Evaluation of foliar fungal endophyte incidence in field-grown transgenic Bt white spruce trees

2006 ◽  
Vol 84 (10) ◽  
pp. 1573-1580 ◽  
Author(s):  
F.O.P. Stefani ◽  
J.A. Bérubé
Keyword(s):  
White Spruce ◽  
Fungal Endophyte ◽  
Potato Dextrose Agar ◽  
Species Level ◽  
Chain Reaction ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Reference Sequences ◽  
Spruce Needles ◽  
Restriction Group

A total of 770 transgenic Bt white spruce needles were collected and plated on potato dextrose agar to determine their foliar endophyte diversity. The ribosomal internal transcribed spacer regions for 310 foliar endophytes were amplified by polymerase chain reaction (PCR) and digested using CfoI and MspI, which created 21 restriction groups. Isolates from each restriction group were sequenced and compared with reference sequences in GenBank. Eighteen sequence groups were obtained, of which five were identified at the species level. The most common endophytic fungi identified by PCR-RFLP was Lophodermium piceae (incidence of 74.5%). The second and third most common ones were Hypoxylon fragiforme (3.63%) and Lophodermium nitens (3.18%). A statistical analysis performed on the most common endophyte groups showed no statistical difference in endophyte frequency or distribution between the control white spruce needles (nontransgenic) and saplings with constructs containing the reporter gene GUS or the Bt Cry1A(b) gene and kanamycin.

scholarly journals CYP27B1 Gene Polymorphism rs10877012 in Patients Diagnosed with Colorectal Cancer

Nutrients ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 998
Author(s):  
Maria Latacz ◽  
Jadwiga Snarska ◽  
Elżbieta Kostyra ◽  
Konrad Wroński ◽  
Ewa Fiedorowicz ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Vitamin D ◽  
Fragment Length Polymorphism ◽  
Intestinal Cells ◽  
Chain Reaction ◽  
The Third ◽  
Pcr Rflp ◽  
Study Population ◽  
Polymerase Chain ◽  
Peripheral Leukocytes

Colorectal cancer (CRC) is the third most commonly occurring cancer worldwide. Intestinal cells are CYP27B1 gene expression sites and, as a consequence, they are capable of converting pro-vitamin D into the active paracrine and autocrine forms. It was demonstrated that rs10877012 polymorphism in the CYP27B1 gene influenced the circulating vitamin D level. This provided a rationale for determining the role that this polymorphism plays in the risk of developing colon cancer. In this study, we investigated the association of rs10877012 (T/G) polymorphism in the CYP27B1 gene with CRC susceptibility. The study population (n = 325) included CRC patients (n = 106) and healthy controls (n = 219). DNA was extracted from peripheral leukocytes and analyzed for the CYP27B1 polymorphism using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. We found an association between the presence of the T allele at the polymorphic site (odds ratio (OR) = 2.94; 95% CI 1.77–4.86; p < 0.0001) and a decreased CRC incidence.

scholarly journals Prevalence and diversity of Arcobacter spp. in retail chicken meat in Turkey

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Celenk Molva ◽  
Halil Ibrahim Atabay
Keyword(s):  
Polymerase Chain Reaction ◽  
Multiplex Pcr ◽  
Chicken Meat ◽  
Species Level ◽  
Waterborne Pathogens ◽  
Chain Reaction ◽  
Retail Markets ◽  
Specific Polymerase Chain Reaction ◽  
Polymerase Chain ◽  
Retail Chicken Meat

Arcobacters are food and waterborne pathogens associated with human and animal infections. The objective of the present study was to investigate the prevalence and diversity of <em>Arcobacter</em> spp. in commercially sold chicken meat in İzmir region of Turkey. For this purpose, 100 samples including legs (n=40), 17 chicken quarters (n=17), drumstickers (n=16), breasts (n=11), wings (n=10), and carcasses (n=6) were collected from different retail markets. A total of 65 isolates were confirmed as <em>Arcobacter</em> spp. from 55 samples by genus-specific polymerase chain reaction (PCR). The prevalence of <em>Arcobacter</em> spp. was 32.5, 81.3, 64.7, 72.7, 83.3, and 50% for legs, drumstickers, chicken quarters, breasts, carcasses and wings, respectively. Based on the multiplex-PCR, most of the isolates were identified as <em>A. butzleri</em> (n=45, 80%), followed by <em>A. cryaerophilus</em> (n=2, 3.6%), <em>A. skirrowii</em> (n=1, 1.8%) and 17 isolates (30.9%) could not be identified at the species level.

