Genbinesia Journal of Biology
The Genbinesia Journal of Biology particularly focuses on the core disciplines in biology, they are: astrobiology, bacteriology, behavioural science, biochemistry, biodiversity, bioethics, bioinformatics, biomathematics, biophysics, biopolymers, biostatistics, biotechnology, botany, cell biology, conservation, crystallography of macromolecules, developmental biology, ecology, entomology, evolutionary biology, genetics, genomics, glycobiology, immunology, macromolecules, marine & aquatic biology, mathematical & computational biology, medicine, microbiology, molecular biology, mycology, nanoscience & nanotechnology, neurobiology, neuroscience, ornithology, paleobiology, paleontology, parasitology, pharmacology, physiology, plant biology, proteins & peptides, proteomics, radiation biology, reproductive biology, soil biology, structural biology, systems biology, techniques in biology, theoretical & mathematical biology, virology, zoology, and interdisciplinary applications in biology.
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<![CDATA[Contribution of the Mangrove ecosystem to the Gastropod community at Pantai Bahagia village, Muara Gembong, West Java ]]>
<![CDATA[Dwijaya, Bayu Awifan]]>;
<![CDATA[Krisnanti, Sukma Awifan]]>;
<![CDATA[Ramdhani, Ardo]]>
<![CDATA[ Genbinesia Journal of Biology Vol. 1 No. 1 (2021): November 2021 ]]>
Publisher : <![CDATA[Generasi Biologi Indonesia ]]>
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DOI: 10.55655/genbinesia.v1i1.2
<![CDATA[The Mangrove ecosystem of Muara Gembong has been under continuing stress by land occupation, land conversion, and abrasion. This research was aimed to reveal the mangrove and gastropods community structure circumstance. A contribution of the environmental factor was also assessed to evaluate the interaction among them and to track the changes of the ecosystem. This research was conducted by purposive sampling in 3 sampling sites, these were a full reforestation site (A), a central site, that was exist by natural process (B), also a moderate reforestation site (C), with 3 sampling replication each site. About 4 mangrove species within shoreline has been progressively important as a protective flood barrier and abrasion at Muara Gembong. The highest gastropod diversity was found in the B1 site, while the highest dominance was found in A2. The C2 site is the only site that showed us a uniform dispersion of gastropods when the other sites showed a clumped dispersion. It can be implied that the ecosystem has been gradually degraded. Eigen and loading value from Canonical Correspondence Analysis (CCA) revealed that a gastropods community was holistically affected by pH, basal area, canopy, substrate, and TDS. The community of gastropods was influenced 62.14% by pH, and 34.29% by basal area. while the highest dominance was found in A2. The C2 site is the only site that showed us a uniform dispersion of gastropods when the other sites showed a clumped dispersion. It can be implied that the ecosystem has been gradually degraded.]]>
<![CDATA[Vaccine construction for human papilloma virus (HPV) type 16 and 18 Infection using in silico approach to combat cervical cancer ]]>
<![CDATA[Dharmawan, Muhammad Alsyifaa]]>;
<![CDATA[Ansori, Arif Nur Muhammad]]>;
<![CDATA[Dian, Farida Aryani]]>;
<![CDATA[Probojati, Rasyadan Taufiq]]>;
<![CDATA[Tamam, Muhammad Badrut]]>;
<![CDATA[Kharisma, Viol Dhea]]>
<![CDATA[ Genbinesia Journal of Biology Vol. 1 No. 1 (2021): November 2021 ]]>
Publisher : <![CDATA[Generasi Biologi Indonesia ]]>
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DOI: 10.55655/genbinesia.v1i1.3
