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3BIO: Journal of Biological Science, Technology and Management
Published by Institut Teknologi Bandung
ISSN : -     EISSN : 26558777     DOI : http://dx.doi.org/10.5614%2F3bio.2020.2.1
Core Subject : Science, Agriculture, Engineering,
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Immunology & microbiology Neuroscience
3Bio: Journal of Biological Science, Technology and Management is an interdisciplinary peer-reviewed journal in a wide aspect related to the field of life sciences and other related fields of study. The journal aims to promote scientific discourse and disseminate research on various branches and applications of bio-science, biotechnology and bio-based management. This journal invites original empirical research, literature reviews, theoretical or methodological contributions, or short communications on, but not limited to, the following topics: - Ecology and Biosystematics - Microbiology - Genetics and Molecular Biology - Animal Development and Physiology - Plant Development and Physiology - Entomology - Biomedical science - Biochemistry - Agronomy - Forestry - Bioengineering - Bioethics - Management of Biological Resources The journal also invites contributions from other associated disciplines. This journal is an open-access journal. Readers may read, download, copy, distribute, print, search, or link to the full texts of these articles without any charge, provided that readers acknowledge the Creative Commons attached to the articles. All submitted papers are reviewed by at least two referees before being accepted for publication, following a double-blind review process. This journal is delivered in an academic English and rigorously edited to provide a quality standard of a scientific journal. This journal is managed by the School of Life Sciences and Technology, Institut Teknologi Bandung, Indonesia.
Arjuna Subject : Ilmu Pertanian dan Biologi (Semua) - Ilmu Pertanian dan Biologi (Lain-Lain)
Articles 68 Documents
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A Stand Structure and Composition and Model for Estimating Stand Volume Potential at the Citragaluh Sustainable Community Forest Management Unit, Subang Regency, West Java Wilhelmus Medhavi; Tien Lastini; Endang Hernawan
3BIO: Journal of Biological Science, Technology and Management Vol. 5 No. 1 (2023)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2023.5.1.4

Abstract

In general, community forest management is still limited to the management of individual farmers so that it affects diversity, especially in the form of stands. This study aimed to explore the stand structure and composition characteristics and develop a model for estimating the potential stand volume at the Citragaluh community forest management unit with 55 observation plots based on a combination of slope and density classes. The data taken includes slope; plant species; plant coordinates; planting pattern and spacing; tree diameter, tree height, and canopy density. The results of plot observations showed that the cropping pattern of Citragaluh Community Forest Management Unit (CFMU) consisted of monoculture (10.9%), mixed stands (20%), agroforestry (29%), dry fields (27.27%), wet fields (9%), bamboo stands (1.8%) and built-up area (1.8%). The trees species found were Jeungjing, Mahogany, Teak, Tisuk, Sobsi, Akasia, and Puspa. Based on the results of stratification, diameter distribution, and stand volume, mixed gardens were the best cropping pattern. This research proves the role of community forest as a transition between plantation forest and natural forest based on the stand form and composition. The stand volume potential estimator model chosen was linear with the equation Y = 0.074X1 + 2.924 X2 - 1.679 where X1 = slope and X2 = Normalized Difference Vegetation Index (NDVI). The values of R2 models are 51.3%. The average potential for the Citragaluh is 119,835 m3/ha, which tends to be higher than other community forest studies.
Relationship of Land Cover Heterogeneity and Insecticide Use with Arthropod Community Structure in Rice Agroecosystems Restu Utari Dewina; Devi N. Choesin
3BIO: Journal of Biological Science, Technology and Management Vol. 6 No. 1 (2024)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2024.6.1.4

Abstract

Rice agroecosystems generally experience two kinds of environmental stresses, i.e., a decrease in the heterogeneity of land vegetation types due to the development of settlements in the border zone and the excessive use of insecticides. Both of these factors are known to affect the structure of the arthropod community in rice agroecosystems. However, studies related to the effects of these two stresses in shaping the structure of arthropod communities have not been widely carried out, especially during the planting period in the rainy season. This study aims toanalyze the relationship between land cover heterogeneity and insecticide use with the taxonomic and functional diversity of arthropods in thealpha, beta, and gamma dimensions. The study was conducted during the rainy season (October–March) on four rice agroecosystem sites in Bandung, West Java. Data was collected 30 and 50 days after planting (DAP). Arthropod samples were identified, and their taxonomic andfunctional diversity was calculated using the Shannon entropy formula (D). In general, land cover heterogeneity was positively correlated withthe value of arthropod taxonomic and functional diversity, especially in the early vegetative phase of rice plants (30 DAP). In con- trast,insecticides (g/m2) were negatively correlated with the value of arthropod diversity. The composition of arthropod species locally was relativelythe same except in the rice agroecosystem with the lowest land cover heterogeneity and the highest use of insecticides. Additionally, thecoefficient value of the insecticide variable has more influence on the value of arthropod diversity than the variable coefficient of land coverheterogeneity.
An Evaluation of Stevia rebaudiana Leaf-Axillary Shoot Formation, Cultured in MS Medium Supplemented with IAA-BAP and MS Medium Supplemented with Kinetin Andira Rahmawati; Victor Emmanuel; Iriawati Iriawati; Khalilan Lambangsari; Rizkita Rachmi Esyanti; Roohaida Othman; Aldo Nathan Dela Simamora; Bugy Suwito
3BIO: Journal of Biological Science, Technology and Management Vol. 5 No. 1 (2023)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2023.5.1.1