scholarly journals Associations of biochemical changes and maternal traits with mutation 1843 (C>T) in the RYR1 gene as a common cause for porcine stress syndrome

2016 ◽  
Vol 19 (2) ◽  
pp. 75-80 ◽  
Author(s):  
ZT Popovski ◽  
B Tanaskovska ◽  
E Miskoska-Milevska ◽  
S Andonov ◽  
S Domazetovska
Keyword(s):  
Fragment Length Polymorphism ◽  
Protein Product ◽  
Biochemical Changes ◽  
Chain Reaction ◽  
Maternal Characteristics ◽  
Stress Syndrome ◽  
Pcr Rflp ◽  
Porcine Stress Syndrome ◽  
Heterozygous Carriers ◽  
Polymerase Chain

AbstractStress syndrome is usually caused by a mutation in theryanodine receptorgene(ryr1) and it is widely studied in humans and swine populations. The protein product of this gene plays a crucial role in the regulation of calcium transport in muscle cells. A G>T mutation in the humanryr1gene, which results in the replacement of a conserved arginine at position 614 where a leucine occurs at the same position as the previously identified Arg→Cys mutation reported in all cases of porcine stress syndrome (PSS). Porcine stress syndrome affects biochemical pathways in stress-susceptible individuals during a stress episode and some biochemical parameters that were used as markers for diagnostic purposes. Also, PSS has remarkable influence on the maternal characteristics of sows. This study dealt with different genotypes for PSS and its association with possible biochemical changes and maternal traits of sows. Seventy-three reproductive sows genotyped for PSS by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) were included in this survey. Sixty of them were stress-free (NN), 11 were heterozygous carriers (Nn) and two animals were homozygous (nn) for the 1843 (C>T) mutation. Significant differences in non stress induced animals with different PSS genotypes were found in the values of creatine phoshokinase (CPK), lactate dehydrogenase (LDH), alkaline phosphatase (AP) and aspartate aminotransferase (AST). Regarding the maternal traits, our study showed that stress susceptible animals (nn) have an increased number of stillborn piglets and a reduced number of newborn piglets compared with heterozygous and normal animals.

scholarly journals Identifikasi Keragaman Gen DGAT1 serta Asosiasinya terhadap Karakteristik Karkas dan Sifat Perlemakan Domba

2019 ◽  
Vol 6 (2) ◽  
pp. 259
Author(s):  
Asep Gunawan ◽  
Ratna Sholatia Harahap ◽  
Kasita Listyarini ◽  
Cece Sumantri
Keyword(s):  
Polymerase Chain Reaction ◽  
Single Nucleotide Polymorphism ◽  
Fragment Length Polymorphism ◽  
Nucleotide Polymorphism ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Dgat1 Gene ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Restriction Fragment Length

