scholarly journals Sus sp. DNA ENCODING cyt b GENE DETECTION TEST ON SOFT GEL CANDY SAMPLES USING PCR METHOD

2021 ◽  
Vol 4 (1) ◽  
pp. 14
Author(s):  
Latifatoel Chilmi ◽  
Tri Susilowati ◽  
Yuanita Rachmawati ◽  
Saiku Rokhim ◽  
Inggrit Tyautari
Keyword(s):  
Aging Treatment ◽  
Positive Control ◽  
Cyt B ◽  
Dna Encoding ◽  
Gene Encoding ◽  
Animal Bone ◽  
Pcr Product ◽  
Pcr Method ◽  
Main Components ◽  
Cyt B Gene

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.

scholarly journals Sus sp. DNA Encoding cyt b Gene Detection Test on Meat Grinding Samples Using Conventional PCR

2020 ◽  
Vol 2 (2) ◽  
pp. 40-45
Author(s):  
Miftahul Lathif Adzakiyyi ◽  
Tri Susilowati ◽  
Saiku Rokhim ◽  
Yuanita Rachmawati
Keyword(s):  
Conventional Polymerase Chain Reaction ◽  
Positive Control ◽  
Pcr Analysis ◽  
Processed Meat ◽  
Cyt B ◽  
Dna Encoding ◽  
Pcr Method ◽  
The Government ◽  
C 30 ◽  
Cyt B Gene

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.

scholarly journals Allele-Specific PCR for the Detection of Azoxystrobin Resistance in Didymella bryoniae

Plant Disease ◽  
2014 ◽  
Vol 98 (12) ◽  
pp. 1681-1684 ◽  
Author(s):  
Mavis J. Finger ◽  
Venkatesan Parkunan ◽  
Pingsheng Ji ◽  
Katherine L. Stevenson
Keyword(s):  
Dna Sequences ◽  
Cyt B ◽  
Didymella Bryoniae ◽  
Specific Pcr ◽  
Pcr Product ◽  
Allele Specific ◽  
Polymerase Chain ◽  
Sensitive Allele ◽  
Cyt B Gene ◽  
Allele Specific Pcr

Gummy stem blight (GSB), caused by the fungus Didymella bryoniae, is considered the most widespread and destructive disease of watermelon in the southeastern United States. The quinone outside-inhibiting (QoI) fungicide azoxystrobin (AZO), which inhibits mitochondrial respiration by binding to the outer, quinone-oxidizing pocket of the cytochrome bc1 (cyt b) enzyme complex, was initially very effective in controlling GSB. However, resistance to AZO has been observed in D. bryoniae in many watermelon-producing regions. In this study, the DNA sequences of partial cyt b genes of four AZO-resistant (AZO-R) and four AZO-sensitive (AZO-S) isolates of D. bryoniae confirmed the amino acid substitution of glycine by alanine at the 143 codon (G143A) in the AZO-R isolates tested. Allele-specific primers were designed to detect the resistant or sensitive allele at codon 143 of the cyt b gene, which amplified a 165-bp polymerase chain reaction (PCR) product from genomic DNA of nine AZO-R and nine AZO-S isolates of D. bryoniae, respectively. The primer pairs did not amplify DNA from other pathogens tested in the study. The results indicated that the PCR assays developed in the study were specific in differentiating AZO-R and AZO-S isolates and could facilitate AZO resistance detection in D. bryoniae.

scholarly journals Amino acid diversity on the basis of cytochrome b gene in Kacang and Ettawa Grade goats

2017 ◽  
Vol 42 (3) ◽  
pp. 135 ◽  
Author(s):  
D. A. Lestari ◽  
S. Sutopo ◽  
E. Kurnianto
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Marker ◽  
Cytochrome B ◽  
Genomic Dna ◽  
Cyt B ◽  
Specific Amino Acid ◽  
Pcr Method ◽  
Cyt B Gene ◽  
Amino Acid Diversity

