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All Journal JBIO: jurnal biosains (the journal of biosciences) Indonesian Journal of Tropical and Infectious Disease Biota Bioeksperimen: Jurnal Penelitian Biologi Journal of Tropical Biodiversity and Biotechnology Indonesia Journal of Halal Indonesian Journal of Halal Research Journal of halal product and research (JHPR) Jurnal Riset Biologi dan Aplikasinya Sains dan Matematika Genbinesia Journal of Biology BIOTROPIC
Yuanita Rachmawati
UIN Sunan Ampel Surabaya
Religion Agriculture, Biological Sciences & Forestry Humanities Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Dentistry Earth & Planetary Sciences Economics, Econometrics & Finance Education Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics Public Health Social Sciences Veterinary Other

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Optimization of Various ITS rDNA Amplification Protocol of Yeast Isolated from Giant Honey Beehives (Apis dorsata) Choiriyah, S.Si, Chumaidatul; Firdhausi, Nirmala Fitria; Tyastirin, Esti; Rachmawati, Yuanita; Hadi, Moch. Irfan
Jurnal Riset Biologi dan Aplikasinya Vol. 3 No. 2 (2021)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jrba.v3n2.p80-87

Abstract

Indonesia is a country with high variability of microorganisms, including bacteria, yeast, and fungi. Yeast isolates could be isolated from the honeycomb of Apis dorsata. Molecular approaches were used to identify yeast using ribosomal DNA gene sequences, called the ITS gene. The optimum condition for DNA extractions and amplifications are needed for the successfully of molecular identification. Therefore, it is necessary to optimize the DNA extraction and amplification of several protocols to obtain good identification results. This study aimed to compare the effects of DNA extraction with various temperatures and different amplification protocols. LIPI reference DNA extraction protocol with the boiling method and variations in incubation time of 10, 15, and 20 minutes at a temperature of 98° C. Meanwhile, for the amplification of yeast DNA using a variety of different amplification protocols. The results showed the optimal time of incubation was 10 minutes in K1 isolates with DNA purity of 1.896. meanwhile, for isolates K2, K3, and K4 each with a purity of 2.246, 2.335, and 1.748. optimal DNA amplification results were indicated by the presense of DNA bands for each sample K1, K2, K3, and K4, namely 503, 542, 492, and 526 bp. In this study, it can be concluded that the optimal incubation time for the extraction process is 10 minutes. In addition, the optimal amplification protocol was shown in the DNA bands in all sample.
Frequency of ABO blood system type alleles in students of UIN Sunan Ampel Surabaya Kautsar, Radinal; Putri, Siti Aisyah Bisri; Azzhahara, Nabillah Ayu; Aini, Humayra Qurrata; Pradiptaadi, Brian Pramana Aprilio; Nabila, Salsa; Arrohmah, Robiatush Sholichah; Rachmawati, Yuanita
Genbinesia Journal of Biology Vol. 1 No. 3 (2022): July 2022
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v1i3.27

Abstract

The commonly used human blood group system is the ABO system. Determination of blood group is important in blood transfusion activities. The purpose of this study was to determine the frequency of the ABO blood group system and the frequency of the ABO blood group allele in students of the Biology and Science Education study program at UIN Sunan Ampel Surabaya. Determination of blood group was carried out by the Slide Test method which was carried out randomly with a sample of 90 people. Determination of blood group is done by the principle of agglutination that occurs between antigens and antibodies. The results showed the frequency of blood group ABO system: A (20%); B (24%); AB (10%); O (46%). IA allele frequency (0.13); IB (0.07); IO (0.8). The proportion of the highest frequency of blood type is blood type O. These results indicate that the distribution of blood type O among students at UIN Sunan Ampel Surabaya is relatively the same as the results of other studies conducted in Indonesia.
In silico research of anti-CHIKF phytoconstituent-based from Physalis peruviana leaves via molecular docking and dynamics analyses Setiyowati, Putri Ayu Ika; Mahbubillah, M. Ainul; Aini, Nur Sofiatul; Rachmawati, Yuanita
Genbinesia Journal of Biology Vol. 3 No. 1 (2023): November 2023
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v3i1.62

