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"This book highlights the latest breakthrough developments in bioinformatics. It presents a series of timely, in-depth reviews, drug clinical trial studies, biodiversity informatics and thematic issues. In addition, it includes insightful reviews on advances in computational molecular/​structural biology, which address areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Innovations in these fields have direct impacts on key issues related to healthcare, medicine, genetic disorders, the development of agricultural products, renewable energy, and environmental protection. Written by respected leaders in the field and covering a wide range of topics involving the integration of biology with computer and information science, the book offers an ideal basis for teaching at the undergraduate and graduate levels. It can also be used for self-instruction by research investigators interested in applying bioinformatics-based analytical methods and information technologists working with academic and industrial laboratories."

"Momentum disahkannya UU no. 33 tahun 2014 tentang Jaminan Produk Halal menjadi acuan awal pengembangan metode deteksi molekuler DNA porsin terhadap kehalalan produk. Undang-undang ini mewajibkan seluruh produk yang masuk dan beredar di Indonesia tersertifikasi halal, termasuk tidak boleh mengandung fragmen babi. Deteksi dilakukan pada jumlah sekelumit jejak DNA yang masih tersisa di dalam gelatin cangkang kapsul setelah melalui proses pembuatan yang panjang dengan pH dan suhu ekstrim. Untuk itu, optimasi metode ekstraksi sangat berperan penting agar mendapatkan jumlah DNA yang memadai.Tujuan penelitian ini adalah mendapatkan metode optimal perolehan DNA dan menentukan kondisi optimal metode deteksi molekular DNA porsin menggunakan metode Polymerase Chain Reaction yang sensitif. Metode PCR yang digunakan adalah PCR duplex dan PCR nested dengan target sekuens DNA ATP8 dan Cytb. Optimasi dilakukan pada metode ekstraksi DNA dengan mengubah jumlah replikat sampel, modifikasi komposisi proses resuspensi dan pelisisan sel, jumlah campuran saat tahap awal isolasi DNA, serta pemekatan pada tahap akhir pengisolasian DNA.Hasil optimasi menunjukan jumlah replikat gelatin optimum adalah delapan sampel ekstraksi. Optimasi PCR dilakukan dengan membandingkan metode PCR duplex dan PCR nested pada uji sensitivitas, serta optimasi kondisi masing-masing PCR tersebut. Hasil positif mengandung DNA porsin dinyatakan dengan terbentuknya dua amplikon 212bp dan 398bp pada PCR duplex atau satu amplikon 387bp pada PCR nested. Dari enam titik konsentrasi DNA yang diujikan pada uji sensitivitas, PCR nested dapat mendeteksi konsentrasi DNA hingga 1 fg/ ??l sedangkan PCR duplex yang hanya dapat mendeteksi hingga 1 ng/ ??l. Deteksi terhadap sampel kapsul suplemen menunjukan bahwa terdeteksi DNA porsin dalam sampel dengan metode PCR nested dan PCR duplex. Metode duplex dan nested PCR dapat diterapkan sebagai metode deteksi awal secara kualitatif namun tidak kuantitatif.

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Halal product assurance regulation, which was established under Law no. 33 year 2014, gave a major impact for the development of molecular detection method of porcines DNA in a product. This law obliges all products in Indonesia to have halal status, included no pigs fragment at all. Traces amount of DNA from gelatin and capsule shell which was still remaining after long manufacturing process under extreme pH and temperature, were detected and amplified. Thus, optimization of DNA extraction method is important to get the sufficient amount of DNA.

The aims of this study are to obtain an optimum DNA collection method and to determine optimum condition of sensitive molecular detection method of porcines DNA using PCR. The sequence DNA targets ATP8 and Cytb were amplified using duplex and nested PCR methods. The optimization on number of sample replication, on composition mix in resuspension and cell lysis process, on the amount of the solution used when starting the DNA isolation process, and the final concentration of DNA isolation process have done.

