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All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences BULETIN OSEANOGRAFI MARINA Jurnal Kelautan Tropis Indonesian Journal of Oceanography
Wahyuningsih, Candra
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Agriculture, Biological Sciences & Forestry Decision Sciences, Operations Research & Management Earth & Planetary Sciences Environmental Science

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Molecular Docking Studies of Marine Sulfated Polysaccharides: Exploring Green Seaweed’s Role Against SARS-CoV-2 Spike Glycoprotein Herida, Azalia Puspa; Kusumaningrum, Hermin Pancasakti; Zainuri, Muhammad; Sabdono, Agus; Subagiyo, Subagiyo; Wahyuningsih, Candra
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 29, No 4 (2024): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.29.4.567-575

Abstract

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is a virus responsible for the infectious disease of COVID-19 (Coronavirus Disease 2019), whose development is still being monitored. One way to deal with the virus’s development is by searching for natural-based medicines that prevent and treat SARS-CoV-2 infection. The abundant biodiversity can be used as a source of treatment. Among many natural resources, seaweed is one of the natural resources rich in bioactive components. Sulfated polysaccharide is one of the potential bioactive compounds in seaweed because it has antiviral effects and the potential to treat SARS-CoV-2. This research aims at increasing the potential of Karimunjawa green seaweed sulfate polysaccharides for antiviral capabilities in SARS-CoV-2 through molecular docking. This research began with identifying the morphology of Karimunjawa seaweed. Identify the components of sulfated polysaccharide compounds based on literature studies according to the species that have been identified. Analysis of the antiviral ability of SARS-CoV-2 based on its binding ability to the SARS-CoV-2 target protein through a molecular docking computational program and testing drug compounds using the Lipinski rule. Based on the research results, it is known that the seaweed obtained from Karimunjawa based on morphology, belongs to the genus Kappaphycus. Molecular docking with a ligand and spike glycoprotein (6LZG) resulted in the hexadecanoic acid compound having a binding free energy of -5.3 kcal.mol-1, which was the compound with the lowest yield compared to other test compounds. The prediction of the physicochemical properties of all test compounds fulfills Lipinski's five rules and has the potential to be used as medicinal compounds.
Molecular Characterization of Nannochloropsis sp. Based on tufA Genetic Marker and Potential Test of Nannochloropsis sp. as a Cadmium (Cd) Heavy Metal Bioremediation Agent Setyowati, Sulis; Kusumaningrum, Hermin Pancasakti; Zainuri, Muhammad; Suprihadi, Agung; Doktorasaintifika, Heradita Kaniaazzahra; Herida, Azalia Puspa; Wahyuningsih, Candra; Jannah, Siti Nur; Wijanarka, Wijanarka
Buletin Oseanografi Marina Vol 14, No 1 (2025): Buletin Oseanografi Marina
Publisher : Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/buloma.v14i1.66422

Abstract

Cadmium (Cd) heavy metal pollution not only affects aquatic ecosystems but also has toxic effects on human health. Bioremediation using microalgae Nannochloropsis sp. is considered more economical and sustainable for overcoming heavy metal pollution. This study aims to molecular characterization of Nannochloropsis sp. with tufA gene markers, determine the effect of different Cd concentrations on the growth and morphology of Nannochloropsis sp. and the ability of Nannochloropsis sp. to absorb Cd concentrations. The methods used include DNA isolation, quantitative and qualitative DNA analysis, amplification of tufA gene, sequencing result analysis, phylogenetic tree analysis, and bioremediation test. The results of molecular characterization showed that Nannochloropsis sp. has similarities with N. oceanica strain BR2 plastid (CP044614.1) with 60% bootstrap value. Nannochloropsis sp. grew at different Cd concentration (0, 2, 4, and 6 ppm) but optimal at 0 ppm Cd concentration. Morphology of Nannochloropsis sp. showed morphological differences in the cell structure. The cell was broken and the color turned increasingly clear. Different concentrations of Cd metal on Nannochloropsis sp. growth significantly affected the decline in Nannochloropsis sp. growth. Nannochloropsis sp. has the potential to absorb heavy metal Cd with an efficiency that increases as the concentration reaching 62.6% at 6 ppm. It can be concluded that molecular characterization using the tufA marker was effective in showing that Nannochloropsis sp. had closed relation with N. oceanica strain BR2 plastids. Cadmium (Cd) exposure significantly reduced growth and caused cell damage, while Nannochloropsis sp. effectively adsorbed Cd and lowering Cd levels by 3.76 ppm.
Molecular Characterization of Microalgae Thalassiosira sp. Based on Genetic Marker tufA and Potential Test for Bioremediation of Heavy Metal Lead (Pb) Izzudin, Maulana Zidan; Kusumaningrum, Hermin Pancasakti; Zainuri, Muhammad; Nurhayati, Nurhayati; Jannah, Siti Nur; Wahyuningsih, Candra; Herida, Azalia Puspa; Doktorasaintifika, Heradita Kaniaazzahra
Jurnal Kelautan Tropis Vol 28, No 1 (2025): JURNAL KELAUTAN TROPIS
Publisher : Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jkt.v28i1.25463

