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Biology, Medicine, & Natural Product Chemistry

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Published by Universitas Islam Negeri Sunan Kalijaga Yogyakarta

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Biochemistry, Genetics & Molecular Biology Medicine & Pharmacology Public Health

BIOLOGY, MEDICINE, & NATURAL PRODUCT CHEMISTRY, this journal is published to attract and disseminate innovative and expert findings in the fields of plant, animal, and microorganism secondary metabolite, and also the effect of natural product on biological system as a reference source for researchers in these fields, and with the aim to set international standards in their methodology.

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Articles 404 Documents

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Stability of T-DNA Integration in Phalaenopsis “Sogo Vivien” Transgenic Orchid Carrying 35S::Gal4::AtRKD4::GR Endang Semiarti; Exsyupransia Mursyanti; Ahmad Suyoko; Faiza Senja Widya Perdana; Catharina Tri Widyastuti; Aditya Nur Subchan
Biology, Medicine, & Natural Product Chemistry Vol 7, No 1 (2018)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Orchid is an elegant ornamental plant and favoured by the society. Phalaenopsis "Sogo vivien" is a mini-sized orchid with an interesting white-striped purple petals. This study was aimed to analyze the stability of the integration of embryonic gene carrier T-DNA from Arabidobsis AtRKD4 into the P. "Sogo vivien" genome produced in 2016. The study was conducted in 3 stages: 1) Transgenic plant phenotype analysis (1 year old); 2) Examination of T-DNA integration in orchid genotypes using PCR. 3) Analysis of transgenic plant leaf explants’ ability to produce somatic embryo in vitro. In vitro cultures were performed on the base medium of New Phalaenopsis (NP), plus various concentrations of TDZ (0, 1, 2 mg.L-1) and IBA (0, 1, 2 mg.L-1) or without TDZ and IBA as controls. The transgenic Phalaenopsis ‘Sogo vivien’ were transferred to pot mediums via ex vitro with two treatments: the first leaves were cut as explants for in vitro culture, and the plants were transferred to the mixture of fern medium with shavings of bark. The integration of T-DNA in the genome was detected by DNA genome amplification from the second leaves using the AtRKD4 gene primers and the POH1 gene. The results showed that the highest number of somatic embryo (SE) propagules or protocorm like bodies (PLBs) amounted to 27 were derived from transgenic plant # 2 cultured on NP + 2 mg.L-1 TDZ +1 mg.L-1 IBA medium. The presence of AtRKD4 transgenes were detected with the amplification of 380 bp of the RKD4 gene from the genome of transgenic plant # 2 by using PCR. There were 2 out of 15 plants that positively carry the AtRKD4 gene and produce SE. Thus, the stability of the AtRKD4 carrier T-DNA integration in the genomes of transgenic plants was 13.3%.

Comparison of detergent and CTAB method for isolation of DNA from Salak ( Salacca zalacca (Gaert.) Voss. Ã¢â‚¬ËœPondohÃ¢â‚¬â„¢) Arfa, Namira Nur; Daryono, Budi Setiadi; Reflinur, Reflinur
Biology, Medicine, & Natural Product Chemistry Vol 7, No 1 (2018)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

This study conducted in Laboratory of Molecular Biology, Balai Besar Bioteknologi dan Sumberdaya Genetik Pertanian (BB- Biogen) Bogor. The aims of this study are to determine and comparing the quantity,Ã‚Â quality and the efficiency of DNA isolation result using detergent method and CTAB method.Ã‚Â The parameters observed in this study are the value of DNA concentration, purity, and visualization result using gel electrophoresis. The samples are the leaves of Salak Ã¢â‚¬ËœPondohÃ¢â‚¬â„¢ (Salacca zalacca (Gaert.) Voss.). Detergent method is a method which was developed by Faculty of Biology UGM, it has simple method and relatively affordable cost. Meanwhile, CTAB method is one of the commonly used methods of DNA isolation protocol with relatively expensive cost.Ã‚Â Detergent method used detergent in the cell wall separation and protein removal in the sample. The CTAB method used Cetyltrimethyl ammonium bromide (CTAB) for cell membrane separation in the sample. The research methods included DNA isolation with detergent and CTAB methods, PCR analysis and electrophoresis. Data analysis was done quantitatively Ã‚Â using spectrophotometric method and qualitative used electrophoresis method. The result of the study Ã‚Â showed that DNA isolation usingÃ‚Â CTAB method showed higher purity compared with detergent method with the purity values ranging from 1,3- 1,4 . Meanwhile, the concentration of DNA in the detergent method was higher than that of CTAB with the highest concentration of 1730 Ã‚Âµg/ml. There is no difference between theÃ‚Â quality of genomic DNA isolated by CTAB and detergent methods.

