Berkala Penelitian Hayati

The content of secondary metabolites and total flavonoid levels of Miswak Wood (Salvadora persica) extract by kinetic maceration

2026-01-09T08:52:13+00:00

Miswak wood is empirically used to clean teeth, as it is known to have antibacterial activity mediated by its secondary metabolite . As a potential plant, miswak wood contains various secondary metabolite compounds, such as flavonoid terpenoid, steroid, alkaloid, saponin, and tannin. The levels and types of active compounds extracted from the extraction process depend on the nature of the solvent used. This study compares the total flavonoid levels of miswak wood with methanol, n-butanol, and ethyl acetate solvents. This study used an experimental design from an in vitro laboratory. This study uses samples of miswak wood extract extracted using the kinetic maceration method using methanol, n-butanol, and ethyl acetate solvents. Then, the extraction results will be qualitatively analyzed through phytochemical screening to see the presence or absence of flavonoid compounds, saponins, tannins, phenolics, alkaloids, terpenoids, and steroids, and quantitative phytochemical screening will be carried out to determine the level of flavonoid compounds in miswak wood extract using UV-vis spectrometry. Data analysis used non-parametric Kruskal-Wallis, followed by a post-hoc comparison test. Extract of miswak wood by kinetic maceration method showed positive for secondary metabolite compounds of flavonoids, alkaloids, terpenoids, phenolics, tannins in methanol, n-butanol, and ethyl acetate solvents, while saponins were only negative in ethyl acetate solvent. Determination of flavonoid compound levels showed ethyl acetate contained as much as 99.15 ± 8.14 mgEQ/g, then n-butanol as much as 62.08 ± 6.10 mgEQ/g, and methanol as much as 13.23 ± 7.47mgEQ/g significance test (P<0.05). Post-hoc pairwise Wilcoxon test showed significant results (p<0.05). This shows the type of solvent that influences flavonoid levels. The types of compounds that can be withdrawn by methanol and n-butanol solvents are more than the ethyl acetate solvent. The highest flavonoid levels were found in ethyl acetate solvent, and the lowest in methanol solvent.

Evaluation of Immunohistochemistry and H&E Staining for Detection of Tumor Budding in Colorectal Cancer

2026-01-09T08:47:24+00:00

Background/ Objective: Tumor budding (TB) is an established prognostic marker in colorectal cancer (CRC) and is defined as single tumor cells or clusters of up to four cells at the invasive front. While the International Tumor Budding Consensus Conference (ITBCC) recommends hematoxylin and eosin (H&E) as the standard for TB evaluation, immunohistochemistry (IHC) with pan-cytokeratin may improve detection in histologically challenging cases. The current study aims to compare TB assessment using H&E and pan-cytokeratin IHC and evaluate its association with clinicopathological parameters in CRC.

Methods: A retrospective analysis was conducted on 98 CRC cases resected between 2017 and 2022. TB was graded according to ITBCC 2016 criteria on H&E and cytokeratin-stained sections (clone AE1/AE3). Associations with clinicopathological features were analyzed using Chi-square or Fisher’s exact tests, with p ≤ 0.05 considered significant.

Results: On H&E, TB was positive in 61 cases (62.2%): Bd1 (29.6%), Bd2 (15.3%), Bd3 (17.3%). On IHC, TB was positive in 67 cases (68.4%): Bd1 (32.7%), Bd2 (19.4%), Bd3 (16.3%) (p < 0.001 for increased detection). High TB (Bd2–Bd3) correlated significantly with advanced pathological stage (p < 0.001), higher T stage (p < 0.001), lymph node metastasis (p < 0.001), vascular invasion (p = 0.002), perineural invasion (p = 0.003), and desmoplasia (p = 0.017).

Conclusion: Pan-cytokeratin IHC improves TB detection compared with H&E, especially in morphologically complex areas, and high TB is strongly associated with aggressive tumor features. Selective IHC use may enhance diagnostic accuracy and prognostic assessment in CRC.

