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1. New high-sensitive rhAmp method for A1 allele detection in A2 milk samples

Author:
Giglioti, Rodrigo; Gutmanis, Gunta; Katiki, Luciana Morita; Okino, Cintia Hiromi; de Sena Oliveira, Márcia Cristina; Vercesi Filho, Anibal Eugênio
Source:
Food chemistry 2020 v.313 pp. 126167
ISSN:
0308-8146
Subject:
single nucleotide polymorphism,   etc   ; DNA; alleles; animals; beta-casein; detection limit; gastrointestinal system; genotyping; melting; milk; peptides;     Show all 11 Subjects
Abstract:
... Cows’ milk may contain two types of β-casein: A1 and A2. A1 digestion is associated with the release of β-casomorphine-7 peptide, which can cause adverse gastrointestinal effects. Two methods – high-resolution melting (HRM) and rhAmp® SNP genotyping – were developed to identify the β-casein gene (CSN2) A1 and A2 alleles directly in milk. DNA milk samples from 45 animals were examined and 10 sample ...
DOI:
10.1016/j.foodchem.2020.126167

2. Rhythm and blues: Influence of CLOCK T3111C on peripheral electrophysiological indicators of negative affective processing

Author:
Armbruster, Diana; Brocke, Burkhard; Kirschbaum, Clemens; Witt, Stephanie H.; Lesch, Klaus-Peter; Strobel, Alexander
Source:
Physiology & behavior 2020 v.219 pp. 112831
ISSN:
0031-9384
Subject:
single nucleotide polymorphism,   etc   ; alleles; electromyography; electrophysiology; emotions; genetic variation; homozygosity; oral contraceptives; physiological response; women;     Show all 10 Subjects
Abstract:
... Dysfunction in the circadian system has been linked to emotion regulation and mood disorders with genetic variation in clock genes as likely contributors. Here, we focused on endophenotypes of affective processing and investigated in two independent samples of healthy individuals (n₁=99, n₂=108) whether genotypes of a functional single nucleotide polymorphism (SNP) in the gene encoding CLOCK (CLOC ...
DOI:
10.1016/j.physbeh.2020.112831

3. Single-nucleotide polymorphism (SNP) genotyping assays for the varietal authentication of ‘Nebbiolo’ musts and wines

Author:
Boccacci, Paolo; Chitarra, Walter; Schneider, Anna; Rolle, Luca; Gambino, Giorgio
Source:
Food chemistry 2020 v.312 pp. 126100
ISSN:
0308-8146
Subject:
single nucleotide polymorphism,   etc   ; DNA; Vitis vinifera; databases; fraud; genotype; genotyping; polymerase chain reaction; red wines; winemaking;     Show all 10 Subjects
Abstract:
... ‘Nebbiolo’ (Vitis vinifera L.) is renowned for its use in producing monovarietal high-quality red wines, such Barolo and Barbaresco. The fight against fraud to safeguard high-quality productions requires an effective varietal identification system applicable in musts and wines. ‘Nebbiolo’-specific single-nucleotide polymorphisms (SNPs) were identified starting from available databases and 260 geno ...
DOI:
10.1016/j.foodchem.2019.126100

4. A functional SNP in the synaptic SNAP25 gene is associated with impulsivity in a Colombian sample

Author:
González-Giraldo, Yeimy; Forero, Diego A.
Source:
3 Biotech 2020 v.10 no.3 pp. 134
ISSN:
2190-572X
Subject:
single nucleotide polymorphism,   etc   ; behavior disorders; binding sites; genes; genotype; microRNA; synaptosomes;     Show all 7 Subjects
Abstract:
... The aim of the current study was to test the hypothesis that a functional polymorphism in the synaptosome associated protein 25 (SNAP25) gene could be associated with impulsivity scores in a sample of young Colombian subjects. Impulsivity has been postulated as an endophenotype for several psychiatric disorders of high epidemiological relevance. There is a need for the study of additional candidat ...
DOI:
10.1007/s13205-020-2110-0
PubMed:
32154047
PubMed Central:
PMC7036081

5. Structured gene‐environment interaction analysis

Author:
Wu, Mengyun; Zhang, Qingzhao; Ma, Shuangge
Source:
Biometrics 2020 v.76 no.1 pp. 23-35
ISSN:
0006-341X
Subject:
single nucleotide polymorphism,   etc   ; biometry; chromosomes; diabetes; etiology; gene expression; genotype-environment interaction; melanoma;     Show all 8 Subjects
Abstract:
... For the etiology, progression, and treatment of complex diseases, gene‐environment (G‐E) interactions have important implications beyond the main G and E effects. G‐E interaction analysis can be more challenging with higher dimensionality and need for accommodating the “main effects, interactions” hierarchy. In recent literature, an array of novel methods, many of which are based on the penalizati ...
DOI:
10.1111/biom.13139
PubMed:
31424088
PubMed Central:
PMC7028505