ABSTRAK Karakteristik karkas dan sifat perlemakan pada daging domba dikontrol oleh banyak gen salah satunya gen DGAT1 (Diacylglycerol Acyltransferasel 1). Penelitian ini bertujuan mengidentifikasi SNP (Single Nucleotide Polymorphism) gen DGAT1 pada titik mutasi g.8539 C>T dan asosiasinya terhadap karakteristik karkas dan sifat perlemakan pada domba Indonesia. Total sampel domba yang digunakan sebanyak 150 buah terdiri dari 35 sampel domba compass agrinak (DCA), 36 sampel domba barbados cross (DBC), 41 sampel domba komposit garut (DKG), 20 sampel domba ekor gemuk (DEG), dan 18 sampel domba ekor tipis (DET). Karakteristik karkas dan sifat perlemakan diukur dari domba jantan berumur 10-12 bulan. Identifikasi keragaman DGAT1|ALuI dianalisis dengan metode PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). Hasil keragaman gen DGAT1 bersifat polimorfik dalam DET dan DEG, sedangkan DCA, DBC, dan DKG bersifat monomorfik. Dua genotipe disebut CC dan  CT ditemukan dalam DET dan DEG. Titik mutasi gen DGAT1 berasosiasi (P<0.05) dengan karakteristik karkas, yaitu bobot dan panjang karkas. Selain itu, keragaman gen DGAT1 juga berasosiasi signifikan (P<0.05) dengan asam lemak jenuh, yaitu asam stearat (C18:0) dan asam arakidat (C20:0) dan asam lemak tak jenuh tunggal, yaitu asam oleat (C18:1n9c). Gen DGAT1 memiliki kontribusi dalam karakteristik karkas dan komposisi asam lemak pada domba.Kata Kunci: domba, gen DGAT1, karakteristik karkas, PCR-RFLP, sifat perlemakan                                                              ABSTRACT            Characteristic of carcass and fatness traits of sheep is regulated by many genes such as DGAT1 (Diacylglycerol Acyltransferasel 1) gene. The research was aimed to investigate SNP (Single Nucleotide Polymorphism) of DGAT1 and its association with characteristic of carcass and fatness traits in Indonesian sheep. A total sample of sheeps used 150 rams of 10–12 months consisted 35 samples of compas agrinak sheep (CAS), 36 of barbados cross (BCS), 41 of garut composite (GCS), 20  of javanese fat tailed (JFT), and 18 of javanese thin tailed (JTT). Identification variant of DGAT1|ALuI were performed by PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). The results of polymorphism of DGAT1 were found in JTT and JFT. However, SNP of DGAT1 in CAS, BCS and GCS were monomorfic. Two genotype namely CC and CT were found in JTT and JFT populations. A SNP of the DGAT1 was associated (P<0.05) with characteristic of carcass, including weight and length of carcass. The variant of DGAT1 was associated too with saturated fatty acids (SFA) including stearic acid (C18:0) and arachidic acid (C20:0), and mono unsaturated fatty acid (MUFA) including oleic acid (C18:1n9c). The DGAT1 gene was contribute to characteristic carcass and fatty acid composition in sheep.Keywords: DGAT1 gene, characteristic carcass, fatness traits, PCR-RFLP, sheep

scholarly journals Etude de l’implication du polymorphisme fonctionnel Arg72Pro du gène TP53 dans la survenue du cancer colorectal et du carcinome Basocellulaire dans la population de l’Ouest Algérien

2017 ◽  
Vol 1 (2) ◽  
Author(s):  
Rym Abderrahmane ◽  
Lotfi Louhibi ◽  
Amina Boubekeur ◽  
Fatima Zohra Moghtit ◽  
Abdellah Boudjema ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Restriction Fragment ◽  
Cancer Colorectal ◽  
Facteurs De Risque ◽  
Chain Reaction ◽  
Biologie Moléculaire ◽  
Pcr Rflp ◽  
Cycle Cellulaire ◽  
Gene Tp53 ◽  
Polymerase Chain

Introduction - Le gène TP53 a fait l’objet de très nombreux travaux. Sa nature polymorphe et son rôle central dans la régulation du cycle cellulaire ont mis en évidence son potentiel de gène candidat dans la susceptibilité et la survenue de différents cancers. Bien que plusieurs polymorphismes du gène TP53 aient été étudiés comme facteurs de risque pour différents cancers, le plus largement étudié est le polymorphisme Arg72Pro (rs1042522), à l’origine d’une substitution d’une Arginie (Arg) en Proline (Pro) ou inversement, connu pour ses différentes fonctions biologiques.Notre objectif est d’explorer la participation du polymorphisme (SNP) Arg72Pro du gène TP53, dans l’expressivité du cancer colorectal (CCR) et du carcinome basocellulaire (CBC) dans une population de l’Ouest Algérien.Matériels et Méthodes - Le déséquilibre de transmission allélique de ce SNP a été réalisé sur une population constituée de 116 individus atteints de CCR, 50 sujets atteints de CBC et enfin une population contrôle constituée de 121 individus sains,par la technique de Biologie Moléculaire PCR/RFLP (Polymerase Chain Reaction/Restriction Fragment LengthPolymorphism).Résultats - L’association du marqueur Arg72Pro avec le CBC a montré une augmentation significative de l’allèle Pro chez les cas par rapport aux contrôles (54% vs 46%, OR=8,85 [4,98-16,03], p<10-7). Cet allèle semble conférer un risque important dedévelopper le CBC. Par ailleurs, les résultats n’ont montré aucune différence significative entre les sujets atteints de CCR et les contrôles, ce qui pourrait exclure son implication dans la survenue du CCR dans notre population (p>0.05).Conclusion - Le polymorphisme Arg72Pro du gène TP53 peut être considéré comme marqueur de risque pour le CBC mais pas pour le CCR.

scholarly journals MDR1 polymorphisms are not related to Xeliri and Xelox chemoresistance in colorectal cancer