Result showed that the optimum numbers of replication for gelatin are eight times. Optimization of PCR was done by comparing nested PCR and duplex PCR for sensitivity test, also for both PCR conditions. Two amplicon of 212bp and 398bp in duplex PCR or one amplicon of 387bp in nested PCR were obtained only in sample that positive contains porcines DNA. Six different concentrations of template DNA that has been carried out for sensitivity test in both methods showed that nested PCR can detect as low as 1fg l DNA while duplex PCR can only detect 1ng l DNA concentration as the lowest. Porcines DNA has been detected in all capsule shell samples. Optimized duplex and nested PCR method could be applied as early qualitative detection."

"ABSTRAKPenelitian mengenai optimasi teknik hidrolisis selubung mucilage untuk meningkatkan konsentrasi dan kemurnian DNA Cyanobacteria filamen lurus yang ditumbuhkan pada medium dengan dan tanpa unsur nitrogen telah dilakukan. Penelitian bertujuan untuk mengetahui pengaruh homogenisasi dengan glass beads dan penambahan nitrogen pada medium terhadap penghilangan selubung mucilage strain Cyanobacteria filamen lurus. Strain Cyanobacteria yang digunakan adalah SO-24, SO-115, dan SO-163. Masing-masing strain uji ditumbuhkan di medium Blue-Green 11 BG-11 dengan dan tanpa unsur nitrogen, kemudian dilakukan homogenisasi dengan glass beads, hidrolisis selubung, dan ekstraksi DNA. Efektivitas optimasi teknik hidrolisis dilihat berdasarkan hasil pengamatan mikroskopik dengan dan tanpa pengecatan negatif, serta berdasarkan hasil pengukuran konsentrasi dan kemurnian DNA. Hasil penelitian menunjukkan proses homogenisasi tidak memberikan pengaruh terhadap penghilangan selubung mucilage, sedangkan penambahan nitrogen pada medium memengaruhi penghilangan selubung mucilage pada ketiga strain uji. Teknik hidrolisis efektif untuk menghilangkan selubung mucilage strain SO-24 pada medium dengan dan tanpa unsur nitrogen. Sementara itu, strain SO-115 dan SO-163 hanya efektif pada medium dengan unsur nitrogen. Ketiga strain uji menghasilkan konsentrasi DNA yang rendah yaitu berkisar dari 1,58 mdash;4,52 ng/ L dengan kemurnian DNA di bawah 1,8.

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ABSTRACTResearch on the optimization of hydrolysis techniques to improved DNA concentration and purity of filamentous Cyanobacteria which were grown in medium with and without nitrogen content has been conducted. The research aims to know the effect of homogenization with glass beads and addition of nitrogen in medium on mucilage sheath removal of filamentous Cyanobacteria. Strains of Cyanobacteria was used is SO 24, SO 115, and SO 163. Each strain was grown in Blue Green 11 BG 11 medium with and without nitrogen content, and then homogenized with glass beads, hydrolyzed process, and DNA was extracted. The effectivity of hydrolysis techniques was achieved based on microscopic observation with and without negative staining, and based on measuring result of DNA concentration and purity. The result showed that homogenization process doesn rsquo t affect mucilage sheath removal, however addition of nitrogen affects mucilage sheath removal. The hydrolysis techniques effective on mucilage sheath removal from strain SO 24 which was grown in medium with and without nitrogen content. Meanwhile, for strain SO 115 and SO 163 were effective only in medium with nitrogen content. The result of DNA concentration showed that all of strains showed low DNA concentration with value range from 1,58 mdash 4,52 ng L with DNA purity was below 1,8."