Keywords: tumor budding, colorectal cancer, immunohistochemistry, pan-cytokeratin, H&E, prognosis

Assessment of Escherichia coliContamination in Catfish (Clarias gariepinus) Sold at Traditional Markets in Blitar, Indonesia

2026-01-16T22:06:09+00:00

Catfish is easy to cultivate and is in high demand by consumers. Traditional markets are one of the main places in Blitar for buying and selling catfish. However, catfish are susceptible to infection caused by E. coli. Therefore, the level of E. coli as an indicator of catfish hygiene in two traditional markets in Blitar needs to be studied. This research employed a descriptive method that included interviews, sampling, and testing the level of E. coli using the MPN. The result indicated the average level of E. coli contamination on catfish at Pon Market was 13.8 MPN/g, while at Templek Market was 9.13 MPN/g. Both of them exceed the threshold set by SNI 7388-2009, which stated the maximum limit for fresh fish’s E. coli level is <3 MPN/g. The average level of E. coli contamination at Pon Market is higher than Templek Market due to differences in the catfish handling by sellers after being taken from catfish cultivator. Catfish stored for longer periods in conditions of insufficient water can cause the deterioration of the catfish’s health, so that it was more easily infected by pathogens, such as E. coli. Poor equipment and environmental hygiene conditions are also factors that cause catfish to be potentially infected by pathogenic bacteria. Therefore, sellers must pay more attention to catfish hygiene and handling so that it is free from E. coli contamination. Also, the consumers should cook the catfish properly to prevent the transmission of E. coli.

Comparative Analysis of Oxygen Availability and Demand in Klojen and Kedungkandang Districts, Malang City, Using NDVI-Based Vegetation Assessment

2026-01-16T23:03:22+00:00

Urban areas face increasing ecological pressures due to growing population density, transportation, and land use conversion, which trigger environmental imbalances. This study aims to analyze the balance between oxygen availability and oxygen demand in Kedungkandang and Klojen Districts, Malang City, using the Normalized Difference Vegetation Index (NDVI) derived from Sentinel-2 imagery as the basis for estimating oxygen supply. The analysis covers the period from 2019 to 2024 and employs a quantitative spatial approach. Oxygen demand was calculated based on oxygen consumption from humans, motor vehicles, and livestock, while oxygen availability was estimated by converting NDVI values into biomass, carbon stock, and annual oxygen production from vegetation. This approach provides a comprehensive overview of the vegetative ecosystem’s capacity to support oxygen balance within urban environments. The results indicate that Kedungkandang District has higher oxygen availability compared to Klojen District due to its wider and more continuous vegetation cover. In contrast, Klojen District experiences an increasing oxygen deficit each year, driven by population growth and the dominance of built-up areas. This disparity underscores the existence of ecological imbalances among urban subregions in Malang City. If the oxygen balance is unmet, strategic expansion of urban green spaces, especially in high-deficit districts, is necessary to achieve sustainable urban environmental management.

Spatial Identification of Carbon Stock Hotspots for Urban Climate Mitigation Planning: Remote Sensing Analysis of Malang City, Indonesia

2026-01-16T23:09:28+00:00

Urban expansion in tropical cities threatens carbon storage through vegetation-to-built conversion. Malang City, Indonesia, experiences accelerating vegetation loss due to urban sprawl. Here, spatially detailed assessments linking vegetation conversion to carbon dynamics remain absent, limiting evidence-based climate governance. This study thus employs high-resolution remote sensing integrated with spatial analysis to quantify carbon stock dynamics and identify priority intervention zones in a rapidly urbanizing tropical city context. Understanding carbon loss magnitude and geographic concentration is essential for targeted interventions. Google Dynamic World satellite data were processed through Google Earth Engine and validated against ground truth. Carbon stocks were estimated with international standard and reclassified according to national greenhouse gas mitigation guidelines. Linear regression characterized temporal trends; spatial analysis identified carbon release hotspots and sequestration opportunity areas. Results show that Malang City experienced significant annual carbon stock decline, representing a considerable overall loss. Carbon release hotspots concentrated in southern and southeastern urban-fringe zones due to vegetation-to-built conversion, while sequestration areas remained in fragmented northern and eastern patches. Hotspot permanence classification identified areas requiring urgent protection and areas retaining restoration potential. Spatially-explicit hotspot identification provides municipalities with an actionable framework for climate-responsive planning and targeted mitigation. This study demonstrates method applicability to other tropical cities seeking evidence-based urban carbon policy.

