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INDONESIA
HAYATI Journal of Biosciences
Published by Institut Pertanian Bogor
ISSN : 19783019     EISSN : 20864094     DOI : -
Core Subject : Science, Agriculture,
Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences
HAYATI Journal of Biosciences (HAYATI J Biosci) publishes articles and short communication in tropical bioscience fields such as development, biotechnology, biodiversity and environmental issues. HAYATI J Biosci covers wide range of all life forms topics including virus, microbes, fungi, plants, animal and human. HAYATI J Biosci has been also indexed/registered in Crossref, DOAJ, CABI, EBSCO, Agricola and ProQuest.
Arjuna Subject : -
Articles 1,091 Documents
 80   81   82   83   84 
DNA Barcoding of Six Commercially Important Groupers (Epinephelidae) from Langsa, Aceh, Indonesia Fadli, Nur; Jumiati, Sri; Razi, Nanda Muhammad; Damora, Adrian; Muchlisin, Zainal A.; Dewiyanti, Irma; Ramadhaniaty, Mutia; Harnelly, Essy; Habib, Ahasan; Siti-Azizah, Mohd Nor
HAYATI Journal of Biosciences Vol. 31 No. 2 (2024): March 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.2.328-335

Abstract

Groupers are among the fish groups that are difficult to recognize due to their high morphological similarities. Therefore, molecular techniques, particularly DNA barcoding, are extensively utilized to differentiate this fish group. This study aimed to analyze and validate six grouper species belonging to the Epinephelidae family that were harvested from Langsa district waters in Aceh province, Indonesia, based on DNA barcode data. It was conducted from June to December 2021, with the fish specimens collected from fishers at fish landing sites and the fish market in Langsa City, Aceh province. A total of 22 grouper sequences belonging to six species were generated, namely Epinephelus coioides, E. bleekeri, E. malabaricus, E. erythrurus, E. sexfasciatus and Mycteroperca poecilonotus (formerly Epinephelus poecilonotus). Genetic distance within these species ranged from 0.10 to 0.73% (average: 0.40%). Notably, E. malabaricus and E. coioides exhibited the closest genetic kinship (4.07%), while E. sexfasciatus and M. poecilonotus displayed the greatest genetic distance (19.33%). This study provides the first DNA reference for grouper in Langsa district, Indonesia, with significant implications for future sustainable grouper management.
The Study of Exogenous Auxin and Cytokinins in Embryogenesis and Fiber Genes Expression during In Vitro Regeneration of Cotton (Gossypium hirsutum L.) Mufadilah, Mitha Aprilia; Thamrin , Nurhaliza; Puspito, Agung Nugroho; Ubaidillah, Mohammad
HAYATI Journal of Biosciences Vol. 31 No. 3 (2024): May 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.3.517-529

Abstract

The efficiency of regeneration media, based on the morpho-cytochemical response and embryogenesis gene expression of widely cultivated cotton in Indonesia (Gossypium hirsutum L.), needs to be studied further. This study's objectives are to identify the effect of 2,4-D and IBA hormones on the morphology and induction of cotton callus; to determine the effect of regeneration media on the morphology, cytochemical, and gene expression of cotton plant during embryogenesis. This study was conducted by inducing cotton callus on MS0 medium, MS Basal + 0.1 mg/L 2,4-D and MS Basal + 0.1 mg/L IBA. The best callus induction results were regenerated on the regeneration media, namely M1 (MS Vitamin + 0.01 ppm 2,4-D + 0.3 ppm IBA + 0.5 ppm Kinetin), M2 (MS Vitamin + 0.01 ppm 2,4-D + 0.5 ppm IBA + 0.5 ppm Kinetin), M3 (MS Vitamin + 0.00 ppm 2,4-D + 0.3 ppm IBA + 0.5 ppm Kinetin), and M4 (MS Vitamin + 0, 00 ppm 2,4- D + 0.5 ppm IBA + 0.5 ppm Kinetin). The embryogenesis gene expression was observed. The best morphological results for callus induction were obtained on MS Basal + 0.1 mg/L 2,4-D medium with a compact and white callus, indicates high embryogenic and regeneration ability. The highest percentage of regenerated callus parameters was found in M2 media and further confirmed by cytochemical characterization. Embryogenesis genes expressed were GhSERK1, GhSERK2, LEC, GhWUS, and GhWOX11. Other fiber-related genes GhMYB25-like, GhHD-1, and F3H were also expressed during the embryogenesis.
Genomics and Phylogeny of Rhodotorula glutinis and Rhodotorula kratochvilovae Isolated from the Northern Peruvian Andes Vásquez Villalobos, Víctor Javier; Hidalgo-Arteaga, Angely Meryl Alessandra; Sosa-Becerra, Roxana Beatriz; Soriano-Bernilla, Bertha Soledad; de Moura Ferreira, Maurício Alexander; Batista da Silveira, Wendel
HAYATI Journal of Biosciences Vol. 31 No. 4 (2024): July 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.4.793-802