"Sifat transpor muatan pada molekul DNA untai ganda dan DNA G4 telah dipelajari. Kami menggunakan dua model DNA yang direpresentasikan secara matematis dengan menggunakan model Hamiltonian tight binding. Model yang pertama adalah DNA untai ganda dengan panjang 32 pasangan basa yang disusun secara random. Transpor muatan untuk molekul DNA ini dipelajari dari probabilitas transmisi dan karakteristik I-V dengan memvariasikan hopping elektron inter-strand tegak lurus. Peningkatan hopping electron inter-strand tegak lurus menyebabkan probabilitas transmisi dan arus meningkat, tetapi saat temperaturnya dinaikkan probabilitas transmisi dan arus menurun. Model kedua adalah DNA G4, Sifat transpor muatan pada molekul ini dipelajari dari panjang lokalisasi dengan panjang 102 pasangan basa, density of states dan karakteristik I-V masing-masing dengan 32 tumpukan tetrad guanin, yang diberi pengaruh medan listrik dan temperatur, Probabilitas transmisi dan panjang lokalisasi dihitung menggunakan metode transfer matriks. Formula landauer Buttiker digunakan untuk menghitung karakteristik I-V. Metode fungsi green untuk menghitung probabilitas transmisi dan density of states. Hasil perhitungan medan listrik dan temperatur terhadap sifat transpor muatan yaitu menurunkan panjang lokalisasi, density of states, dan arus, saat meningkatnya medan listrik dan temperatur.

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The charge transport property on double-stranded DNA and G4 DNA molecules has been studied. We use two DNA models that are mathematically represented using Hamiltonian tight binding models. The first model is double stranded DNA with length of 32 base pairs arranged randomly. The charge transport for this DNA molecule is studied from transmission probabilities and I-V characteristics by varying of electron hopping in perpendicular inter-strand. Increased of electron hopping in perpendicular inter-strand causes the transmission and current probabilities to increase, but when temperature is increased the transmission probabilities and current is decrease. The second model is DNA G4. The charge transport property in this molecule is studied from localization length with length of 102 base pairs, density of states and I-V characteristics with 32 stacks of guanine tetrads respectively that influenced of electric field and temperature. Transmission probability and localization length are calculated using matrix transfer method. The buttiker landauer formula is used to calculate the I-V characteristics. Green function method for calculating transmission probability and density of states. The result of electric field and temperature calculation on charge transport leads to decreasing localization length, density of states, and current, when increasing of electric field and temperature."

"Latar Belakang: Endometriosis merupakan penyakit multifaktorial yang mempengaruhi 10% wanita usia subur. Diketahui bahwa gen EGFR dan MMP-2 mengalami peningkatan ekspresi pada endometriosis sehingga memiliki peran dalam perkembangan endometriosis, dan gen yang dapat meregulasi sitoskeleton. Tujuan dari penelitian ini adalah untuk mengevaluasi hubungan antara tingkat metilasi gen EGFR dan MMP-2 dengan ekspresi mRNA-nya pada jaringan endometriosis peritoneum.Metode Penelitian: Penelitian ini menggunakan desain cross sectional. Sampel yang digunakan sebanyak 20 wanita endometriosis dan 20 wanita bukan endometriosis yang usianya sekitar 20-45 tahun. Pada wanita endometriosis diambil jaringan endometriosis peritoneum dengan tindakan laparoskopi, sedangkan 20 wanita bukan endometriosis diambil jaringan endometrium normal dengan tindakan mikrokuretase. Tingkat metilasi DNA gen EGFR dan MMP-2 dianalisis dengan metode Methylation Specific PCR (MSP) dan Ekspresi mRNA gen EGFR dan MMP-2 dianalisis dengan metode qRT-PCR.Hasil: Tingkat metilasi DNA pada gen EGFR dan MMP-2 mengalami hipermetilasi. Pada gen EGFR, tingkat metilasi DNA antara jaringan endometriosis peritoneum dibandingkan dengan jaringan endometrium normal terdapat perbedaan yang bermakna (p=0,001), sedangkan pada gen MMP-2 tingkat metilasi DNA-nya tidak terdapat perbedaan yang bermakna (p=0,596) antara jaringan endometriosis peritoneum dibandingkan dengan jaringan endometrium normal. Nilai ekspresi relatif mRNA EGFR dan MMP-2 mengalami peningkatan ekspresi pada jaringan endometriosis peritoneum. Penelitian ini tidak menunjukkan korelasi yang bermakna antara tingkat metilasi dengan tingginya ekspresi mRNA baik gen EGFR maupun MMP-2. (gen EGFR (p=0,947 dan r=-0,016) dan gen MMP-2 (p=0.769 dan r=0.070)Kesimpulan: Tingginya ekspresi mRNA EGFR dan gen MMP-2, kemungkinan bukan hanya disebabkan karena faktor metilasi DNA, melainkan faktor lainnya.

