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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

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

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

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

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

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

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

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

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

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

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.
Nada Nisrina Maulidya, Siti Rohimah, Zakiyah Ramadany, Tri Ratnasari, Mukhamad Su'udi
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 138-144; doi:10.24252/bio.v8i2.13278

Indonesia has high biodiversity for plant species, including orchids with medicinal potential such as Phalaenopsis deliciosa. Generally, morphological characters, especially in flowers are used for orchids identification. However, when the plants are not in the flowering period, the identification becomes difficult. Therefore an alternative method, such as molecular identification (DNA barcoding) needs to be applied for the best solution. This research, which was conducted with three different markers found that the identity level of matK, rbcL, and ITS to other orchids species was 99-98%, 98%, and 94-96%, respectively. Furthermore, matK and ITS showed high specificity for Phalaenopsis deliciosa, and are therefore recommended as the best molecular identification marker of genus Phalaenopsis.
, Abiyyayumna Rif’At Chasnaurosyiqoh, Joseph Chohansandhika, Feren Putri Sholiha, Nurachmad Bagas Indriarto, Budi Setiadi Daryono
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 172-184; doi:10.24252/bio.v8i2.15648

In this study the genetic resource of Pelung chicken from Cianjur, West Java, Indonesia, was exploited. Pelung chicken has a higher body weight growth, unique meat flavor, and superior posture, compared with other indigenous breeds. Kamper chicken line selective breeding program was conducted, to increase the performance of Pelung breed by crossing with Layer Lohmann Brown-Classic. The Layer Lohmann Brown-Classic is an imported laying-type breed, which is widely known for its reproductive performance, based on the egg productivity. This study aims to use quantitative genetic method in estimating the commercial and reproductive traits' performance of Kamper chicken line. Based on commercial, phenotypic and reproductive traits, the progenies in Kamper chicken line have significant improvements, compared to the parental cross of Pelung and Layer Lohmann Brown-Classic. The quantitative genetic method was used in describing and underlying some phenomenon, in the selective breeding program. Although quantitative genetic method is utilized in basic breeding program with significant precision and rapidness, it is only used in the preliminary study, for the advanced type. Therefore, the addition of quantitative trait loci (QTL), provide a more thorough genetic examination, and play a role in selective breeding program.
, Wien Kusharyoto
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 225-233; doi:10.24252/bio.v8i2.15805

DNA is widely used to construct heterologously expressed genes. The adaptation of the codons to the host organism is necessary in order to ensure sufficient production of proteins. The GC content, codon identity and the mRNA from the translation site are also important in the design of the gene construct. This study performed a strategy for the design of synthetic gene encoding HPV52 L1 protein and several analyses at the genetic level to optimize its protein expression in the Escherichia coli BL21(DE3) host. The determination of the codon optimization was performed by collecting 75 HPV52 L1 protein sequences in the NCBI database. Furthermore, all the sequences were analyzed using multiple global alignments by Clustal Omega web server. Once the model was determined, codon optimization was performed using OPTIMIZER and the web server of the IDT codon optimization tool based on the E. Coli B. The generated open reading frame (ORF) sequence was analyzed using Restriction mapper web server to choose the restriction site for facilitating the cloning stage, which is adjusted for pJExpress414 expression vector. To maximize the protein expression level, the mRNA secondary structure analysis around the ribosome binding site (rbs) was performed. A slight modification at the 5’-terminal end waa carried out in order to get more accessible rbs and increasing mRNA folding free energy. Finally, the construction of the synthetic gene was confirmed to ensure that no mutation occurs in the protein and to calculate its Codon Adaptation Index (CAI) and GC content. The above strategy, which leads to a good ORF sequence with the value of the free mRNA folding energy around rbs, is -5.5 kcal / mol, CAI = 0.787 and GC content 49.5%. This result is much better than its original gene. This result is much better compared to its native gene. Theoretically it is possible that this synthetic gene construct generates a high level protein expression in E. coli BL21 (DE3) under the regulation of the T7 promoter.
Wilson Lamayi Danbature, Zaccheus Shehu, Muhammad Mustapha Adam, Ahmed Mohammed Bello
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 126-132; doi:10.24252/bio.v8i2.17581