Abstract

Stevia rebaudiana leaves can be used as a sweetener alternatives because they contain steviol glycoside derivative compounds, including steviosides and rebaudioside-A. Propagation of Stevia is more optimally carried out using in vitro culture when compared to conventional propagation through seeds or cuttings. This study aimed to evaluate the formation and growth of Stevia shoots and leaves in MS medium containing a mixture of IAA and BAP with MS medium containing kinetin only, as well as evaluating the use of a liquid medium containing kinetin. Stevia was initiated from apical shoot then grown in MS medium containing a mixture of IAA and BAP with MS medium containing kinetin only. Stevia was subcultured every 4 weeks. Several parameters measured were number of axillary shoots and number of leaves. It was transferred into a liquid medium for 7 days. The results showed that the formation and growth of axillary buds and leaves at the initiation stage were better in medium containing IAA and BAP compared to medium containing single hormone kinetin. At the stage of shoot multiplication and maintenance, cultivation in semi-solid medium containing kinetin showed more leaves and axillary shoots compared to that cultivated in semi-solid medium with the addition of IAA and BAP. Plants acclimatized in liquid medium supplemented with 1 ppm kinetin showed fast plant growth but were not accompanied by sturdy stem growth. The presence of brownish color on certain parts of the plant such as in some leaves and stems was also observed. 
The Behavioral Response of Komodo Dragons (Va- ranus komodoensis OUWENS, 1912) During Mating and Nesting Periods towards Tourist Presence in Loh Buaya, Komodo National Park Aditya Dimas Pramudya; Achmad Sjarmidi
3BIO: Journal of Biological Science, Technology and Management Vol. 5 No. 1 (2023)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2023.5.1.2

Abstract

It has been recognized in many studies that wildlife tourism practices might generate a negative impact on wildlife, particularly during the reproductive period. Some wildlife may lower their sensitivity towards tourist presence, for instance in Komodo. Understanding to what extenthabituation occurs in Komodo would be necessary for tourism management in Komodo National Park (KNP). Therefore, this study aimed to identify the response of Komodo to tourist presence during mating and nesting activities. The observation was conducted in Loh Buaya, which is one of the tourism sites in KNP. Komodo’s responses were divided into (1) avoidance; (2) neutral; and (3) aggressive under categorized stimulus: tourist number (i.e., < 5 persons; 5-10 persons; and > 10 persons) and distance (i.e., < 5 m; 5-10 m; and > 10 m). Correlation analysis was performed to identify any influences on mating and nesting activities. Our results revealed that Komodo inhabiting tourism facilities havebeen habituated to tourist presence. Different tourist frequencies did not influence Komodo mating activities (r(20)= 0.036, p=0.873), the nest preparing activity (i.e., digging proportion; r(22)= 0.054, p=0.803) and the guarding activity (i.e., nesting proportion; r(22)= 0.314, p=0.135).Nevertheless, our results indicated possible impacts due to tourism activities and its supporting facilities, such as dominated mating pairs, threats to female reproductive success, and human-Komodo conflicts. Therefore, habituation evi- dence must be carefully considered in order todevelop more corresponding strategies and achieve sustainable tourism practices.
Artificial Neural Networks (ANN) to Model Microplastic Contents in Commercial Fish Species at Jakarta Bay Andriwibowo Andriwibowo; Adi Basukriadi; Erwin Nurdin; Vita Meylani; Nenti Rofiah Hasanah; Zulfi Sam Shiddiq; Sitiawati Mulyanah
3BIO: Journal of Biological Science, Technology and Management Vol. 6 No. 1 (2024)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2024.6.1.3

