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Results in Journal Biogenesis: Jurnal Ilmiah Biologi: 155

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Arifin Surya Dwipa Irsyam, Muhammad Rifqi Hariri, Ashari Bagus Setiawan, Rina Ratnasih Irwanto, Asih Perwita Dewi
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.12199

Abstract:
Calcareous soil and dry climate are characteristic of Madura Island, located on the east coast of Java, Indonesia. The group of flowering plants that adapted to these conditions is the genus Cleome L. (Cleomaceae). In 1963, Backer and Bakhuizen van den Brink Jr. only listed three species of Cleome from Madura, i.e., C. aspera J.König ex DC., C. gynandra L., and C. viscosa L. Since then, the updated data on the genus Cleome of Madura is not provided yet. Therefore, this study aimed to provide updated information on the genus in Madura island. The botanical exploration was conducted at Bangkalan, Sampang, Pamekasan, and Sumenep in December 2019 to January 2020. The two additional species, namely C. chelidonii L.f. and C. rutidosperma DC., were reported for the first time in Madura. Both species were considered as the newly distributional record for the island. Cleome chelidonii was found in Gapura Tengah (Sumenep Regency), and C. rutidosperma was collected from Kamal (Bangkalan Regency). The botanical information on both species is presented, including the updated key to the Cleome of Madura Island. This study provides updated information on genus Cleome in Madura and reporting the existence of Cleome chelidonii and Clome rutidosperma from the island. The presence of both species was considered as a newly distributional record.
Akhmad Rezki Purnajaya, Wisnu Ananta Kusuma, Medria Kusuma Dewi Hardhienata
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.12002

Abstract:
The prediction of Compound-Protein Interactions (CPI) is an essential step in the drug-target analysis for developing new drugs as well as for drug repositioning. One challenging issue in this field is that commonly there are more numbers of non-interacting compound-protein pairs than interacting pairs. This problem causes bias, which may degrade the prediction of CPI. Besides, currently, there is not much research on CPI prediction that compares data sampling techniques to handle the class imbalance problem. To address this issue, we compare four data sampling techniques, namely Random Under-sampling (RUS), Combination of Over-Under-sampling (COUS), Synthetic Minority Over-sampling Technique (SMOTE), and Tomek Link (T-Link). The benchmark CPI data: Nuclear Receptor and G-Protein Coupled Receptor (GPCR) are used to test these techniques. Area Under Curve (AUC) applied to evaluate the CPI prediction performance of each technique. Results show that the AUC values for RUS, COUS, SMOTE, and T-Link are 0.75, 0.77, 0.85 and 0.79 respectively on Nuclear Receptor data and 0.70, 0.85, 0.91 and 0.72 respectively on GPCR data. These results indicate that SMOTE has the highest AUC values. Furthermore, we found that the SMOTE technique is more capable of handling class imbalance problems on CPI prediction compared to the remaining three other techniques.
Nova Mujiono, Ristiyanti M Marwoto, Heryanto Heryanto
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.13212

Abstract:
Faunistic study on the malacofauna of Simeulue Island was carried out in 2017 after 104 years from the last collection in 1913. 3 locations with 13 stations were observed. 20 families and 50 species of aquatic and terrestrial molluscs were identified. The occurrences of 4 local endemic species were still found and 19 new distributional records were added to the previous list. However, 5 previously listed species were not found in the present study. Through the present study, the accumulative number of malacofauna from Simeulue Island will be around 54 species. 19 species were reported for the first time, including 3 introduced species and 1 new records for Indonesia. 4 local endemic species were still found there after 104 years gone by.
Taufik Muhammad Fakih, Mentari Luthfika Dewi, Eky Syahroni
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.13871

