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All Journal BIOTROPIA - The Southeast Asian Journal of Tropical Biology Biosaintifika: Journal of Biology & Biology Education Narra J Biosaintifika: Journal of Biology & Biology Education
Dafip, Muchamad
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Health Professions Immunology & microbiology Medicine & Pharmacology Public Health Veterinary

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Biochemical and Histopathology Analysis of Liver Damage in Hypercholesterolemic Rats Induced by Tomato Extract Iswari, Retno Sri; Dafip, Muchamad; Rifa'i, Muhammad
Biosaintifika: Journal of Biology & Biology Education Vol 12, No 3 (2020): December 2020
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v12i3.23337

Abstract

Hypercholesterolemia is a condition caused by high cholesterol consumption. Tomatoes is well known has cholesterol-lowering effects. However, high consumption of tomato shall be concerned especially prooxidant potential that may damage the organ, especially in liver. This study aims to understand the effect of hypercholesterolemic and tomato administration to the rat’s liver, which is monitored using aspartate transaminase (AST), alanine transaminase (ALT) and histological condition. A total 24 of 12-weeks-old male-rats divided into 4 groups, equally. The K1 as normal group consist of placebo-treatment rats; K2 group as hypercholesterolemia group induced with high-cholesterol diet and 2 ml of cholesterol; K3 group was hypercholesterolemia rats treated with 20 mg of atorvastatin; and the last is K4 group was cholesterol rats supplemented with 16 mg/ day of tomato extract. All samples were treated for 60 days. The highest levels of AST and ALT level was 76.39 U/L and 45.40 U/L, respectively, was found in K2. Then, K4 is not significantly different from K3 and K1 and significantly different from K2. The scoring results showed that all groups experienced damage in the form of parenchymal degeneration, fat degeneration and necrosis. From this study it can be concluded that tomato extract gives a protection to the liver from cholesterol-oxidation damage effect. The updating information about how tomato inhibite liver fattening. The liver condition probably can be considered as biomarker-related hypercholesterolemia and developed a diagnostic marker to prevent increases metabolic disorder in community.
Dietary Steamed Tomato Inhibits Hyper-production of Inflammatory Markers and Enhance miR-29b-3p Expression in Atherosclerosis Rats Dafip, Muchamad; Iswari, Retno Sri; Kartika, Aprilia Indra; Reki, Winarto; Gasem, Muhammad Husein; Fitria, Meutia Srikandi
Biosaintifika: Journal of Biology & Biology Education Vol. 16 No. 1 (2024): April 2024
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v15i1.782

Abstract

Atherosclerosis is triggered by cholesterol accumulation in endothelial layers that induces the production of inflammatory cytokines, including TNF-α, IL-6, and IL-10. This condition disrupts microRNA homeostasis like miR-29b-3p, generally maintaining artery health. Steamed tomatoes contain higher antioxidant properties than raw, which might be better against atherosclerosis. However, its influence on inflammation and miR-29b-3p balance remains unclear. This study aims to elucidate the effect of steamed tomatoes on the TNF-α, IL-6, and IL-10 levels and miR-29b-3p expression under atherosclerosis conditions. Sprague Dawley male rats were equally divided into K1 group of healthy rats given a placebo; K2 group was atherosclerosis rats induced with 2 m of cholesterin/ 200 g/KgBW per day, then K3 and K4 groups were atherosclerosis rats supplemented with 20 mg/ 200 g/KgBW per day of atorvastatin and 16 mg/ 200 g/KgBW per day of steamed-tomato extract for 60 days. Steamed tomato decreases cytokine level in the K4 group and significantly differs from all groups (p < 0.050). This study showed that increased proinflammatory cytokine, including TNF-α and IL-6, is hypothetically involved in plaque formation and lamina layer destruction in endothelial. Steamed tomato supplementation also significantly increases miR-29b-3p expression to 0.98 ± 0.33 log10 fold change higher than K2 and K3 (p = 0.000). This study demonstrated the potential of steamed tomatoes to improve dyslipidemia, atherosclerosis-related inflammation, and miRNA homeostasis. This research provides additional knowledge regarding determining the expression of miR-29b-3p, which has the potential to be developed as a diagnostic or therapeutic target.
Research trends in microRNA profiling as a biomarker for lung adenocarcinoma via liquid biopsy: A bibliometric analysis Kartika, Aprilia I.; Dafip, Muchamad; Wijayanti, Nastiti; Heriyanto, Didik S.; Haryana, Sofia M.; Taroeno-Hariadi, Kartika W.
Narra J Vol. 5 No. 1 (2025): April 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i1.1372

