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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Jurnal Biologi Udayana Biotropika BIOMA : Jurnal Biologi Makassar BIOEDUSCIENCE 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) Biosaintifika: Journal of Biology & Biology Education
Turhadi Turhadi
(Scopus ID: 57207793599), Universitas Brawijaya
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemistry Education Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience Public Health Social Sciences

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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.
Efektivitas Larutan Kultur Unsur Hara dengan Penambahan Agar Sebagai Media Evaluasi Padi Dalam Kondisi Toksisitas Besi Turhadi Turhadi; Miftahuddin Miftahuddin; Hamim Hamim; Munif Ghulamahdi
BIOEDUSCIENCE Vol 5 No 1 (2021): BIOEDUSCIENCE
Publisher : Universitas Muhammadiyah Prof. Dr. Hamka

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22236/j.bes/516395

Abstract

Background: Evaluation of the tolerance level of rice to iron (Fe) toxicity stress can be done using a hydroponic system in a nutrient culture solution under a controlled condition. This study aimed to obtain a nutrient culture solution that effective as a medium for evaluating the response of rice under Fe toxicity stress condition. Methods: This experiment was carried out by comparing the effectiveness of three kinds of nutrient culture media, namely Yoshida's Half-Strength solution (HSY), Yoshida's Half-Strength + 0.2% agar solution (HSYA), and Yoshida's Full-Strength + 0.2% agar solution (FSYA) using two rice genotypes, Inpara 5 (sensitive to Fe toxicity) and Mahsuri (tolerant to Fe toxicity). Leaf bronzing level, plant dry weight, and pH of nutrient culture media were observed in this experiment. Results: The results showed that the stress response as represented by the bronzing score in Inpara 5 leaves was known to be higher than that of Mahsuri in the three nutrient culture media. The decrease of root and shoot dry weight in Inpara 5 was higher than that of Mahsuri. In addition, the decrease in the pH of nutrient culture solution media without an agar addition (HSY) occurred faster than the media with the agar addition (HSYA and FSYA). Conclusion: The HSYA and FSYA media exhibited a similar pattern of pH declining but causing significant differences in growth responses between Inpara 5 and Mashuri indicating the HSYA medium is considered more efficient compared to the FSYA medium because it only requires a smaller amount of agar.
Rekaman baru Scopellaria marginata (Cucurbitaceae) dari Malang, Jawa Timur, Indonesia Estri Laras Arumingtyas; Turhadi Turhadi Turhadi; Rodiyati Azrianingsih; Mufidah Afiyanti; Mentari Putri Pratami; Briliyan Natalina Sudarjayanti; Fifi Mar’atun Solihah
Jurnal Biologi Udayana Vol 27 No 2 (2023): JURNAL BIOLOGI UDAYANA
Publisher : Program Studi Biologi, Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Udayana

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24843/JBIOUNUD.2023.v27.i02.p06

Abstract

Scopellaria merupakan salah satu genus dalam Cucurbitaceae yang hanya terdiri dari dua jenis yaitu S. diversiflora dan S. marginata. Kedua jenis tersebut belum pernah dilaporkan sebelumnya di wilayah Jawa Timur. Penelitian ini bertujuan untuk mengkarakterisasi Scopellaria marginata yang ternaturalisasi di Kota Malang, Jawa Timur. Jenis Scopellaria marginata dilaporkan sebagai rekaman baru untuk Jawa Timur dengan ciri batang memiliki rambut agak kasar (scarbid-hairy); tepi daun denticulate, rambut pada daun bagian adaksial yaitu rough-hairy dan bagian abaksial coarsely hairy; bentuk buah bervariasi, meliputi bulat (globose), oval (elliptic), dan fusiform; ukuran biji 3.0-4.4 mm, warna whitish, dan tepi distinctly square-margined. Jenis ini ditemukan merambat pada tanaman lain dan menjalar di atas permukaan tanah. Deskripsi dan persebaran jenis ini disajikan dalam tulisan ini.
In Silico Evaluation of rbcL, matK, and psbA-trnH Regions on the Genus Spatholobus (Fabaceae) Muwaffiq Faza, Ahmad; Khairunnisa Hidaya, Amira; Fatma Yona, Hafidza; Talitha Pangestu, Twistka; Shafala Safa, Muhammad; Suyanto, Eko; Turhadi, Turhadi; Fatchiyah, Fatchiyah
Jurnal Riset Biologi dan Aplikasinya Vol. 6 No. 2 (2024)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jrba.v6n2.p73-81

Abstract

Spatholobus is a genus that belongs to the Fabaceae that is known to contain various bioactive compounds and distributed across Asia, including Indonesia. However, exploration of Spatholobus in Indonesia is still rare. Therefore, DNA barcoding is used to support the exploration and conservation of Spatholobus in Indonesia. However, there is no universal marker that can be used across all plant species. In addition, there are still few studies related to DNA barcoding within the genus Spatholobus. The purpose of this study was to evaluate the rbcL, matK, and intergenic spacer psbA-trnH regions in silico that can be used as DNA barcodes for the genus Spatholobus. This study began with a sequence search on the NCBI database including the rbcL, matK, and intergenic spacer psbA-trnH genes   in the genus Spatholobus and Phaseolus coccineus as the outgroup. Each sequence was then aligned with ClustalW. Then, a phylogenetic tree was constructed using the Maximum-Likelihood (ML) with 1000× bootstrap. As a result, the rbcL, matK, and psbA-trnH regions can be used as markers for DNA barcoding in the genus Spatholobus with different specifications. The rbcL and matK can be used to distinguish Spatholobus at the genus level, while the psbA-trnH can be used to distinguish Spatholobus at the species level.
Pemetaan Spesies Asing Invasif Hydrocotyle leucocephala Cham. & Schltdl. di Kebun Raya Bogor Fifi Mar’atun Solihah; Muhammad Rifqi Hariri; Turhadi Turhadi
Bioscientist : Jurnal Ilmiah Biologi Vol 12, No 1 (2024): June
Publisher : Department of Biology Education, FSTT, Mandalika University of Education, Indonesia.