Abstract

Chikungunya fever (CHIKF) is an infectious disease that has similar symptoms with dengue fever (DF). Several drugs have been offered to treat both dengue (DENV) and chikungunya virus (CHIKV). Investigating anti-CHIKF potential from nearby plants is one strategy to produce potential drug to reduce CHIKF in endemic countries. Physalis peruviana is one the promising object to be new anti-CHIKV drug candidate. This study aimed to analyze the anti-CHIKV agents from leaf parts of P. peruviana. Ligand and protein samples were collected from multiple sources. The phytoconstituents were evaluated their drug-likeness properties throughout SwissADME webservers. Selected ligands then docked via PyRX and measured the output by binding affinity. Visualization of the best outputs was carried out using BIOVIA Discovery Studio. CABS-flex was carried out to screen the RMSF of molecular dynamics activity of the best complex. The result showed that 1,2-benzenecarboxylic acid had the lowest binding affinity following suramin as control with -5.1 and -11.1 kcal/mol after targeting E2 domain protein of CHIKV. This led to the conclusion that 1,2-benzenecarboxylic acid could be forecast as predictive anti-CHIKF therapeutic candidate. Additional in vitro and in vivo studies are needed to validate this outcome.
Composition and Zonation of Mangrove Vegetation in Ujung Pangkah, Gresik, Indonesia Mabruroh, Arofatul Syabina; Firdhausi, Nirmala Fitria; Bahri, Saiful; Rachmawati, Yuanita; Munir, Misbakhul
Bioeksperimen: Jurnal Penelitian Biologi Vol 10, No 2: September 2024
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v10i2.23819

Abstract

Ujung Pangkah Gresik is a significant mangrove area with both ecological and economic functions. Ecologically, it prevents seawater intrusion and abrasion, while economically, it supports sectors like tourism, forestry, fisheries, and ecotourism. This research aims to identify mangrove species diversity and zoning patterns in Ujung Pangkah using survey methods to assess diversity, density, dominance, importance value, and zoning. Four species were found (Avicennia marina, Avicennia officinalis, Rhizophora stylosa, Ceriops tagal) with 454 individuals. The diversity value is moderate at 1.86. The highest and lowest densities were 0.52 and 0.01, respectively. Avicennia marina is the dominant species with an importance index of 273.69. The area has a mixed zoning pattern.
Sus sp. DNA Encoding cyt b Gene Detection Test on Meat Grinding Samples Using Conventional PCR Adzakiyyi, Miftahul Lathif; Susilowati, Tri; Rokhim, Saiku; Rachmawati, Yuanita
Indonesian Journal of Halal Research Vol. 2 No. 2 (2020): August
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/ijhar.v2i2.8489

Abstract

Micro-entrepreneurs with basic ingredients of processed meat such as meatball who do not have a meat grinder, generally using meat grinder at the public market. The problem that occurs is that there is no clear regulation from the Government regarding the guarantee of the halal meat grinding in the Regional Company. This needs to be enhanced as a study, considering that the grinding material does not only come from Halal substances. The purpose of this study was to test pig DNA in meat grinding samples at PD Pasar Surya Surabaya City by using the conventional Polymerase Chain Reaction (PCR) method. DNA was isolated from 11 PD Pasar Surya meat grinding samples, then spectrophotometry was performed. Spectrophotometry results showed that all samples have high DNA concentrations. The primer used is the cyt b pig gene encoder. Predenaturation is performed at a temperature of 95°C-5 minutes, denaturation of 95°C-45 seconds, annealing 60°C-30 seconds, extension 72°C-40 seconds, and post extension 72°C-5 minutes. The results of PCR analysis were determined by the emergence of DNA bands of ± 149 bp as markers of pig DNA. The results showed negative on sample or no pig contamination in 11 samples tested. While the pig sample as positive control showed a band of ± 149 bp. These results prove that at 11 points of the location of meat grinding there is no contamination of pig DNA.
End Point Polymerase Chain Reaction for Porcine Detection on Food Product of UIN Sunan Ampel Surabaya Canteen Rokhim, Saiku; Tyautari, Inggrit; Firmansyah, M. Aliffiyan; Rachmawati, Yuanita
Indonesian Journal of Halal Research Vol. 3 No. 1 (2021): February
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/ijhar.v3i1.11149

Abstract

Halal food means food that permitted under Islamic law and fulfills about requirements. The absence of information about halal food contained in UIN Sunan Ampel Surabaya (UINSA) campus area causes related research to be carried out. This study aims to determine the porcine DNA contamination on food around UINSA area using molecular technology. Twenty two samples used were foods that contain meat and may contain pork obtained from canteens around UINSA area, analyzed using Polymerase Chain Reaction (PCR) method. The analysis was started with DNA isolation of 22 food samples, electrophoresis, PCR, then visualization gel electrophoresis. Primer gene coding for cytochrome b (cyt b) which produces 149 bp of DNA fragments. The results showed that no porcine contamination in 22 food samples, while the positive control showed a band of 149 bp. End point PCR method potentially to detect porcine DNA contaminants in food products around UINSA. Therefore the food is halal and safe for consumption.
CmBGI Gene Expression encoding β-glucosidase in melon (Cucumis melo L.) under stress condition Yuanita Rachmawati; Ganies Rizaa Aristya; Budi Setiadi Daryono
Biotropic : The Journal of Tropical Biology Vol. 1 No. 2 (2017): Biotropic, Volume 1, Nomor 2, 2017
Publisher : Program Studi Biologi, Fakultas Sains dan Teknologi, Universitas Islam Negeri Sunan Ampel Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29080/biotropic.2017.1.2.1-8

