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All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences BULETIN OSEANOGRAFI MARINA Jurnal Kelautan Tropis Berkala Bioteknologi Cendekia Journal of Pharmacy
Herida, Azalia Puspa
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Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Medicine & Pharmacology

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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.
Analisis Pigmen Karotenoid dan Uji Aktivitas Antibakteri Serta Karakterisasi Daerah Penanda ITS dari Nannochloropsis oculata Herida, Azalia Puspa; Kusumaningrum, Hermin Pancasakti; Kusdiyantini, Endang
Berkala Bioteknologi Vol. 3, No. 1, April 2020
Publisher : Berkala Bioteknologi

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Nannochloropsis oculata merupakan mikroalga yang umum digunakan pada pakan tambahan budidaya hewan laut. Mikroalga N. oculata mampu menghasilkan pigmen karotenoid salah satunya β-karoten berfungsi sebagai antioksidan serta senyawa bioaktif yang berpotensi sebagai agen antibakteri. Penamaan mikroalga N. oculata dari Gondol Bali hanya dilakukan berdasarkan pengamatan mikrobiologis, karakterisasi biokimia, dan ekofisiologis tetapi belum dianalisis hingga tingkat molekuler. Identifikasi molekuler mikroalga dapat dilakukan pada daerah penanda ITS (Internal Transcribed Spacer) hingga di tingkat spesies. Tujuan penelitian yaitu, menganalisis kandungan pigmen karotenoid berupa β-karoten, menguji kemampuan N. oculata sebagai agen antibakteri, serta karakterisasi molekuler N. oculata menggunakan daerah penanda ITS. Metode penelitian ini meliputi kultivasi mikroalga, analisis pigmen β-karoten, uji antibakteri kultur N. oculata, isolasi DNA menggunakan metode Doyle & Doyle, amplifikasi daerah ITS menggunakan primer ITS 4 dan ITS 5, sekuensing DNA hasil amplifikasi, analisis filogenetik melalui program BLAST, Clustal X, NJ Plot, dan MEGA 6. Hasil penelitian diketahui bahwa analisis pigmen β-karoten mengalami peningkatan kadar β-karoten selama masa kultur dan menurun pada fase stasioner. Kadar β-karoten tertinggi sebesar 0,08 µg/mL. Kultur N. oculata mampu menghambat pertumbuhan bakteri uji dengan kategori hambat sedang terhadap bakteri Gram negatif Eschericia coli dan Gram positif Staphylococcus aureus. Amplifikasi daerah penanda ITS menggunakan metode PCR menghasilkan sekuens sebesar 985 bp. Hasil BLAST menunjukkan N. oculata memiliki kemiripan sekuen sebesar 99,43% dengan N. oceanica. Penelitian ini disimpulkan bahwa N. oculata memiliki pigmen β-karoten yang dihasilkan selama masa pertumbuhan mikroalga. Kultur N. oculata yang mampu menghambat pertumbuhan bakteri uji dengan semakin banyak volume yang diberikan daya hambat yang dihasilkan semakin besar. N. oculata berdasarkan pohon filogenetik berkerabat dekat dengan sekuen referensi N. oceanica strain IMP-BG-006.
SALTED FISH PRESERVATION MENGGUNAKAN HERBS EDIBLE COATING DARI NANOPARTIKEL BAWANG PUTIH, DAUN PANDAN DAN SERAI DAPUR Doktorasaintifika, Heradita Kaniaazzahra; Nurkertamanda, Denny; Shasabila, Analies Devi; Kusumaningrum, Hermin Pancasakti; Sugiarti, Lilis; Wahyuningsih, Candra; Herida, Azalia Puspa; Hapsari, Hererapratita Aysha
Cendekia Journal of Pharmacy Vol 9, No 3 (2025): Cendekia Journal of Pharmacy
Publisher : Institut Teknologi Kesehatan Cendekia Utama Kudus

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31596/cjp.v9i3.385

Abstract

Global consumption trends show a tendency to choose natural food preservatives, especially those derived from plants, especially to avoid chemical and synthetic preservatives that are harmful to health. Nanotechnology is an important development and an efficient choice to extend the shelf life of food. This study aims to create and carry out seafood preservation using herbs edible coating from garlic nanoparticles, pandan leaves and lemongrass to determine its use as a preservative for salted mackerel and tigawaja salted fish. As a comparison, a mixture of the three ingredients. The study used four treatments where each was repeated 3 times. A hedonic test was also carried out in the form of observations of dryness, color, texture and odor of salted fish. The research method consisted of making garlic nanoparticle extract, pandan leaf extract, lemongrass extract, and a mixture of the three ingredients followed by microscopic observation. Antibacterial activity was carried out using the TPC test. The hedonic test was carried out to see the potential of consumers for the product. Furthermore, a PASS analysis was carried out to see the potential of antimicrobial compounds in the three ingredients. The results showed that the edible coating layer was made into nanoparticle form. Edible coating from pandan is most suitable for use on salted mackerel. Edible coating from garlic is most suitable for use on tigawaja salted fish. The TPC test results showed that garlic, pandan and lemongrass were able to prevent microbial growth effectively for 48-96hours and have the potential to be used as edible coating.
Co-Authors Agus Sabdono Chatarina Umbul Wahyuni Denny Nurkertamanda Doktorasaintifika, Heradita Kaniaazzahra Endang Kusdiyantini Hapsari, Hererapratita Aysha Hermin Pancasakti Kusumaningrum Izzudin, Maulana Zidan Lilis Sugiarti Muhammad Zainuri Nurhayati Nurhayati Shasabila, Analies Devi Siti Nur Jannah Subagiyo Subagiyo Sulis Setyowati, Sulis Wahyuningsih, Candra Wijanarka Wijanarka