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All Journal JBIO: jurnal biosains (the journal of biosciences) Indonesian Journal of Tropical and Infectious Disease Biota Journal of Tropical Biodiversity and Biotechnology BIOTROPIC The Journal of Tropical Biology 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
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 Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics Public Health Social Sciences Veterinary Other

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Karakter Gen CmBG1 Melon (Cucumis melo) pada Pengaruh Cekaman Tanah Karst Ganies Riza Aristya; Budi Setiadi Daryono; Yuanita Rachmawati
Sains dan Matematika Vol. 3 No. 1 (2014): Oktober, Sains & Matematika
Publisher : Universitas Negeri Surabaya

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Abstract

Lahan kritis berkapur, karst, memberikan cekaman abiotik pada tanaman karena hambatan hidrasi dan nutrisi. Asam absisat (ABA) adalah hormon yang diekspresikan tumbuhan pada kondisi cekaman abiotik. CmBG1 merupakan salah satu gen peregulasi hormon ABA pada melon yang akan terakumulasi saat tumbuhan mengalami cekaman. Tujuan penelitian ini adalah mendeskripsikan pengaruh lahan kritis karst terhadap ekspresi gen CmBG1 secara kualitatif dan kuantitatif melon hasil turunan kultivar TACAPA, yaitu kultivar PT dan AT yang ditanam pada medium tanah karst dari wilayah Agroekosistem II dan III Yogyakarta (Gunungsewu, Dlingo, maupun Sentolo). cDNA library diperoleh dari reverse transcription isolat RNA. cDNA diamplifi kasi dengan primer spesifi k, kemudian dispektrofotometri pada λ260 nm untuk mengetahui konsentrasi gen CmBG1. Ekspresi gen dianalisis dengan real time PCR dengan gen referensi Cm-actin. Uji kualitatif dilakukan dengan elektroforesis gel agarosa 1,5%. Hasil penelitian menunjukkan gen CmBG1 terdeteksi dengan ukuran ±1258 bp pada kultivar PT dan AT. Konsentrasi gen CmBG1 melalui spektrofotometri menunjukkan semua kultivar yang ditanam pada media kontrol memiliki konsentrasi yang lebih rendah bila dibandingkan media tanam dengan perlakuan lahan kritis baik Gunungsewu, Dlingo, maupun Sentolo. Hasil ini sama dengan uji ekspresi gen CmBG1 menggunakan analisis kuantitatif real time PCR. Karsts critical land gives abiotic stresses in plants because of hydration and nutrition disturbances. Abscisic acid (ABA) is a hormone that expressed in the plant in abiotic stress conditions. CmBG1 is one of the regulatory genes encoding hormone ABA in melon plants which is accumulated in stress condition. The purpose of this study was to describe the infl uence of karsts critical land on the genes expression of CmBG1 melon cultivars PT and AT qualitatively and quantitatively. The plants were grown in medium karst land of Agroecosystems II and III of Yogyakarta (Gunungsewu, Dlingo, and Sentolo). Total RNA was extracted from leaf tissue then Reversed Transcriptase (RT-PCR) to collect cDNA library. cDNA was amplifi ed using specifi c primer. Spectrophotometry was conducted in λ260 nm and electrophoresis run in 1.5% agarose gel. Control band and reference gene chosen in Real Time PCR was Cm-Actin. CmBGI band (± 1258 bp) was showed both on PT and AT. 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 PT and AT melons when they are grown under stress condition. This result show similarly when using real time PCR.
DETEKSI KONTAMINAN FRAGMEN DNA PENGKODE cyt b BABI PADA SAMPEL SOFTGELLCANDY TAK BERLABEL HALAL Yuanita Rachmawati; Saiku Rokhim; Misbakhul Munir; Eva Agustina
Indonesia Journal of Halal Vol 1 (1) 2018
Publisher : Pusat Kajian Halal Undip

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (205.92 KB) | DOI: 10.14710/halal.v1i1.3115

