In Silico Analysis of the cadF Gene and Development of a Duplex Polymerase Chain Reaction for Species-Specific Identification of Campylobacter jejuni and Campylobacter coli

The genus Campylobacter is of great importance to public health because it includes several species that may cause diarrhea. These species may be found in water, food and in the intestinal tract of chickens. This study investigated the presence of Campylobacter jejuni and Campylobacter coli in chicken abattoirs in São Paulo State, Brazil. A total of 288 samples of feces, feathers, scald water, evisceration water, chiller water, and the rinse water of eviscerated, not eviscerated and chilled carcasses were collected in six chicken abattoirs. Polymerase Chain Reaction (PCR) was performed in Campylobacter spp.-positive isolates using the gene HIP, specific for hippuricase enzyme from Campylobacter jejuni and aspartokinase gene, specific to detect Campylobacter coli. The percentage of positive isolates of Campylobacter jejuni was 4.9% (14/288). Isolation was greater in feces samples (22%, 8/36). One sample was positive for the species C. coli. In conclusion, the results indicate that it is necessary to improve quality control for Campylobacter spp. in chicken abattoirs.

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Isolasi dan Karakterisasi Barcode DNA Tanaman Nusa indah putih (Mussaenda frondosa) Berdasarkan Gen matK

Jurnal MIPA ◽

10.35799/jm.4.2.2015.8527 ◽

2015 ◽

Vol 4 (2) ◽

pp. 111

Author(s):

Jein Damanis ◽

Lidya Irma Momuat ◽

Meiske S. Sangi ◽

Maureen Kumaunang

Keyword(s):

Polymerase Chain Reaction ◽

In Silico ◽

Dna Barcode ◽

In Silico Analysis ◽

Chain Reaction ◽

Plant Dna ◽

Barcode Dna ◽

Reverse Primer ◽

Polymerase Chain ◽

Silico Analysis

Telah dilakukan penelitian untuk menentukan urutan nukleotida dari barcode DNA tanaman Nusa indah putih berdasarkan gen matK dan mengkarakterisasi matK tanaman nusa indah putih dengan analisis in-silico. Isolasi DNA dari tanaman Nusa indah putih telah dilakukan berdasarkan manual prosedur dari InnuPrep Plant DNA kit yang dilanjutkan dengan amplifikasi dengan metode Polymerase Chain Reaction (PCR) menggunakan primer forward matK-1RKIM-f dan primer reverse matK-3FKIM-r kemudian dielektroforesis dan disekuensing. Sekuensing tanaman Nusa indah putih menghasilkan kromatogram yang berkualitas tinggi, dengan panjang sekuens 843 bp. Hasil Analisis in-silico menunjukan matK tanaman nusa indah putih bersifat basa, stabil, dan berinteraksi baik dengan air.A study to determine the nucleotide sequence of the DNA barcode Nusa indah putih plants based on gene matK and to characterize the matK of Nusa indah putih plant using in-silico analysis had been done. Isolation of DNA from Nusa indah putih plant was conducted by manual procedures of InnuPrep Plant DNA kit, followed by amplification using Polymerase Chain Reaction (PCR) method using matK-1RKIM-f as forward primer and matK-3FKIM-r as reverse primer then electrophoresis and sequenced. Nusa indah putih plants sequencing produced a high-quality chromatogram produce, with a length of 843 bp sequences. Results of in-silico analysis showed that matK Nusa indah putih plant is a base, stable, and well-interacted with water.

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Penentuan Barcode DNA berdasarkan Gen matK dan Analisis In-silico MatK Rumput Macan (Lantana camara L.)

Jurnal MIPA ◽

10.35799/jm.4.1.2015.6900 ◽

2015 ◽

Vol 4 (1) ◽

pp. 24

Author(s):

Billy L. Mokoagow

Keyword(s):

