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All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences Biota Journal of Tropical Biodiversity and Biotechnology Journal of Multidisciplinary Applied Natural Science
Putri, Wahyu Aristyaning
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Energy Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics

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Functional 3D Structure Analysis of Quasispecies Variants of Hepatitis B Virus Surface and Core Protein in Advanced Liver Disease and Chronic HBV Infection Patients in Indonesia: In Silico Samuel Johanes Aldrian Mahulette; Adhisa Fathirisari Putri; Azki Afidati Putri Anfa; Yoshihiko Yano; Jajar Setiawan; Putri, Wahyu Aristyaning
Biota Vol 10 No 2 (2024): Jurnal Biota 2024
Publisher : Faculty of Science and Technology Universitas Islam Negeri Raden Fatah Palembang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19109/Biota.v10i2.21681

Abstract

Hepatitis B Virus (HBV) is an endemic virus and belongs to Hepadnaviridae family. This virus can result in variations of quasispecies due to its high rate of mutation. A quasispecies variant is a small population and develops as a result of mutation and can become a wild-type population. This research aims to study and carry out 3D modeling on 12 in-house full sequence HBV genome isolates from Indonesia and obtain predictive visualization data to become a reference for further research leading to the production of anti-virals and natural treatments for HBV. 12 in-house full HBV genome sequences obtained from previous research were used to carry out 3D modeling and structural analysis of the surface protein, core protein, and polymerase protein. Analysis was carried out in silico using programs available online. Phylogenetic analysis was carried out using MEGA11, translation of nucleotides into protein sequences using the ExPAsy Translate portal, physiochemical analysis using ProtParam portal, and functional domain testing using the MOTIF tool from GenomeNet. Then 3D modelling using Phyre2 and SWISS-MODEL. The major mutation of the S protein occurs in L21S and mutations in the C protein mainly occur in P79Q and S87G. The model for S Protein from homology structure prediction is not reliable thus it still needs more templates from experimental techniques. While C Protein structure prediction can provide information for further research in alternative natural antiviral treatment.
Expression, Characterisation and Structural Homology Modelling of Recombinant Mercuric Reductase of Streptomyces sp. AS2 Khasanah, Anis Uswatun; Putri, Wahyu Aristyaning; Rahayu, Hanum Mukti; Sembiring, Langkah; Purwestri, Yekti Asih
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 4 (2024): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.88773

Abstract

Mercury pollution poses a significant environmental challenge worldwide, prompting extensive efforts over the past two decades to combat its detrimental effects. Cloning merA from Streptomyces sp. AS2 (Accession numbers LC026157) into the expression vector pET-28c (+) marks a critical advancement in this field, necessitating further investigation into the expression and structural analysis of the resulting recombinant mercuric reductase protein. This study aimed to optimise the expression and characterise the structural MerA protein. The study involved the expression of merA from AS2 isolate in the host Escherichia coli BL21 and the measurement of mercuric reductase using SDS-PAGE. Induction of E. coli BL21 was optimized by adding IPTG concentration and incubation time. Purification of mercuric reductase was attempted using ammonium sulphate precipitation, dialysis, and column chromatography. Protein structural characterisation was conducted using computational modelling tools Swiss-Model and Phyre2. Expression of merA from AS2 isolate was successfully performed in E. coli BL21, with SDS-PAGE showing a dominant band in the 55-70 kDa range using IPTG concentration 1 and 1,2 mM and 18-hour incubation time. The specific activity of mercuric reductase was obtained at an enzyme concentration of 294.07 Unit/mg. Protein structural characterisation revealed homology with Lysinibacillus sphaericus (Swiss-Model) and similar folding to c5c1Yc, a known mercuric reductase from the same species using Phyre2. The successful expression of recombinant pET-28c (+)-MerA in E. coli BL21 offers new opportunities for bioremediation efforts targeting mercury contamination. 
Global Perspectives on Environmental Microbiome Research: Current Status and Future Directions Putri, Wahyu Aristyaning; Subiastuti, Aprilia Sufi; Wulandari, Cahyo; Rachman, Mifta Pratiwi; Sebastian, Alfino; Siregar, Abdul Rahman; Himawan, Tyas Ikhsan; Priyono, Dwi Sendi; Sofyana, Neng Tanty; Purwestri, Yekti Asih; Nugrahapraja, Husna; Wibowo, Anjar Tri
Journal of Multidisciplinary Applied Natural Science Vol. 5 No. 2 (2025): Journal of Multidisciplinary Applied Natural Science
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/jmans.2774-3047.266