Abstract

Genomes of oleaginous yeast strains Rhodotorula glutinis CON-5 and Rhodotorula kratochvilovae POR-3, isolated from areas in the northern Peruvian Andes using SPAdes, were sequenced and assembled applying Illumina and de novo. Genomes of 20,515,696 and 20,738,185 bp, respectively, were determined. From the structural and functional annotations, the Basidiomycota phylum showed a similarity of 76.8% and 86.5% with 6,976 and 8,124 pairs of proteins in both yeasts respectively, with homologues in the UniProt data bank. Using OrthoVenn, a relationship between both yeasts was obtained from 450 orthologous groups. Likewise, the above-mentioned yeasts and R. toruloides (oleaginous Basidiomycota) showed 1,574 orthologous groups, indicating a good relationship. Construction of phylogenetic trees of genes encoding metabolic enzymes was also carried out, based on the ITS sequences which showed that CON-5 and POR-3 have a greater relationship with R. graminis. Their phylogenetic relationship was ascertained and determined that the enzymes involved in the metabolism of CON-5 and POR-3 are related to each other. It was also found that the protein sequences of the Basidiomycota phylum differ from Ascomycota. The study showed functional evidence regarding the lipid accumulation phenotype, an important aspect in the context of obtaining lipids or oleochemicals.
Sequence-Structure Based Comparison of Structurally Homologous Thermophilic and Mesophilic Polyethylene Terephthalate (PET) Hydrolases Hasan, Khomaini; Ulfah, Maria; Nurhayati, Niknik; Sabbathini, Gabriela Christy; Wulandari, Sri Rezeki; Putra, I Gede Eka Perdana; Helianti, Is
HAYATI Journal of Biosciences Vol. 31 No. 2 (2024): March 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.2.348-356

Abstract

Protein structure has a direct impact on thermostability. Deviations in the primary sequence can affect structural changes, leading to alterations in thermostability properties. However, the molecular basis of protein thermostability is unspecified; thus, elucidation of key factors that role particular protein thermostability is required when engineering proteins to be thermostable. To address this challenge, the amino acid composition, hydrophobicity/hydrophilicity ratio, cysteine bridges, and intrinsic features of two structurally homologous but different thermostability, poly(ethylene terephthalate) hydrolase (PETase) were compared. According to the findings, thermostable and thermolabile PETases have similar folds, compactness, and disulfide bridges. Interestingly, an abundance gap of aromaticity, hydrophobic cluster area, polar amino acid and hydrogen bond network compositions demonstrated dominant trends of variations for both PET hydrolases, indicating a pivotal role of these features in the thermostability of PET hydrolase. Furthermore, increased hydrophobic amino acid frequency in the inner surface of thermostable proteins contributed significantly to thermostability by forming more internal hydrophobic interactions and a less hydrophobic patch. There are no consistent trends in insertions and deletions between both PETases. Taken together, these observations demonstrate that hydrophobicity and hydrogen bond networks are essential factors in thermostability of thermostable PETase.
Diversity of 17 Genotypes of Taro Based on Anatomy and Nutritional Value of Tuber Cahyanti, Lutfy Ditya; Didy Sopandie; Edi Santosa; Heni Purnamawati
HAYATI Journal of Biosciences Vol. 31 No. 3 (2024): May 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.3.465-473

Abstract

Indonesia is one of the countries with the greatest diversity of taro variety, while the study of taro's morphology and nutritional characteristics is limited. The aim of this study was to evaluate the anatomical of plant and nutritional value of taro tuber. This research observed fourteen genotypes of Colacasia esculenta (7 Eddoe types, 7 Dasheen types) and 3 Xanthosoma genotypes. In three blocks of replications, the eddoe and Xanthosoma genotypes were cultivated using cormel and the dasheen genotypes with sucker. Plant anatomy (leaf, stem, and root) and tuber nutritional characteristics were analyzed. From this research, explained that stomata and epidermis number, length from stomata and epidermis, number leaf epidermis, length of leaf and stem epidermis, also length of root epidermis, endodermis, cortex, and stele among 17 genotypes of taro were statistically different. The diversity of taro based on the nutrition content of tuber between 17 genotypes of taro was considered high, as represented by water, ash, fat, protein, carbohydrate, energy, and glucomannan, which were statistically different.
Extract of Red Okra Pod (Abelmoschus esculentus L. Moench) Chemoprevents N-Methyl-N-Nitrosourea-Induced Kidney Proximal Tubular Cells Damage Achhlam, Divany Hunaimatul; Wahyuningsih, Sri Puji Astuti; Hapsari, Lukiteswari Dyah Tri; Soepriandono, Hari; Dewi, Firli Rahmah Primula
HAYATI Journal of Biosciences Vol. 31 No. 6 (2024): November 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.6.1061-1070