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33394/bioscientist.v12i1.10841

Abstract

The presence of undocumented alien flora threatens Indonesia’s flora richness and diversity due to unpredictable invasion risks. Hydrocotyle leucocephala is an alien flora that has been reported as invasive in Sri Lanka and Nigeria and has distributed to Indonesia. Therefore, mapping the distribution and describe the morphological of Hydrocotyle leucocephala is necessary to detect the initial introduction or further spread of this species. The data collection was carried out by exploring the Bogor Botanical Gardens. Environmental factors are measured and documented where Hydrocotyle leucocephala occurs. For observation, Hydrocotyle leucocephala was taken and their morphology described. As a results, Hydrocotyle leucocephala was spread over vak V.L, V.G, V.M, IX.D, VIII.B and parking lot near the conservation building in the Bogor Botanical Gardens. It is also known that Hydrocotyle leucocephala is a creeping herbaceous plant with glabrous stems, kidney-shaped leaves, white flowers without petals and green fruit with persistent styles.
Distribusi Jenis Asing Invasif Melothria pendula L. (Cucurbitaceae) di Kawasan Konservasi Ilmiah Kebun Raya Bogor Cristina Mega Meyfiani Kekung; Iin Pertiwi A Husaini; Turhadi Turhadi
Bioscientist : Jurnal Ilmiah Biologi Vol 12, No 2 (2024): December
Publisher : Department of Biology Education, FSTT, Mandalika University of Education, Indonesia.

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33394/bioscientist.v12i2.12369

Abstract

Melothria pendula is belong to Cucurbitaceae family and originates from America continent. Previous research reported findings of M. pendula in several regions in Indonesia, such as in Bogor Botanical Gardens (KRB) as invasive species. The appearance of M. pendula in KRB has not yet been inventoried. As invasive species, M. pendula has the potential to be a threat to collection and native plants. This research aims to report the distribution of M. pendula in the scientific conservation area of KRB and measure the abiotic factors in the locations where M. pendula was found. This research was exploratory method which was carried out by exploring and morphological characterization of M. pendula. Measurement of abiotic factors, including temperature, air humidity, light intensity, and wind speed at each site where M. pendula was found. QGIS is used to mapping the distribution of M. pendula. Based on this study showed that there were 40 individuals of M. pendula which found distributed randomly in 15 sites (VG, VD, VB, XXIVA, IIM, IIC, IIP, XVI.VII, IVF, XXIVB, IIO, XVF, XXIIA, IIK, and seedling area) in KRB. M. pendula habitats in KRB characterized by forest land cover type with temperature of 31.1 ± 0.96 ℃, air humidity of 69 ± 2.73%, light intensity 3183.9 ± 3095 lux, and wind speed 0.7 ± 0.51 m/s.
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.
DNA QR Code Using Internal Transcribed Spacer 1 (ITS1) Region of Commercial Cucumber Varieties (Cucumis sativus L.) Turhadi, Turhadi; Padmana, I Made Dhena Radya; Azrianingsih, Rodiyati
Jurnal Riset Biologi dan Aplikasinya Vol. 7 No. 1 (2025)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jrba.v7n1.p1-7

Abstract

DNA Quick Response (DQR) is an accurate, efficient, fast, and cost-effective alternative to PCR-based or other sequencing methods. DQR is the method integrated seamlessly with digital systems. The DQR could be apply as effective approach to preventing seed counterfeiting, for example in cucumber. This study aimed to identify DNA barcodes based on the ITS1 region and develop DQR for commercial cucumber varieties in Indonesia. Two cucumber varieties, namely cv. Mars and cv. Makka were used. The genomic DNA was extracted using commercial DNA purification kit. The DQR for these two cucumber varieties were developed based on experimental data from the ITS1 region. The efficiency and characterization of ITS1 region were evaluated through homology analysis using BLAST-NCBI and DQR development. The DQR of cucumber cv. Mars and cv. Makka based on ITS1 region were successfully developed. The length of the ITS1 region encrypted in the QR code was 496 bp and 437 bp for cv. Mars and cv. Makka, respectively. The A-T and G-C proportions for cv. Mars were 45.2% and 54.8%, respectively, while for cv. Makka, the A-T and G-C proportions were 42.6% and 57.4%, respectively. Our findings are valuable for genetic labeling and authentication of horticultural crops, especially cucumber.
Co-Authors . Hamim . Miftahudin . PRIYONO Abdullah Abdullah Aliarani Rosyidiana Putri 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 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 Luchman Hakim Maharani, Fira Shabrina Bintang Masna Maya Sinta Mentari Putri Pratami Miftahuddin Miftahuddin Miftahuddin Miftahudin . Mufidah Afiyanti Muhammad Rifqi Hariri Muhammad Rifqi Hariri Muhammad Wisam Wira Sakti Munif Ghulamahdi Muwaffiq Faza, Ahmad Nabila Shafa Yumna Salsabila Nandagesta Aurelia Shafa Wagmi Nashafi, Azizuddin Muhammad Nuraini Rosyadah Padmana, I Made Dhena Radya 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 Yohanna Sisilia Grace Sirait Yuli Setiawati