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All Journal Biospecies Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Jurnal Biologi Udayana Biotropika BIOMA : Jurnal Biologi Makassar BIOEDUSCIENCE Indonesian Journal of Chemistry Menara Perkebunan Agro Bali: Agricultural Journal Jurnal Riset Biologi dan Aplikasinya JSMARTech : Journal of Smart Bioprospecting and Technology Jurnal Biosense Bioscientist : Jurnal Ilmiah Biologi Tri Dharma Mandiri: Diseminasi dan Hilirisasi Riset Kepada Masyarakat (Jurnal Pengabdian Kepada Masyarakat) BIO-CONS: Jurnal Biologi dan Konservasi Biosaintifika: Journal of Biology & Biology Education
Turhadi Turhadi
(Scopus ID: 57207793599), Universitas Brawijaya
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Decision Sciences, Operations Research & Management Education Energy Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience Public Health Social Sciences

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Journal : JSMARTech : Journal of Smart Bioprospecting and Technology

 1 
Phylogenetic construction of Green Algae Based on the rbcL Gene Aliarani Rosyidiana Putri; Galuh Arkana; Haikal Ageng Maulana; Septhyanti Aprilia Kavitarna; Rayhan Yugo Nurul Maulana; Muhammad Wisam Wira Sakti; Turhadi Turhadi; Fatchiyah Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol. 4 No. 1 (2023): JSMARTech Volume 4, No. 1, 2023
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2023.004.01.25

Abstract

Chlorophyta (green algae) is one of the algae that can be found in (both oceans and freshwater lakes) as well as land with temperate to dry climates. Chlorophyta or green algae can be found in oceans, freshwater lakes, temperate land, and dry climate land.  In addition, chlorophyta can also be found in semi-aquatic environments, such as rocks, moist soil, and moist tree bark. This study aims to analyze the phylogenetic relationship among chlorophyta species based on rbcL gene to classify the diversity of green algae in Indonesia. The green algae gene rbcL sequence with 20 species was obtained from NCBI. The sequences obtained were aligned with ClustalW and the mutation patterns were analyzed. The aligned sequences were made phylogenetic trees by MEGA-X with the Maximum Parsimony method and 1000 bootstrap. The total percentage of transversions that occurred was 10.75%, while the percentage of transitions was 7.85%. The construction of the phylogenetic tree shows that the chlorophyta species are grouped based on their habitat in the same clade. Clad 1 consists of genera Chlorella, Coccomyxa, and Volvox with freshwater habitats and a genus of Parachlorella with soil habitat. Clade 2 consists of genera Chlorococcum, Tetradesmus, Crucigenia, and Desmodesmus with freshwater habitats and a genus of Chlorococcum with soil habitats. Clad 3 consists of genera Ulva and Chlorella salina with marine habitat. The furthest pairwise distance analysis results were shown by Coccomyxa subellipsoidea and Sargassum schnetteri with a value of 1.18902. The kinship of the species of the Chlorophyta division based on the rbcL gene is divided into 3 clade separated by habitat. The phylogenetic tree in the Chlorophyta division shows that the rbcL gene is sensitive enough to separate among genera and can be utilized in phylogenetic studies.
Phylogenetic Analysis of UreABC Protein in Ureolytic Bacteria as Self-Healing Agent in Concrete Amalia Danti Safa Audia; Else Vilia Setiawan; Giral Baines Mora; Grace Christy; Nabila Shafa Yumna Salsabila; Firda Nuri Asyhari; Turhadi Turhadi; Fatchiyah Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol. 4 No. 2 (2023): JSMARTech Volume 4, No. 2, 2023
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2023.004.02.49

Abstract

Concrete is one of Indonesia's most widely used materials in infrastructure development because it is strong enough to withstand pressure, adaptable, and has relatively low maintenance costs. Bacteria are potential agents that can be used to close cracks in concrete. Therefore, this research is aimed to determine which bacteria can produce the enzyme urease based on constructing a phylogenetic tree, the ability to produce spores, and the characteristics of ureolytic bacteria. This study used four sequences of ureolytic bacteria that code for ureABC, namely Bacillus, Clostridium, Pseudomonas, and Enterobacter, with Micrococcus terreus as the outgroup. The four bacterial groups with outgroups were aligned and phylogeny constructed using the Neighbor-Joining (NJ) method with 1000 replication and grouped based on genetic distance in MEGA-X software. Then further screening was carried out based on the ability to form endospores and the characteristics of ureolytic bacteria. Phylogenetic analysis shows that the bacterial groups Bacillus, Enterobacter, Clostridium and Pseudomonas have a fairly close kinship, the construction is based on proteins, genus, cell shape, gram characteristics, and habitat. The ureolytic bacteria group predicted to have the highest potential as a biomaterial agent comes from Bacillus sp. and Clostridium sp. due to its ability to form endospores. Ureolytic activity is indicated by an increased pH value and urea degradation activity due to ammonification with Bacillus sp. having a pH of 6.0-8.0. In contrast, the pH value of Clostridium sp. is unknown because further research is needed in vitro.
A Virtual Inhibition of Anti-diabetic Activity of Bioactive Compounds in Harp (Sandoricum koetjape (Burm. f.) Merr.) Elvina Rashida Khairi; Rahmi Izzati; Raissa Kendra Ainiyah; Salma Wahid Marseti; Nuraini Rosyadah; Turhadi Turhadi; Fatchiyah Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol. 4 No. 2 (2023): JSMARTech Volume 4, No. 2, 2023
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2023.004.02.41