The objectives of study were to identify and assess the amino acid diversity of Cytochrome b (Cyt b) gene, genetic marker and characteristic of specific amino acid in Kacang and Ettawa Grade goat. Nineteen heads of Kacang goat (KG) and twelve heads of Ettawa Grade goat (EG) were purposively sampled. The genomic DNA was isolated by Genomic DNA Mini Kit (Geneaid) and amplified Cyt b using PCR method with CytbCapF and CytbCapR primers and was sequenced. The results showed that there were two specific amino acids that distinguish KG and EG goat with C. hircus and C. aegagrus and four specific amino acids that distinguish KG and EG goat with C. falconeri, but there were no specific amino acids can be used as a genetic marker to distinguish between Kacang and EG goat. In conclusion, specific amino acids in Cyt b gene can be used as a genetic marker among KG and EG goat with 3 goat others comparator.

scholarly journals Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome B gene

2020 ◽  
Vol 13 (1) ◽  
pp. 96-103
Author(s):  
Dorothea Vera Megarani ◽  
Herjuno Ari Nugroho ◽  
Zahrah Prawita Andarini ◽  
Yura Dwi Risa B. R. Surbakti ◽  
Rini Widayanti
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Cytochrome B ◽  
Genetic Characterization ◽  
Phylogenetic Study ◽  
Cyt B ◽  
Phylogenetic Structure ◽  
Mitochondrial Cytochrome B ◽  
Sperata Seenghala ◽  
Cyt B Gene

Aim: This study aimed to determine the genetic characterization and phylogenetic structure of Indonesian indigenous catfish using cytochrome B (Cyt B) sequences. Materials and Methods: The genomes of 26 catfishes caught from nine rivers from nine different geographical locations around Indonesia were analyzed. The tissue isolation method was used to isolate the total genome of the fishes. Furthermore, polymerase chain reaction was done to amplify the mtDNA Cyt B using the CytBF and CytBR primers. Following sequencing, the analysis of genetic variation and the phylogenetic relationship was performed using MEGA version X software. Results: Cyt B gene sequencing attained a total of 1139 nucleotides encrypting 379 amino acids for all samples. The ClustalW alignment program using MEGA X software revealed 395 substituted nucleotides, which then translated into 63 amino acid variation sites among all 26 samples. No amino acids in catfish BB were different compared to catfish PM, MP, and KR2,3. Catfish MS had one modified amino acid; KR1 and KS had two different amino acids; BF had 38 different amino acids; EM had 31 different amino acids; and BSBJ had 26 different amino acids compared to catfish BB. The most significant alteration of amino acids was between catfish EM and BF (49 amino acids). Conclusion: Indonesian catfish were divided into five clades based on the Cyt B gene. Samples KR and MP (Sumatra); MS and BB (Kalimantan); and PM (Java) were clustered with Hemibagrus nemurus and Hemibagrus wyckioides (Bagridae family). Samples from Kalimantan (KS) and one sample of KR (KR1) from Sumatra were clustered with Sperata seenghala and Hemibagrus spilopterus (Bagridae family). Samples from Java (BSBJ) were clustered with Pseudolais pleurotaenia (Pangasiidae family). Samples EM (Java) were together with Mystus cavasius (Bagridae family). Samples from West Papua were clustered with Potamosilurus latirostris (Ariidae family).

scholarly journals The polymorphism of ETR1 gene in autochthonous apple cultivars

Genetika ◽  
2007 ◽  
Vol 39 (3) ◽  
pp. 387-394 ◽  
Author(s):  
Sladjana Maric ◽  
Radovan Boskovic ◽  
Milan Lukic
Keyword(s):  
Plant Hormone ◽  
Allelic Polymorphism ◽  
Ethylene Receptor ◽  
Gene Encoding ◽  
Fruit Storage ◽  
Specific Pcr ◽  
Pcr Product ◽  
Apple Cultivars ◽  
Storage Ability

Ethylene is a plant hormone, which plays an important role in the ripening of climacteric fruits such as the apple. We studied allelic polymorphism of the ETR1 gene, encoding ethylene receptor, in 23 autochthonous apple cultivars. The polymorphism was revealed by combining the gene specific PCR and restriction of PCR product. Four alleles of the ETR1 gene (a, b, c and d) were detected, and their possible association with the fruit storage ability examined.

scholarly journals Kajian Penanda Genetik Gen Sitokrom b DNA Mitokondria Ikan Lais dari Sungai Kampar Riau