Prevalence and intensity of ectoparasites in Nile Tilapia (Oreochromis niloticus) at BBI Babadan and BBI Bendogerit Blitar Regency

2026-01-16T23:16:04+00:00

The availability of high quality fish seeds is a key factor in the success of tilapia (Oreochromis niloticus) cultivation. The fry phase is particularly vulnerable to disease, especially ectoparasites that can inhibit fish growth. This study aims to analyze the prevalence and intensity of ectoparasites in tilapia seeds at the BBI Babadan and the BBI Bendogerit, located at Blitar Regency. The fish samples used were 15 tilapia fish measuring 4-8 cm, which were taken randomly from each pond in each Fish Seed Center. Examination of ectoparasites in tilapia seeds (O. niloticus) was carried out on the surface of the fish's body, including external organs such as gills and fins, under a microscope at 100x magnification. The results of the study have found 11 species of ectoparasites in the BBI Babadan and 7 species of ectoparasites in the BBI Bendogerit. The level of Trichodina sp. parasite attack on tilapia in the Babadan BBI showed the highest prevalence, with a prevalence value of 100%. The Apiosoma sp. species at BBI Babadan exhibited the highest parasite intensity, with an intensity of 23 individuals. Water quality measurements at both BBIs showed pH and NH₃ levels exceeding the established limits, potentially causing stress and deteriorating fish condition. Sustainable management is essential to suppress parasitic infections and improve the quality of tilapia fry in cultivation.

Comprehensive Review : Phytochemical and The Potential of Cocoa (Theobroma cacao L.) As An Antibacterial Agent

2026-01-17T06:20:27+00:00

Cocoa (Theobroma cacao L.) belongs to the genus Theobroma and the family Sterculiaceae. This plant is one of the leading plantation commodities in Indonesia. This review aims to discuss the potential of Theobroma cacao L. as an antibacterial by reviewing its botanical characteristics, phytochemicals, bioactivity and providing scientific evidence for future research. This review was compiled from the results of literature searches via the Google Scholar, ResearchGate, Science Direct, and Springer-Link search engines using the keywords "Cocoa Phytochemical and Antibacterial Activity", "Antibacterial activity of cocoa" and other relevant keywords. The articles obtained were selected based on inclusion and exclusion criteria and then discussed narratively. Based on several research results that have been reviewed, it is reported that the cocoa plant contains phytochemicals as groups of saponins, flavonoids, polyphenols, tannins, alkaloids, terpenoids, and steroids. These compounds are known to have antibacterial activity by inactivating microbial cell adhesins and enzymes, disrupting the transport of proteins in the inner layers of cells, cell wall polypeptides so that cell wall formation is less than perfect, damaging bacterial cell membranes and followed by the release of intracellular compounds until cell lysis occurs.

Computational Docking and Virtual Screening of Thymus vulgaris as Potential Inhibitors for Multi-Drug-Resistant Tuberculosis (MDR-TB) Target Proteins

2026-02-13T15:01:29+00:00

MDR-TB is a worldwide problem; according to the World Health Organisation (WHO), TB is the second most infectious killer after COVID-19, even above HIV and AIDS. With rising resistance to current antibiotics and limited solutions, the urgent discovery of new, effective, and affordable antibacterials with low toxicity is imperative to combat MDR-TB strains. Multidrug-Resistant tuberculosis (MDR-TB), caused by mycobacterium tuberculosis, is resistant to ethambutol (EMB), which has been widely ported worldwide. EMB resistance is caused by mutations in the embB gene, which encodes the arabinosylindoylacetylinositol synthase enzyme. The mutations are found in M306L, M3306L + E378A, M306V, and D1024N. Caryophyllene oxide, Bisabolene, and Trans-caryophyllene are essential components of the medicinal plant Thymus vulgaris. Hence, this study will introduce an in silico phytochemical-based approach for discovering novel bacterial agents, exploring the potential of a computational approach in therapeutic discovery. This study focuses on screening all these phytochemicals, Caryophyllene oxide, Bisabolene, and Trans-Caryophyllene, as a potential drug candidate to combat MDR-TB infection through a molecular docking approach.