Abstract

The environmental microbiome plays an important role in various ecosystems around the world, influencing nutrient cycling, disease dynamics and ecosystem stability. This bibliometric analysis provides a comprehensive overview of the current state and future directions of environmental microbiome research from a global perspective from 2009–2024. Through systematic examination of Scopus publications, 2154 documents were found. The results show a significant increase in the number of publications since 2017 and a peak in 2024. The most cited document was "The hidden world within plants: Ecological and evolutionary considerations for defining functioning of microbial endophytes" with 1887 citations and “Structure and function of the global ocean microbiome” with 1843 citations. The most productive countries in environmental microbiome research are the United States (n = 748), China (n = 533), India (n = 308), Germany (n = 172) and the United Kingdom (n = 157). Microbiome, microbial community, microfolora, microbiota, microbiology, bacteria, and bacterium are the most popular topics that will continue to develop in the future. Although the United States has published the highest total number of papers, more recent studies have predominantly been published from China, indicating shift in the centre of study from the United States to China. Insights gained from this analysis contribute to a deeper understanding of the environmental microbiome research landscape, guiding future research priorities and collaborations in the field.
Valorization of Shrimp Shell Waste: Comparative Phytochemical Composition and Bioactivity of Parapenaeus longirostris and Aristeus antennatus Zeghdoudi, Essaid; Nouar, Ahmed; Cheurfa, Mohammed; Noun, Chaimaa; Mohammadi, Imane Kouider; Putri, Wahyu Aristyaning; Domingues, Valentina Fernandes
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 31, No 1 (2026): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.31.1.8-14

Abstract

The valorization of marine by-products represents a promising approach for discovering novel bioactive compounds. This study presents a comparative phytochemical and bioactivity assessment of shrimp shell waste extracts from Parapenaeus longirostris and Aristeus antennatus species, which are prevalent on Algerian coasts. The objective of this study is to evaluate their potential as a source of biologically active compounds, with a particular focus on those compounds that possess anti-inflammatory and antidiabetic properties. The methodology entailed the extraction of chemical compounds. The subsequent procedure involved the utilization of shrimp residues, which were then subjected to a comprehensive compositional analysis. This analysis was then followed by an evaluation of their biological activity. The results obtained demonstrated the presence of biologically effective compounds, with the extracts exhibiting notable anti-inflammatory and antidiabetic activity. White shrimp (P. longirostris) was found to be particularly efficacious in both activities, showing particular promise in diabetes-related inhibition. This finding indicates the potential of valorization. It is evident that these marine by-products have the potential to serve as a promising natural resource for the development of value-added products. It is evident that these initiatives facilitate novel advancements in the domains of health and industry, thus underpinning the blue economy within the paradigm of sustainable development.
Co-Authors Abdul Rahman Siregar, Abdul Rahman Adhisa Fathirisari Putri Anjar Tri Wibowo Azki Afidati Putri Anfa Cahyo Wulandari Cheurfa, Mohammed Domingues, Valentina Fernandes Himawan, Tyas Ikhsan Jajar Setiawan Khasanah, Novita Uswatun LANGKAH SEMBIRING Mohammadi, Imane Kouider Nouar, Ahmed Noun, Chaimaa Nugrahapraja, Husna Priyono, Dwi Sendi Rachman, Mifta Pratiwi Rahayu, Hanum Mukti Samuel Johanes Aldrian Mahulette Sebastian, Alfino Sofyana, Neng Tanty Subiastuti, Aprilia Sufi Yekti Asih Purwestri Yoshihiko Yano Zeghdoudi, Essaid