<![CDATA[Human papillomavirus (HPV) is a virus that causes infection on the surface of the skin and has the potential to cause cervical cancer. This viral infection is characterized by the growth of warts on the skin in various areas of the body, such as the arms, legs, mouth, and genital area. Because the virus can endanger health, it is necessary to design an HPV vaccine to overcome this problem. In this study, we performed a study characterization of HPV types 16 and 18 sequences to obtain immunogenic epitopes retrieved from the National Center for Biotechnology Information (NCBI) web server. Then, epitope prediction was performed using the immune epitope database (IEDB) web server and selected to get the best vaccine candidate for HPV types 16 and 18. We recommend 16P1 as an epitope-based peptide vaccine candidate for HPV type 16 and 18P4 for type 18. Both vaccine candidates are antigenic, non-allergenic, and non-toxic. The 16P1 and 18P4 have the lowest global energy values among the other candidates. However, further research is needed to be able to develop the best vaccine (in vitro and in vivo experiments).]]>
<![CDATA[Comercial yeast samples DNA extraction using universal kit ]]>
<![CDATA[Robiatush Sholichah Arrohmah]]>;
<![CDATA[Radinal Kautsar]]>
<![CDATA[ Genbinesia Journal of Biology Vol. 1 No. 1 (2021): November 2021 ]]>
Publisher : <![CDATA[Generasi Biologi Indonesia ]]>
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DOI: 10.55655/genbinesia.v1i1.4
<![CDATA[Yeast is a microorganism that is relatively difficult to obtain its DNA mass. This is caused by the content of cell walls with a thick and rigid composition, such as chitin. This study aims to provide information on the best concentration and purity of the DNA extraction results of various types of commercial yeast in different samples weight. The method used is based on Universal Kit procedure with modification. This study indicates that differences in concentration or sample weight do not affect the DNA concentration and purity ratio value of each yeast sample. Each best result obtained from Jago (Rhizopus oligosporus), Raprima (Rhizopus oligosporus) and Fermipan (Saccharomyces cerevisiae) in 50 mg sample, NKL (Saccharomyces cerevisiae) yeast in 40 mg. Recomendation weight samples to extract DNA of Rhizopus oligosporus and Saccharomyces cerevisiae isolates are between 40 mg to 50 mg. The contamination factor causes the difference in the value of purity in each sample during DNA extraction.]]>
<![CDATA[Clarias batrachus linnaeus, 1758 (siluriformes, clariidae): new records of threatened catfish from Bawean Island, Indonesia ]]>
<![CDATA[Tamam, Muhammad Badrut]]>;
<![CDATA[Ramadani, Aisyah Hadi]]>;
<![CDATA[Valen, Fitri Sil]]>
<![CDATA[ Genbinesia Journal of Biology Vol. 1 No. 1 (2021): November 2021 ]]>
Publisher : <![CDATA[Generasi Biologi Indonesia ]]>
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DOI: 10.55655/genbinesia.v1i1.5
<![CDATA[Clarias batrachus Linnaeus, 1758 is one of catfish in Indonesia. The spread of Clarias batrachus in Indonesia have generally in mainland of Sumatra, Borneo and Java. In 2019 we report for the first time the presence of C. batrachus on Bawean, a small, isolated island, conservation area in the middle of Java Sea. A description of morphological characters of a specimen are provided. Presence of C. batrachus on Bawean Island caused by the geographical reason and human introduction factors.]]>
<![CDATA[Viroinformatics study: polytope mapping of envelope glycoprotein to tackle HIV-2 infection and develop vaccine candidate ]]>
<![CDATA[Kharisma, Viol Dhea]]>;
<![CDATA[Widyananda, Muhammad Hermawan]]>;
<![CDATA[Probojati, Rasyadan Taufiq]]>;
<![CDATA[Ansori, Arif Nur Muhammad]]>;
<![CDATA[Murtadlo, Ahmad Affan Ali]]>;
<![CDATA[Tamam, Muhammad Badrut]]>;
<![CDATA[Wicaksono, Adhityo]]>;
<![CDATA[Turista, Dora Dayu Rahma]]>
<![CDATA[ Genbinesia Journal of Biology Vol. 1 No. 1 (2021): November 2021 ]]>