Abstract:
The new coronavirus (SARS-CoV-2), which caused the global pandemic Coronavirus Disease-2019 (COVID-2019), has infected nearly 206 countries. There is still little information about molecular compounds that can inhibit the development of infections caused by this disease. It is crucial to achieving the discovery of competent natural inhibitor candidates, such as antiviral peptides, because they have a variety of biological activities and have evolved to target biochemical machinery from different pathogens or host cell structures. In silico studies will be carried out, including protein-peptide docking and protein-protein docking, to identify, evaluate, and explore the affinity and molecular interactions of the Magainin-1 and Magainin-2 peptide molecules derived from frog skin (Xenopus laevis) to the main protease macromolecule (Mpro) SARS-CoV-2, and its effect on the ACE-2 receptor (Angiotensin Converting Enzyme-2 Receptor). Protein-peptide docking simulations show that both peptide molecules have a good affinity for the active site area of the SARS-CoV-2 Mpro macromolecule. These results were then confirmed using protein-protein docking simulations to observe the ability of the peptide molecule in preventing attachment to the ACE-2 receptor surface area. In silico studies show that Magainin-2 has the best affinity, with a bond free energy value of −3054.53 kJ/mol. Then the protein-protein docking simulation provided Magainin-2 was able to prevent the attachment of ACE-2 receptors, with an ACE score of 1697.99 kJ/mol. Thus, through in silico research, it is hoped that the Magainin peptide molecule can be further investigated in the development of new antiviral peptides for the treatment of infectious diseases of COVID-19.
Muhammad Abdul Malik Al-Furqon , Yanti Yanti, Salim Salim, Harish Muhammad
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.13137

Abstract:
The high concentration of detergent in the aquatic ecosystem potentially affects the physiological condition of the fish by disrupting the respiration process and changing the concentration of blood components and chemistry. The purpose of this study was to determine the condition of the hematological parameters of tilapia (Oreochromis niloticus) exposed to wastewater from the laundry industry. Each treatment was stocked with five fish per aquarium (50 x 30 x 30 cm). This study used a completely randomized design (CRD) technique with six treatments and three replications: P0 (0%) as a control, P1 (1%), P2 (2%), P3 (3%), P4 (4%) and P5 (5%) with each treatment exposed to a specific concentration of wastewater and residues. The results showed that the hemoglobin levels of treatments were decreasing, with the lowest mean of hemoglobin level found in the P2 (7.05 gr%), and the lowest concentration on the 30th day was 7.71 gr%. There were no significant effects of wastewater to the number of erythrocytes and leucocytes among treatments (P>0.05). While there were increasing levels of hematocrit, the largest mean level was found in the P4 treatment with a value of 24.11%, and the largest mean on the 20th day of observation showed a value of 23.51%. Wastewater from the laundry industry can affect the hematological condition of tilapia by decreasing the hemoglobin concentration and increasing the hematocrit levels above the normal condition.
Djong Hon Tjong, Anugrah Viona Agesi, Dewi Imelda Roesma
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.13019

Abstract:
The true frog species, Odorrana hosii, found in West Sumatera Indonesia, has high morphological differentiation and also estimated has high genetic variation. A total of 35 O. hosii at a seven location have analyzed using DNA microsatellite markers. Genetic variation of five microsatellite loci provided the highest value of expected heterozygosity (He) for the population in Padang (He = 0.618), while the lowest was the population in Merapi (He = 0.427). There are genetic differences in moderate levels among populations of O. hosii in West Sumatra (FST = 0.108) with inbreeding intrapopulation value (FIS = -0.559), and high value of gene flow among the populations (Nm = 2.061). This study becomes the first molecular data for establishing effective population management conservation.
Oktira Roka Aji, Larasati Haliimah Roosyidah
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.12009

