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All Journal International Journal of Evaluation and Research in Education (IJERE) HAYATI Journal of Biosciences Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Jurnal Pendidikan Humaniora Jurnal Pendidikan Sains El-Hayah : Jurnal Biologi Journal of Education and Learning (EduLearn) Biotropika KEMBARA Jurnal Pendidikan Biologi Indonesia Bioeksperimen: Jurnal Penelitian Biologi JURNAL KONFIKS Indonesian Language Education and Literature Jurnal Pendidikan: Teori, Penelitian, dan Pengembangan Jurnal Kajian Pembelajaran Matematika KREDO : Jurnal Ilmiah Bahasa dan Sastra THE JOURNAL OF MUHAMMADIYAH MEDICAL LABORATORY TECHNOLOGIST BIOEDUKASI Biosfer: Jurnal Pendidikan Biologi Diglosia: Jurnal Kajian Bahasa, Sastra, dan Pengajarannya English Language and Literature International Conference (ELLiC) Proceedings Edubiotik : Jurnal Pendidikan, Biologi dan Terapan Jurnal Pendidikan dan Pengajaran Guru Sekolah Dasar (JPPGuseda) Jurnal Ilmiah Mandala Education (JIME) Journal of Saintech Transfer Satwika : Kajian Ilmu Budaya dan Perubahan Sosial Hasta Wiyata JENTERA: Jurnal Kajian Sastra Jurnal Onoma: Pendidikan, Bahasa, dan Sastra Bio-Inoved : Jurnal Biologi-Inovasi Pendidikan Ghancaran: Jurnal Pendidikan Bahasa dan Sastra Indonesia Edunesia : jurnal Ilmiah Pendidikan Jurnal Riset Biologi dan Aplikasinya Jurnal Kesmas Untika Luwuk: Public Health Journal Majalah Ilmiah Gema Maritim Education and Linguistics Knowledge Journal (Edulink) JOLLT Journal of Languages and Language Teaching Wahana Dedikasi : Jurnal PkM Ilmu Kependidikan Marine Science and Technology Journal Journal of English Education Program (JEEP) Proceeding Biology Education Conference Berkala Penelitian Hayati Borneo Journal of Biology Education (BJBE) Journal of Education Research Bahasa dan Seni: Jurnal Bahasa, Sastra, Seni, dan Pengajarannya ELECTRUM: The English Language and Education Spectrum Jurnal Pembelajaran Sastra Journal of Language, Literature, and Arts (JoLLA) JURNAL SAINS DAN TEKNOLOGI MARITIM UNNES International Conference on ELTLT Journal of Literature and Education EduInovasi: Journal of Basic Educational Studies Ngabekti: Jurnal Pengabdian kepada Masyarakat PROSIDING SEMINAR NASIONAL DAN INTERNASIONAL HIMPUNAN SARJANA-KESUSASTRAAN INDONESIA Prosiding Seminar Nasional Pengabdian kepada Masyarakat (SINAPMAS) Edubiotik : Jurnal Pendidikan, Biologi dan Terapan Proceeding Mulawarman International Conference on Tropical Public Health
Dwi Listyorini
Universitas Negeri Malang
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Journal : Jurnal Riset Biologi dan Aplikasinya

 1 
The Comparison of SARS-CoV-2, SARS-CoV, and MERS-CoV Genome and Spike Protein Variations Fikriani, Choirun Nita; Ardana, I Kade Karisma Gita; Listyorini, Dwi
Jurnal Riset Biologi dan Aplikasinya Vol 3, No 1 (2021)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jrba.v3n1.p38-44

