this activity was aimed to increase the knowledge and skills of adolescents in carrying out their roles as heatlh counselors for early detection of cervical cancer. The training activities was conducted at the Minas Health Center located in the Minas District, Siak Regency on August 27, 2019. The training activities were attended by 24 (twenty four) students who serve as youth health counselor in Minas District. Analysis of training achievement showed a significant increase in the level of knowledge of participants about cervical cancer after counseling from a total knowledge score of 7.67 ± 1.55 to 11.00 ± 2.21 (p <0.001).Keywords: Adolescent, Cervical cancer, Counselor, Early detectionAbstrak. Kanker serviks merupakan penyakit keganasan keempat terbanyak pada wanita dan merupakan salah satu penyebab kematian terbanyak akibat kanker. Kanker serviks stadium dini pada umumnya tidak bergejala sehingga diperlukan program skrining untuk melakukan deteksi dini sehingga pasien tidak datang dalam kondisi kanker serviks stadium lanjut. Upaya promotif dan preventif berbasis pemberdayaan masyarakat merupakan strategi yang terbaik untuk menurunkan jumlah penderita kanker serviks stadium lanjut di Indonesia. Untuk meningkatkan kesadaran masyarakat tentang pentingnya deteksi dini kanker serviks diperlukan keterlibatan semua unsur dari pemerintah, swasta dan masyarakat. Oleh karena remaja merupakan kelompok yang potensial berperan secara aktif sebagai kader penyuluh deteksi kanker serviks maka tujuan kegiatan pengabdian ini adalah untuk meningkatkan pengetahuan dan keterampilan remaja dalam menjalankan peran sebagai penyuluh deteksi dini kanker serviks. Kegiatan pelatihan berlangsung di Puskemas Minas yang berada dalam wilayah Kecamatan Minas, Kabupaten Siak pada tanggal 27 Agustus 2019. Kegiatan pelatihan diikuti oleh 24 (dua puluh empat) siswi yang merupakan kader kesehatan remaja di Kecamatan Minas. Analisis tingkat ketercapaian pelatihan menunjukkan terjadinya peningkatan yang bermakna pada tingkat pengetahuan peserta tentang kanker serviks setelah penyuluhan yaitu dari total skor pengetahuan 7.67 ± 1.55 menjadi 11.00 ± 2.21 (p < 0.001).Kata Kunci: Remaja, Kanker serviks, Penyuluh, Deteksi Dini
Computational design of ancestral and consensus sequence of apical membrane antigen 1 (AMA1) of Plasmodium spp Rizky Nurdiansyah; Rahmat Azhari Kemal
Acta Biochimica Indonesiana Vol. 2 No. 2 (2019): Acta Biochimica Indonesiana
Publisher : Indonesian Society for Biochemistry and Molecular Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32889/actabioina.v2i2.40

Abstract

Background: It is important to design a malaria vaccine targeting all human malaria parasites as well as non-human primate parasites to eradicate malaria and prevent zoonotic malaria. Apical membrane antigen 1 (AMA1) protein is shared by human-infecting Plasmodium species. Ancestral sequence reconstruction (ASR) and consensus sequence construction on AMA1 might be able to overcome the antigenic distinction between those species. Objective: We aimed to computationally design the ancestral and consensus sequence of Plasmodium AMA1 protein and analyze the sequences for its putative immunogenicity. Methods: We utilized bioinformatics software to computationally design ancestral and consensus sequences of AMA1 protein. AMA1 protein sequences of human-infecting Plasmodium and non-human primate Plasmodium were retrieved from PlasmoDB. ASR was designed using MEGA X while consensus was inferred using UGENE. Phylogenetic tree consisting of existing Plasmodium sequences and the ancestral sequence was constructed using IQTREE webserver and visualized with FigTree. Results: Phylogenetic analysis showed that Plasmodium spp. were divided into 2 major groups, P. falciparum (Clade F) and non-falciparum (Clade NF) thus three ancestral and consensus sequences were designed based on each clade and both clades at once. Reconstructed ancestral sequences were located as sister branch for naturally occurring strains. On the contrary, consensus sequences are located within the branch of corresponding naturally occurring strains. Sequence analysis showed the presence of CD8+ T cell epitope in all computationally-designed sequences. Conclusion: Ancestral and consensus AMA1 sequences are potential for further studies as a malaria vaccine candidate.
Optimization of multiplex PCR composition to screen for SARS-CoV-2 variants of concern Maya Savira; Enikarmila Asni; Rahmat Azhari Kemal
Acta Biochimica Indonesiana Vol. 4 No. 2 (2021): Acta Biochimica Indonesiana
Publisher : Indonesian Society for Biochemistry and Molecular Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32889/actabioina.58

Abstract

Background: The ongoing COVID-19 pandemic has led to the emergence of several variants of concern. To rapidly identify those variants, screening samples for whole-genome sequencing (WGS) prioritization could be performed. Objective: We optimized the polymerase chain reaction (PCR) screening method to identify the mutation in spike and ORF1a regions. Methods: We adopted primers targeting mutation in spike and ORF1a region from another study. We optimized the PCR screening method using kits readily available in Indonesia. Firstly, we compared N1 and N2 primers as internal positive control. We also compared GoTaq® 1-Step RT-qPCR System and Indonesia TFRIC-19 BioCOV-19 for the multiplex reaction. We used the optimized composition to screen SARS-CoV-2 positive samples from April – June 2021. Samples with spike and/or ORF1a target failure were subjected to whole genome sequencing (WGS). Results: The results demonstrated the N2 BioCOV-19 reaction as the optimized multiplex PCR composition for spike and ORF1a mutations screening. Whole-genome sequencing has shown that a sample with spike and ORF1a targets failure to be Alpha variant, while other samples with single target failure as non-variants of concern. Therefore, a multiplex RT-PCR composition has been optimized to detect mutation in spike and ORF1a regions. Conclusion: We have optimized a multiplex RT-PCR composition to detect mutation in spike and ORF1a regions.
Pengetahuan, Sikap dan Praktik Analis Kesehatan di Rumah Sakit X Provinsi Riau tentang Vaksinasi Hepatitis B Huriatul Masdar; Sri Intan Agusmai; Rahmat Azhari Kemal; Fajri Marindra Siregar; Dedi Afandi
Jurnal Ilmu Kedokteran Vol 16, No 1 (2022): Jurnal Ilmu Kedokteran
Publisher : Fakultas Kedokteran Universitas Riau

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26891/JIK.v16i1.2022.30-35

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Hepatitis B is still one of public health problems in the world including in Indonesia. The most vulnerable group to hepatitis B virus exposure is healthcare workers including clinical laboratory technicians. The best way to prevent hepatitis B infection is by getting vaccination. Therefore clinical laboratory technicians are among prioritized subject in getting hepatitis B vaccination. However, hepatitis B vaccination for healthcare workers is not an obligation yet. The purpose of this study was to determine the knowledge, attitude and practice of hepatitis B vaccination among clinical laboratory technicians at X Hospital of Riau Province. This descriptive cross-sectional study was carried out between October 2021 and January 2022. Overall, 38 clinical laboratory technicians were recruited for this study. The Kolmogorov-Smirnov test is used to determine the relationship between knowledge with attitudes and practice. The results showed that 52.6% of respondents had good knowledge, 57.9% had a positive attitude and 68.4% had not been vaccinated against hepatitis B. Based on the results of bivariate analysis, there was no relationship between knowledge and attitude (p>0.05) or practice (p>0.05). Although more than 50% of respondents had good knowledge and attitude, the low number of clinical laboratory technicians in getting the hepatitis B vaccine remains a particular concern.