Abstract

The prevalence of type 2 diabetes mellitus (DMT2) has increased worldwide over the last 3 decades. This prompted the researchers to consider the medical benefits of plants, including harp (Sandoricum koetjape). In Indonesia, harp is a common medicinal herb used to cure fever, colic, vaginal discharge, diarrhea, and bloating. harp also contains substances like flavonoids, tannins, or quinones that have anti-diabetic properties. This study aims to determine the potential compound from the harp plant in inhibiting the breakdown of sugar using molecular docking to minimize the buildup of sugar in the blood. Bioactive compounds of harp were obtained from earlier studies and collected from KNApSAcK database. The physicochemical properties of the compounds were analyzed by using SwissADME and PASS Online. Using the CB-Dock server and the receptors α-amylase and α-glucosidase retrieved from RCSB PDB, along with acarbose as a control, the selected compounds were examined for their molecular interactions and binding affinities. Molecular interactions were visualized using Biovia Discovery Studio 2019. The result showed that three compounds were discovered to show potential as antidiabetic medicines out of the 54 active compounds that were screened using SwissADME. Those three compounds are sandorinic acid A, sandorinic acid B, and quercetin with the absolute value of free binding energy ranging from -7.2 to -9.6 kcal/mol. By targeting residues found in amylase and glucosidase, sandorinic acid A, sandorinic acid B, and quercetin have binding sites that are similar to acarbose. The three bioactive compounds quercetin, sandorinic acid a, and sandorinic acid b that are found in harp are expected to have the potential to be agents of type 2 diabetes mellitus.
Virtual Prediction of The Potency of Common Jasmine (Jasminum officinale L.) Bioactive Compounds as Anti-Aging Agents for Natural Sunscreen Fathiyah Nurul Izzah; Dawama Nur Fadlilah; Yohanna Sisilia Grace Sirait; Nandagesta Aurelia Shafa Wagmi; Abdullah Abdullah; Turhadi Turhadi; Fatchiyah Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol. 3 No. 2 (2022): JSMARTech Volume 3, No. 2, 2022
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2022.003.02.73

Abstract

UV exposure causes protein denaturation in the skin, leading to wrinkles and photoaging. Matrix metalloproteinases (MMPs) are enzymes that degrade the matrix and are associated with destruction processes like skin aging. Tyrosinase is the rate-limiting enzyme in the melanin synthesis process. We predict that Jasminum officinale L. bioactive compounds can be used as inhibitors for MMP1, MMP3, and tyrosinase. This study aims to compare the potential of bioactive compounds in Jasminum officinale L. as an inhibitor for the MMP1, MMP3, and tyrosinase receptors to prevent anti-aging. Vanillin, hydroxytyrosol, salicylic acid, 3,4-dihydroxy benzoic acid, oleoside-11-methyl ester, ursolic acid, oleanolic acid, and jasminine were retrieved from PubChem database as ligands, to dock with MMP1, MMP3, and tyrosinase as receptors that were retrieved from RCSB PDB. ADMET analysis was performed using pKCSM. Target-based virtual screening was performed using AutoDock Vina in PyRx. Visualization and interactions of amino acid residues was performed using Biovia Discovery Studio 2021. The complex structure was analyzed by molecular dynamics using the CABS-Flex 2.0 website. The oleoside-11-methyl ester compound has the highest potential as an MMP1 inhibitor, the 3,4-dihydroxy benzoic acid compound has the potential to inhibit MMP3, and hydroxytyrosol has the potential to inhibit tyrosinase involved in skin aging because it has low toxicity, highest binding affinity, and low fluctuations based on RMSF values in molecular dynamics simulations. Thus, this study indicated that bioactive compounds in common jasmine (Jasminum officinale L.) can be used as a candidate for organic sunscreen.
Phylogenetic Study of Several Parasitic Plant Species Based on The atp-1 Gene Sequence Pratama, Ardo Cahya; Karuniasari, Nadaa; Rahmadini, Agnia Fadillah; Ezra, Achmad; Hose, Victor Alvianoes Guterez; Turhadi, Turhadi; Suyanto, Eko; Fatchiyah, Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol. 5 No. 2 (2024): JSMARTech Volume 5, No. 2, 2024
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2024.005.02.57