Abstract

Jakarta Bay is known as one of the marine ecosystems that have been contaminated by microplastics. Despite massive loads of microplasticcontamination, Jakarta Bay is also habitat to potential commercial fish species, including anchovy Stolephorus commersonnii and mackerel Rastrelliger kanagurta. While information on the microplastic contents and their determining factors is still limited, the goal of this study was touse artificial neural networks (ANN) as a novel and useful tool to model the determinants of microplastic content in fish in Jakarta Bay, using fish weight and length as proxies. Inside the stomachs of S. commersonnii and R. kanagurta, the order of microplastics from the highest to thelowest was fiber > film > fragment > pellet. Based on the RMSE values of 3.199 for S. commersonnii and 2.738 for R. kanagurta, the ANNmodel of fish’s weight + length ~ pellet was found to be the best fitted model to explain the correlation of fish weight and length with microplastic content in the stomach. The results indicate that ANN is suitable for solving large, complex problems in determining and projecting microplastic contents and provides better estimates that can be used to manage R. kanagurta and S. commersonnii along with microplastic contamination threats.
The Primer Design and Optimization of Annealing Temperature for Analysis of Glutathione Reductase Gene Expression in Rice (Oryza sativa L.) Annisa Khaira; Afifatul Achyar; Zulyusri Zulyusri; Yusni Atifah; Dwi Hilda Putri; Violita Violita
3BIO: Journal of Biological Science, Technology and Management Vol. 5 No. 1 (2023)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2023.5.1.3

Abstract

Glutathione Reductase (GR) belongs to the NADPH-dependent flavoprotein oxidoreductase family and is found in both prokaryotes and eukaryotes. The GR gene is considered to play a key role in the elimination of oxidative reaction products by looking at the level of gene expression of GR rice in dealing with  drought stress using qPCR. One of the important steps to develop a specific, effective and efficient qPCR is the primer design. Several studies analyzing GR gene expression in rice have also designed primers. However, the primer still lacks an ideal characteristic of primer, as it still has a secondary structure. This studies aims to design rice GR specific primers and optimize the annealing temperature for GR gene expression analysis on rice. Primers were designed using the  Primer3 and Geneious Prime and checked for specificity using the Primer-BLAST tool. The selected primer pairs were then optimized for annealing  temperature using gradient PCR. The best primer design results were GR-Forward 5’-ACGATTGCAGCCAGTGAAGA-3’ and GR-Reverse 5’-TGCGGCAATACTATCAACATCC-3’, with an amplicon length of 204 bp, primer base lengths of 20 and 22 nucleotides, Tm values of 60°C and 58.9°C, %GC of 50% and 45.5%, respectively. This primer pair had no secondary structure, both hairpin and self dimer. Gradient PCR showed the optimum annealing temperature for this primer pair was 52.2oC so that the primer can be used as a specific primer to analyze  the GR gene expression in rice using qPCR.
The In Silico Characterization of Lycopene Forming Phytoene Desaturase (CrtI) Protein from Wheat Leaf Rust Fungi (Puccinia triticina) Yehezkiel Vieri Polandos; Fenny Martha Dwivany; Karlia Meitha
3BIO: Journal of Biological Science, Technology and Management Vol. 5 No. 2 (2023)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2023.5.2.1

Abstract

Carotenoid is a highly economical compound with a variety of bioactivities. However, 98% of total carotenoid used is still being manufactured by chemical-based synthesis, reducing bioactivities and is not environmentally friendly, hence the use of biofortification approach is sought.Lycopene forming phytoene desaturase (CrtI) is one of the key enzymes with the potential to develop as bioparts in recombinant carotenoid biosynthesis. CrtI from Puccinia triticina and Blakeslea trispora are considered as promising candidates due to the high amount of carotenoid inthe fungi. This research aims to characterize CrtI enzyme from P. triticina and B. trispora and the interaction with substrate, i.e.,15 cis-phytoene. The results showed that CrtI from P. triticina protein has 2 unique motifs, determining the three-dimensional CrtI protein structure. According to docking analysis, CrtI enzyme from P. triticina is predicted to bind to the substrate more spontaneously as indicated by the lower energy of affinity (-8.3 kcal mol-1) and more residues interaction compared to CrtI from Blakeslea trispora. In conclusion, the CrtI protein from P. triticina is suggested as the candidate for further exploration to design expression in a recombinant system.
A Short Note on Asteraceae as Traditional Food and Medicinal Plants in Cihanjawar Village, Purwakarta Regency, West Java Reza Raihandhany; Angga Dwiartama; Rina Ratnasih
3BIO: Journal of Biological Science, Technology and Management Vol. 5 No. 1 (2023)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2023.5.1.5