2019 ◽  
Author(s):  
Ayat B. Al-Ghafari ◽  
Areej M. Alqahtani ◽  
Suzan N. Alturki ◽  
Huda Abdulaziz Al Doghaither ◽  
Hanaa M. Tashkandi ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Drug Response ◽  
Fragment Length Polymorphism ◽  
Protective Role ◽  
Genotype Distribution ◽  
Chain Reaction ◽  
P Glycoprotein ◽  
Significant Difference ◽  
Pcr Rflp ◽  
Polymerase Chain

Abstract Background Multidrug resistance member 1 (MDR1) is located on chromosome 7 and encodes P-glycoprotein (Pgp), which is universally accepted as a drug resistance biomarker. MDR1 polymorphisms may change either the protein expression or function, suggesting its possible association with cancers, including colorectal cancer (CRC). Thus, this study aimed to determine the effects of MDR1 polymorphisms on the drug response of Saudi CRC patients.Methods DNA samples were obtained from 62 CRC patients and 100 healthy controls. The genotypes and allele frequencies of the MDR1 polymorphisms G2677T and T1236C were determined by polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP).Results No significant difference was observed in the genotype distribution and allele frequency of T1236C between the CRC the patients and the controls. However, G2677T was found to play a highly significant protective role against the progression of CRC. Moreover, the results showed that none of the genotypes in SNPs T1236C and G2677T affected chemoresistance to Xeliri and Xelox.Conclusions T1236C in the MDR1 gene is not related to CRC risk, and G2677T protects against the development of CRC. Both MDR1 polymorphisms are not associated with the risk of chemoresistance.

scholarly journals Chilean Salmon Sushi: Genetics Reveals Product Mislabeling and a Lack of Reliable Information at the Point of Sale

Foods ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1699
Author(s):  
Valentina Prida ◽  
Maritza Sepúlveda ◽  
Claudio Quezada-Romegialli ◽  
Chris Harrod ◽  
Daniel Gomez-Uchida ◽  
...  
Keyword(s):  
Chinook Salmon ◽  
Food Production ◽  
Fragment Length Polymorphism ◽  
Coho Salmon ◽  
Chain Reaction ◽  
Production Chain ◽  
Point Of Sale ◽  
Pcr Rflp ◽  
Seafood Products ◽  
Polymerase Chain

Species diagnosis is essential to assess the level of mislabeling or misnamed seafood products such as sushi. In Chile, sushi typically includes salmon as the main ingredient, but species used are rarely declared on the menu. In order to identify which species are included in the Chilean sushi market, we analyzed 84 individual sushi rolls sold as “salmon” from sushi outlets in ten cities across Chile. Using a polymerase chain reaction-restriction fragment length polymorphism protocol (PCR-RFLP), we identified mislabeled and misnamed products. Atlantic salmon was the most common salmonid fish used in sushi, followed by coho salmon, rainbow trout, and Chinook salmon. We found a total of 23% and 18% of the products were mislabeled and misnamed, respectively. In 64% of cases, the salesperson selling the product could not identify the species. We also identified the use of wild-captured Chinook salmon samples from a naturalized population. Our results provide a first indication regarding species composition in Chilean sushi, a quantification of mislabeling and the level of misinformation declared by sales people to consumers. Finally, considering that Chinook salmon likely originates from a non-licensed origin and that sushi is an uncooked product, proper identification in the food production chain may have important consequences for the health of consumers.

Extraction of microsporidial DNA from modified trichrome-stained clinical slides and subsequent species identification using PCR sequencing

Parasitology ◽  
2008 ◽  
Vol 135 (6) ◽  
pp. 701-703 ◽  
Author(s):  
K. S. CHAN ◽  
T. H. KOH
Keyword(s):  
Polymerase Chain Reaction ◽  
Species Identification ◽  
Environmental Samples ◽  
Species Level ◽  
Molecular Techniques ◽  
Chain Reaction ◽  
Clinical Specimens ◽  
Polymerase Chain ◽  
Pcr Conditions ◽  
Hiv Negative

SUMMARYMolecular techniques involving polymerase chain reaction (PCR) and sequencing provide a relatively simple and objective means of identifying microsporidia to species level. We modified previously described methods of DNA extraction and PCR conditions for identification of microsporidia from museum slides, clinical specimens and environmental samples and successfully identifiedVittaforma corneaein 11 out of 13 cases of microsporidial infection from used trichrome-stained slides of corneal scrapings from HIV-negative patients with keratoconjunctivitis.

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