Abstract

Abstrak Softgellcandy adalah permen bertekstur lunak yang diproses dengan penambahan komponen hidrokoloid seperti agar, gum, pektin, pati, kaegenan, gelatin dan lain-lain yang digunakan untuk modifikasi tekstur sehingga menghasilkan produk yang kenyal. Sayangnya distribusi Softgellcandy di pasaran seringkali terlepas dari pengawasan lembaga berwenang. Banyak ditemukan bermacam merk Softgellcandy yang tidak berBPOM maupun tidak berlabel Halal. Gelatin menjadi titik kritis kehalalan Softgellcandy. Penelitian ini menguji 15 sampel Softgellcandy tak berlabel halal yang dijual bebas di Surabaya dengan primer pengkode fragmen DNA cytochrome b Babi. Metode yang digunakan adalah konvensional PCR pada suhu 98oC-2 menit; 95oC-30 detik; 61oC-30 detik; 72oC-40 detik; dan 72oC-3 menit, selama 30 siklus. Visualisasi hasil PCR menggunakan elektroforesis 2% gel agarosa menunjukkan dari 15 sampel, 8 sampel terindikasi kontaminan DNA babi ditandai dengan pita DNA sebesar ±149bp. Pemerintah perlu melakukan monitoring lebih ketat terkait peredaran produk makanan tak berlabel halal yang dijual bebas di pasaran, mengingat Halal menjadi issue yang sangat sensitif di negara dengan mayoritas penduduk muslim terbesar di dunia ini. Karena halal adalah suatu keharusan. Keywords: Softgellcandy, cyt b Babi, PCR
Sus sp. DNA encoding Cyt b gene detection test on soft gel candy samples using PCR method Latifatoel Chilmi; Tri Susilowati; Yuanita Rachmawati; Saiku Rokhim; Inggrit Tyautari
Journal of halal product and research (JPHR) Vol. 4 No. 1 (2021): Journal of Halal Product and Research (JHPR)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jhpr.vol.4-issue.1.14-19

Abstract

Softgel candy is soft-textured confectionery processed by the addition of several components such as gum, pectin, starch and gelatin, to obtain a supple product and packed after aging treatment first. Gelatin is one of the main components in the manufacture of soft candy derived from the hydrolysis of collagen connective tissue and animal bone that serves as the nature of gelling agents, stabilizers or emulsifiers. However, the gelatin used in products not yet labeled halal Indonesian Council of Ulama (MUI) is particularly vulnerable to pork gelatin, since pork gelatin is cheaper than cattle. The purpose of this study was to test the contaminants of pig DNA on 17 samples of soft candles not labeled halal MUI. This research used Polymerase Chain Reaction (PCR) method. Seventeen samples were isolated by DNA, then spectrophotometry was performed, followed by PCR. The PCR product is run electrophoresis. Visualize the DNA with a UV gel documentation. Primer used is primer gene encoding cyt b DNA pork. Results showed that 17 samples were negative contaminants, while the positive control of pork showed a DNA band of 149 bp. This shows that Softgel Candy 17 samples do not contain pork gelatin.
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

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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.    
Optimization of RNA Extraction from Aedes aegypti and Aedes albopictus Saiku Rokhim; Ninik Fadhillah; Radinal Kautsar; Humayra Qurrata Aini; Yuanita Rachmawati
Biotropic : The Journal of Tropical Biology Vol. 7 No. 1 (2023): Biotropic, Volume 7 Nomor 1, 2023
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.v7i1.1781