Abstract

Research related to the development of diagnostic biomarkers in lung adenocarcinoma in various countries is important. Research on microRNA as a biomarker in lung adenocarcinoma varies depending on the population, specimen, and technology used for profiling and validation. The aim of this study was to map and analyze bibliometric data of publications related to the topic of microRNA as a candidate biomarker in lung adenocarcinoma and to determine any potential research gaps. A total of 8,506 articles were collected from Crossref, Google Scholar, Semantic Scholar, PubMed, and Scopus databases using Harzing's Publish or Perish platform. A systematic search was conducted using four keywords: “profiling,” “validating,” “microRNA,” and “lung adenocarcinoma,” and synonyms of these keywords based on the MeSH on NCBI. The data extraction process followed the chart from PRISMA-P. The article’s elimination was conducted using Mendeley Desktop and then was analyzed based on the authors' keywords using VOSviewer and Biblioshiny. A bibliometric analysis of 692 relevant articles identified four primary research clusters: (1) microRNA (19 keywords), which highlights its potential as a biomarker for early detection and diagnosis; (2) lung adenocarcinoma (18 keywords), reflecting advancements in lung cancer research; (3) liquid biopsy (19 keywords), emphasizing the growing interest in non-invasive diagnostic methods; and (4) bioinformatics (nine keywords), underscoring the role of computational approaches in transcriptomic analysis. As a primary topic, microRNAs have become a focal point of research for diagnosing lung cancer across various stages and as biomarkers for cancer cell proliferation, invasion, migration, and metastasis. Numerous studies have demonstrated the successful application of microRNAs in lung cancer diagnosis in the last decade, although the reported types of microRNAs are inconsistent. Therefore, further research on this topic should be continuously conducted, particularly to validate the types of microRNAs and the types of environments that influence them.
Characterization and Evaluation of Tobacco Stem Waste Liquid Smoke as an Eco-Friendly Tofu Bio-preservation Purwantisari, Susiana; Rasyid, Rido Baharudin Ar; Wardana, Tegar Pratama Kayong; Arfieta, Frisca; Wibisono, Shafa’ Khairunnisa; Jaya, Myra Ivana Yulia; Dafip, Muchamad
Biosaintifika: Journal of Biology & Biology Education Vol. 17 No. 3 (2025): November 2025
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v17i3.21552

Abstract

Tofu preservation often uses unsafe chemicals, especially formaldehyde, that trigger health problems in humans. Therefore, it is necessary to develop preservation methods that are both effective and safe for human health. Liquid smoke derived from tobacco stem waste is well known to contain antioxidant and antimicrobial properties that may be suitable for use as a preservative compound for tofu. This study aims to evaluated the potential of tobacco stem liquid smoke as a natural preservative by analyzing its chemical profile, antimicrobial efficacy, and impact on tofu characteristics. Tofu samples were soaked in 0%, 5%, and 15% liquid smoke solutions and stored at room temperature for 24 hours. GC-MS analysis confirmed the presence of key compounds: phenolics (51.21%), fatty acids (30.82%), and ketones (17.96%). The treatment significantly improved preservation metrics, reducing the microbial load by up to 81% and lowering the pH to 5.1. The moisture content was reduced while protein levels were proportionally maintained. The 15% concentration provided the highest antimicrobial effect, enhanced aroma, and imparted a distinctive smoky flavor, yet the treatment was preferred by panelists for its better preservation of original color and soft texture. These findings highlight the potential of tobacco stem liquid smoke as a natural, low-cost preservative for tofu, promoting the valorization of biomass waste into value-added products.
CHARACTERIZATION OF MICROBIAL DIVERSITY AND FATTY ACID COMPOSITION IN THE INTESTINE OF HEALTHY DOMESTIC DUCKS : MICROBIAL COMMUNITY AND FATTY ACIDS PROFILE IN DUCKS INTESTINE Susanti, R; Rahayu Utami, Nur; Dafip, Muchamad
BIOTROPIA Vol. 33 No. 1 (2026): BIOTROPIA Vol. 33 No. 1 January 2026
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11598/btb.2026.33.1.2451