One of the objectives of nanotechnology is to synthesize effective nanoinsecticides in a bid to reduce the prevalence of the numerous diseases caused by mosquitoes. This synthesis is even more vital in cases where phytochemicals from plants extracts are used as reducing agents. In this study, phytochemical screening of aqueous sprout extract of Palmyra palm (Borassus aethiopum) was performed, in accordance with some established methods and the results confirmed the presence of alkaloids, flavonoids, saponins, coumarins, glycosides, tannins, phenols as well as quinines, however, sterols, steroids and terpenoids were not detected. Subsequently, the sprout extract was used as a reducing agent in the synthesis of silver nanoparticles (AgNPs). Characterization with Fourier transform infrared and Ultraviolet-visible spectrometry was then carried out to confirm the synthesis. In addition, the AgNPs were further analyzed for larvicidal potency against 1st, 2nd 3rd and 4th instars Culex quinquefasciatus mosquito larvae, at interval concentrations of 5, 10, 20, 25 and 50 ppm. The LC50 and LC90 values discovered to be 9.103 ppm and 134.463 ppm with a correlation of 0.815, as well as 10.316 ppm and 118.810 ppm with a correlation of 0.801, for the 1st and 2nd instars, respectively. Meanwhile, the 3rd and 4th instars had LC50 and LC90 values of 17.585 ppm and 179.052 ppm, respectively, with a correlation of 0.807. This study provides a basis for extracting and analyzing the reduction potential of the phytochemicals present in the sprout extract, as well as the application of AgNPs, in controlling mosquito larvae population.
Suci Rizki Nurul Aeni, Ni'matul Murtafi'Ah, Handarini Handarini
Biogenesis: Jurnal Ilmiah Biologi, Volume 8, pp 119-125; doi:10.24252/bio.v8i2.12274

The Citarum River was regarded as the World’s dirtiest river in 2018, characterized by a Basin situated adjacent to several textile and electroplating industries. Hexavalent chromium metal (Cr6+) is a toxic, carcinogenic heavy metal found in the wastes of these industries. Furthermore, biosorption with biological adsorbents, including Saccharomyces cerevisiae and Rhizopus oryzae, is an alternative method for treating water polluted with heavy metals. This study therefore aims to adsorb Cr6 + heavy metals from Citarum River water using S. cerevisiae and R. oryzae biomass in two locations: Nanjung and Pangauban, with various biomass concentrations and stirring speeds. For this study, 0.25, 0.5, and 0.75 g of R. oryzae suspension, as well as 250, 500, and 750 µ of S. cerevisiae were used as adsorbent, while rotated at speeds of 250 rpm, 750 rpm and 1500 rpm. Subsequently, the Cr6 + metal content was measured using a UV-Vis spectrophotometer at a wavelength of 525 nm, and calculated based on a standard curve. The results showed S. cerevisiae and R. oryzae are able to reduce the levels of Cr6+ in Citarum river water. The most reduction was obtained with the highest concentration of the adsorbents, 750 µ for S. cerevisiae and 0.75 g for R. oryzae, at the speed of 1500 rpm. S. cerevisiae and R. oryzae have great potential as biosorbents for the in situ remediation of Citarum River contaminated with heavy metals.
Retno Susilowati, Nailirrohmah Hidayatin, Amalia Rizka Diana, Tri Kustono Adi
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.11973

Diabetes initiates augmented damage in levels of nuclear and mitochondrial DNA in males. As a result, the sperm DNA is affected, as well, leading to lower levels of fecundity and influencing reproductive health. This study aims to improve male reproductive function and oxidative stress status in diabetic rats. Combination High Fat Diet (HFD) and Streptozotocin (STZ) injection 30 mg/kg intraperitoneally are the initiations of DM-2 for 14 weeks. Treat therapy using 80% ethanol extract of black cumin seeds takes five weeks. Based on parametric test on ANOVA test results followed by Duncan Multiple Range Tests on the concentration, abnormalities of spermatozoa and Super Oxide Dismutase (SOD) effects and the Kruskal-Wallis test followed by the Mann-Whitney test on non-parametric data of the spermatozoa motility and Malondialdehyde (MDA) levels, showed that obtaining black cumin dose 48 is an effective dose in improving sperm quality and stress oxidation level. It has the same effect with metformin, even has MDA level less than normal rats. This study finds out Ns-48 is an effective dose of ethanol extract of black cumin seeds to improving spermatozoa quality and stress oxidation level, so that it becomes valuable information for research related to the improvement of reproductive function in diabetes mellitus disease.
Erlia Narulita, Gerda Permata Aji, Bevo Wahono, Siti Murdiyah, Ria Yulian
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.11280

