Articles
<![CDATA[KARAKTER GEN CMBG1 MELON (CUCUMIS MELO) PADA PENGARUH CEKAMAN TANAH KARST ]]>
<![CDATA[Aristya, Ganies Riza]]>;
<![CDATA[Daryono, Budi Setiadi]]>;
<![CDATA[Rachmawati, Yuanita]]>
<![CDATA[ Sains & Matematika Vol 3, No 1 (2014): Oktober, Sains & Matematika ]]>
Publisher : <![CDATA[Sains & Matematika ]]>
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<![CDATA[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.]]>
<![CDATA[Karakter Gen CmBG1 Melon (Cucumis melo) pada Pengaruh Cekaman Tanah Karst ]]>
<![CDATA[Aristya, Ganies Riza]]>;
<![CDATA[Daryono, Budi Setiadi]]>;
<![CDATA[Rachmawati, Yuanita]]>
<![CDATA[ Sains & Matematika Vol 3, No 1 (2014): Oktober, Sains & Matematika ]]>
Publisher : <![CDATA[Sains & Matematika ]]>
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<![CDATA[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.]]>
<![CDATA[Optimization of PCR Protocol for the Identification of Yeasts Isolated from Apis mellifera Honeycomb based on the ITS rDNA ]]>
<![CDATA[Ayudya Fitri Arifa]]>;
<![CDATA[Nirmala Fitria Firdhausi]]>;
<![CDATA[Irul Hidayati]]>;
<![CDATA[Yuanita Rachmawati]]>;
<![CDATA[Moch. Irfan Hadi]]>
<![CDATA[ Biota Vol 8 No 2 (2022): Jurnal Biota 2022 ]]>
Publisher : <![CDATA[Faculty of Science and Technology Universitas Islam Negeri Raden Fatah Palembang ]]>
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DOI: 10.19109/Biota.v8i2.10181
<![CDATA[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.]]>
<![CDATA[DETECTION OF PIG DNA FRAGMENTS IN HALAL UNLABLED LIPSTICK SAMPLES USING CONVENTIONAL PCR ]]>
<![CDATA[Misbakhul Munir]]>;
<![CDATA[Siti Malihatus Sa'adah]]>;
<![CDATA[Siti Latifa]]>;
<![CDATA[Nabila Ayu]]>;
<![CDATA[Oki Rahmatirta W]]>;
<![CDATA[Najwa Maulidina P]]>;
<![CDATA[Ameliora C E]]>;
<![CDATA[Eko Prasetya]]>;
<![CDATA[Yuanita Rachmawati]]>
<![CDATA[ JBIO: jurnal biosains (the journal of biosciences) Vol 7, No 1 (2021): Jurnal Biosains ]]>
Publisher : <![CDATA[Universitas Negeri Medan ]]>
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DOI: 10.24114/jbio.v7i1.23707
<![CDATA[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.]]>
<![CDATA[DNA BARCODING EDELWEISS (Anaphalis longifolia) ASAL SUMATERA UTARA MENGGUNAKAN SEKUEN GEN maturase K ]]>
<![CDATA[Eko Prasetya]]>;
<![CDATA[Hary Prakasa]]>;
<![CDATA[Miftahul Jannah]]>;
<![CDATA[Yuanita Rachmawati]]>
<![CDATA[ JBIO: jurnal biosains (the journal of biosciences) Vol 6, No 3 (2020): Jurnal Biosains ]]>
Publisher : <![CDATA[Universitas Negeri Medan ]]>
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DOI: 10.24114/jbio.v6i3.22403
<![CDATA[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.]]>
<![CDATA[Karakter Gen CmBG1 Melon (Cucumis melo) pada Pengaruh Cekaman Tanah Karst ]]>
<![CDATA[Ganies Riza Aristya]]>;
<![CDATA[Budi Setiadi Daryono]]>;
<![CDATA[Yuanita Rachmawati]]>
<![CDATA[ Sains dan Matematika Vol. 3 No. 1 (2014): Oktober, Sains & Matematika ]]>
Publisher : <![CDATA[Universitas Negeri Surabaya ]]>
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<![CDATA[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.]]>
<![CDATA[DETEKSI KONTAMINAN FRAGMEN DNA PENGKODE cyt b BABI PADA SAMPEL SOFTGELLCANDY TAK BERLABEL HALAL ]]>
<![CDATA[Yuanita Rachmawati]]>;
<![CDATA[Saiku Rokhim]]>;
<![CDATA[Misbakhul Munir]]>;
<![CDATA[Eva Agustina]]>
<![CDATA[ Indonesia Journal of Halal Vol 1 (1) 2018 ]]>
Publisher : <![CDATA[Pusat Kajian Halal Undip ]]>
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DOI: 10.14710/halal.v1i1.3115
<![CDATA[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]]>
<![CDATA[Sus sp. DNA encoding Cyt b gene detection test on soft gel candy samples using PCR method ]]>
<![CDATA[Latifatoel Chilmi]]>;
<![CDATA[Tri Susilowati]]>;
<![CDATA[Yuanita Rachmawati]]>;
<![CDATA[Saiku Rokhim]]>;
<![CDATA[Inggrit Tyautari]]>
<![CDATA[ Journal of halal product and research (JPHR) Vol. 4 No. 1 (2021): Journal of Halal Product and Research (JHPR) ]]>
Publisher : <![CDATA[Universitas Airlangga ]]>
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DOI: 10.20473/jhpr.vol.4-issue.1.14-19
<![CDATA[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.]]>
<![CDATA[In Silico Analysis of Inhibitor Potential of Punicalagin Compound in Pomegranate (Punica granatum) Against NS5 DENV-3 Protein ]]>
<![CDATA[Kautsar, Radinal]]>;
<![CDATA[Rachmawati, Yuanita]]>;
<![CDATA[Rokhim, Saiku]]>;
<![CDATA[Sucipto, Teguh Hari]]>;
<![CDATA[Damayanti, Mamik]]>;
<![CDATA[Ramadhani, Aisyah Hadi]]>
<![CDATA[ Indonesian Journal of Tropical and Infectious Disease Vol. 12 No. 1 (2024) ]]>
Publisher : <![CDATA[Institute of Topical Disease Universitas Airlangga ]]>
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DOI: 10.20473/ijtid.v12i1.52320
<![CDATA[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. ]]>
<![CDATA[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 ]]>
<![CDATA[Prasetya, Eko]]>;
<![CDATA[Lazuardi, Lazuardi]]>;
<![CDATA[Harahap, Fauziyah]]>;
<![CDATA[Rachmawati, Yuanita]]>;
<![CDATA[Yusuf, Yusnaeni]]>;
<![CDATA[Al Idrus, Said Iskandar]]>;
<![CDATA[Prastowo, Puji]]>
<![CDATA[ Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December ]]>
Publisher : <![CDATA[Universitas Gadjah Mada ]]>
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DOI: 10.22146/jtbb.76956
<![CDATA[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. ]]>