Abstract:
Anthracnose is a plant disease that can infect a variety of plants worldwide. Fungal pathogen groups are the cause of anthracnose, one of which is Colletotrichum acutatum. Morinda citrifolia is famous for having antimicrobial activity. This study aims to determine the antifungal activity of M. citrifolia leaves extract against the growth of the fungus C. acutatum. The extract solvent used was 96% ethanol. The experiment consisted of five treatments (0%, 20%, 40%, 60% and propineb 0.1% as positive control). The method used in this study was the poisoned food technique. In this technique, C. acutatum was grown on PDA media mixed with M. citrifolia leaves extract. Antifungal activity was observed based on reduced mycelium growth compared to control. Observations were made every day by measuring the diameter of the fungus mycelium for eleven days. The analysis showed that 60% M. citrifolia leaves extract effectively inhibited the growth of the mycelium C. acutatum on the eleventh day of observation.
Teuku Reza Efianda, Uci Elfana Sari, Humeira Humeira, Kiki Rishki Ananda
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.11510

Abstract:
Cyprinus carpio is an economically crucial freshwater commodity in Indonesia and across the globe. Fish demand has a rising trend, which not in line with productivity. Innovation and aspects of food safety are the primary keys to increasing productive capacity. Therefore, the utilization of Manihot utilissima leaves as an alternative to improve national fish's productivity rate is a worthy consideration. They have multiple nutrients, including protein and fat needed by C. carpio seeds. This study aims to determine the optimal dose of M. utilissima supplementation to increase the productivity of C. carpio seeds. The methodology consisted of four treatments (0.5 mL/250 g, 10 mL/250 g, 15 mL/250 g) with four replications for 21 days. The outcome showed that P4 treatment (15 mL) could increase the relative growth rate by 21.10%/day, and it decreased the feed conversion ratio by 0.84. However, there is no significant effect on the survival rate. The study concludes that P4 treatment (15 mL) has positively increased the relative growth rate of C. carpio, and decreased its feed conversion ratio.
Afif Muhammad Akrom, Soedarmanto Indarjulianto, Yanuartono Yanuartono, Trini Susmiati, Alfarisa Nururrozi, Slamet Raharjo, Rief Ghulam Satria Permana, Puveanthan Nagappan Govendan
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.11115

Abstract:
Phenotypic sexing of birds is a common practice among the songbird-keeping community, yet it is based on non-reputable information. This study aims to determine the sex of canaries (Serinus canaria) based on the alignment of the eye with the beak line. A total of 26 samples, consisting of six samples of one-month-old canaries (three males and three females based on PCR examination), 20 samples of six-month-old canaries (10 proven breeding pairs) were used in this study. The birds' heads were photographed from the sides, and then the positions of the eyes were compared with the shadow alignment of the beak. The results provided that 5 young birds and 10 adult birds have a beak line alignment under the eye, while 10 adult birds and 1 young bird have a beak line alignment across the eye. The accuracy of sexing using this method was 100% for both female and male adult canaries. However, this result could not be applied to sample that are not yet sexually mature, as 2 young male birds were found to have beak alignment below the eye. It can be concluded that sexing adult canaries can be performed by observing the eye and beak line's alignment.
Melewanto Patabang, Julianus Dising, Adrin Adrin, Aah Ahmad Almulqu
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.10212

Abstract:
Eucalyptus urophylla is one of the typical plants of the Province of East Nusa Tenggara, Indonesia whose distribution includes the islands of Timor, Alor, Wetor, Flores, Adonara, Lomblen, and Pantar. The best land for the growth of E. urophylla is an area with rainfall above 1000 mm every year. E. urophylla dominate the island of Timor hence the potential to absorb carbon and store it in biomass as part of climate change mitigation. This study aims to determine the allometric equation model to predict the potential of E. urophylla stem biomass. Calculation of the amount of stem biomass based on allometric equations is an analytical method used in this study. The sample trees used in equation modeling is 100 trees as a result of the inventory. The equations that can be used to estimate the biomass potential of the stem of E. urophylla in Timor Island were ln = -2.12 + 2.472 ln ( ) and (R2= 0.98); ln = -3.617 + 1.046 ln and (R2= 0.99); and ln = -3.510 + 2.157 ln ( ) + 0.983 ln and (R2= 0.99). The stem biomass potential with the model I amounting to 276.877 tons ha-1, model II of 279.671 tons ha-1, and model III of 280.209 tons ha-1.
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