Foodborne disease caused by Escherichia coli contamination is increasing every year. It also followed by elevating of drug-resistance of E. coli. Bacteriophage can be an alternative for therapy infection. This study aimed to determine synergism effect of bacteriophage ϕPT1b which has a high rate virulence to E. coli and phage-antibiotics (tetracycline and amoxicillin) synergy. The indigenous bacteria isolates were KR, MJ, KP, PT, PR. Five bacteriophages used namely ϕKR1b, ϕKR2, ϕPT1a, ϕPT1b, and ϕMJ1b. Virulence test was used to determine the ability of each phage in reducing E. coli. Treatment to examine synergism of phage ϕPT1b and antibiotics were P1: amoxicillin, P2: ϕPT1b, P3: ϕPT1b + Amx = 1:1, P4 : ϕPT1b + Amx = 2:1, P5: ϕPT1b + Amx = 1:2, P6 : tetracycline, P2: ϕPT1b, P7: ϕPT1b + Tet = 1:1, P8 : ϕPT1b + Tet = 2:1, and P9: ϕPT1b + Tet = 1:2. The virulence test showed that isolate ϕPT1a with 106 CFU/ml had the highest ability in reducing E. coli. While, the result of synergism test indicated that the synergism of bacteriophage and antibiotics differ significantly (P ≤ 0.05). The best ratios of synergism were 1:1 (ϕPT1b+tetracycline) and 2:1 (ϕPT1b+amoxicilline). In summarize, phage-antibiotic synergy (ϕPT1b with tetracycline/amoxicilline) can reduce the level of antibiotic resistance in isolated E. coli.
Ani Sulistiyani, Syamsul Falah, Triadiati Triadiati
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.11686

Vetiver grass (Chrysopogon zizanioides, Poaceae) is the leading commodity in Garut Regency, Indonesia, the second-largest producer in the world of vetiver oils. The content of vetiver oils is strongly influenced by the environment, for example, drought stress. Drought stress causes plants to adapt by producing secondary metabolites such as essential oils. This experiment aimed to analyze growth, phytocomponents and obtaining the best quality of vetiver grass accessions under drought stress. The results showed that root and shoot dry biomass were significantly affected by the interaction between drought stress duration and vetiver grass accession. The root dry biomass of Kamojang accession decreased by 25.4%, while Cilawu increased by 5% for 4 days of drought stress. The root length and shoot length were not significantly affected by the treatment. The highest root/shoot length ratio was Verina, and the lowest one was Cisarua. The highest increase in proline occurred in Cilawu accession (85.7%), while the lowest was Verina (6.67%). Essential root oils contain 53 types of phytocomponents, dominated by sesquiterpenes, being khusimol, the highest type. The Cilawu is the best accession based on growth and content rendement.
Rahadian Yudo Hartantyo, Helen Eko Putro, Epa Yohana Toga Torop, Laksmindra Fitria, Mulyati Mulyati
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.11168

Several physiological alterations that arise in response to hypoxemia conditions when diving are intended to protect oxygen-sensitive organs from the hypoxic condition. Hippocampus, known for its central function in memory formation, is sensitive to hypoxic conditions. This research aimed to study the effect of voluntary diving exercise (VDE) on the hippocampus-dependent learning performance of rats. Rats were divided into control and diving groups, with swim and voluntary diving exercises every day for 60 days, respectively. Observation of memory consolidation was carried out using Morris Water Maze (MWM) and Novel Object Recognition (NOR) tests. In the MWM test, the escape latencies in the diving group were shorter than those in the control group. Consistent results were obtained in the MWM probe trial which the time spent in the target quadrant was significantly longer in the diving group. Moreover, the diving group spent more time exploring the novel object in the NOR test. Based on the results, we can conclude that 60 days VDE significantly improves hippocampus-dependent learning capacity in trained rats.
, Hidayatun Muyasyaroh, Abdul Aziz Jaziri, Nada Itorul Umam
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.10826

Protease is an important enzyme widely produced by microorganisms applied in food, health, and industry. Mangrove ecosystem, a rich microorganism habitat, accounted as a new resource for isolating the proteolytic bacteria. The purpose of this study was to identify protease-producing bacteria from mangrove ecosystems in the Tuban area, Indonesia. Three isolates that produced the gelatinase was successfully isolated from mangrove sediments. Bacterial isolates were then tested for extracellular gelatinase. The results showed that isolate T1 had high gelatinase activity. Two isolates (isolates T2 and T3) produced moderately gelatinase enzymes. Molecular identification revealed that isolate T1 is Enterobacter hormaechei.
Nova Mujiono, Ristiyanti M Marwoto, Heryanto Heryanto
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.13212

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

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.
, Yanti Yanti, Salim Salim, Harish Muhammad
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.13137

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.
, Anugrah Viona Agesi, Dewi Imelda Roesma
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.13019

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.
Teuku Reza Efianda, Uci Elfana Sari, Humeira Humeira, Kiki Rishki Ananda
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.11510

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

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

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.
Oktira Roka Aji, Larasati Haliimah Roosyidah
Biogenesis: Jurnal Ilmiah Biologi, Volume 8; doi:10.24252/bio.v8i1.12009