Abstract

The distinction between parasitic and non-parasitic plants can be determined by analyzing the atp-1 gene, which plays a vital role in respiration and is known for its high mutation rate. This study analyzed the kinship of parasitic plant subclass species through the construction of a phylogenetic tree based on atp-1 gene sequences. The atp-1 gene sequences of parasitic and non-parasitic plants with a total of 29 species were obtained from NCBI. The sequences were then aligned with ClustalW and analyzed for mutation patterns. Sequences that have been aligned, phylogenetic trees were made with MEGA11 software with the Maximum Likelihood method and analyzed using the iTOL website. The sequences were analyzed for similarity and kinship with Matrix Coefficient and Haplotype Construction. The atp-1 gene proved that parasitic plants (hemiparasites) are furthermore related to non-parasitic plants compared to holoparasite parasitic plants. Besides that, the kinship of parasitic plants can be analyzed by several methods, namely matrix coefficient to measure similarity, DnaSP to analyzing haplotype, and haplotype network to find out detailed information on mutations that occur. Matrix coefficients can also be used to measure specific similarities between species. It was found that the same subclass had high similarities, for example the species Santalum album and Heisteria parvifolia with a genetic distance value of 0.00574. Meanwhile, different subclasses have low similarity, such as Cassytha filiformis and Ombrophytum with a genetic distance value of 0.07871. This study shows that the atp-1 gene is effective in analyzing the kinship between parasitic and non-parasitic plants. Hemiparasites are genetically closer to non-parasitic plants than holoparasites, with higher genetic similarity within the same subclass.
Co-Authors . Hamim . Miftahudin . PRIYONO Abdullah Abdullah Aliarani Rosyidiana Putri Althoriq, Luthfi Amalia Danti Safa Audia Amin Setyo Leksono Aminudin Afandhi Anisa Zairina Annisa Aulya Aksa Asmini Budiani Bagyo Yanuwiadi Baharuddin, Muh. Fikry Bedjo Bedjo Briliyan Natalina Sudarjayanti Cristina Mega Meyfiani Kekung Dawama Nur Fadlilah Deden Sukmadjaya Dian Siswanto Dini Astika Sari Eko Suyanto Else Vilia Setiawan Elvina Rashida Khairi Estri Laras Arumingtyas Ezra, Achmad fatchiyah . Fatchiyah Fatchiyah Fatchiyah Fatchiyah Fatchiyah Fatchiyah Fathiyah Nurul Izzah Fatma Yona, Hafidza Fauziatul Fitriyah Faza, Ahmad Muwaffiq Fifi Mar’atun Solihah Fifi Mar’atun Solihah Firda Nuri Asyhari Galuh Arkana Giral Baines Mora Grace Christy Haikal Ageng Maulana Hamim Hamim Hamim Hamim Hayati Minarsih Hayati Minarsih Hayati Minarsih Hose, Victor Alvianoes Guterez Husaini, Iin Pertiwi A Iin Pertiwi A Husaini Imron RIYADI Imron Riyadi Irfan Mustafa Karuniasari, Nadaa Kekung, Cristina Mega Meyfiani Khairunnisa Hidaya, Amira Kurniawan, Jessica Amadea Luchman Hakim Maharani, Fira Shabrina Bintang MARTIANSYAH, Irfan Masna Maya Sinta Mentari Putri Pratami Miftahuddin Miftahuddin Miftahuddin Miftahudin . Mufidah Afiyanti Muhammad Rifqi Hariri Muhammad Rifqi Hariri Muhammad Wisam Wira Sakti Mulyani, Melza Munif Ghulamahdi Muwaffiq Faza, Ahmad Nabila Shafa Yumna Salsabila Nandagesta Aurelia Shafa Wagmi Nashafi, Azizuddin Muhammad Nuraini Rosyadah Padmana, I Made Dhena Radya Palis, Christine Natalia Pratama, Ardo Cahya Rahmadini, Agnia Fadillah Rahmi Izzati Raissa Kendra Ainiyah Rayhan Yugo Nurul Maulana Riza Arief Putranto Rizka Tamania Saptari Rodiyati Azrianingsih Rodiyati Azrianingsih Salma Wahid Marseti Septhyanti Aprilia Kavitarna Serafinah Indriyani Serafinah Indriyani Setiyanto, Afif Eka Rahma Shafala Safa, Muhammad Solihah, Fifi Mar’atun Suharjono Suharjono Sustiprajitno Sustiprajitno Talitha Pangestu, Twistka Titin Andri Wihastuti Umar, Ja’far Yohanna Sisilia Grace Sirait Yuli Setiawati