2018 ◽  
Vol 10 (1) ◽  
pp. 6
Author(s):  
Roza Elvyra ◽  
Dedy Duryadi Solihin
Keyword(s):  
Species Diversity ◽  
Molecular Marker ◽  
Phylogenetic Relationship ◽  
Cytochrome B ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Phylogenetic Marker ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

The mitochondrial cytochrome b (cyt-b) gene as a phylogenetic marker of lais fish Kryptopterus schilbeides from Kampar River in Riau has been studied. This is a prelimininary research on the utility of cyt-b gene as a molecular marker to obtain species diversity and phylogenetic relationship among Kryptopterus fishes from Kampar River. The primers of L14841 and H15149 were used to amplify the cyt-b gene. The results showed that K. schilbeides has isoleusine at site-81 and metionine at site-114; K. schilbeides from Kampar River and K. schilbeides from GenBank form a phylogeny cluster at 45% value.

scholarly journals First Report of a Group 16SrII Phytoplasma Associated with Witches'-Broom of Eggplant in Oman

Plant Disease ◽  
2011 ◽  
Vol 95 (3) ◽  
pp. 360-360 ◽  
Author(s):  
A. M. Al-Subhi ◽  
N. A. Al-Saady ◽  
A. J. Khan ◽  
M. L. Deadman
Keyword(s):  
Nested Pcr ◽  
Solanum Melongena ◽  
Positive Control ◽  
Rrna Gene ◽  
Direct Pcr ◽  
First Report ◽  
Pcr Product ◽  
Pcr Products ◽  
Broom Disease ◽  
Phytoplasma Infection

Eggplant (Solanum melongena L.) belongs to the family Solanaceae and is an important vegetable cash crop grown in most parts of Oman. In February 2010, plants showing phyllody symptoms and proliferation of shoots resembling those caused by phytoplasma infection were observed at Khasab, 500 km north of Muscat. Total genomic DNA was extracted from healthy and two symptomatic plants with a modified (CTAB) buffer method (2) and analyzed by direct and nested PCR with universal phytoplasma 16S rDNA primers P1/P7 and R16F2n/ R16R2, respectively. PCR amplifications from all infected plants yielded an expected product of 1.8 kb with P1/P7 primers and a 1.2-kb fragment with nested PCR, while no products were evident with DNA from healthy plants. Restriction fragment length polymorphism (RFLP) profiles of the 1.2-kb nested PCR products of two eggplant phyllody phytoplasma and five phytoplasma control strains belonging to different groups used as positive control were generated with the restriction endonucleases RsaI, AluI, Tru9I, T-HB8I, and HpaII. The eggplant phytoplasma DNA yielded patterns similar to alfalfa witches'-broom phytoplasma (GenBank Accession No. AF438413) belonging to subgroup 16SrII-D, which has been recorded in Oman (1). The DNA sequence of the 1.8-kb direct PCR product was deposited in GenBank (Accession No. HQ423156). Sequence homology results using BLAST revealed that the eggplant phyllody phytoplasma shared >99% sequence identity with Scaevola witches'-broom phytoplasma (Accession No. AB257291.1), eggplant phyllody phytoplasma (Accession No. FN257482.1), and alfalfa witches'-broom phytoplasma (Accession No. AY169323). The RFLP and BLAST results of 16S rRNA gene sequences confirm that eggplant phyllody phytoplasma is similar to the alfalfa phytoplasma belonging to subgroup 16SrII-D. To our knowledge, this is the first report of a phytoplasma of the 16SrII-D group causing witches'-broom disease on eggplant in Oman. References: (1) A. J. Khan et al. Phytopathology 92:1038, 2002. (2) M. A. Saghai-Maroof et al. Proc. Natl. Acad. Sci. USA, 81:8014, 1984.