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.
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

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

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.
Andri Maulidi, Mohamad Jakaria, Nurul Fitriyana, Muhammad Rizki
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i2.10072

A large number of forests at Munggu Village, Ngabang District, Landak Regency have been converted into oil palm and rubber plantations. As consequences, natural habitats in the region have been fragmented and species diversity, including herpetofauna, has been decreased. This study aimed to assess herpetofauna diversity in four different habitats in Munggu Village: (1) forests, (2) Landak river, (3) tourist areas, and (4) rubber plantations. Data collection used Visual Encounter Survey (VES) for 8 days.[u1] The results showed that the total of 24 herpetofauna species: 15 amphibians’ species (4 families) and 9 reptiles species (6 families) have been recorded from the four sampled areas. Of the four locations 11 species were found in river habitat in the forest, 4 species in the location of Landak river, 8 species in tourism sites and 9 species in rubber plantations. The Shannon-Wiener (H') diversity index in all four habitats was classified as moderate. In the river location in the forest, H' was 2.14, in the Landak river it was 1.28, in the tourism sites it was 1.71 and in the rubber plantation it was 1.87. However, the evenness index (E) for the herpetofauna community in all four locations was >0.80. Habitat loss and habitat destruction are among the causes of decline in amphibian and reptile populations. Knowing the diversity of herpetofauna, it is hoped that the community and stakeholders can collaborate to secure the herpetofauna in Munggu Village.
Yohanes Bare, Dewi Ratih Tirto Sari, Yoga Tribakti Rachmad, Gabriella Candrakirana Krisnamurti, Agustina Elizabeth
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i2.9847

Inflammation was signs of pathological or abnormality in tissue to give an alert as a trouble signal to the system. Therapeutic using NSAIDs has some side effects. This research explored the potential role of chlorogenic acid as natural therapeutic compound to inhibit the inflammation target such as COX-2 by interaction model. The research method used in this study was the molecular docking approach, which binds ligand and protein. Protein data provided by Protein Data Bank (ID: 6cox) while, chlorogenic acid obtain from PubChem (CID: 1794427). We docked COX-2 and chlorogenic acid using Hex 8.0.0. Visualization and analysis of the molecular interactions of chlorogenic acid and COX-2 conducted by the Discovery Studio Client 4.1 software. Chlorogenic acid has a high permeability and is easily absorbed based on five Lipinski Rule. Interestingly, we found Fifteen amino acid was binding with chlorogenic acid that formed by hydrogen bond and van der Waals.The interaction between ligand-protein results in energy binding -327.59cal/mol. Chlorogenic acid has a potential role to inhibit inflammation pathway by inhibiting COX-2. We predicted chlorogenic acid has a potential as therapy anti-inflammatory to suppress COX-2 as mediator inflammation.
Putu Ayu Damayanti, Budi Setiadi Daryono,
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i2.9493

GK-Bro (Gallus gallus Linnaeus, 1758) is a hybrid chicken from crossing between ♀ F2 Broiler ♂ F2 Golden Kamper that have variation of phenotypic character. To meet the market’s demand, GK-Bro must have prime phenotypic character in both quantity and quality. This research aims to examine the phenotype character that occur in GK-Bro by the character of feet morphometry, crest’s shape, feather’s color, and feet’s color. The parental chicken are crossed in Innovation and Agriculture Centre of Gadjah Mada University (Indonesia) and produce 11 chickens with five males and six females filial. The filial are maintained intensively and qualitative data were observed at the end of seven weeks, classified based on the percentage of the phenotypic class. Quantitative characters that observed were tibia and femur length after seven weeks, using control pelung, broiler, and F1 broiler. Quantitative data showed that the average length of the tibia and femur of GK-Bro is lower when compared to the control but the ratio of feet morphometry is closer to pelung. Qualitative data classified crest form in one class, feather’s color in 4 classes and feet’s color in 3 class.
Hery Fajeriadi, Dharmono Dharmono
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i2.7647

Indonesia as the largest archipelago country in the world has a vast coastline. Various types of ecosystems are scattered on the coast, one of which is coastal forest. One of the functions of coastal forests is as a habitat for flora, including rattan siit (Daemonorops melanochaetes, Blume.). Siit rattan has a fairly stable commercial value on the market. Its strong structure makes it attractive, not only nationally, even internationally. This study aims to determine the population structure of siit rattan in the coastal forest of Tabanio Village, Takisung District, Tanah Laut Regency. Data collection was done with total roaming techniques, namely along the coastal forest with a width of 50 m and a length of one thousand m to the south. The results of the study were analyzed descriptively. The age of siit rattan (Daemonorops melanochaetes, Blume.) includes a wide base pyramid, without any stopping or decaying of growth in the pre-reproductive and reproductive phases. Natality rattan siit went well, and almost did not experience mortality because the coastal forest of Tabanio Village was guarded by custom by the local community. Environmental factors that inhibit the reproductive rate of siit rattan are air temperatures that were too high from the optimal temperature of siit rattan breeding.
Hasan Basri, Meilinda Pahriana Sulastri
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i2.9315

