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"[This book offers an overview of state-of-the-art in non amplified DNA detection methods and provides chemists, biochemists, biotechnologists and material scientists with an introduction to these methods. In fact all these fields have dedicated resources to the problem of nucleic acid detection, each contributing with their own specific methods and concepts. This book will explain the basic principles of the different non amplified DNA detection methods available, highlighting their respective advantages and limitations. Non-amplified DNA detection can be achieved by adopting different techniques. Such techniques have allowed the commercialization of innovative platforms for DNA detection that are expected to break into the DNA diagnostics market. The enhanced sensitivity required for the detection of non amplified genomic DNA has prompted new strategies that can achieve ultrasensitivity by combining specific materials with specific detection tools. Advanced materials play multiple roles in ultrasensitive detection. Optical and electrochemical detection tools are among the most widely investigated to analyze non amplified nucleic acids. Biosensors based on piezoelectric crystal have been also used to detect unamplified genomic DNA. The main scientific topics related to DNA diagnostics are discussed by an outstanding set of authors with proven experience in this field., This book offers an overview of state-of-the-art in non amplified DNA detection methods and provides chemists, biochemists, biotechnologists and material scientists with an introduction to these methods. In fact all these fields have dedicated resources to the problem of nucleic acid detection, each contributing with their own specific methods and concepts. This book will explain the basic principles of the different non amplified DNA detection methods available, highlighting their respective advantages and limitations. Non-amplified DNA detection can be achieved by adopting different techniques. Such techniques have allowed the commercialization of innovative platforms for DNA detection that are expected to break into the DNA diagnostics market. The enhanced sensitivity required for the detection of non amplified genomic DNA has prompted new strategies that can achieve ultrasensitivity by combining specific materials with specific detection tools. Advanced materials play multiple roles in ultrasensitive detection. Optical and electrochemical detection tools are among the most widely investigated to analyze non amplified nucleic acids. Biosensors based on piezoelectric crystal have been also used to detect unamplified genomic DNA. The main scientific topics related to DNA diagnostics are discussed by an outstanding set of authors with proven experience in this field.]"

"A rapid and simple to amplify genomic DNA sequences nanking mini-Tn5 transposon insertion was developed....."

"Penelitian ini mengembangkan metode deteksi spesies babi (Sus scrofa) pada sampel daging campuran menggunakan automasi ekstraksi DNA magLEAD gC. DNA dianalisis menggunakan PCR dan TaqMan probe RT-PCR dengan primer spesifik untuk gen Cytochrome c oxidase I (COI), Cytochrome b (Cytb), dan NADH5 dehydrogenase 5 (ND5). Hasil menunjukkan bahwa ekstraksi DNA otomatis menghasilkan konsentrasi DNA 129,4–388,5 ng/μL pada daging mentah dan 66,4–89,5 ng/μL pada bakso dengan rasio kemurnian A260/A280 dan 260/A230 > 1,8. Primer COI, Cytb dan ND5 dapat mendeteksi DNA babi. PCR dan RT-PCR in vitro menunjukkan ketiga primer hanya mendeteksi DNA babi. Efisiensi amplifikasi RT-PCR primer COI, Cytb, dan ND5 adalah 144,14% (R2=0,982), 88,05% (R2=0,998), dan 81,25% (R2=0,997) dengan batas deteksi 0,0001 ng/μL, 0,001 ng/μL, dan 0,001 ng/μL. Primer/probe Cytb dan ND5 mendeteksi bakso dengan campuran daging babi hingga 0,1% (w/w).

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This study developed a method to detect pig species (Sus scrofa) in mixed meat samples using automated DNA extraction with the magLEAD gC. DNA was analyzed using PCR and TaqMan probe RT-PCR with specific primers for the genes Cytochrome c oxidase I (COI), Cytochrome b (Cytb), and NADH5 dehydrogenase 5 (ND5). Results showed that automated DNA extraction produced DNA concentrations of 129.4–388.5 ng/μL in raw meat and 66.4–89.5 ng/μL in processed meatballs with purity ratios A260/A280 dan 260/A230 > 1.8. The COI, Cytb and ND5 primers could be used to detect pig DNA. In vitro PCR and RT-PCR showed that all three primers only detected pig DNA. The RT-PCR amplification efficiency for COI, Cytb, and ND5 primers were 144,14% (R2=0,982), 88,05% (R2=0,998), dan 81,25% (R2=0,997) with detection limits of 0.0001 ng/μL, 0.001 ng/μL, and 0.001 ng/μL. The Cytb and ND5 primers/probes detected meatballs with pig meat content as low as 0.1% (w/w)."

"Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes w."