6. The first evidence of an association between a polymorphism in the endocannabinoid-degrading enzyme FAAH (FAAH rs2295633) with attention deficit hyperactivity disorder

Author:
Ahmadalipour, Ali; Mehdizadeh Fanid, Leila; Zeinalzadeh, Narges; Alizadeh, Maedeh; Vaezi, Helaleh; Hassanpour Aydinlou, Zahra; Noorazar, Seyed Gholamreza
Source:
Genomics 2020 v.112 no.2 pp. 1330-1334
ISSN:
0888-7543
Subject:
single nucleotide polymorphism,   etc   ; alleles; amide hydrolases; cannabinoids; children; fatty acids; gene frequency; genotype; genotyping; risk;     Show all 10 Subjects
Abstract:
... Several single nucleotide polymorphisms (SNPs) of the fatty acid amide hydrolase (FAAH), the degrading enzyme of the endocannabinoids, have been shown to be associated with many neuropsychiatric disorders. Here, FAAH rs2295633 was studied in ADHD and case-control healthy children. There was a significant difference in the allele frequency (P = .04) and genotype distribution (P = .04) of the FAAH r ...
DOI:
10.1016/j.ygeno.2019.07.024

7. A real-time PCR assay based on a specific mutation of PstS1 gene for detection of M. bovis strains

Author:
Ji, Lingyun; Jiang, Yi; Li, Guilian; Zhao, Xiuqin; Wan, Kanglin
Source:
Biologicals 2020
ISSN:
1045-1056
Subject:
single nucleotide polymorphism,   etc   ; DNA; Mycobacterium bovis; Mycobacterium tuberculosis; genes; monitoring; quantitative polymerase chain reaction; rapid methods;     Show all 8 Subjects
Abstract:
... The Mycobacterium tuberculosis complex (MTBC) is composed of several genetically related and pathogenic mycobacterial species, including M. tuberculosis, M. bovis and M.africanum et al. In our previous study, we found that M. bovis strains had a unique SNP located in position 1055 in the sequence of the pstS1 gene in which a T was substituted by a C. In this study, specific primers and MGB probes ...
DOI:
10.1016/j.biologicals.2020.01.007

8. Detecting sequence variants in clinically important protozoan parasites

Author:
Calarco, Larissa; Barratt, Joel; Ellis, John
Source:
International journal for parasitology 2020 v.50 no.1 pp. 1-18
ISSN:
0020-7519
Subject:
single nucleotide polymorphism,   etc   ; Plasmodium; Protozoa; Toxoplasma; genes; microsatellite repeats; mutation rate; parasites; pathogenicity; pathogens; phylogeny; pipelines;     Show all 12 Subjects
Abstract:
... Second and third generation sequencing methods are crucial for population genetic studies, and variant detection is a popular approach for exploiting this sequence data. While mini- and microsatellites are historically useful markers for studying important Protozoa such as Toxoplasma and Plasmodium spp., detecting non-repetitive variants such as those found in genes can be fundamental to investiga ...
DOI:
10.1016/j.ijpara.2019.10.004

9. Identification of deleterious SNPs and their effects on BCL11A, the master regulator of fetal hemoglobin expression

Author:
Das, Sankha Subhra; Chakravorty, Nishant
Source:
Genomics 2020 v.112 no.1 pp. 397-403
ISSN:
0888-7543
Subject:
single nucleotide polymorphism,   etc   ; B-cell lymphoma; binding sites; genes; hemoglobin; leukemia; ligands; mutants; post-translational modification;     Show all 9 Subjects
Abstract:
... The B-cell lymphoma/leukemia 11A protein (encoded by BCL11A gene) is a key regulator of fetal-to-adult hemoglobin switching as seen in post-natal life. Although genetic polymorphisms like SNPs in BCL11A gene are expected to affect fetal hemoglobin (HbF) expression levels, yet their implications are poorly studied. This study utilizes a computational approach to identify the deleterious SNPs which ...
DOI:
10.1016/j.ygeno.2019.03.002