Physiological Response of 'Segreng' Rice Plant (Oryza sativa L.) to Biogas Sludge at Wukirsari Village, Cangkringan, Sleman Dwi Umi Siswanti; Nindy Senissia Asri; Mifta Arlinda; Arianda Poetri Shofia Rochman; Akrima Syahidah
Biology, Medicine, & Natural Product Chemistry Vol 7, No 1 (2018)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Wukirsari Village, Cangkringan District is belong to Merapi Mountain’s slopes which located between the Gendol River and Yellow River. Nowadays, we faced the problem of anorganic fertilizer overused such as Urea, ZA, TSP/SP-36 and KCl in agriculture land. The effort to return the soil organic compound can be done by added some organic compounds or microbial bio -organic fertilizer. Sludge is fermented biodigester yield and it has lost its gas. The aim of this research was to understand the physiological response and optimum dose of biogas as planting medium to ‘Segreng’ Rice planted in the rice field of Wukirsari Village, Cangkringan District, Sleman Regency. This research was done on greenhouse scale and rice field scale. The treatment given on 0; 1; 1,5; 2 and 2,5 liters per 100 m2 of rice field areas, and given on 0; 4; 8; 12; and 24 ml per 5 kg soil on polybags. Data were taken in three repetitions. The vegetative growth parameters included plant height, number of leaves, number of seedlings and chlorophyll content, while generative growth parameters measured included NRA levels, dried biomass including crown/stem, roots, filled grains, empty grains, and total weight and number of filled grains, empty rains, and the number of panicles. The result were tested with ONE WAY ANOVA (Analysis of Variance) with SPSS version 19 for Windows and followed by Duncan's Multiple Range Test with 95% significance level (α = 0.05). Generally, the result showed that biogas sludge can increase the vegetative and generative growth of rice plant ‘Segreng’ on polybag scale and rice field scale. The rice plant on polybag with 4 ml biogas sludge was significantly different on the vegetative growth and chlorophyll content, while the rice plant on polybag with 8 ml biogas sludge was significantly different on the generative growth and NRA levels.

Quercetin: the bioactive compound from Allium cepa L. as anti-inflammation based on in silico screening Mohamad Amin; Kurniawan Setia Putra; Ihya Fakhrurizal Amin; Nanda Earlia; Dina Maulina; Betty Lukiati; Umie Lestari
Biology, Medicine, & Natural Product Chemistry Vol 7, No 1 (2018)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Inflammation is a tissue injury that occurs due to physical trauma or microbiological substances that involve the activities of many cell types. Inflammation can be prevented using the natural medicines from Allium cepa L. Quercetin is one of the bioactive compounds found in Allium cepa L and has been reported to have anti-inflammatory activity. The natural medicines have been used to minimize non-steroidal anti-inflammatory drugs. This study aims to investigated the modeling structures and the protein receptor from quecertin in inflammation mechanism and their optimization of the effectiveness in the human body. The bioinformatics tools used in this study are the database of quercetin compounds, Pubchem and Swis Target Prediction protein prediction databases, PyRx 0.8 molecular docking software, ligand docking, and binding site analysis with PyMOL and LigPlus software. The results from in silico show that quercetin compounds can interact with Muscleblind-like protein 1 target protein with a Binding Affinity minus value which is not much different from the dexamethasone compound. Dexamethason is a standart because it is a corticosteroid drug that can be used as an anti-inflammatory to reduce inflammation, allergic reactions, arthritis and other inflammatory diseases.