Abstract

ARTICLE HIGLIGHTS- Healthy duck gut shows rich bacterial diversity dominated by Firmicutes.- Duck intestine is enriched in saturated fatty acids compared to the feed.- Short chain fatty acids in duck intestine greatly exceed those in the feed.- Genera Lactobacillus and Ruminococcus are key markers of duck gut health.- Palmitic, stearic, and vaccenic acids emerge as major intestinal lipids.ABSTRACTFatty acids exhibit antibacterial properties and serve as metabolic substrates for intestinal bacteria, shaping the composition of the microbiota and the synthesis of microbial metabolites. This study aimed to analyze the duck intestinal microbiota community and its fatty acid profile. This study utilized 25 healthy domestic ducks (Anas platyrhynchos) sourced from an intensive laying farm in Central Java, Indonesia. An exploratory observational research design was employed to analyze data obtained from this study. The intestinal bacteria of duck samples were analyzed using Next-Generation Sequencing (NGS), and fatty acid components using Gas Chromatography–Mass Spectrometry (GC-MS). Duck feed samples were analyzed for nutritional composition using proximate analysis and fatty acid composition using GC-MS. The Simpson and Shannon indices revealed rich microbial diversity in the duck intestine. The abundance of bacteria was dominated by several phyla, such as Firmicutes (82.58%), Actinobacteria (12.25%), and Bacteroidetes (4.27%). The Firmicutes/Bacteroidetes ratio was 19.32, with the intestine containing greater proportion of saturated fatty acids (74.32%) compared to unsaturated fatty acids (33.62%). Additionally, the concentration of short-chain fatty acids (SCFAs) in the duck’s intestine was 15.72 times greater than that found in the feed. Microorganisms, including Bacteroides (2.88%), Faecalibacterium (0.16%), Prevotella (0.08%), Butyricicoccus (0.67%), Ruminococcus (2.2%), Oscillospira (0.02%), and Mucisspirillum (0.018%) are genera that produce SCFA. Bacteria capable of synthesizing medium-chain fatty acids (MCFA) were identified, namely Ruminococcaceae UGC-005 (1.85%) and Acinetobacter (0.005%). Bacteria producing saturated long-chain fatty acids (LCFA) were identified, namely Lactobacillus (12.12%), Prevotella (0.08%), and Alistipes (0.13%). Bacteria capable of producing polyunsaturated fatty acids (PUFA) metabolites including conjugated linoleic acid (CLA) and conjugated linolenic acid (CLnA) were identified, namely Propionibacterium (0.004%), Lactobacillus (12.12%), and Bifidobacterium (0.21%). In summary, the intestinal microbiota of healthy ducks exhibits considerable diversity and a high diversity index. Various bacterial genera contribute to the production of SCFA, MCFA, and LCFA, as well as the conversion of PUFA into CLA and CLnA metabolites. This baseline microbiota–fatty acid profile can guide microbiota-informed feed optimization and candidate probiotic selection to support SCFA production, gut health, and productivity, and it provides a reference for monitoring dysbiosis and evaluating dietary interventions in intensive duck production systems.
Co-Authors Aprilia Indra Kartika, Aprilia Indra Arfieta, Frisca Fitria, Meutia Srikandi Gasem, Muhammad Husein Heriyanto, Didik S. Jaya, Myra Ivana Yulia Kartika W. Taroeno-Hariadi Kartika, Aprilia I. Martien Herna Susanti Nastiti Wijayanti Nur Rahayu Utami Rasyid, Rido Baharudin Ar Reki, Winarto Retno Sri Iswari rifa'i, Muhammad Sofia M. Haryana Susiana Purwantisari Wardana, Tegar Pratama Kayong Wibisono, Shafa’ Khairunnisa