Moreover, the interaction of amino acid analysis, in silico pharmacokinetics, compound target prediction, pathway enrichment analysis, and Molecular Dynamics (MD) simulations were conducted for further investigation. Caryophyllene oxide, Bisabolene, and Trans-Caryophyllene also showed a strong binding affinity against these mutations. in silico pharmacokinetic analysis highlights the potency as a drug candidate, showing strong Adsorption, Distribution, Metabolism, and Excretion (ADME) properties in combination with low toxicity.

(BCF) of Lead (Pb) and Copper (Cu) in Mangrove Roots as an Indicator of Heavy Metal Accumulation

2026-02-26T04:03:20+00:00

Mangrove ecosystems play a crucial role in trapping, storing, and accumulating heavy metals from surrounding waters and sediments, making them important bioindicators for environmental monitoring and conservation in coastal areas. Heavy metals such as Lead (Pb) and Copper (Cu) can accumulate in mangrove tissues, and their distribution between plant organs and sediments can be evaluated through the Bioconcentration Factor (BCF). This study aimed to assess the BCF values of Pb and Cu in mangrove roots and sediments in the Mangrove Tahura Ngurah Rai, Bali. Sampling was conducted using a purposive random sampling method at several stations representing different mangrove zones. Sediment and root samples from four mangrove speciesRhizophoraapiculata, Rhizophora mucronata, Bruguiera gymnorrhiza, and Sonneratia albawere collected during low tide. Heavy metal concentrations were measured using Atomic Absorption Spectrophotometry (AAS). The BCF values were calculated as the ratio between the concentration of heavy metals in roots and those in sediments. The results showed that all species had BCF values < 1, classifying them as excluders. The highest Pb BCF value was 1.00 in Rhizophora mucronata and the highest Cu BCF value was 1.13 in Rhizophoraapiculata. Mean Pb BCF values were higher than Cu in all species, with Rhizophora apiculata (0.65±0.22) and Rhizophora mucronata (0.64±0.33) exhibiting greater accumulation potential than Bruguiera gymnorrhiza and Sonneratia alba. Variations in BCF values were influenced by root morphology, zonation, and ion uptake ability. These findings highlight the superior potential of Rhizophoraapiculata and Rhizophora mucronata for heavy metal uptake, underscoring their role in mangrove-based phytoremediation and coastal environmental conservation

Microbial Community Dysbiosis and Functional Perturbations in Colorectal Cancer Patients

2026-03-10T15:02:29+00:00

Colorectal cancer (CRC) has a very close association with Dysbiosis, a phenomenon causing alterations in the microbiome of gut. Some of the recent research implicates that gut microbiome plays a key role in colorectal carcinogenesis, where CRC patients often displays an imbalance in gut bacteria (dysbiosis) marked by depletion of beneficial microbes and proliferation of pro-inflammatory microbial species. Aim of our study was to carry out gut microbiome profiling of CRC patients alongside publicly accessible healthy datasets to inspect changes in microbial diversity, its taxonomic shifts, and functional obstructions. We carried out 16S rRNA gene sequencing of faecal samples, assessing alpha diversity and beta diversity, and used PICRUSt2 for predicting microbial metabolic pathways and metabolites. The CRC gut microbiome showcased a significant reduction in alpha diversity, pointing out an anticipated loss of microbial richness. Taxonomic profiling revealed depletion of health-associated commensals, notably short-chain fatty acid (SCFA) producers such as Faecalibacterium, alongside an enrichment of opportunistic and potentially pathogenic genera. Functional prediction analysis indicated corresponding losses in microbial metabolic capacity: CRC samples were deficient in pathways for SCFA biosynthesis (e.g., butyrate production) and B-vitamin biosynthesis (e.g., folate, cobalamin), among other nutrient metabolism pathways, suggesting a collapse of beneficial functions. Altogether, dysbiosis linked to CRC was evidently clear in both community structure and in its function, with almost half of microbial pathways significantly altered. These findings emphasize the relevance of gut microbiome disturbances with CRC. The depletion of beneficial microbes and their metabolites in CRC patients has potential clinical implications, from using microbial signatures as non-invasive diagnostic markers to restoring microbial balance as a therapeutic strategy.