Polymerase Chain Reaction ◽

In Silico ◽

Dna Barcode ◽

In Silico Analysis ◽

Lantana Camara ◽

Chain Reaction ◽

Barcode Dna ◽

Matk Gene ◽

Polymerase Chain ◽

Silico Analysis

DNA barcoding merupakan metode identifikasi spesies menggunakan potongan DNA pendek yang disebut barcode DNA. Gen matK merupakan gen standar untuk penentuan barcode DNA tanaman. Penelitian ini bertujuan untuk menentukan barcode DNA tumbuhan rumput macan (L. camara L.) berdasarkan gen matK, serta melakukan analisis in-silico terhadap produk gen matK tumbuhan rumput macan (L. camara L.) dengan kerabat terdekatnya. Gen matK L. camara L. telah berhasil diamplifikasi dengan Polymerase Chain Reaction (PCR) menggunakan primer forward matK-1RKIM-f dan primer reverse matK-3FKIM-r. Analisis terhadap sekuens matK L. camara L. menunjukkan bahwa barcode DNA tumbuhan rumput macan (L. camara L.) terdiri dari 843 nukleotida. Selanjutnya, hasil analisis in-silico menunjukkan bahwa matK Lantana camara L. bersifat basa, stabil, dan dapat berinteraksi baik dengan air.DNA barcoding is a method of species identification using short pieces of DNA called DNA barcode. matK is a standard gene to determine DNA barcode of a plant. The aim of this research was to determine the DNA barcode of Rumput Macan plant (Lantana camara L.) based on matK gene, as well as in-silico analysis of the product matK gene Rumput Macan (L camara L.) with its closest relatives. L. camara L. matK gene was successfully amplified by Polymerase Chain Reaction (PCR) using forward primer MATK-1RKIM-f and reverse primer MATK-3FKIM-r. Analysis of the matK sequence of L. camara L. showed that the barcode DNA of rumput macan plant (L. camara L.) consisting of 843 nucleotides. Furthermore, the result of in-silico analysis showed that the matK of L camara L. is alkaline, stable, and able to interact well with water.

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Identifikasi Barcode Tumbuhan Gedi Merah (Abelmoschus manihot L. medik) dan Gedi Hijau (Abelmoschus moschatus) Berdasarkan Gen matK

Jurnal MIPA ◽

10.35799/jm.3.2.2014.5863 ◽

2014 ◽

Vol 3 (2) ◽

pp. 120

Author(s):

Yusuf R. Fattah ◽

Vanda S. Kamu ◽

Max R. J. Runtuwene ◽

Lidya I. Momuat

Keyword(s):

Polymerase Chain Reaction ◽

Dna Barcoding ◽

In Silico ◽

Dna Barcode ◽

In Silico Analysis ◽

Chain Reaction ◽

Barcode Dna ◽

Matk Gene ◽

Polymerase Chain ◽

Silico Analysis

Gedi (Abelmoschus L.) merupakan tumbuhan tropis. Tumbuhan ini memilki efek farmakologis. Masyarakat Minahasa mengkonsumsi daun gedi yang direbus tanpa diberi bumbu sebagai obat tradisional untuk menurunkan kadar kolesterol, antihipertensi dan antidiabetes. Suatu metode baru untuk mengidentifikasi dan menganalisis keanekaragaman genetika spesies telah dikembangkan dengan menggunakan potongan gen standar yang dikenal dengan teknik DNA barcoding. Salah satu gen yang terdapat pada tumbuhan yaitu gen matK telah digunakan sebagai gen standar untuk barcoding. Pada penelitian ini telah dilakukan isolasi DNA total dan gen matK penanda barcode DNA dari gedi merah dan gedi hijau, serta analisis in-silico terhadap produk gen matK gedi merah, gedi hijau, dan kerabat terdekatnya. Gen matK diisolasi dan diamplifikasi menggunakan metode Polymerase Chain Reaction (PCR) menggunakan primer forward (5’-CGTACAGTACTTTTGTGTTT ACGAG-3’) dan primer reverse (5’-ACCCAGTCCATCTGGAAATCTTGGTTC-3’). Hasil pengurutan nukleotida DNA barcode matK menunjukkan bahwa sebanyak 828 pb matK berhasil diisolasi untuk tumbuhan gedi merah dan tumbuhan gedi hijau. Urutan nukleotida matK gedi merah dan gedi hijau menunjukkan tingkat kemiripan yang tinggi, yaitu > 95%. Selain itu, hasil analisis in-silico menunjukkan bahwa protein MatK gedi dan kerabat terdekatnya bersifat hidrofobik.Gedi (Abelmoschus L.) is a tropical plant. This plant has the pharmacological effects. Minahasan people consumed boiled gedi without any spices addition to lower cholesterol level, blood pressure, and glucose level. A new method for identifying and analyzing the genetic diversity of species has been developed using standard gene known as DNA barcoding technique. One of the genes found in plants called matK gene was used as standard for DNA barcoding. In this research, identification of DNA barcode of red gedi and green gedi based on matK gene, and in-silico analysis on the matK gene products of red gedi, green gedi, and its closest relatives gedi have been done. matK gene was isolated with Polymerase Chain Reaction (PCR) using forward primer (5'-CGTACAGTACTTTTGTGTTTACGAG-3') and reverse primer (5'-ACCCAGTCCATCTGGAAATCTTGGTTC-3'). Barcode DNA of red and green gedi showed 828 bp nucleotide sequence based on matK gene. In addition, matK of both gedi showed high similarity, i.e. >95%. Furthermore, in-silico analysis of MatK gedi and its closest relative showed that this protein is hidrophobic.

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