Abstract

CmBGI is the enzymatic genes encoding β-glucosidase that involved in Abscisic Acid (ABA) metabolism of Cucumis melo L. β-glucosidase promotes the accumulation of glucose, fructose, and sucrose, and it might act as a regulator that mediates melon fruit ripening both climacteric and nonclimacteric. ABA mediates adaptive responses to abiotic and biotic stresses. Agricultural Balitbang in 1997 showed that there were approximately 158.600 ha of degraded land scattered in three zones of agroecosystems in Yogyakarta (DIY). One of them is Dlingo Bantul area which has a karst type critical land area. Karst provides stress to the certain plant growth. One way to conserve critical land is making this area for agriculture. Cultivar TACAPA and TA were superior melons that have been developed by Genetic Laboratory of Biology Faculty UGM. This preliminary research was conducted to examine molecular characterization of CmBGI gene expression in cultivar TACAPA and TA which are planted in normal condition medium and in critical land medium treatment. Total RNA was extracted from leaf tissue then Reversed Transcriptase (RT-PCR) to collect cDNA library. cDNA was amplified using specific primer. Spectrophotometry was conducted in λ260 nm and electrophoresis run in 1.5% agarose gel. Control of band chosen was Cm-Actin. CmBGI gene concentration of TACAPA and TA in normal condition medium are in succession 578.5 and 579.4 μg/ml then for critical land medium treatment 743.4 and 773.5 μg/ml. CmBGI band was showed both of TACAPA and TA as ± 1258 bp. Cm-actin was showed band of DNA as ± 445 bp. CmBGI gene concentration in critical land medium treatment which is given greater stress on melons are higher than normal condition. This suggests that the CmBGI gene is expressed more in cultivar TACAPA and TA melons when they are grown under stress condition.
Phenotipical Characters of Melon (Cucumis melo L.) in Response to Karst Critical Land Yuanita Rachmawati; Budi Setiadi Daryono; Ganies Riza Ariestya
Biotropic : The Journal of Tropical Biology Vol. 2 No. 1 (2018): Biotropic, Volume 2, Nomor 1, 2018
Publisher : Program Studi Biologi, Fakultas Sains dan Teknologi, Universitas Islam Negeri Sunan Ampel Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29080/biotropic.2018.2.1.1-10

Abstract

Yogyakarta Agroecosystem has 158,600 ha of critical land spread over three zones. Two areas are Karst Land, located on Agroecosystem II includes Gunungsewu Hills, Gunungkidul and III covers Dlingo Bantul Hills and Sentolo Hills Kulon Progo Regency.. Karst Land is certainly provides stress to plants. These research purposes are examining the phenotype character of superior melon Cultivar TACAPA compare to parents and offsprings phenotypes. The phenotype characters are based on plant height, leaf number, time of melon flowering, water content of plants, and fruit and seed productivity. This experiment was done by Split Plot Design with Completely Randomized Design (CRD) with 4 kinds of treatment (control plant media, Gunungsewu, Dlingo, and Sentolo), 7 experimental units cultivars: TACAPA, TA, TP, PT, AT, Action 434, PI 371795), and 4 replications. Research result reveals that most of the phenotypic characters including plant height, number of leaves, fruit weight, and number of seeds produced have relatively no significant effect between treatment and control, while the phenotypic first time flowering time and water content of the plant, have a noticeable difference.
Comparison of DNA Isolation Results with Simple Methods and Kits in Samples of Psidium guajava Leaves Yuanita Rachmawati; Romyun Alvy Khoiriyah
Biotropic : The Journal of Tropical Biology Vol. 2 No. 2 (2018): Biotropic, Volume 2, Nomor 2, 2018
Publisher : Program Studi Biologi, Fakultas Sains dan Teknologi, Universitas Islam Negeri Sunan Ampel Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29080/biotropic.2018.2.2.93-99