Abstract

Heavy metal lead (Pb) pollution in aquatic environments poses a serious threat to aquatic ecosystems and human health. The microalga Thalassiosira  sp. has potential as a bioremediation agent for heavy metals; however, further studies are needed to maximize its capability. This study aims to molecularly characterize Thalassiosira  sp. using the tufA gene, evaluate the effects of Pb on growth and cell morphology, and assess its Pb uptake efficiency. Methods included DNA isolation, phylogenetic analysis, growth measurement using a hemocytometer, Pb uptake testing via ICP-OES, and cell morphology analysis. Results showed that the tufA gene could molecularly characterize Thalassiosira  sp., with a phylogenetic similarity of 99.53% to Conticriba weissflogii (MH571875.1). Pb significantly inhibited growth at concentrations of 0.03 ppm and 0.05 ppm and caused cell aggregation and pigment degradation at higher concentrations (2 ppm). This microalga exhibited the highest Pb uptake efficiency at lower concentrations (0.03–0.05 ppm), reaching 100%, while at 2 ppm, the efficiency decreased to 40%. This study highlights the potential of Thalassiosira  sp. in remediating Pb, providing a foundation for the development of microalgae-based biotechnological applications.
Sebaran Nitrat dan Ammonium di Wilayah Mangrove Mojo, Kabupaten Pemalang Parry, Markus Julio; Zainuri, Muhammad; Indrayanti, Elis; Lukman, Annisa Aulia; Jihadi, Muhammad Shulhan; Wahyuningsih, Candra
Indonesian Journal of Oceanography Vol 7, No 3 (2025): Indonesian Journal of Oceanography
Publisher : University of Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ijoce.v7i3.26529

Abstract

Wilayah Mojo terletak di pantai utara Pulau Jawa tepatnya di Kabupaten Pemalang, yang merupakan daerah potensial dan memiliki  kawasan mangrove strategis yang berperan penting dalam ekowisata, produksi tambak, dan keseimbangan ekosistem pesisir. Di tengah tingginya aktivitas antropogenik seperti industri, pelabuhan, pemukiman, dan pertanian yang berdampak pada peningkatan konsentrasi nutrien, penelitian ini penting untuk dilakukan dengan tujuan mengidentifikasi konsentrasi dan sebaran horizontal nitrat dan ammonium sebagai indikator kualitas perairan. Sampel diambil dari 14 stasiun yang mewakili empat daerah yaitu laut, pantai, sungai, dan laguna. Nitrat dianalisa dengan metode reduksi cadmium (SNI 6989.79:2011) menggunakan spektrofotometer UV-Vis dengan panjang gelombang 543 nm. Analisa ammonium dengan metode oksidasi (SNI 06-6989.30-2005) menggunakan spektrofotometer UV-Vis pada panjang gelombang 640 nm. Hasil penelitian menunjukkan konsentrasi tertinggi berada pada daerah sungai yaitu nitrat dengan kisaran nilai antara 0,355–1,608 mg/L dan ammonium dengan kisaran nilai antara 0,029–0,056 mg/L, dan secara perlahan mengalami penurunan ke arah laut mengikuti pola arus. Hasil penelitian diharapkan dapat menjadi masukan dalam penentuan strategi pengelolaan perairan yang efektif dan berkelanjutan guna mengantisipasi gangguan pada kualitas perairan, menjaga kelestarian ekosistem mangrove dan mendukung kesejahteraan masyarakat pesisir.
Co-Authors Agus Sabdono Doktorasaintifika, Heradita Kaniaazzahra Elis Indrayanti Herida, Azalia Puspa Hermin Pancasakti Kusumaningrum Izzudin, Maulana Zidan Jihadi, Muhammad Shulhan Lukman, Annisa Aulia Muhammad Zainuri Nurhayati Nurhayati Parry, Markus Julio Siti Nur Jannah Subagiyo Subagiyo Sulis Setyowati, Sulis Suprihadi Wijanarka Wijanarka