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Background: Endometriosis is a multifactorial disease that affects 10% of women of childbearing age. It is known that the EGFR and MMP-2 genes have increased expression in endometriosis and thus have a role in the development of endometriosis, and genes that can regulate the cytoskeleton. The purpose of this study was to evaluate the relationship between the level of methylation of the EGFR and MMP-2 genes with their mRNA expression in peritoneal endometriosis tissue.

Method: The study used a cross sectional design. The sample used was 20 women with endometriosis and 20 women without endometriosis who were around 20-45 years old. In endometriosis women are taken to peritoneal endometriosis tissue by laparoscopic, while 20 women without endometriosis are taken to normal endometrial tissue by microcuretase. The levels of EGFR and MMP-2 gene methylation were analyzed by the Methylation Specific PCR (MSP) method and the mRNA expression of the EGFR and MMP-2 genes were analyzed by the qRT-PCR method.

Results: The level of DNA methylation in the EGFR and MMP-2 genes was hypermethylated. In the EGFR gene between peritoneal endometriosis tissue compared to normal endometrial tissue there were significant differences (p=0,001), whereas in the MMP-2 gene there was no significant difference (p=0.596) between peritoneal endometriosis tissue compared to normal endometrial tissue. The relative expression value of EGFR and MMP-2 mRNA has increased expression in peritoneal endometriosis tissue. This study did not show a significant correlation between the level of methylation and the high mRNA expression in both the EGFR and MMP-2 genes. (EGFR gene (p=0.947 and r=-0.016) and MMP-2 gene (p=0.769 and r=0.070)

Conclusion: The high expression of EGFR mRNA and MMP-2 gene, the possibility is not only due to hypermethylation factors, but other factors."

"Latar belakang: Telah dilaporkan bahwa terdapat perubahan pada ekspresi dari ribuan gen di jaringan endometrium endometriosis, termasuk diantaranya adalah gen FN1 dan RAC1. Perubahan ekspresi gen tersebut dapat disebabkan oleh mekanisme epigenetik seperti perubahan tingkat metilasi DNA pada gen.Tujuan: Mengetahui tingkat metilasi DNA pada gen FN1 dan RAC1 serta ekspresi mRNAnya pada jaringan endometrium subjek endometriosis dan nir-endometriosis.Metode: Penelitian ini merupakan cross sectional dengan jumlah sampel sebanyak 40 dari jaringan endometrium subjek endometriosis dan subjek nir-endometriosis. Sampel diambil dengan teknik mikrokuretase di RSUPN Ciptomangunkusumo dan RS Fatmawati Jakarta. Pada jaringan kemudian dilakukan isolasi DNA dan RNA. Pada isolat DNA dilakukan konversi bisulfit, MSP, elektroforesis dan analisis intensitas pita menggunakan software ImageJ untuk mendapatkan data persentase tingkat metilasi DNA. Pada isolat RNA dilakukan qRT-PCR untuk mendapatkan ekspresi relatif mRNA gen FN1 dan RAC1.Hasil: Analisis persentase tingkat metilasi DNA promotor menunjukkan terdapat perbedaan bermakna (p=0,022) pada gen FN1 pada pasien endometriosis (37,95%) dibandingkan nir-endometriosis (59,22 %), sedangkan pada gen RAC1 tidak terdapat perbedaan bermakna (p=0,63) dengan tingkat metilasi subjek endometriosis (28.45%) dan subjek nir-endometriosis (26.11%). Penelitian ini juga melaporkan terjadinya peningkatan ekspresi relatif mRNA gen FN1 dan RAC1 dibandingkan dengan subjek nir-endometriosis, namun secara statistik tidak terdapat perbedaan bermakna (p>0,05). Tidak terdapat korelasi bermakna antara tingkat metilasi gen FN1 dan RAC1 dengan ekspresi mRNAnya.Kesimpulan: Terjadi penurunan tingkat metilasi yang bermakna pada gen FN1 di jaringan endometrium endometriosis, namun tidak berkorelasi dengan peningkatan mRNA nya. Tidak terdapat perbedaan bermakna tingkat metilasi dan ekspresi mRNA pada gen RAC1 di jaringan endometrium subjek endometriosis dibandingkan dengan nir endometriosis.