Japanese quail (Coturnix coturnix japonica) is one of the livestock sectors that is efficient in providing nutrition, both from eggs and meat. This study aims to examine the effect of provision of standard organic feed and organic feed containing cassava leaves, turmeric powder and ginger on increasing the percentage of carcasses and internal organs Japanese quail (Coturnix coturnix japonica). This study used an experimental method with a completely randomized design pattern. The test animals used were 30 females Japanese quail which were divided into 3 groups, i.e. P0: control (given commercial feed); P1: given standard organic feed (corn, soybeans, bran and fish meal); P2: given organic feed (corn, soybeans, bran, fish meal, cassava leaves, turmeric and ginger powder). Each group was treated with 5 replications. Data obtained were analyzed using analysis of variance (ANOVA) and continued with Duncan test with a confidence of 95% (P>0.05). The results showed that the provision of organic feed could not increase the percentage of carcass, heart and liver, but could increase the percentage of Japanese quail gizzard (Coturnix coturnix japonica).
Efry Roziaty, Putri Agustina, Siti Naily Rohmah
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i2.6336

The concept of epiphytic plants is a critical plant that determines the processes that occur in ecosystems. Epiphytic plants especially Bryophytes or commonly moss is one of primary productivity. This study aims to record any epiphytic moss in their natural habitat in the Jumog Waterfall Forest Ngargoyoso in Karanganyar Tawangmangu Central Java. The method used in this study was purposive sampling, this method using exploration techniques. Field data observed were epiphytic plants from the Bryophyte groups (moss plants). The results showed that there were five moss colonies namely Bryum billardieri, Octoblepharum albidum, Leucobryum aduncum, Heteroscyphus coalitus and Pogonatum neesii, in 3 different zones of phorophytes, name zone I, II and III.
Eva Septiyana, Sri Darmanti, Nintya Setiari
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i2.10146

Red okra fruit has high nutritional value and fiber but still has low production. Monosodium glutamate (MSG) consists of sodium and glutamic acid. In plants, sodium can role of replacing potassium, stomata physiology, and chlorophyll biosynthesis. Glutamate as the nitrogen donor in primer metabolism and gibberellic acid precursor. The assumption that MSG in plants has a positive impact. This research aimed to examine the effect of MSG and the optimum dosage for enhances of growth and production. This research was conducted with Completely Randomized Designs (CRD) with one factor, is the MSG dosage (0, 3, 6, and 9 g). Quantitative data were analyzed using analysis of variant (ANOVA) dan Duncan’s Multiple Range Test (DMRT) at a 95% confidence level. The result shows that the MSG treatment enhances the growth of the okra based on parameters of plant’s height, fresh weight of plant, dry weight of plant and the width of the leaf and enhances the production of the okra based on the flowering time, the number of the flower, the number of the fruit, the percentage of flower becoming fruit, the weight of fruit, width of fruit, and the diameter of the fruit. The optimal dosage of MSG for okra production and growth is 3 g/plant.
Dion Satrio Pambudi, Agus Nuryanto, Romanus Edy Prabowo
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i2.10205

Labridae is a large and diverse fish family. Many species under Labridae inhabits Indonesian coral reefs. However, limited scientific data are available on ornamental fish diversity in Labridae from the South Coast of West Java. The purpose of the research is to give information about species diversity and phylogenetic relationships among species of Labridae fish family in the South Coast of West Java. This research will be conducted using a survey method with a purposive sampling technique. The observed parameters include morphometric and meristic characters and evolutionary relationships among species within Labridae family species collected from the South Coast of Sukabumi and Garut, West Java. Morphological data will be analyzed descriptively based on morphometric and meristic data. Species-level identification performed by referring to the available identification guide book. Phylogenetic relationships will be analyzed statistically using cladistics method as implemented in PAUP 4.0 applying maximum parsimony algorithm. The cladogram has a consistency index of 0.563, indicating low homoplasy and proved that the tree was the most parsimonious. Labridae formed monophyletic clade compared to Acanthurus maculiceps, and Cheilio inermis was basal species while the others derived species.
Isna Mustafiatul Ummah, I Wayan Swarautama Mahardhika, Budi Setiadi Daryono
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i2.9993

