Biogenesis: Jurnal Ilmiah Biologi

Journal Information
ISSN / EISSN : 2302-1616 / 2580-2909
Current Publisher: Universitas Islam Negeri Alauddin Makassar (10.24252)
Total articles ≅ 169
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, Dedy Darnaedi, Ismail Rachman, Teguh Triono, Campbell O. Webb
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 203-209; doi:10.24252/bio.v8i2.15697

Abstract:
Indonesia is one of the world’s biodiversity hotspots. It is estimated to be the home of 9.5% flowering plant species, making it the seventh country with the highest biodiversity. Plant data collection is necessary to ascertain the level of plant biodiversity, as such data help in conservation efforts and long-term management. One of the methods applied is the collection of plants, with the purpose to acquire as much data about its biological resources. The collected specimen are then gathered and processed into a herbarium to be used as an information source in managing biological resources. Unfortunately, there are some difficulties related to the making and management of a herbarium. Digital herbarium are one of the potential solutions to the limitations of the traditional herbarium. It is a collection of plant pictures, replete with every step of productivity (leaf, flower, fruit) and the main characteristics of the plant species. It is an effective method for the identification and collection of plant biodiversity in Indonesia. About 2149 plants have been gathered from Borneo, Seram, Waigeo, Flores and Sulawesi which consisted of 152 family, 512 genus, and 1,832 species, with a total of 30391 pictures of plant parts. From the experiment conducted on 672 specimens, it achieved 98.8 % accuracy on the family level and 80.1 % accuracy on the genus level, while the species level reached 78.8%. The results showed that digital herbarium can be used to conduct identification and data collection of plant biodiversity. Furthermore, this method is simple, cheap and relatively easier to conduct. The output is a catalog of plant species in specific areas, which provides better understanding about plant identification and biodiversity, enhances conservation practices, and provides better long-term protection for Indonesian plant biodiversity.
Yohanes Bare, Maria Helvina, Gabriella Chandrakirana Krisnamurti, Mansur S
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 210-218; doi:10.24252/bio.v8i2.15704

Abstract:
Hypertension has become the third highest cause of death in Indonesia. The condition is correlated with angiotensin-converting enzyme (ACE), and possibly managed with the use of drugs. In addition, some natural compounds, including 6-shogaol and 6-gingerol from ginger, are used to decrease blood pressure. However, the mechanism and binding site of these compounds to ACE protein is currently unclear. This study, therefore, aims to investigate the potential role of these compounds as an angiotensin-converting enzyme inhibitor. The ACE protein was downloaded from Protein Data Bank (PDB) database with the ID: 3bkk, while the 6-shogaol (CID: 5281794) and 6-gingerol (CID: 44559528) ligands were obtained from the PubChem database. Meanwhile, molecular docking was established using HEX 8.0.0 software. The analysis examined the amino acid residues and the bonds formed from these interactions. According to the results, fourteen amino acid residues were formed by the interaction between 6-shogaol and ACE, while the interaction between 6-gingerol and ACE formed eight amino acids. Also, thirteen amino acid residues in the novelty binding site of ACE were discovered to be blocked by the ligands from ginger. Therefore, the compounds have potential roles as inhibitors, and this possibly helps to prevent regulation of the renin-angiotensin system. These interactions also formed hydrogen bonds, as well as electrostatic, unfavorable, and hydrophobic sites, making the binding stronger than others.
Abdulridha Taha Sarhan
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 195-202; doi:10.24252/bio.v8i2.16802

Abstract:
The normal field soil environment safeguarded, via indigenous microbes in a native manner, with the aim of turning herbicide waste into productive bio-resources, through fungi activities. This study aims to determine the effective role of soil indigenous fungi on 2,4-D herbicide degradation. The research was conducted over a period of six weeks, on Iraqi cereal field. A total of eight fungi species, belonging to six genera, (Aspergillus candidus L. ATCC 1002, A. niger T. ATCC 16888, Curvularia lunata W. B1933, Penicillium sp. L. 1809, Rhizopus stolonifer L. B9770, Stachybotrys atra C. 1837, Trichoderma harzianum R. IOC 3844, and T. lignorum T. Hartz 1872), were isolated from the soil. During the exposure periods, fungal populations were differently affected, upon treatments with herbicide. The applied herbicide treatments showed different effects on growth and development of the isolated fungi. The results showed that, five of the eight fungi species (C. lunata B1933, Penicillium sp. 1809, R. stolonifer B9770, T. harzianum IOC 3844, and T. lignorum Hartz 1872) were greatly enhanced by the treatment process. However, two fungi (S. atra 1837, and A. candidus ATCC 1002) were affected negatively by the herbicide, while one (A. niger ATCC 16888) remained unaffected. Once extracted from the soil of wheat fields in Iraq, the fungus S. atra 1837, was first isolated. The highest inhibitory effect was caused by 2,4-D herbicide, on the toxigenic fungus S. atra, causing its disappearance from the field at the last week of application. The laboratory experiments showed similar herbicide effects on the isolated fungi at low and moderate levels, while those at the high level (800 µg /ml) were toxic. These results showed that the herbicide 2,4-D treatments have substantial effects on microbial population in the field. When applied at recommended field rate, the herbicide causes transient impacts on fungal population growth and biodiversity, with the majority of the organism becoming responsible for 2,4-D mineralization in the soil. Therefore, the use of 2,4-D herbicide does not only control weed population, but it also affects microbial activities, especially indigenous fungi in the soil.
Mohd Yunus Shukor
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 219-224; doi:10.24252/bio.v8i2.17419

