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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 Aristya, Ganies Riza; Daryono, Budi Setiadi; Rachmawati, Yuanita
Sains & Matematika Vol 3, No 1 (2014): Oktober, Sains & Matematika
Publisher : Sains & Matematika

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

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 ?260 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 ?260 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.
Karakter Gen CmBG1 Melon (Cucumis melo) pada Pengaruh Cekaman Tanah Karst Aristya, Ganies Riza; Daryono, Budi Setiadi; Rachmawati, Yuanita
Sains & Matematika Vol 3, No 1 (2014): Oktober, Sains & Matematika
Publisher : Sains & Matematika

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

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.
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 | Full PDF (924.346 KB) | 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 | Full PDF (712.581 KB) | 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 | Full PDF (589.56 KB) | 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
Optimization of PCR Protocol for the Identification of Yeasts Isolated from Apis mellifera Honeycomb based on the ITS rDNA Ayudya Fitri Arifa; Nirmala Fitria Firdhausi; Irul Hidayati; Yuanita Rachmawati; Moch. Irfan Hadi
Biota Vol 8 No 2 (2022): Jurnal Biota 2022
Publisher : Faculty of Science and Technology Universitas Islam Negeri Raden Fatah Palembang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19109/Biota.v8i2.10181

Abstract

Yeast is a microorganism that can be found in honeycomb. Yeast identification is a process to find and identify new species. One of which is molecular identification of yeast with rDNA sequences in the ITS region. Before carrying out molecular identification, it is necessary to optimize yeast DNA amplification methods to obtain good DNA sequences that ease the yeast identification process. The purpose of this study was to discover the optimum PCR (Polymerase Chain Reaction)protocols for the identification of yeasts isolated from Apis mellifera honeycomb based on the ITS rDNA. This study used 3 PCR (Polymerase Chain Reaction) protocols, i.e., from Kanti et al. (2018), Ediningsari (2008), and Maulana (2011). This results study shows that the optimum PCR protocol was from Maulana (2011), which produced clear and whole DNA fragment luminescences.
DETECTION OF PIG DNA FRAGMENTS IN HALAL UNLABLED LIPSTICK SAMPLES USING CONVENTIONAL PCR Misbakhul Munir; Siti Malihatus Sa'adah; Siti Latifa; Nabila Ayu; Oki Rahmatirta W; Najwa Maulidina P; Ameliora C E; Eko Prasetya; Yuanita Rachmawati
JBIO: jurnal biosains (the journal of biosciences) Vol 7, No 1 (2021): Jurnal Biosains
Publisher : Universitas Negeri Medan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24114/jbio.v7i1.23707

Abstract

From a Muslim perspective, it is very important to know the content, raw materials, and processing of the raw materials used in the cosmetic products used. One type of cosmetics that is most often used is lipstick. However, many lipsticks circulating in Indonesia are not equipped with a halal logo. One of the ingredients for lipstick is pork derivatives. These pig derivatives can be detected using PCR. Based on this background, this study aims to test the presence of pig DNA in lipstick samples that have not been certified halal on the market using 4 combinations of pig DNA fragments coding primers by using the conventional PCR method. Five commercial lipstick samples were selected by purposive sampling. DNA isolation was carried out according to the Wizard Promega Universal Kit. The PCR process was carried out with temperature optimization as follows: Predenaturation 98oC: 2 minutes, denaturation of 95oC: 30 seconds, Annealing 61oC: 30 seconds, Extension 72oC: 40 seconds, and Postextension 72oC: 3 minutes. The results showed that of the 5 samples tested by PCR using 5 kinds of primer combination, none of the samples were suspected to contain pork DNA. DNA isolation is the most difficult step in the lipstick sample detection process. Even though the detection result is negative, it is necessary to carry out further tests which become the Gold Standard of DNA-based testing using Real Time PCR.
DNA BARCODING EDELWEISS (Anaphalis longifolia) ASAL SUMATERA UTARA MENGGUNAKAN SEKUEN GEN maturase K Eko Prasetya; Hary Prakasa; Miftahul Jannah; Yuanita Rachmawati
JBIO: jurnal biosains (the journal of biosciences) Vol 6, No 3 (2020): Jurnal Biosains
Publisher : Universitas Negeri Medan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24114/jbio.v6i3.22403

Abstract

Anaphalis longifolia merupakan anggota dari family Asteraceae yang tersebar di dataran tinggi Eropa, Amerika, hingga Asia. Penelitian tentang tanaman ini masih terbatas pada studi habitat, sedangkan penelitian terkait identifikasi molekuler masih belum dilakukan. Penelitian ini bertujuan untuk menganalisis DNA barcode dari A. longifolia menggunakan sekuen matK gene. Sampel yang diperoleh dari Sumatera Utara kemudian di Isolasi DNA, di amplifikasi menggunakan primer spesifik, lalu disequencing. Hasil sequencing dianalisis menggunakan program Molecular Evolution Genetics Analysis (MEGA) Version X. Hasil penelitian menunjukkan bahwa sekuen matK gen berhasil diamplifikasi pada panjang 800-850 kb. Hasil analisis pohon filogenetik menunjukkan bahwa sekuen matK gene dapat mengelompokkan A. longifolia. Pada sekuen matK gene A. longifolia, AT content lebih tinggi dibandingkan dengan GC conten. Jarak genetik yang diperoleh berkisar 0-0.0014. Hasil analisis alignment sekuen matK gene menunjukkan terdapat 1521 karakter yang dapat diamati, 1403 karakter conserved site, 118 karakter variable site, 9 karakter parsimony informative site, dan 7 karakter single nucleotide polymorphism (SNP) site. Sekuen matK gene dapat digunakan sebagai DNA barcoding untuk mengidentifikasi A. longifolia. Hasil penelitian ini diharapkan dapat memberikan informasi penting dalam konservasi A. longifolia.
End Point Polymerase Chain Reaction for Porcine Detection on Food Product of UIN Sunan Ampel Surabaya Canteen Saiku Rokhim; Inggrit Tyautari; M. Aliffiyan Firmansyah; Yuanita Rachmawati
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.
Sus sp. DNA Encoding cyt b Gene Detection Test on Meat Grinding Samples Using Conventional PCR Miftahul Lathif Adzakiyyi; Tri Susilowati; Saiku Rokhim; Yuanita Rachmawati
Indonesian Journal of Halal Research (IJHAR) 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.
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