On the recent classification of native Indonesian chicken, there are 31 breeds of chicken. Highly circulated chicken breed in Indonesia is fast-growing broiler that includes several strains such as Cobb 500, Hubbard, Hybro, Isa Hyline, and Hisex. Fast-growing broiler chickens have rapid growth, with excessive fat deposition on chicken carcass which implicates a health problem and unfavorable meat quality. Gama Ayam Research Team conducted selective breeding which produces two new chicken breed Kamper and Kambro. Further selective breeding then crossbred female F1 Kamper and male BC1 (backcross I) Kambro. In this research morphological traits, productive performance and genotyping of PPAR gene related to fat deposition gene and blood lipid content in Gama Ayam were identified. Based on data analysis hybrid chickens morphological traits it concluded that Gama Ayam has a significant variation based on feather color. The productive performance was determined with the feed-conversion ratio (FCR) value which was 3.17. Genotyping of PPAR gene resulted in four polymorphisms that formed 14 haplotypes groups. Based on blood lipid content analysis of cholesterol content, triglycerides content, HDL and LDL, Gama Ayam have significantly lower content of cholesterol (107.05 mg/dl), LDL (44.71 mg/dl) and triglycerides (22.41 mg/dl). PPAR gene polymorphisms are not correlated with blood lipid content in Gama Ayam. A significantly strong correlation between PPAR gene polymorphism on the bodyweight of Gama Ayam at 49-days-old. Triglyceride level, cholesterol level and LDL level in Gama Ayam were lower than broiler chicken. Further research with a larger population size and sex classification of hybrid chicken must be conducted to validate the results.
Donan Satria Yudha, Wulan Rahmani Akmal, Rury Eprilurahman
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i2.10174

The research about frogs and toads diversity in the Code River, Province of Daerah Istimewa Yogyakarta (DIY) had been done in 2012 (Yudha et al, 2013). Now, after five years passed, we conduct monitoring activities to updating its diversity and distribution. After five years, we consider that there are many changes along the river that influenced habitat condition for frogs and toads which live along and near the river. Some of the changes are unused land became human settlement or paddy fields and waste land. The purpose of this research is to monitor the diversity of frogs and toads after five years along Code River. The method used was line transect combine with visual encounter surveys (VES) and river bank cruising. Results show that the species number of frogs and toads found in 2012 were slightly higher compare to 2017. The frogs and toads on upstream part were diverse in 2017 compare to 2012 due to natural restoration of riparian vegetation occur on upstream. The frogs and toads on midstream part were less diverse in 2017 compare to 2012 due to increasing human activities near the river and less riparian vegetation. The frogs and toads on downstream part were also less diverse in 2017 compare to 2012 due to increasing human activities near the river and more household waste stuck on riparian vegetation. There was variation of anurans diversity after five years due to changing on physical condition of the river and human activities near the river.
Suparti Suparti, Lina Agustina, Putri Agustina, Resti Rahmawati
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i1.6102

Potato Dextrose Agar (PDA) is the most media to grow the mushrooms, but the price of this media is expensive. Thus we need alternative media that easy and cheap to get it. This study aims to determine the growth of Aspergillus niger in alternative Artocarpus communis and Artocarpus heterophyllus seeds media. This research was an experimental study using a completely randomized design (CRD) one factor was the type of media is PDA (M0), Artocarpus communis seed media (M1), Artocarpus heterophyllus seed media (M2) and using the test mushrooms A. niger (J1). Inoculation of A. niger used agar block method for 3 days with a temperature of 28°C. Parameter of research was colony diameter and sporulation of A. niger. Data obtained with qualitative and quantitative methods. The result of this research showed that the best growth for Aspergillus niger was after 72 hours incubation. Colony diameter continually in PDA media, Artocarpus communis media, and Artocarpus heterophyllus media is 4.7 cm, 4.3 cm, and 4.1 cm with heavy sporulation. Therefore, Artocarpus communis and Artocarpus heterophyllus seeds media can be utilized as a substitution of PDA media for the growth of mushrooms.
Agus Nuryanto, Rani Eva Dewi, Hendro Pramono
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i1.6352