Publisher : <![CDATA[Generasi Biologi Indonesia ]]>
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DOI: 10.55655/genbinesia.v1i1.6
<![CDATA[Human Immunodeficiency Virus type 2 (HIV-2) has been identified to exhibit an ability to resist antiretroviral administration and many scientists has predicted increases in the pathogenicity of HIV-2. The development of a vaccine against the type 1 virus (HIV-1) infection has reached the phase 3 clinical trial stage, but currently there is no information on the development of a vaccine against HIV-2. Vaccine development to trigger an increase in the coverage of the expansion of protection can be done through B cell polytope. This study aims to provide an important preliminary for the construction of vaccine candidates by identifying the peptides that make up the B cell polytope in the HIV-2 envelope glycoprotein region. The HIV-2 sequence was obtained from the database. The study followed by 3D modelling, prediction of linear B-cell epitope mapping, antigenicity, allergenicity, peptide properties, and immune simulation was carried out via a webserver. The 3D structure of the peptide was displayed through molecular visualization software. The results showed that the 23-mer peptides E1 'HPRYTGVKNIRDITLTEPGRGSD', F1 'NFIENRKGTQHN' 12-mer, M1 'YLKDQARLNS' 10-mer, N1 'PWVNDSIQPNWNNMTWQQWELQVRD' 25-mer, and O1 'KLQNSWNMGVQTO' can be used as a candidate polytope HIV-2 vaccine because it is recognized by B cells is an antigenic peptide with stable molecule, non-allergenic. The peptides trigger proliferation and activation of B cells to produces a humoral response and work as functionally protective antibody for neutralization of HIV-2. Key words: Acquired Immune Deficiency Syndrome, B-cell, Bioinformatics, Human Immunodeficiency Virus, Retrovirus]]>
<![CDATA[Exploring active compounds of kelor (Moringa oleifera Lam.) leaves as an alternative medicine to improve immunity in facing COVID-19 via in silico study ]]>
<![CDATA[Hikam, Agus Mohammad]]>;
<![CDATA[Mubarakati, Nurul Jadid]]>;
<![CDATA[Probojati, Rasyadan Taufiq]]>;
<![CDATA[Widyananda, Muhammad Hermawan]]>;
<![CDATA[Kharisma, Viol Dhea]]>;
<![CDATA[Ansori, Arif Nur Muhammad]]>
<![CDATA[ Genbinesia Journal of Biology Vol. 1 No. 1 (2021): November 2021 ]]>
Publisher : <![CDATA[Generasi Biologi Indonesia ]]>
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DOI: 10.55655/genbinesia.v1i1.7
<![CDATA[SARS-CoV-2 is a new strain of coronavirus (CoV) that was identified in Wuhan in 2019. This virus is known to have the ability to reduce human immunity. Kelor (Moringa oleifera) is a potential natural resource in Indonesia, which is very abundant and contains several metabolic compounds such as phenolics, flavonoids, saponins, cytokines, and caffeoylquinic acid, which was reported to show antioxidants, antibacterial and antiviral. This study aims to predict the biological activity, physicochemical properties, toxicity, and affinity-interactions of the active compounds of M. oleifera leave. The active compounds of M. oleifera were obtained from the KNApSAcK and PubChem. Analysis of the bioactivity of the compounds using the Way2Drug Pass Online. Analysis of drug-likeness and toxicity using the Lipinski web server and pkCSM. Docking is done using Autodock vina software to analyze the interaction of the compounds with Mpro. The results indicate that the compound astragalin is the compound with the highest affinity value, namely -8.7 (kcal/mol), compared to lopinavir as a control compound with an affinity value -6.6 (kcal/mol). The types of bonds in astragalin compounds are hydrogen bonds with amino acids Glutamine 127 and Arginine 298. From these results, it is predicted that astragalin compounds have the highest potential as alternative drugs to increase body immunity against the COVID-19.]]>