Abstract

RNA extraction is the critical initial stage in analyzing certain gene expressions, further analysis using Real Time PCR technology, and performing virus detection. However, the process of extracting RNA is often hampered by the risk of contamination, resulting in low concentrations of RNA and low purity of RNA. This is often an obstacle in extracting mosquito RNA especially detecting Dengue Virus (Den-V). Dengue virus (Den-V) can cause dangerous diseases in humans such as Dengue Fever (DHF) which is transmitted through the bites of Aedes aegypti and Aedes albopictus mosquitoes. This study aims to find out the effective steps for extracting RNA from Aedes aegypti and Aedes albopictus mosquitoes. The method being compared is a commercial RNA extraction kit with modification (addition of β-mercaptoethanol) and without modification. The results showed that the best DNA concentration and purity were obtained in mosquito samples from modified process. The purity ratio of RNA extracted without modification was 1.971 (0.021 ± 0.800) while with modification it was 2.003 (0.011 ± 0.112). Aedes aegypti had a better average concentration of 7.146 µg/ml for unmodified RNA and 7.613 µg/ml for modified RNA. This research is expected to be a reference for further studies on viruses in Aedes aegypti and Aedes albopictus.
In Silico Analysis of Inhibitor Potential of Punicalagin Compound in Pomegranate (Punica granatum) Against NS5 DENV-3 Protein Kautsar, Radinal; Rachmawati, Yuanita; Rokhim, Saiku; Sucipto, Teguh Hari; Damayanti, Mamik; Ramadhani, Aisyah Hadi
Indonesian Journal of Tropical and Infectious Disease Vol. 12 No. 1 (2024)
Publisher : Institute of Topical Disease Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/ijtid.v12i1.52320

Abstract

Indonesia is one of the Dengue Virus (DENV) endemic areas which are dominated by DENV-2 and DENV-3. Until now, no specific drug therapy has been found to cure Dengue Virus Infection (DVI). Punicalagin is one of the active compounds that have the potential to be used as an antiviral. Unfortunately, not many studies have used punicalagin as a DENV antivirus. This study aims to determine the inhibitory potential of punicalagin compounds against NS5 DENV-3 protein through molecular docking. Molecular docking was performed using AutoDock Tools, ChemDraw, and Discovery Studio Visualizer. The target protein used is NS5 DENV-3 protein with PDB ID code: 4V0Q. The ribavirin compound was used as a positive control. The results obtained show that the punicalagin compound has the ability to attach to target receptors in the C-Terminal domain complex. This docking produces a bond free energy (ΔG) of -6.39 kcal/mol. This result is better than the ΔG of the control compound. Punicalagin's Inhibition Constant (Ki) value also showed better results than ribavirin. So it can be seen that the compound punicalagin effectively inhibits DENV replication and has the potential as a DENV drug candidate. 
Region of Nuclear Ribosomal DNA (ITS2) and Chloroplast DNA (rbcL and trnL-F) as A Suitable DNA Barcode for Identification of Zingiber loerzingii Valeton From North Sumatera, Indonesia Prasetya, Eko; Lazuardi, Lazuardi; Harahap, Fauziyah; Rachmawati, Yuanita; Yusuf, Yusnaeni; Al Idrus, Said Iskandar; Prastowo, Puji
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.76956

Abstract

Zingiber loerzingii Valeton is one of the species in the Zingiberaceae family found throughout Aceh and North Sumatra, Indonesia, with slimy flowers, yellowish white color, and dark orange stamens. Z. loerzingii is endemic in North Sumatra with a very limited distribution. The International Union for Conservation of Nature and Natural Resources classifies this plant into the vulnerable ones category. This study aims to examine the potential of DNA barcoding from nuclear DNA (ITS2) and DNA chloroplasts (rbcL and trnL-F) to identify Z. loerzingii plants. The research sample was obtained from two main distribution areas of Z. loerzingii in North Sumatra, Indonesia, namely Sibolangit Nature Reserve and Tangkahan Conservation Forest. The results showed that all the DNA barcode markers used were able to classify Z. loerzingii into the same group in the phylogenetic analysis. ITS marker is the most effective marker for classifying Zingiberaceae species compared to rbcL and trnL-F markers. The ITS2 marker has the lowest level of intraspecific and intraspecific genetic distance overlap compared to the rbcL and trnL-F markers. This research is expected to provide information related to the DNA barcode of Z. loerzingii in an effort to conserve this rare plant. 
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.
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.
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 Mahbubillah, M. Ainul Mashita Andiana, Mashita Miftahul Jannah Miftahul Lathif Adzakiyyi 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 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