Commerson’s anchovy (Stolephorus commersonnii) is a small pelagic fish that live in a group and its existence is very abundant in Segara Anakan Cilacap. This anchovy is widely consumed by communities live around Segara Anakan. This leads to a high exploitation rate. Exploited populations generally have low genetic diversity. This study aims to evaluate genetic diversity of commerson’s anchovy population in Segara Anakan Cilacap inferred from PCR-RFLP of the cytochrome c oxidase 1 (CO1) gene. This study was conducted from January to April 2018 and used survey method by applying random sampling. As many as 30 samples of anchovy were taken. Genomic mtDNA was isolated using modified Chelex method. Partial sequences of the COI gene were amplified using a pair forward commercially available primer. The lengths of 650 base pair of the PCR products were digested with four restriction enzymes. The HindIII enzyme produces PCR-RFLP fragment with the size of 416 bp and 234 bp lengths, VspI produces 435 bp and 214 bp, CO1-TaqI produces 556 bp and 94 bp and RsaI produces 319 bp, 183 bp, and 148 bp fragments, respectively. The PCR-RFLP fragments were obtained from all samples but they produced uniform band pattern for all 30 anchovy individuals. These results indicated that the anchovy population in Segara Anakan Cilacap has monomorphic allele for all PCR-RFLP markers. Hence, it can be concluded that genetic homogenity was observed on anchovy population in Segara Anakan Cilacap as inferred from PCR-RFLP COI gene.
, Lia Rahayu
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i1.5786

Data from the Malang City Health Office shows the increasing number of refill drinking water depots in the city of Malang until 2013 there were 163 drinking water depots scattered in each Malang Subdistrict. The purpose of this study was to determine the contamination of Escherichia coli refill drinking water in drinking water depots in Malang. The samples taken were 20 refill drinking water depots in Malang. Sampling is done by simple random sampling. Escherichia coli examination using the Most Probable Number Test. Of the 20 samples tested, 2 samples met the requirements of drinking water quality according to PERMENKES and 18 other samples containing the number of coliform bacteria exceeding the maximum limit of 0 per 100 ml of water. There were Escherichia coli in 10 samples while 8 other samples contained other coliform bacteria.
, Elis Kartika, Lizawati Lizawati
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i1.5990

Opencast mining caused heavy deforestation and barren land in Jambi. This ex-mining land must be reclaimed by planting crops based on biofertilizers containing mycorrhizae, this is a potential alternative that provides benefit both agronomy plant and ecosystem specially replanting with oil palm. Those are the technology for reclamation ex-coal mining soil. This research aim is to examine the effect of four combinations indigenous isolate of Arbuscular Mycorrhizae Fungi (AMF), which is originated from ex-coal mining soil that combined with Phosphorous fertilizers to minimize utilizing P fertilizer at oil palm pre-nursery, to improve soil fertility, and seedling growth. Hence, this research was arranged in factorial experiment with 2 factors, using a complete randomized design with three replications. The first factor is five different mycorrhizae isolates, representing a broad range of endomycorrhizae fungi, there are: without indigenous AMF, isolate of Glomus sp. 3, isolates of Glomus sp. 6, isolates of Glomus sp. 15 and isolates of Glomus sp. 16. The second factor is P fertilizer: control (without P fertilizers), fertilizer dosage P 25%, 50%, 75%, and 100%. Variables measured are shoot height, number of leaves per plant, total leaf area per plant, and plant stem diameter. The data were analyzed by analysis of variance to see whether there was an interaction between the MVA isolate and the P fertilizer dosage. The result showed a significant effect on palm oil seedling growth, shoot height, number of leaves per plant, total leaf area per plant but there is no interaction on the stem diameter. Plants that are inoculated with mycorrhizae have greater P content in leaves than those not inoculated. The types of isolated Glomus sp.3 and dosage P 75% of recommended dosage, give the best seedling growth. This research concluded that inoculation with AMF could minimize P fertilizers doses.
Muhammad Efendi, Rugayah Rugayah
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i1.6239

Farah Nadia Karima, Mulyati Sarto
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i1.7292

Stress is a psychiatric/psychological disorder characterized by a sense of disability, despair, anhedonia, decreased activity, and pessimism. Stress can affect the physiological condition of the body with symptoms of lipid metabolism disorders. Chlorella vulgaris is a microalgae that is known to have the potential as an alternative antidepressant drug. The study was conducted to determine the lipid profile of blood wistar strain rats after stress induction and the effect of administration of Chlorella vulgaris on blood lipid profiles of stress-induced wistar rats. This research is an experimental study using 5 treatments with 25 models of Rattus norvegicus wistar strain, 2 months old. The treatment group consisted of 1 control group, 1 stress group, and 3 groups of treatment variations, namely the treatment of antidepressant medication, the treatment of administration of cultivated Chlorella vulgaris, and the treatment of commercial Chlorella. Stress induction is carried out by treatments that given to the rats randomly, namely cold water, warm water, wet cage, dark-light cycle, and sound wave exposure for 40 days. Examination of blood lipid profiles was carried out on Day 0 after mice were acclimated, day 40 after rats were induced stress, and day 56 after rats were given treatment of cultivated Chlorella vulgaris. The results obtained were the stress conditions of the lipid profile of the wistar strain of rats which had increased were total cholesterol levels of the control group and triglyceride levels in all groups while those who had decreased were cholesterol levels other than the control group, HDL levels in all groups, and LDL levels all groups. Giving Chlorella vulgaris had effect on decreasing total cholesterol levels, triglyceride levels, and LDL levels along with increasing HDL levels.
Ganies Riza Aristya, Rezika Alyza
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i1.5250