Abstract:
Several models are available to determine the effect of temperature on the growth rate of microorganisms on substrates. An example is Arrhenius model, which is very popular because it has few parameters. For the first time, a discontinuous chevron-like graph of apparent activation energy based on the Arrhenius plot on the growth of 2-chloro-4-nitrophenol by Cupriavidus sp. is reported. The plot of ln mm against 1/T shows a discontinuous chevron-like graph for the entire investigated temperature range with an inflection at 27.75°C. This indicates that the existence of 2 activation energies for growth on 2-chloro-4-nitrophenol ranges from 20 to 40°C. Furthermore, a regression analysis from 20–25°C and 30–40°C results in activation energies of 88.71 kJmol-1 and 75.16kJ mol-1, respectively. This is probably the first time a Chevron-like graph was observed for the Arrhenius plot on the effect of temperature on the growth rate of 2-chloro-4-nitrophenol.
, Aadrean Aadrean, Henny Herwina
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 133-137; doi:10.24252/bio.v8i2.12642

Abstract:
The Black-crowned Night heron (Nycticorax nycticorax) is a known visitor in Sumatra with more sighting records in the eastern side of the island. Meanwhile, on the west, it was historically recorded from only two offshore islands, namely Nias and Enggano. During the waterbird survey from early 2018 at Pasir Jambak Beach of Padang City in the coastline of West Sumatra, a Night heron was spotted among the colony of mixed egret species. This is the first record of its kind in the province of West Sumatra, although, previous records cover almost all provinces in Sumatra. The summary of the compiled records of this species indicates that it is probably a vagrant along the western coastline, while it visits more frequently on the eastern side.
Yani Suryani, Opik Taupiqurrohman
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 185-194; doi:10.24252/bio.v8i2.15696

Abstract:
In the manufacture of universal peptide vaccines, it is necessary to analyze the amino acids of the various candidates. Therefore, this study aims to examine the amino acids of the spike glycoproteins of SARS-CoV, SARS-CoV-2, and MERS CoV. The method used is the alignment of the amino acid spike glycoprotein between SARS-CoV with SARS-CoV-2, MERS CoV with SARS-CoV-2, and SARS-CoV with MERS-CoV using web-based software water emboss. The analysis result showed that SARS and SARS CoV-2 were very similar with 87% similarity and 76.4% identity values. In contrast, SARS-CoV-2 with MERS and SARS with MERS were very different, having similarity and identity values of less than 70%. Therefore, it is reasonable to conclude that spike glycoprotein's peptide is only useful from attacks by the SARS-CoV and SARS-CoV-2 viruses.
Lizawati Lizawati, Zulkarnain Zulkarnain, Neliyati Neliyati
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 111-118; doi:10.24252/bio.v8i2.11769

Abstract:
Conventional vegetative propagation is the process in which new plants are grown from a variety of sources, seeds, cuttings and other parts of the plants. Therefore, the conventional vegetative propagation of liberica coffee by cutting or grafting of stems is hampered by the limited number of stem or branches, which can be used as propagating materials. In addition, the tissue culture technique is another method used to propagate liberica coffee. This study aims to investigate an efficient protocol for embryogenic callus development from leaf explants of Coffea liberica cv. Liberika Tungkal Komposit. The explants used are immature leaves of fully opened liberica coffee. The medium used was Murashige and Skoog (MS) composition supplemented with vitamins, 3% sucrose and solidified with 0.7% agar, and the medium pH was adjusted to 5.8 ± 0.1. The experiment was arranged in a factorial randomized block design, and the first factor was 2.4-D (2.0, 3.0, 4.0, and 5.0 ppm) and then the second factor was BAP (0.0, 0.5, and 1.0 ppm). The results showed that the application of 2.4-D and BAP significantly improved the distribution of callus proliferation on cultured explants. The use of 2.0 ppm 2.4-D + 1.0 ppm BAP resulted in the fastest callus proliferation (19 days after culture initiation). In general, the application of different levels of 2.4-D and BAP successfully induced friable with nodular morphology callus on young leaf explant of liberica coffee. It is believe that the callus has embryogenic capacity and will undergo embryogenesis when transferred to a suitable medium composition.
Agus Nuryanto, Dian Baghawati, Kusbiyanto Kusbiyanto, Moh Husein Sastranegara, Farida Nur Rachmawati
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 145-156; doi:10.24252/bio.v8i2.15532