"Jumlah pengidap virus HIV di Indonesia terus meningkat dari jenis penularannya, lebih banyak melalui cairan genital daripada plasma darah. Deteksi HIV diperlukan untuk pencegahan dan pengobatan. Teknik yang lazim digunakan adalah amplifikasi DNA dengan metode PCR. Penelitian ini bertujuan menerapkan teknik amplifikasi DNA metode LAMP yang baru-baru ini dikembangkan sebagai ganti PCR karena lebih spesifik, sensitif dan efisien. LAMP menggunakan pasangan primer yang unik, sepasang primer forward dan sepasang backward yang masing-maing terdiri dari primer panjang untuk polimerisasi DNA dem sepasang primer pendek untuk melepas rantai baru DNA sehingga reaksi bisa dilakukan pada suhu tetap. Reaksi LAMP menggunakan enzim Bst DNA polymerase pada suhu 65°C dilakukanterhadap isolat genom RNA HW sudah dikonfirmasi keberadaannya dengan metode PCR."

"Deteksi DNA adduct dapat dijadikan sebagai pendekatan untuk mendeteksi dini risiko kanker. Salah satu produk kerusakan oksidatif DNA adalah 8-hidroksi-2’-deoksiguanosin (8-OHdG). Penelitian ini dilakukan untuk mendeteksi 8-OHdG secara in vitro dan in vivo. Studi in vitro dilakukan dengan inkubasi 2’-deoksiguanosin dengan H2O2 dan akrilamida pada variasi pH 7,4 dan 8,4 selama 24 jam dalam suhu 37 oC. Kemudian hasil inkubasi dianalisis menggunakan HPLC. Sedangkan secara in vivo dilakukan deteksi 8-OHdG dalam urin pasien kanker paru stadium III-IV, urin perokok, dan urin non perokok dengan menggunakan LCMS/MS. Pada validasi instrumen HPLC diperoleh nilai regresi linier 0,9985, nilai LOD dan LOQ sebesar 6,108 ppb dan 20,361 ppb. Sedangkan untuk LCMS/MS diperoleh nilai regresi linier sebesar 1, nilai LOD dan LOQ sebesar 1,819 ppb and 6,066 ppb. Hasil penelitian menunjukkan bahwa paparan H2O2 dan akrilamida dapat membentuk 8-OHdG. Konsentrasi 8-OHdG yang terbentuk dari inkubasi 2-deoksiguanosin dan H2O2 serta 2-deoksiguanosin, H2O2, dan akrilamida maksimum pada pH 8,4 yakni sebesar 2,151 ppm dan 2,617 ppm. 8-Hidroksi-2’-Deoksiguanosin terdeteksi dalam urin pasien kanker paru, perokok, dan non perokok masing-masing sebesar 4,668 – 19,919 ppb, 6,873 – 12,111 ppb, -0,502 – 6,578 ppb. Nilai rata-rata konsentrasi 8-OHdG dalam sampel urin pasien kanker paru, perokok dan non perokok masing-masing sebesar 9,710 ppb, 10,226 ppb, dan 3,080 ppb.

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DNA adduct detection could be an approach to early detection of risk cancer. One of oxidative DNA damage products is 8-hydroxy-2’-deoxyguanosine (8-OHdG). This study was conducted to detect DNA adduct 8-OHdG in vitro and in vivo. In vitro study was started to incubate 2’-deoxyguanosine added by H2O2 and acrylamide in various pH for 24 hours at 37 oC. Then the result was analyzed with HPLC. In vivo study was conducted detection 8-OHdG in urine of lung cancer patients with stage III-IV disease, smokers and non smokers using LCMS/MS. Instrument validation (HPLC) was yielded linear regression value 0,9985, LOD and LOQ as much as 6,108 ppb and 20,361 ppb as well as validation instrument of LCMS/MS was yielded linier regression value 1, LOD and LOQ as much as 1,819 ppb and 6,066 ppb.The results of study found exposure of H2O2 to 2-deoxyguanosine induced 8-OHdG formation and the addition of acrylamide increased 8-OHdG formation. The highest 8-OHdG level obtained by incubation of 2’-deoxyguanosine and H2O2 then 2’deoxyguanosine, H2O2 and acrylamide at pH 8,4 as much as 2,151 ppm and 2,617 ppm. 8-Hydroxy-2’-Deoxyguanosine was detected in urine of lung cancer patients, smokers and non smokers respectively 4,668 – 19,919 ppb, 6,873 – 12,111 ppb, -0,502 – 6,578 ppb. The mean value of 8-hydroxy-2’-deoxyguanosine in urine of lung cancer patients, smokers and non smokers as much as 9,710 ppb, 10,226 ppb, and 3,080 ppb."