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It has been reported that there was a changes in the expression of thousands of genes in endometrial endometriosis tissues, including the FN1 and RAC1 genes. Changes in gene expression can be caused by epigenetic mechanisms such as DNA methylation in genes.

Objective: To determine the level of DNA methylation in FN1 and RAC1 genes and their mRNA expression in endometrial tissue of endometriosis and non-ndometriosis.

Method: This study was designed as cross sectional with a total sample of 40 of endometrial tissues in the subject of endometriosis and non-endometriosis. Samples were taken by microcuretase at Ciptomangunkusumo and Fatmawati Hospital, Jakarta. DNA and RNA was isolated. DNA isolates were converted by bisulfite procedure, MSP conversion, electrophoresis, analyzed intensity of the band which appeared on gel electrophoresis using ImageJ software to obtain the percentage data of DNA methylation level. In RNA isolates, it was analyzed using qRT-PCR methode to obtain the relative mRNA expression level.

Results: Analysis of percentage of DNA methylation level showed significant differences (p=0.022) in the FN1 gene (37.95%) compared to non-endometriosis (59.22%), whereas in the RAC1 gene there was no significant difference (p=0,63) with methylation level of endometriosis subjects (28.45%) and non-endometriosis subjects (26.11%). For relative mRNA expression of FN1 and RAC1 genes showed no significant differences (p> 0.05). For correlation in endometrial endometriosis showed no significant between the rate of methylation of the FN1 and RAC1 genes with their mRNA expression.

Conclusion: There was a significant decrease in DNA methylation level of FN1 gene in endometrial endometriosis tissues, but it did not correlate with the increasing in its mRNA expression. There was no significant difference in DNA methylation level and mRNA expression of RAC1 gene in endometrial tissues of endometriosis subjects compared to non-endometriosis."

"Kriopreservasi adalah salah satu prosedur yang termasuk ke dalam serangkaian TRB. Prosedur ini telah secara rutin diaplikasikan untuk penggunaan spermatozoa di masa depan. Namun, pada praktiknya, spermatozoa yang dikriopreservasi akan mengalami penurunan kualitas terutama pada kemampuan motilitasnya, hingga menyebabkan kematian spermatozoa. Penurunan pada parameter spermatozoa pasca thawing diyakini paling utama disebabkan karena produksi berlebih dari ROS akibat kejutan suhu dan osmotik selama proses pembekuan dan pencairan. Pada penelitian ini, dilakukan suplementasi antioksidan dengan vitamin C, ALA, dan pentoksifilin pada medium kriopreservasi untuk dianalisis pasca thawing terhadap beberapa parameter di antaranya kualitas spermatozoa, kadar MDA, Indeks Fragmentasi DNA (IFD), dan apoptosis spermatozoa melalui ekspresi caspase-3 pada subyek normozoospermia dan non-normozoospermia. Hasil menunjukkan secara umum antioksidan vitamin C, ALA, dan pentoksifilin cenderung meningkatkan kualitas spermatozoa pasca thawing dengan meningkatkan motilitas, cryosurvival dan viability rate. Secara signifikan, peningkatan kualitas spermatozoa pasca thawing ditunjukkan oleh pentoksifilin dengan meningkatkan motilitas pasca thawing dan cryosurvival rate. Ketiga antioksidan cenderung menurunkan konsentrasi MDA dan apoptosis, namun hanya vitamin C yang menurunkan IFD.