Abstract

N-Methyl-N-Nitrosourea (MNU) is a compound that induces oxidative stress resulting in high levels of oxidants and damage to body cells. Red okra contains polyphenol and flavonoid active ingredients as antioxidants. This study aims to analyze the effect of ethanol extract of red okra pods (ROPE) on oxidant levels, antioxidant enzymes, and damage to rat kidney proximal tubule cells due to NMU. This study used 30 rats divided into six treatment groups, namely CN (normal), N (negative control; MNU 50 mg/kg BW), P (positive control; MNU and MTX 50 mg/kg BW), T1 (MNU and ROPE 50 mg/kg BW), T2 (MNU and ROPE 100 mg/kg BW), and T3 (MNU and ROPE 200 mg/kg BW). The treatment was carried out on all groups after eight weeks. The results indicate that malondialdehyde (MDA) and nitrogen oxide (NO) decrease with the ROPE treatment. The glutathione reductase (GSH) activity as an antioxidant enzyme increased T1 and T2, while glutathione peroxidase (GPx) showed an increase in T2 and T3. Furthermore, the biochemical marker of the rat kidney showed lower blood urea nitrogen (BUN) and creatinine (Cre) levels in all treatment groups. Then, the repair of damaged proximal tubule cells showed an increase in normal cells and lower swollen cells; however, there was a degradation in necrotic cells in T2 and T3. It can be indicated that the ROPE can act as an antioxidant that can reduce MDA and NO levels, increase GSH and GPx levels, and reduce damage to proximal renal tubule cells due to MNU.
Cloning and Production of Antigen 85A Mycobacterium tuberculosis for Diagnostic Latent Tuberculosis: a Preliminary Study Agus, Rosana; Sjafaraenan; Samara, Yulianti; Massi, Muhammad Nasrum
HAYATI Journal of Biosciences Vol. 31 No. 2 (2024): March 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.2.374-381

Abstract

The main challenge in the management of Tuberculosis (TB) is diagnosing quickly and accurately, especially Latent Tuberculosis Infection (LTBI). LTBI detection was carried out using the Tuberculin Skin Test (TST) and Interferon Gamma Release Assay (IGRA). In TB endemic areas, these two examinations have limitations, so current research is directed at finding specific antigens for the diagnosis of LTBI. One of the potential proteins is Antigen 85A (Ag85A) Mycobacterium tuberculosis (Mtb) encoded by Fibronectin-binding protein A (FbpA). The Ag85 complex induces the proliferation of T-cells and interferon-gamma in most healthy individuals infected with Mycobacterium tuberculosis, Mycobacterium leprae, and BCG-vaccinated mice, making it a potential antigen. This study aims to clone and produce recombinant protein Ag85A from Mtb in Escherichia coli BL21. The methods used were ligation to the pET-32a expression vector, transformation to Escherichia coli BL21, and production of protein by IPTG induction. Characterization of recombinant clones by colony PCR and sequencing. The results obtained were that the fbpA gene isolated from Mtb clinical isolate had been amplified, and the PCR product was 900 bp. The production of Antigen 85A has been successfully carried out and produces 44 kDa.
Histological and Molecular Evaluation of the Antiproliferative Activity of Allium ampeloprasum Water Extract Against Oral Mucosa Cell Line (Gingival Cancer) Alwan, Maryam Hameed; Hameed, Zainab; Mandala, Satria
HAYATI Journal of Biosciences Vol. 31 No. 5 (2024): September 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.5.829-835