Abstract

SARS-CoV-2 is a virus that has caused COVID-19 pandemic. This virus is a new variant of the SARS-CoV virus and also closely related to MERS-CoV, which caused similar acute respiratory infections. All these viruses recognize target cells by binding to the Receptor Binding Domain (RBD) on Spike protein with receptors. This study aimed to determine the SARS-CoV-2, MERS-CoV, and SARS-CoV genome structure, Spike protein sequence differences, and variations of RBD’s Receptor Binding Motif (RBM). This research was using data mining approach. Genome sequences were downloaded from NCBI, except for Indonesian samples were downloaded from GISAID. Genomic structures, Spike sequence, and RBD structure were analyzed using Bioedit, followed by protein modelling using SwissModel and PyMol applications. The result showed that the SARS-CoV-2, MERS-CoV, and SARS-CoV genome shared the same genes yet in different numbers and length. SARS-CoV-2 Spike protein sequence was quite similar to SARS-CoV Spike protein, but very different to the Spike protein of MERS-CoV. There were variations of RBD’s RBM structure due to the mutations occurred among these viruses. It is suggested that these differences may increase the affinity between SARS-CoV-2 Spike protein to its hACE2 receptor which caused SARS-CoV-2 becomes more infective and spread wider than SARS-CoV and MERS-CoV, in turn. This result expected to be basic information for the development of SARS-CoV-2 introduction inhibition agent and spreading prevention.
S-D614G Mutation Reveals the Euro-America and East-Asia Origin SARS-CoV-2 Virus Spread in Indonesia Anggraini, Nina Bunga; Listyorini, Dwi
Jurnal Riset Biologi dan Aplikasinya Vol. 3 No. 2 (2021)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jrba.v3n2.p45-53

Abstract

COVID-19 is a pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The first case was found in the city of Wuhan, Hubei province, China. The first case in Indonesia was reported in March 2020 and currently there are 0.5 million cases with a death rate of 3.1%. This rapid increase in cases is thought to due to presence of the mutant strain S-D614G, which causes a faster rate of infection and spread. The purpose of this study was to determine the presence of S-D614G mutations in Indonesian samples in order to find the origin of COVID-19 which was spread in Indonesia based on the Spike gene sequences and the RdRp genes from 25 countries, and one control sequence China/Wuhan-Hu-1 obtained from the NCBI and GISAID databases. Mutation analysis was carried out through multiple alignments using BioEdit software. Phylogenetic tree reconstruction using MEGA6 software with the Neighbor Joining method. This study found mutation of S-D614G in one Indonesian sample, namely the Indonesian/SBY9 sample along with 23 samples from Europe, America, and Africa. The phylogenetic tree reconstruction confirmed these findings; the mutated samples were closely related to samples from these continents, while the non-mutated Indonesian samples were closely related to sample from East Asia. These findings indicate that the origin of the SARS-CoV-2 virus in Indonesia possibly came from the East Asia cluster and the European-American cluster.
The Comparison of SARS-CoV-2, SARS-CoV, and MERS-CoV Genome and Spike Protein Variations Choirun Nita Fikriani; I Kade Karisma Gita Ardana; Dwi Listyorini
Jurnal Riset Biologi dan Aplikasinya Vol. 3 No. 1 (2021)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jrba.v3n1.p38-44

Abstract

SARS-CoV-2 is a virus that has caused COVID-19 pandemic. This virus is a new variant of the SARS-CoV virus and also closely related to MERS-CoV, which caused similar acute respiratory infections. All these viruses recognize target cells by binding to the Receptor Binding Domain (RBD) on Spike protein with receptors. This study aimed to determine the SARS-CoV-2, MERS-CoV, and SARS-CoV genome structure, Spike protein sequence differences, and variations of RBDs Receptor Binding Motif (RBM). This research was using data mining approach. Genome sequences were downloaded from NCBI, except for Indonesian samples were downloaded from GISAID. Genomic structures, Spike sequence, and RBD structure were analyzed using Bioedit, followed by protein modelling using SwissModel and PyMol applications. The result showed that the SARS-CoV-2, MERS-CoV, and SARS-CoV genome shared the same genes yet in different numbers and length. SARS-CoV-2 Spike protein sequence was quite similar to SARS-CoV Spike protein, but very different to the Spike protein of MERS-CoV. There were variations of RBDs RBM structure due to the mutations occurred among these viruses. It is suggested that these differences may increase the affinity between SARS-CoV-2 Spike protein to its hACE2 receptor which caused SARS-CoV-2 becomes more infective and spread wider than SARS-CoV and MERS-CoV, in turn. This result expected to be basic information for the development of SARS-CoV-2 introduction inhibition agent and spreading prevention.
A Genetic Identification of Superbugs from River Streams in State University of Malang Sholekah, Reeno Al Hikmatus; Listyorini, Dwi
Jurnal Riset Biologi dan Aplikasinya Vol. 5 No. 1 (2023)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jrba.v5n1.p27-36