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Cryopreservation is one of the procedures included in a series of TRB procedures. This procedure has been routinely applied for future use of spermatozoa. However, practically, cryopreserved spermatozoa will experience a decrease in quality, particularly in their motility ability, which in turn causing cell death. The decrease in post-thawing spermatozoa parameters is believed to be mainly due to the overproduction of ROS due to temperature and osmotic shock during freezing and thawing. In this study, antioxidant supplementation with vitamin C, ALA, and pentoxifylline was supplemented in cryopreservation medium and carried out for post-thawing analysis of several parameters including spermatozoa quality, MDA levels, DNA Fragmentation Index (DFI), and apoptosis through the activation of caspase-3 expression in normozoospermic and non-normozoospermic subject. The results showed that in general, the antioxidants included vitamin C, ALA, and pentoxifylline improved the quality of post-thawing spermatozoa by increasing motility, cryosurvival, and viability rate. The quality of spermatozoa post-thawing was significantly improved by pentoxifylline, which significantly improved motility and cryosurvival rate. The antioxidants reduced the concentration of MDA and apoptosis insignificantly, yet only vitamin C decreased the DFI."

"Plastik merupakan bahan yang banyak digunakan dalam peralatan keseharaian. Penambahan zat tertentu pada alat berbahan plastik ini diketahui dapat menambah kualitas, yaitu lebih elastis, kuat dan tahan lama. Salah satu bahan aditif yang biasa digunakan yaitu ftalat. Senyawa ftalat dapat berpotensi menghasilkan terjadinya DNA adduct. Penelitian ini mempelajari mengenai pembentukan 8-OHdG akibat paparan senyawa ftalat dan logam Cu (II) secara in vitro dan in vivo pada tikus (Rattus novergicus). Pembentukan 8-OHdG dianalisa secara in vitro dengan menggunakan HPLC, dengan variasi pH, waktu inkubasi dan perbandingan konsentrasi. Sedangkan secara in vivo pada tikus, sampel darah dianalisa menggunakan ELISA Kit dan sampel urin menggunakan instrumen LC-MS/MS. Secara umum, konsentrasi 8-OHdG paling besar pada sampel 2-dG diinkubasi dengan kombinasi larutan H₂O₂, ftalat, dan Cu (II). Pada studi in vitro dengan variasi pH menunjukkan konsentrasi 8-OHdG yang lebih tinggi pada pH 7,4; pada variasi waktu inkubasi lebih besar kosentrasi 8-OHdG pada 32 jam; dan pada variasi konsentrasi lebih besar pada perbandingan 1:20. Hasil studi in vivo menggunakan ELISA Kit, konsentrasi 8-OHdG yang terbentuk menunjukkan nilai paling besar pada sampel darah kelompok tikus terpapar ftalat kombinasi Cu (II) yaitu 5,26 ppb; kelompok tikus terpapar ftalat sebesar 4,29 ppb; dan kelompok tikus kontrol (tanpa paparan) sebesar 2,58 ppb. Sedangkan uji in vivo menggunakan LC-MS/MS pada sampel urin tikus juga menunjukkan konsentrasi 8-OHdG paling besar pada tikus kelompok ftalat kombinasi Cu (II) sebesar 174,1 ppb; dan tikus kelompok ftalat sebesar 156,5 ppb.

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Plastic is a material that is widely used in everyday appliances. The addition of certain substances to plastic tools is known to add quality, namely more elastic, strong and durable. One of the additives commonly used is phthalate. Phthalate compounds can potentially produce DNA adducts. This research studies the formation of 8-OHdG due to exposure to phthalate compounds and Cu (II) metal in vitro and in vivo in rats (Rattus novergicus). The formation of 8-OHdG was analyzed in vitro using HPLC, with variations in pH, incubation time and concentration ratio. While in vivo in rats, blood samples were analyzed using ELISA Kit and urine samples using LC-MS/MS instrument. In general, the concentration of 8-OHdG was greatest in 2-dG samples incubated with a combination of H2O2, phthalate, and Cu (II) solutions. In vitro studies with variations in pH showed higher concentrations of 8-OHdG at pH 7.4; at variations in incubation time the concentration of 8-OHdG was greater at 32 hours; and at variations in concentration greater at a ratio of 1:20. The results of the In vivo study using ELISA Kit, the concentration of 8-OHdG formed showed the greatest value in the blood samples of the rat group exposed to phthalate combined with Cu (II), which was 5.26 ppb; the rat group exposed to phthalate was 4.29 ppb; and the control rat group (without exposure) was 2.58 ppb. While the In vivo test using LC-MS/MS on rat urine samples also showed the highest concentration of 8-OHdG in rats of the Cu (II) phthalate combination group at 174.1 ppb; and rats of the phthalate group at 156.5 ppb."