Abstract

Asteraceae is known as the largest family of flowering plants. Despite some species members being invasive plants, these species are often adopted and utilized by local community groups for food, traditional medicine, and other uses. In our ethnobotanical study of Asteraceae, we identified ways a local Sundanese community group in West Java utilizes a diverse range of species in the family for different purposes. Our study focuses on a Sundanese village called Cihanjawar, located in the regency of Purwakarta, using ethnobotany and ethnomedicine approaches. People of Cihanjawar utilize some species of Asteraceae for food as ‘lalapan’ and traditional medicinal purposes. In-depth, semi-structured interviews with the people of Cihanjawar were conducted to collect primary data regarding the utilization of Asteraceae species as food and traditional medicine. A total of eight species of Asteraceae were found during the field-guided exploration in Cihanjawar Village, which include Acmella paniculata, Ageratum conyzoides, Calyptocarpus vialis, Crassocephalum crepidioides, Dichrocepala integrifolia, Emilia sonchifolia, Erechtites valerianifolia, Sphagneticola trilobata, some of which are considered invasive alien species. The species of A. paniculata, C. crepidioides, E. sonchifolia, Er. valerianifolia is eaten as a raw food (lalapan, Ind.). Then Ag. Conyzoides and C. crepidioides are utilized in traditional medicine. C. vialis, D. integrifolia, and Sphagneticola trilobata are not used by the people of Cihanjawar as food or as traditional medicine.
Optimizing the Wet Fermentation of Ateng Coffee (Arabica) with the Addition of Yeast R1-TKSU and LAB (Leuconostoc suionicum) Inoculum Grace Sabatina; Dea Indriani Astuti; Isty Adhitya Purwasena
3BIO: Journal of Biological Science, Technology and Management Vol. 6 No. 1 (2024)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2024.6.1.5

Abstract

Ateng coffee is an Arabica coffee that generally has a high selling value because of its better taste compared to other coffees. However, ateng coffee has poor post-harvest processing, resulting in low coffee quality and an impact on low coffee selling prices. In this study, optimization ofwet fermentation using yeast R1-TKSU and LAB (Leuconostoc suionicum) inoculums was used to improve the quality of ateng coffee. Treatment variations were fermentation with the addition of yeast, LAB, yeast : LAB 1:1, and there is also a control without the addition of inoculum. Sensory assessment showed that the best cupping score was the sample added by LAB with a total score of 86.5. The contents of malic acid, citric acid, lactic acid, sucrose, fructose, and glucose and ethanol which were analyzed by HPLC were found to be relatively stable ingreen coffee beans. Fermentation added inoculum affects the concentration of acetic acid. Amino acid analysed showed that overall the highest concentration of amino acids in green coffee beans was in the yeast : LAB 1:1 treatment. It can be concluded that controlled wet fermentation with the addition of yeast R1-TKSU and LAB (Leuconsotoc suionicum) inoculums can improve the quality of ateng coffee.  
The Structural Evaluations of SARS-CoV-2 Main Protease (Mpro): A Review for COVID-19 Antivirals Development Strategy Muhammad Hamzah Syaifullah Azmi; Ernawati Arifin Giri-Rachman
3BIO: Journal of Biological Science, Technology and Management Vol. 5 No. 2 (2023)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2023.5.2.2

Abstract

It has been almost four years since the first case of COVID-19 emerged, and the antivirals that could work specifically against SARS-CoV-2with a high efficacy are still under development. Main Protease (Mpro) of this virus plays a crucial role in virion maturation during itsreplication within the host cell. This protein works together with the papain-like protease (PLpro) to cleave polyprotein 1a  and 1ab  into a total of16 functional fragments of non-structural protein. Antiviral with the ability to inhibit the activity of Mpro could potentially prevent the virion replication, and they can be developed to target the catalytic or allosteric site of this protein. Antiviral that works on the catalytic site will act as competitive inhibitors of the substrate peptide which leads to the loss of Mpro function. Targeting the allosteric site (e.g. distal site and dimerization interface) will cause allosteric modu- lation of the protomer which could alter the protein 3D conformation and disrupt the formation of homodimer structure. This will affect the geometry and surface structure of the catalytic site which in turn decreases the affinity of the substrate peptide towards the Mpro catalytic site, resulting in a completeinactivation of the protein. Mutation study of Mpro amino acids sequence also reveals that the mutation frequency for each amino acid position isextremely low and negligible. Moreover, it is found that this protein has 24 mutational cold spot residues scattered within its structure which could be targeted for the development of antivirals due to its highly conserved nature.

Page 5 of 7 | Total Record : 68

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