Abstract

Superbugs revert to bacterial strains, which exhibit resistance to antibiotics. These bacteria could cause some problems in disease treatment and the environment. This research aimed of this study was to identify the presence of superbugs in the river stream that flows through Malang State University campus area. Amoxicillin, tetracycline, and chloramphenicol were selected to test the possible bacterial resistance. Water samples taken from a decided spot were spread over Luria Bertani’s agar on both antibiotic supplemented and antibiotics-free media with no delay. Molecular identification was carried out using 16S rRNA gene DNA barcoding approach, completed with morphological and Gram staining analyses. A total of 16 isolates of gram-negative colonies were found in the form of bacilli, diplobacilli, cocci, and diplococci. The genetic identification of eight resistant colonies led us to suggest that the isolates may belong to Aeromonas, Shigella, and Bacillus. Further studies are still required to get a clearer view of the correct taxonomical position of those resistant isolates.
Co-Authors @Mustaffa, Madiawati Mamat Abdul Ghofur Abdul Gofur Abdul Gofur Abdul Gofur Achmad Rodiansyah Afrabiyas Firyal Hanasepti Agung Andana Agung Andana Agung Wibowo Agung Witjoro Ainul Fitria Mahmudah Aisyah Hidayati Algafari Bakti Manggara Alvian Guntur Prasetya Aziz Alvian Guntur Prasetya Aziz Anastacia Verena Salim Andi Madhihah Manggabarani Anggraini, Nina Bunga Anggun Sari Anjarwati Annasa Sabatia Ardana, I Kade Karisma Gita Arini, Kartika Ayu Dwi Assegaff, Muhamad Farid Asteria, Prima Vidya Aswan Aswan Atik Kurniawati Azizatuz Zahro Badri'ah, Badri'ah Bani Sudardi Caesar Adlu Hakim Caesar Adlu Hakim Choirun Nita Fikriani Choirun Nita Fikriani Cicik Tri Jayanti Dahlia Dahlia Dahlia Dahlia Darmawan, Taufik Delia Wahyu Pangesti Deni Ainur Rokhim Dermawan, Taufik DEWI ARIANI Dewi Ariani Dhikri, Ahmad Saiqu Dhion Meitreya Vidhiasi Dian Ratri Wulandari Didin Widyartono Djoko Saryono Dwi Anggorowati Rahayu Dwi Anggorowati Rahayu Dwi Anggorowati Rahayu Dwita Novitasari Dyati Galuh Pratita Effendi, Desy Irafadillah Eko Agus Suyono Eko Sri Sulasmi Elhah Nailul Khasna Emy Kusumawati Endang Suarsini Endik Deni Nugroho Endik Deni Nugroho Endriawati, Riskha Anggita Erry Hidayanto Evania Yafie Evi Susanti Fadhillah, Rayhan Rizky Fahriani, Dita Karisma Fatchur Rohman Fauziah, Putri Nanda Febrianto, Aziza Restu Fikriani, Choirun Nita Firnanda, Sindy Galina Istiqhfarini GAYUH ELPANUSI, GAYUH ELPANUSI Gracela Noveline Christiana Telaumbanua Habibi, Mohamad Hadi Sowono Hadi Suwono Haryani Haryani Hasbi, Nur Hayuni Retno Widarti Helmi Muzaki Hendra Susanto Herawati Susilo Herdina Rahma