"Perkembangan teknologi menyebabkan praktik pencampuran produk makanan menggunakan substansi non-halal. Dokumen (International Standardization Organization/ Technical Specification) ISO/TS 20224-3: 2020 digunakan sebagai prosedur standar uji deteksi kehalalan berbasis Deoxyribonucleic Acid (DNA) memanfaatkan metode Quantitative Polymerase Chain Reaction (qPCR) yang berlaku secara internasional melalui gen Beta actin (ACTB) sebagai gen target. Namun, kemampuan gen ACTB sebagai gen target belum banyak teruji langsung melalui reaksi PCR sehingga dibutuhkan evaluasi potensi gen target alternatif lain melalui optimasi primer seperti gen Cytochrome b (Cytb) untuk mendeteksi kandungan babi domestik (Sus scrofa domesticus) dan babi hutan (Sus scrofa). Metode yang digunakan terdiri atas desain primer dan probe, optimasi suhu annealing primer dan probe, uji spesifisitas in silico, uji sensitivitas in vitro, serta pengolahan dan analisis data. Adapun sampel yang digunakan untuk uji sensitivitas in vitro adalah pig genomic DNA. Berdasarkan pengujian yang dilakukan, primer dan probe gen Cytb memiliki suhu annealing optimal pada suhu 55°C. Uji spesifisitas in silico membuktikan bahwa sekuens primer dan probe gen Cytb memiliki kemampuan deteksi pada sekuens babi domestik dan babi hutan. Uji sensitivitas menggunakan qPCR pada gen ACTB membentuk kurva standar dengan nilai y=-3,6541x +38,385 dan R2=0,9967, serta LoD sebesar 5 pg/uL. Nilai linearitas (0,9967) dan efisiensi (87,78%) yang dihasilkan masuk ke dalam rentang standar sesuai literatur karena berada ≥0,98 untuk linearitas dan rentang 80%—120% untuk efisiensi. Sementara itu, uji sensitivitas menggunakan qPCR pada gen Cytb membentuk kurva standar dengan nilai y=-2,7222x + 32,196 dan R2= 0,9867, serta LoD sebesar 1 pg/uL. Nilai linearitas (0,9867) yang dimiliki masuk ke dalam rentang standar, tetapi nilai efisiensi (132,99%) melebihi rentang persentase yang baik akibat kemungkinan konsentrasi serial dilusi yang kurang sesuai dan protokol yang belum optimal. Gen Cytb memiliki jangkauan sensitivitas yang lebih baik dibandingkan gen ACTB. Keseluruhan grafik hasil membentuk kurva sigmoid yang valid sebagai hasil uji qPCR. Oleh karena itu, berdasarkan uji spesifisitas in silico dan sensitivitas in vitro yang dilakukan dapat disimpulkan bahwa gen Cytb berpotensi dijadikan gen target altenatif sebagai pengembangan halal kit.