Abstract

Gingival carcinoma is a malignant neoplasm affecting the oral mucosa and is associated with significant morbidity and mortality. Allium ampeloprasum var. porrum water extracts have gotten a lot of attention because of their bioactive components, such as polyphenols, flavonoids, and alkaloids, which have a variety of pharmacological activities, including antiproliferative actions. This study aimed to evaluate the histological and molecular effects of Allium ampeloprasum (leek) water extract on the proliferation of the murine gingival cancer cell line. Histological evaluation was conducted to examine morphological changes induced by extract treatment. Molecular mechanisms underlying the observed histological changes were investigated using real-time polymerase chain reaction (PCR). Expression levels of key genes associated with cell proliferation and apoptosis were assessed. Histological findings revealed a dose-dependent decrease (100, 50, 25, 12.5, and 6.25 µg/ml) in cell density and altered cell shape in the treated cell line. Also, the percentage of inhibition for the oral mucosa cell line was high, with a significant P of 0.006, in the treated group compared to the control group. Additionally, water extract has an IC50 value of 61 g/ml. The P53 fold increment of gene expression is 0.6, which means the expression level in the experimental condition is 60% higher than the control. This study provides evidence for the potential antiproliferative activity of Allium ampeloprasum water extract on the oral mucosa cell line. The observed histological changes, coupled with the modulation of key genes involved in proliferation and apoptosis, suggest that leek water extract may have therapeutic implications in managing oral cancer.
Slow-release Fertilizer Application on Silk (Falcataria moluccana Miq.) and Rice (Oryza sativa L.) Plant Growth and Yield in Agroforestry System Madani, Hilmi Naufal; Wijayanto, Nurheni; Hartoyo, Adisti Permatasari Putri; Solikhin, Achmad
HAYATI Journal of Biosciences Vol. 31 No. 4 (2024): July 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.4.750-767

Abstract

The aim of this experiment is to evaluate the impact of chitosan-NPK slow-release fertilizer (CS-NPK SRF) on the germination and growth of silk tree and rice in different planting patterns, as well as to assess the nutrient release rate of the SRF. The germination test followed a complete randomized design, incorporating a single factor (fertilizer type), namely no fertilizer (F0), SRF CS 0.5% weight 0.03 g (F1), SRF CS 0.5% 0.01 g (F2), SRF CS 0.7% 0.03 g (F3), SRF CS 0.7% 0.01 g (F4), and conventional NPK fertilizer (F5). The growth test utilized a 2-factor split-plot design, with the primary factor being the planting pattern (sengon/rice monoculture-SM/RM and sengon-rice agroforestry-AF) and the second factor being the fertilizer type. Results indicate that F2 and F4 yielded the highest germination and growth values in both plants, although not significantly different from F0. These findings suggest that CS-NPK SRF has the potential to enhance plant growth. The AF pattern exhibited lower growth compared to SM/RM, attributed to plant competition. CS-NPK SRF demonstrated a slower nutrient release (47.65% N; 85.01% P; 31.80% K) compared to conventional fertilizers. This slow release could potentially reduce nutrient loss to the environment while enhancing plant nutrient absorption.
Quantile Normalization for High Throughput Circulating MicroRNA Expression Study using TaqMan® Low Density Array Panels: Supporting Evidence Ahmad, Azmir; Mohamed, Syarah Syamimi; Tumian, Afidalina; Tolos, Siti Marponga; Sivanesan, Vijaya Mohan; Leman, Wan Ishlah; Abdullah, Kahairi; Mohamad, Irfan; Wan Zainon, Wan Mohd. Nazri; Rosla, Luqman; Syed Yussof, Sharifah Nor Ezura; Mark, Paul; Mohamed@Awang, Kamariah; Ramli, Rosdi; Omar, Eshamsol Kamar; Mohd. Yassin, Mohd. Wardah; Mohamad, Mohd. Amin Marwan; Kaderi, Mohd. Arifin
HAYATI Journal of Biosciences Vol. 31 No. 3 (2024): May 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.3.432-442

Abstract

In searching for new biomarkers, high throughput technique has been widely used by researchers, including for gene expression study. However, the reliability and accuracy of results from high throughput study critically depends on appropriate data management, including normalization methods. Data driven normalization has been introduced as a normalization method for high throughput gene expression study. Thus, this study was conducted to evaluate the performance of various data driven and reference genes normalization methods using a high throughput circulating microRNA expression dataset. A quantification cycle (Cq) dataset generated from a high throughput circulating microRNA study was used to test the normalization methods using HTqPCR package in R software. The normalized Cq generated from different methods were compared descriptively using box plot analysis and coefficient of variance. The box plot analysis showed that quantile normalization produced more homogenous Cq distribution, lesser outliers and reduced coefficient of variance as compared to other normalization methods in screening and validation phases. The overview on quantile normalized Cq showed consistency in its level of expression before and after 2-∆∆Cq calculation indicating the reliability of quantile normalized Cq. Quantile normalization is suggested to be used in high throughput miRNA expression study due to its performance in homogenizing the data, reduce outliers and coefficient of variance.

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