Zalita Hikam, Ahmad Faruqil Huda, Marleni Rosalia Ndapa Hudayanto, Reynaldi Januar I Kade Karisma Gita Ardana I Kade Karisma Gita Ardana I Kade Karisma Gita Ardana Ibrohim Iin Murtini Ike Ratnawati Indra Kurniawan Saputra Intan Chairun Nisa Ira Junita Suryantoro Iza, Nikmatul Izdihara Arini Aulia Jamila Wijayanti Jayawarsa, A.A. Ketut Jeni Jeni Jiilan Hani Safitri JK, Adi Kus Rochman Jumain, Jumain Ken Raos Regina Kuncoro, Condro Ayu Mukti Kurniawan Setia Putra Kusubakti Andajani Kusumawati, Emy Laili, Rani Nuzulul Laily Abida Lathif, Yudrik Lathif, Yudrik Lea Assyifa Lestari, Nunik Martin M. Miftahul Aziz M. Nidhamul Maulana Mamat, Madiawati Binti Manggabarani, Andi Madhihah Maria Goretti Indah Della Conseta Mastika Marisahani Ulfah Mauluddin, Imam Mitra Istiar Wardhana Moh. Safii Mohamad Habibi Mona Lisa Mona Lisa, Mona Muh Ade Artasasta Muhammad Habibi Muharramah, Disa Hijratul Muhibbatul Ma'rifah Mulyani, Dita Tri Munika, Risa Dewi Murni Sapta Sari Muslim Mustayah ., Mustayah Muthia Naila Mazieda Mutika, Winnie Tunggal Naailatu Nur Azizah Natasya, Shella Ndzani Latifatur Rofi’ah NIKMATUL IZA Nikmatul Iza Nila Kartika Sari Nila Kartika Sari Nina Bunga Anggraini Ningsih, Husdiani Norman Yoshi Haryono Nur Hasbi Nur Hasbi Nurastuti, Galuh Yuli Nurjannah, Andhika Afifah Nurul Annisa Putri Nurul Annisa Putri Pearlindah Peralindah Peralindah, Pearlindah Pradipta, Dristanta Setya Prasetyani, Rizki Nurul Puguh Darmawan Putra, Kurniawan Setia Putra, Kurniawan Setia Putri, Aldila Rahmita Putri, Cindy Pradina Putri, Nurul Annisa Raden Bambang Sumarsono Radhiyah, Rizqa Rahmawati, Yusi Rahmawati, Yusi Rahmi Masita Ratna Juwita Rayhan Rizki Fadhillah Ria Novita Ayu Komalasari Rina Wahyuningsih Riri Wiyanti Retnaningtyas Riri Wiyanti Retnaningtyas Rismiawati, Riris Risqillah, Ulfa Rizki Nurul Prasetyani Rizkian, Selvi Rizqa Radhiyah Rizqullah Janitra Kristian Abadi Roekhan Roekhan Rohmah, Riska Nur Rohmawati, Uun Rozana, Kennis Sari, Nila Kartika Setiawan, Nur Candra Eka Sholekah, Reeno Al Hikmatus Sholihah, Mar'atus Siti Salina Mustakim Siti Zubaidah Siti Zubaidah Sitoresmi Prabaningtyas Sri Sukaesih Suharti Suharti Suharti Sukiman Sunarmi Susriyati Mahanal Sutejo Sutejo Sutejo Sutejo Tamara, Widia Tita Putri Milasari Triutami, Dwinisari Tunggal Mutika, Winnie Tutut Indria Permana Umrotin, Emilia Utami Sri Hastuti Wahyudi Siswanto Wahyudi Siswanto Wahyuni, Ida Tri Wahyuningtyas, Afifah Fitri Wibowo, Rachmat Ari Wibowo, Rahmat Ari Wigrahanto, Kifan Winda Dwi Astuti Windri Hermadhiyanti Wisnubroto Wisnubroto Wisnubroto, Wisnubroto Wulandari, Dian Ratri Yessi Affriyenni Yudrik Lathif Zelen Surya Minata Zidan Aqillah Rasyid Zuhairi, Aminudin Zulfia, Firda Ama ‘Ainun Sayyidah Zakiyah