Abstract

DNA isolation is one of a series of methods that must be carried out on the basic techniques of Molecular Biology Analysis. Especially PCR-based molecular marking techniques. Many ways are done in DNA isolation. This study discusses the comparison of the results of DNA isolation using two methods. Simple DNA isolation methods and using Kit. Samples of Psidium guajava leaves used were taken from 15 different locations used. In general, DNA isolation methods include three steps, namely destruction, precipitation, and purification. Simple DNA isolation is done with detergents, alcohol groups, which are commonly available in the laboratory. Methods of DNA isolation with KIT are carried out according to the Promega Universal Wizard KIT protocol. The comparison results are seen from spectrophotometric absorption Å230 nm, Å260 nm, Å280 nm, Å320 nm, ratio Å260/Å230, ratio Å260/Å280 to see DNA purity, protein concentration before purification step, and DNA concentration produced. The results showed that there were no statistically significant differences in the results of DNA isolate spectrophotometry. However, the use of KIT with modified protocols is more recommended if researchers want to carry out DNA analysis more precisely and accurately. Keywords: DNA isolation, spectrophotometry, DNA concentration and purity
Chromosome Characterization of Brassicaceae Family Ganies Riza Aristya; Bening Larasati; Galang Riswi Dyatama; Himawan Masyhuri; Febri Yuda Kurniawan; Fauzana Putri; Dian Astriana; Yuanita Rachmawati
Biotropic : The Journal of Tropical Biology Vol. 6 No. 2 (2022): Biotropic, Volume 6 Nomor 2, 2022
Publisher : Program Studi Biologi, Fakultas Sains dan Teknologi, Universitas Islam Negeri Sunan Ampel Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Indonesia is known as a rich country in various agricultural and plantation products, including vegetables such as mustard, broccoli, cabbage, and cauliflower. However, in its cultivation, the products and demand for vegetables are not offset by an increase in the production quality. One of the efforts to improve and enhance the production quality is to identify and characterize chromosomes of plants which will become the basis for plant breeding activities. The purpose of this study was to characterize the number, form and size of the chromosome in cultivars belonging to the Brassicaceae family. The study was carried out using the modified squash method. Chromosomes were prepared by fixation, maceration, and staining, then the mitotic phases were observed using a microscope and optilab, and analyzed using Image Raster 3. The results showed that mitotic time range and chromosome character of six cultivars of the Brassicaceae family were different. Broccoli ('Chief No. 2 1955' and 'Green Super') and cauliflower ('ILONA' and 'TM 126') had a mitotic time range from 04.00 to 09.00 a.m. with 2n chromosome number = 18. Green mustard (‘Juwita’ and ‘TM Jade’) and white mustard ('Sakata' and 'Shuka-shuka') had a mitotic time range from 03.00 to 08.00 a.m. with 2n chromosome number = 20. White cabbage (‘CR ACE' and 'Sehati F1') had a mitotic time range from 04.00 to 09.00 a.m and red cabbage (‘Scarlet’ and ‘Red Globe’) had a mitotic time range from 09.00 to 10.00 a.m. with 2n chromosome number = 18.    
Co-Authors Adzakiyyi, Miftahul Lathif AGUSTINA, EVA Aini, Humayra Qurrata Aini, Nur Sofiatul Ameliora C E Arrohmah, Robiatush Sholichah Ayudya Fitri Arifa Azzhahara, Nabillah Ayu Bening Larasati BUDI SETIADI DARYONO Choiriyah, S.Si, Chumaidatul DAMAYANTI, MAMIK Dian Astriana Eko Prasetya Eko Prasetya, Eko Esti Tyastirin Fauzana Putri Fauziyah Harahap Febri Yuda Kurniawan Firmansyah, M. Aliffiyan Galang Riswi Dyatama Ganies Riza Ariestya Ganies Riza Aristya Hary Prakasa Himawan Masyhuri Humayra Qurrata Aini Inggrit Tyautari Inggrit Tyautari Irul Hidayati Kautsar, Radinal KHOIRIYAH, ROMYUN ALVY Latifatoel Chilmi Lazuardi Lazuardi M. Aliffiyan Firmansyah Mabruroh, Arofatul Syabina Mahbubillah, M. Ainul Mashita Andiana, Mashita Miftahul Jannah Miftahul Lathif Adzakiyyi Misbakhul Munir Misbakhul Munir Moch. Irfan Hadi Nabila Ayu Nabila, Salsa Najwa Maulidina P Ninik Fadhillah Nirmala Fitria Firdhausi Oki Rahmatirta W Pradiptaadi, Brian Pramana Aprilio Puji Prastowo, Puji Putri, Siti Aisyah Bisri Radinal Kautsar Ramadhani, Aisyah Hadi Said . Iskandar Saiful Bahri Saiku Rokhim Setiyowati, Putri Ayu Ika Siti Latifa Siti Malihatus Sa'adah Sri Susila Andayani, Sri Susila Teguh Hari Sucipto, Teguh Hari Tri Susilowati Tri Susilowati Tri Susilowati Tyautari, Inggrit Yusuf, Yusnaeni