Abstract:
The taxonomic status of Anguilla species' in river watershed that empties into Segara Anakan Cilacap is uncertain, thereby making it difficult for further studies to be carried out to determine its genetic in that area. Therefore, this study evaluates Anguilla's taxonomic status and population genetic in Cibeureum and Sapuregel River watersheds. Data were obtained from molecular characterization study using cytochrome c oxidase 1, with fourteen Anguilla specimens collected from two sequenced watersheds. Taxonomic status was determined based on homology and divergence values and monophyly of the samples to the reference species. Meanwhile, genetic divergences among samples to the reference species were calculated based on the Juke-Cantor substitution model in DnaSP6. A homology test was performed using a basic local alignment search tool, with monophyly inferred from the cladogram, which was developed using neighbor-joining and maximum likelihood algorithms in MEGAX with 1000 pseudoreplicates and out-group comparison. Furthermore, population genetic was analyzed through polymorphism, haplotype, nucleotide diversity within the population, divergence, and genetic differences. All calculations conducted in Arlequin 3.5 had Anguilla samples comprising of high (99.23% to 99.84%) to low genetic divergences (0.224% to 1.127%). The result shows that cladogram with all Anguilla samples formed a monophyletic clade with A. bicolor, separated from their taxa. Furthermore, Anguilla samples from both watersheds have low genetic polymorphisms with medium to high haplotype and nucleotide diversity. The population's comparison proved that both populations have low genetic divergence, and no genetic difference based on variance analysis (p=0761). Therefore, Anguilla resources in river watersheds that empty into Segara Anakan are a single genetic conservation unit.
, Ram Kumar Bhakat
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 157-171; doi:10.24252/bio.v8i2.16407

Abstract:
Sacred Groves are tracts of virgin forests, left untouched and protected by local people, because of culture and religious beliefs. These tracts are remnants of the once-dominant flora, reservoirs of the rich biodiversity, and the last refuge for preserving the rich indigenous culture and traditions. For these reasons, the biological and leaf spectra, as well as the conservation status of the current sacred grove vegetation, Maa Mongalmoyee Than (MMT) in Jhargram district of West Bengal, India, have been studied. The results of floristic studies showed 217 MMT's angiosperm species, belonging to 196 genera, distributed under 59 families of 27 orders. Furthermore, Poales (13.82%) and Fabaceae (12.44%) are the dominant order and family, respectively, in terms of species population. Meanwhile, the biological spectrum showed the grove enjoys a "thero-chamaephyte" phytoclimate form, as well as a comparatively undisturbed status, being a sacred grove. Also, the preservation of germplasm within the grove is based on traditional belief in the social system.
G.V.P. Samaranayake, W.A.L.C. Walivita, K.M. Chandimal
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 234-240; doi:10.24252/bio.v8i2.17348

Abstract:
The different surgical techniques and importance in disease treatment were explored by Sushruta, the father of surgery. Furthermore, Anushastra or parasurgical substances and methods from Ayurveda are distinctive in surgical fields as discovered by Sushruta. According to Susruta Samhita, Kshara or alkali are useful for performing excision/removal, incision/cutting, scraping, alleviating three Doshas and several special procedures, and therefore superior to Shastra (sharp instruments) or Anu Shastra (accessory apparatuses). Also, Kshara is derived from diverse Ayurveda plants and applied in different ways to manage various diseases, including bhagandara (fistula-in-ano) and other numerous anorectal conditions. Ksharasutra, a novel drug delivery system, is now popular in Ayurvedic surgery for anorectal Diseases and involves a thread smeared with kshara (alkali) applied to induce both mechanical and chemical cutting and healing. There are 23 Kshara source plants provided by Sushruta. This study implemented a literary analysis of the three plant sources employed to prepare Kshara sutra used for managing Fistula-in-ano.
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