Estimating Giardia cyst viability using RT-PCR

2002 ◽  
Vol 2 (3) ◽  
pp. 107-115 ◽  
Author(s):  
M. Maux ◽  
I. Bertrand ◽  
C. Gantzer ◽  
J. Schwartzbrod
Keyword(s):  
Nested Pcr ◽  
Target Genes ◽  
Molecular Techniques ◽  
Giardia Cyst ◽  
Health Issues ◽  
Structural Protein ◽  
Gene Encoding ◽  
Response To Stress ◽  
Pcr Method ◽  
Giardia Cysts

The aim of this work was to evaluate the use of molecular techniques for the detection of viable Giardia cysts in the environment to assess public health issues. Three target genes were selected: the heat shock protein gene, HSP70, which is expressed in response to stress; the giardin gene, which encodes a structural protein; and, alcohol dehydrogenase E (ADHE), a novel gene encoding an enzyme involved in the metabolism of energy. We tested the efficiency of five protocols for the extraction of either genomic DNA or total RNA from Giardia cysts: two of these protocols were previously cited in the literature and three consisted of commercial DNA extraction kits. The brands of enzyme were determined according to the primers chosen and the amplification conditions were optimised: 2.5 mM MgCl2, 0.5 mM primers and 60°C for annealing temperature. A semi-nested PCR method and an RT semi-nested PCR procedure were developed to detect mRNA from these three genes and to estimate the viability of Giardia cysts.

The genetic analysis of new Polish strains of European brown hare syndrome virus

2014 ◽  
Vol 17 (2) ◽  
pp. 353-355
Author(s):  
E. Kwit ◽  
M. Chrobocińska ◽  
Z. Grądzki ◽  
Ł. Jarosz ◽  
B. Majer-Dziedzic ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Phylogenetic Position ◽  
Brown Hare ◽  
Gene Encoding ◽  
European Brown Hare ◽  
Close Relationship ◽  
Provinces Of Poland ◽  
Pcr Method ◽  
European Brown Hare Syndrome ◽  
Hare Population

Abstract In this paper we describe recently occurring outbreaks of European brown hare syndrome (EBHS) in a captive hare population. The aim of our study was to evaluate the phylogenetic position of detected Polish strains compared to other European strains of EBHSV. Investigations were undertaken in hares from different provinces of Poland. Liver or spleen samples were tested for viral RNA using the RT-nested PCR method and the products were subsequently sequenced. The genetic analysis was based on the fragment of gene encoding viral capsid protein; it revealed a high homology and close relationship between Polish and European EBHSV strains isolated between 2001 and 2011

scholarly journals A new method for rapid detection of Listeria monocytogenes in food

2000 ◽  
Vol 18 (No. 3) ◽  
pp. 103-109 ◽  
Author(s):  
K. Zdeňková ◽  
K. Demnerová ◽  
G. Jeníková ◽  
J. Pazlarová
Keyword(s):  
Listeria Monocytogenes ◽  
Pcr Primers ◽  
Immunomagnetic Separation ◽  
Food Samples ◽  
Special Importance ◽  
Ground Meat ◽  
Specific Detection ◽  
Gene Encoding ◽  
Pcr Method

Listeria monocytogenes represents serious danger for human health. Thus detection of this pathogen in food, which represents its main means of entry into the organism, is a topic of special importance. The original classic methods for the determination of Listeria monocytogenes are in general laborious and time-consuming procedures. In order to address this issue we developed a new rapid method for specific detection of Listeria monocytogenes in food samples. The method consists of three steps: i) enrichment of food microflora (16 h), ii) selective isolation of Listeria sp. exploiting immunomagnetic separation (2–3 h) followed by iii) precise identification of Listeria sp. and Listeria monocytogenes using duplex PCR. PCR primers specific to part of 16S rRNA were used in order to identify the members of Listeria genus. The specific identification of Listeria monocytogenes was accomplished exploiting a pair of primers specific to gene encoding invasion-associated protein – iap (4–5 h). Amplification products, 1003 bp and 593 bp respectively, were separated by electrophoresis and visualized by UV detection. The optimized IMS-PCR method was used to test the presence of Listeria sp. and Listeria monocytogenes in food samples (ground meat, low-fat milk and cheese [olomoucké tvarůžky]). A comparison of the efficiency of the bacteria enrichment step by IMS and centrifugation was also performed. The analysis time including enrichment is less than 24 h. The detection limit for Listeria monocytogenes was found between 101–102 cfu per 25 g of food sample.

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