Cover, Editorial Board, Guidance for Authors, & Table of Contents Riyanto Riyanto
Biology, Medicine, & Natural Product Chemistry Vol 7, No 1 (2018)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Degradation Study of Biodegradable Plastic Using Nata De Coco as A Filler Tiara Nur Elfiana; Anisa Nur Izza Fitria; Endaruji Sedyadi; Susy Yunita Prabawati; Irwan Nugraha
Biology, Medicine, & Natural Product Chemistry Vol 7, No 2 (2018)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Starch is known as a biodegradable raw material that can be degraded by bacteria and microorganisms in the soil. Starch has cellulose which is kind of plant cellulose. This study shows the biodegradation rates of plastic made from Ganyong Canna (Canna edulis Kerr) as a cellulose source which is added with nata de coco as a filler. The biodegradable plastic functional group was confirmed by using FITR. The results show that the O-H group of Ganyong Canna (Canna edulis Kerr) biodegradable plastic is located at wave number 3298.03 cm-1 and shifted to 3290.32 cm-1 after addition of nata de coco. The C-H bonds functional groups in Canna biodegradable plastics and nata de coco plastics are at wave numbers 2920.01 cm-1 and 2916.16 cm-1. While the C-O bonds functional groups in biodegradable starch plastics and nata de coco is shown at wave numbers 995.05 cm-1. The mechanical properties of biodegradable plastics testing are thickness, tensile strength, and elongation based on the ASTM method. The thickness is about 0.1005 mm, the tensile strength of biodegradable plastic is 4,3244 MPa and the elongation value range about 13.9639% while the WVTR range about 14.20 g/m² hours. The results show that the increase of the plastic degradation made from nata de coco occurs between 5% - 38% per days. It is faster than the plastic made from pure Ganyong Canna (Canna edulis Kerr) starch. These results indicate that nata de coco could be added in biodegradable plastic on packaging materials for better degradation.

Comparative Anatomy of Labyrinth and Gill of Catfish (Clarias gariepinus) (Burchell, 1822) and Snakehead Fish (Channa striata) (Bloch, 1793) Ina Karlina; Muhammad Ja’far Luthfi
Biology, Medicine, & Natural Product Chemistry Vol 7, No 2 (2018)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Dumbo catfish (Clarias gariepinus) and Gabus (Channa striata) have additional organ respiratory system structures in the gills, called labyrinth. This organ is a tool for fish to take oxygen directly from the air so that it can live in low oxygen habitats. Both fish have differences at the Order level. Catfish is an order of Siluriformes as Gabus is an order of Perciformes. The purpose of this study was to distinguish the anatomy and histology of the gill structure and labyrinth in both fish. The macroanatomy observation was conveyed by dissection to determine the gill topography in the two fish species. Histology preparations were carried out using the paraffin method and using Hematoxylin-Eosin (HE) staining that showed in the labyrinth organ there were many blood vessels to bind oxygen then distributed to all parts of the fish's body.

Diversity of Angiospermae Plant Class Liliopsida in Mount Nglanggeran Bayu Setya Aji Nugraha; Widodo Widodo; Rendi Yuntara; Normalita Normalita
Biology, Medicine, & Natural Product Chemistry Vol 7, No 2 (2018)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Nglanggeran is a place that has a high plant diversity and there are many unique and unidentified wild plants. This study aims to list liliopside class plants which found around the climbing route. The angiosperm plants in the liliopside class found around the climbing route were successfully identified and consisted of 40 species belong to 17 families.

Link of Nasopharyngeal Carcinoma and Epstein-Barr Virus Sugiyanto Sugiyanto; Lina Aryati; Fajar Adi Kusumo; Mardiah Suci Hardianti
Biology, Medicine, & Natural Product Chemistry Vol 7, No 2 (2018)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Nasopharyngeal Carcinoma (NPC) is a cancer that occurs in nasopharynx which is associated with Epstein-Barr Virus (EBV). Mutation agents in nasopharyngeal neoplasms occur because of EBV infection. Transformation of B-cells due to EBV causes hormone imbalance in lymphoid cells or nasopharyngeal epithelial tissue. Rates of EBV infection have been shown to be prognostic to NPC. The basic level of EBV DNA can be used for stratification prognosis, with higher titers showing greater disease severity and worse outcomes. With mathematical models, there is a correlation between the increase in Epstein-Barr Virus and the increase in Invasive Carcinoma Cells or increase in Nasopharyngeal Carcinoma Cells.

Alizarin Red S-Alcian Blue Staining for Regenerated tail of Common House Gecko (Hemidactylus frenatus) Rakhmiyati Rakhmiyati; Muhammad Ja’far Luthfi
Biology, Medicine, & Natural Product Chemistry Vol 7, No 2 (2018)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Common House Gecko (Hemidactylus frenatus) is one of reptiles that have ability to autotomy their tails. Tail autotomy is a mechanism to protect it self from predators. After the tail broke, there will be wound healing on the tail which is then followed by a tail regeneration event. Original tail and regenerate tail is very different morphologically and anatomically. The original tail is composed of bones while the tail of the regenerate is composed of cartilage. Histochemical staining using Alizarin Red-S Alcian Blue was done to differentiate bone and cartilage. This method will stained bones red while the cartilage will stained blue.

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