"Latar Belakang: Gen MGMT berperan dalam mekanisme perbaikan DNA melalui transfer alkil mencegah terjadinya mutasi gen ? gen terkait orofacial cleft. Metilasi pada promoter gen MGMT mempengaruhi regulasi ekspresi gen tersebut.Tujuan: Mengetahui gambaran kejadian metilasi gen MGMT penderita orofacial cleft.Metode: Dua puluh empat sampel orofacial cleft dan 24 sampel normal dilakukan deteksi status metilasi melalui methylation specific-PCR (MSP).Hasil: Diperoleh 33.3% orofacial cleft berstatus fully methylated dan 66.7% partially methylated. Sedangkan pada kontrol, 100% berstatus partially methylated.Kesimpulan: Terjadi metilasi gen MGMT pada penderita orofacial cleft dan distribusinya berbeda dengan individu normal (p=0.004).

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Background: MGMT gene plays a role in DNA repair mechanisms via the transfer of alkyl to prevent mutation of gene related orofacial cleft. Methylation at MGMT gene promoter has effect in the regulation of gene expression.

Objective: To determine MGMT gene methylation status in orofacial cleft.

Methods: Methylation status were detected in 24 orofacial cleft and 24 healthy individuals samples by methylation-specific PCR (MSP).

Results: 33.3% orofacial cleft were fully methylated and 66.7% were partially methylated. Meanwhile, in control group, 100% were partially methylated.

Conclusion: MGMT gene methylation occurred in orofacial cleft and the distributions are different from healthy individuals (p=0.004)."

"Dengan tersedianya data genom berupa sekuen DNA pada domain publik, banyak peneliti dari berbagai lintas bidang yang memfokuskan penelitian mereka dalam studi genom untuk analisa ekstrasi informasi dan analisa data. Penelitian pada sekuen DNA dilakukan dengan menggunakan metode pengolahan signal digital disebut dengan Genomic Signal Processing (GSP). GSP dapat digunakan untuk mendiagnosis penyakit genetik yang muncul karena mutasi pada sekuen DNA, seperti kanker. Saat ini, kanker menduduki peringkat kedua sebagai penyebab kematian di dunia. Pada tingkat yang paling mendasar, kanker adalah penyakit DNA, dimana perubahan sekuen DNA dan molekul yang berinteraksi dengan DNA pada akhirnya menyebabkan profilerasi sel yng tidak terkendali. Pada skripsi ini, akan dilakukan simulasi untuk membandingkan tranformasi fourier dengan transformasi wavelet dalam mendeteksi kanker. Perancangan diawali dengan mengkonversi sekuen DNA menjadi sekuen numerik menggunakan binary sequence method. Selanjutnya,transformasi fourier / wavelet digunakan untuk menganalisa karakteristik spektral dan IIR Low Pass Filter Butterworth digunakan untuk meningkatkan akurasi dengan menekan noise. Berdasarkan simulasi, diperoleh bahwa transformasi wavelet dapat digunakan untuk mendeteksi kanker melalui analisa sekuen DNA dimana wavelet ortogonal memberikan hasil lebih baik daripada biortogonal. Dibandingkan transformasi fourier, transformasi wavelet memiliki performa yang lebih baik dalam mendeteksi sel kanker.

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With the enormous amount of genomic data of DNA sequence available in the public domain, many researcher from various cross fields have concentrated their research in genomic study for information extraction and data analysis technique that is used to analyze DNA sequences using Digital Signal Processing (DSP) is Genomic Signal Processing (GSP). GSP can be used to diagnose genetic diseases that appear due to mutations in DNA sequences, such as cancer. Cancer is the second leading disease that cause of death in the world. Cancer is the disease of DNA because a permanent change in the DNA can develop cancer cells.

This thesis will design a simulation to compare between fourier transformation and wavelet transformation for cancer detection. The design begins by converting the DNA sequence into numerical sequences using binary sequence method. Furthermore, the fourier/wavelet transform is used to analyze the spectral characteristics of DNA sequence and IIR Butterworth Low Pass Filter is used to improve the accuracy in predicting and identifying cancer cells.

The result of simulation shows that wavelet transform can be used to detect a cancer through DNA sequence analysis. Wavelet transform shows the better performance than fourier transformation. In wavelet transform, orthogonal wavelet give better result that biorthogonal wavelet."

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ABSTRACTOral bacteria are the first human microbiome to encounter the food we eat. To date, most research has focused on the role of oral bacteria in the development and progression of caries and periodontal disease; however, little is known about the microbial communities that maintain a healthy oral cavity. This book, Oral Microbial Communities: Genomic Inquiry and Interspecies Communication, helps readers understand how multispecies microbial communities function to maintain and promote oral health as well as disease. It explores the immense opportunities presented by readily accessible, genetically tractable, genome-sequenced oral species that naturally form multispecies communities. Emphasizing the use of genomic inquiry to probe questions, Oral Microbial Communities examines multispecies community interactions, spatiotemporal organization, and gene function. Readers will find coverage of all the major microbe species currently under investigation by leading oral microbiologists. In particular, the book highlights model systems that study oral bacterial interactions, including biofilm growth using saliva as the source of nutrition."