Strawberry is fruit commodities which originating from the member of Rosaceae and has been widely cultivated in several countries of the world including Indonesia. One of the strawberry cultivars which consumed and cultivate in Indonesia is the strawberry Festival (Fragaria x ananassa D. var. Festival), which was developed in the area of Banyuroto, Magelang. In order to improve the quality and quantity of strawberry plants, polyploidization using colchicine has been employed in previous studies. The objectives of this research were study the chromosome character which include number, size, shape, and karyotype of normal strawberries and treatment strawberries with colchicine (0.05% 36 hours of root and leaf induction, 0.05% 24 hours of root and leaf induction, 0.05% 36 hours of leaf induction, 0.01% 36 hours of root and leaf induction). The results of this research shown that chromosome number difference and degree of ploidy between Fragaria x ananassa var Chandler in America with Fragaria x ananassa var. Festival in Indonesia due to natural mutation. While Festival strawberry control and treatment colchicine have same number chromosome is 2n=4x=28M and there are a difference long sleeve and short sleeve chromosome that may affect the content of chromosome expression and phenotype character are produced. The analysis of flow cytometry showed that treatment strawberry with colchicine has two peaks with intensity fluorescence equal to strawberry control so that it can be interpreted that the ploidy number of strawberries treatment with colchicine is tetraploid.
Angga Prasetyo, Boy Rahardjo Sidharta, Yustina Sri Hartini, Exsyupransia Mursyanti
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i1.6000

Red ginger (Zingiber officinale var. rubrum) has been proven to show anticancer activity. Direct use bioactive compound from red ginger has many obstacles such as large amount of red ginger’s rhizome needed, limitation of planting area, and very long time of harvesting. Utilization of endophytic fungi from red ginger’s rhizome could be an alternative to the problems. The aims of this study were to determine bioactive compound produced by endophytic fungi and toxicity activity based on LC50. Endophytic fungi were isolated from red ginger and were identified macroscopically and microscopically. The bioactive compounds were extracted using ethanol 96%. Flavonoid test was done qualitatively, bioactive compounds were analyzed by Thin Layer Chromatography (TLC), and the toxicity test was done using Brine Shrimp Lethality Assay (BSLA). The present research found two endophytic fungi isolated from red ginger rhizome. Isolate 1 was similar to Mucor sp. and isolate 2 was similar to Trichoderma sp. Phytochemical test revealed bioactive compound extracted from the isolates were contained flavonoid. TLC analysis did not detect quercetin from the bioactive compound extracted from the isolates. LC50 values of the bioactive compound from the isolates were 2.300 and 1.747 µg/ml, respectively. The toxicological results suggest that both isolates produce non-toxic compound to Artemia salina.
Rich Gemilang Simanjuntak, Rury Eprilurahman
Biogenesis: Jurnal Ilmiah Biologi, Volume 7; doi:10.24252/bio.v7i1.7803

The shape of chelae and carapace can be used to distinguish between species of prawn. This study aims to determine the variations in the shape of chelae and carapace in several species belonging to the genus Macrobrachium using analysis of geometric morphometric. This study uses photos of specimens that have been processed with several TPS software. Data analyzed statistically by PCA using the MorphoJ software. Clustering analysis using UPGMA method using PAST software. The results showed the carapace shape grid deformation varied at the tip of the rostrum, the tip of the ocular spine and the lower curvature of the front of the carapace, and the base spines of rostrum. Grid deformation in the shape of chelae varies at the tip of the pollex, the junction between the pollex and the manus on the inferior margin of the propodus, the upper and lower points marking the junction of the dactylus with the propodus. PCA shows the total variation of the carapace shape is 82.66% which is divided into PC1: 75.11% and PC2: 7.55%. While the total variation of the shape of chelae is 87.56% which is divided into PC1: 55.49% and PC2: 32.07%. Clustering analysis shows the grouping of populations of Macrobrachium, the first group is M. latidactylus and M. sintangense, the second group includes M. horstii and M. latimanus. M. lar is a species that shows the similarity of the shape of the carapace and chelae with the two groups. M. rosenbergii and M. pilimanus are on different lines.
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