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Technological developments have led to the practice of mixing food products using non-halal substances. Document (International Standardization Organization/Technical Specification) ISO/TS 20224-3: 2020 is used as a standard procedure for Deoxyribonucleic Acid (DNA)-based halal detection test that is internationally applicable through the Beta actin gene (ACTB) as the target gene. However, the ability of the ACTB gene as a target gene has not been tested directly through PCR reactions, so it is required to evaluate the potential of other alternative target genes through primer optimization such as the Cytochrome b (Cytb) gene to detect domestic pig (Sus scrofa domesticus) and wild boar (Sus scrofa) containment. The method used was comprised of primer and probe design, primer and probe annealing temperature optimization, in silico specificity test, in vitro sensitivity test, and data processing and analysis. The sample used for the in vitro sensitivity test is pig genomic DNA. Based on the tests conducted, primers and probes of the Cytb gene have an optimal annealing temperature at 55°C. The in silico specificity test proved that the primer sequences and Cytb gene probes have the ability to detect domestic pig and wild boar sequences. The sensitivity test using qPCR on the ACTB gene forming a standard curve with a value of y=-3.6541x +38.385 and R2=0.9967, and LoD of 5 pg/uL. The linearity (0.9967) and efficiency (87.78%) values generated are in the standard range according to the literature because they are ≥0.98 for linearity and 80%—120% range for efficiency. Meanwhile, the sensitivity test using qPCR on the Cytb gene is forming a standard curve with a value of y= -2.7222x + 32.196 and R2= 0.9867, and LoD of 1 pg/uL. The linearity value (0.9867) is within the standard range, but the efficiency value (132.99%) exceeds the good percentage range as a result of the possibility of inappropriate serial dilution concentrations and an unoptimal protocol. The Cytb gene has a better sensitivity range than the ACTB gene. The overall result graph forms a sigmoid curve which is valid as a qPCR test result. Therefore, based on the in silico specificity and in vitro sensitivity tests, it can be concluded that the Cytb gene has the potential to be used as an alternative target gene as a halal kit development."

"Pelacakan keabsahan pelabelan pada produk filet ikan dan olahan ikan penting bagi keberlanjutan konservasi spesies dan keamanan konsumen. Identifikasi produk filet ikan dan olahannya sulit dilakukan saat menggunakan pendekatan morfologi atau konvensional. Penelitian ini bertujuan untuk mengetahui ada atau tidaknya kesalahan pelabelan pada produk filet ikan dan olahannya di Jabodetabek dengan menggunakan Full DNA Barcoding dan Mini DNA Barcoding, serta membandingkan efektivitas kedua metode tersebut. Metode DNA barcoding memungkinkan identifikasi spesies ikan dengan menggunakan urutan nukleotida yang khas dari genom mitokondria pada bagian Sitokrom C Oksidase subunit 1 (COI). Metode yang digunakan pada penelitian ini ialah full DNA barcoding dan mini DNA barcoding. Sebanyak 113 dari 116 sampel produk ikan dan olahan ikan yang dikumpulkan dari daerah Jabodetabek berhasil diidentifikasi hingga tingkat spesies dengan menggunakan metode DNA Barcoding. Hasil identifikasi spesies dengan DNA Barcoding dan uji keabsahan menunjukkan 69% sampel memiliki label spesies yang tepat, 6% sampel memiliki label spesies yang tidak sesuai, 22% sampel tidak memiliki label spesies, dan 3% sampel tidak berhasil diidentifikasi. Jumlah keberhasilan amplifikasi mini DNA barcoding 3% lebih tinggi dibandingkan full DNA barcoding.

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Tracking the validity of labeling on fish fillet and processed fish products is one of the key issues in the sustainability of species conservation and food safety. It is difficult to identify fish fillet products and their processed products when using a conventional or morphological approach. This study aims to determine whether or not there is a labeling error in fish fillets and processed products in Jabodetabek using Full DNA Barcoding and Mini DNA Barcoding, and to compare the effectiveness of the two methods. The DNA barcoding method allows the identification of fish species using the typical nucleotide sequences of the mitochondrial genome in the Cytochrome C Oxidase subunit 1 (COI) section. The methods used in this research are full-length DNA barcoding and mini-length DNA barcoding. The result shows that 113 of 116 samples collected from the Jabodetabek area were identified to the species level. The results of species identification using Barcoding DNA and validity tests showed that 69% of samples had proper species labels, 6% of samples had inappropriate species labels, 22% of samples did not have species labels, and 3% of samples were not identified. The number of successful amplification of mini DNA barcoding is 3% higher than that of full DNA barcoding."