10. Identification of male-specific SNP markers and development of PCR-based genetic sex identification technique in crucifix crab (Charybdis feriatus) with implication of an XX/XY sex determination system

Author:
Fang, Shaobin; Zhang, Yin; Shi, Xi; Zheng, Huaiping; Li, Shengkang; Zhang, Yueling; Fazhan, Hanafiah; Waiho, Khor; Tan, Huaqiang; Ikhwanuddin, Mhd; Ma, Hongyu
Source:
Genomics 2020 v.112 no.1 pp. 404-411
ISSN:
0888-7543
Subject:
single nucleotide polymorphism,   etc   ; Charybdis feriatus; breeding programs; females; heterozygosity; homozygosity; males; polymerase chain reaction; sex determination;     Show all 9 Subjects
Abstract:
... In this study, we first identified male-specific SNP markers using restriction site-associated DNA sequencing, and further developed a PCR-based sex identification technique for Charybdis feriatus. A total of 296.96 million clean reads were obtained, with 114.95 and 182.01 million from females and males. After assembly and alignment, 10 SNP markers were identified being heterozygous in males but h ...
DOI:
10.1016/j.ygeno.2019.03.003

11. Identifying geographic origins of the Escherichia coli isolates from food by a method based on single-nucleotide polymorphisms

Author:
Liu, Weili; Zhao, Hong; Qiu, Zhigang; Jin, Min; Yang, Dong; Xu, Qunying; Feng, Hua; Li, Junwen; Shen, Zhiqiang
Source:
Journal of microbiological methods 2020 v.168 pp. 105807
ISSN:
0167-7012
Subject:
single nucleotide polymorphism,   etc   ; Escherichia coli; ancestry; databases; essential genes; food pathogens; multilocus sequence typing; provenance; traceability;     Show all 9 Subjects
Abstract:
... E.coli is an important foodborne pathogen. Rapid and robust tracking of the source of E. coli is the key step to control foodborne infections.In this study, a genotyping and tracing method based on highly discriminatory single nucleotide polymorphisms (SNPs) was developed to investigate the geographical origin of E. coli in food. A highly informative set of 12 SNPs was derived from 4 housekeeping ...
DOI:
10.1016/j.mimet.2019.105807

12. In silico quality assessment of SNPs—A case study on the Axiom® Wheat genotyping arrays

Author:
Lange, Thomas M.; Heinrich, Felix; Enders, Matthias; Wolf, Markus; Schmitt, Armin O.
Source:
Current plant biology 2020 v.21 pp. 100140
ISSN:
2214-6628
Subject:
single nucleotide polymorphism,   etc   ; Triticum aestivum; case studies; computer simulation; computer software; databases; genome; genomics; genotyping; wheat;     Show all 10 Subjects
Abstract:
... Genotyping arrays proved to be an exemplary tool for the simultaneous analysis of a multitude of single nucleotide polymorphisms (SNPs), a special case of genomic variants. By the example of SNPs represented on the Axiom® Wheat HD genotyping array as well as on the Axiom® Wheat Breeder's genotyping array, we applied a three way classification system to assess the quality of SNPs in bread wheat (Tr ...
DOI:
10.1016/j.cpb.2020.100140

13. Dynamics of ascorbic acid content in apple (Malus x domestica) during fruit development and storage

Author:
Lemmens, Eline; Alós, Enriqueta; Rymenants, Marijn; De Storme, Nico; Keulemans, Wannes (Johan)
Source:
Plant physiology and biochemistry 2020 v.151 pp. 47-59
ISSN:
0981-9428
Subject:
single nucleotide polymorphism; single nucleotide polymorphism arrays,   etc   ; Malus domestica; abiotic stress; antioxidants; apple peels; apple pulp; apples; ascorbic acid; biodiversity; biotic stress; cultivars; dehydroascorbic acid; fruiting; genotype; genotyping; germplasm; humans; monitoring; oxidation; plant breeding; shelf life; stress response;     Show all 23 Subjects
Abstract:
... Vitamin C is a crucial antioxidant and cofactor for both plants and humans. Apple fruits generally contain low levels of vitamin C, making vitamin C content an interesting trait for apple crop improvement. With the aim of breeding high vitamin C apple cultivars it is important to get an insight in the natural biodiversity of vitamin C content in apple fruits. In this study, quantification of ascor ...
DOI:
10.1016/j.plaphy.2020.03.006

14. Application of high resolution melting combined with DNA-based markers for quantitative analysis of olive oil authenticity and adulteration

Author:
Chedid, Elsa; Rizou, Myrto; Kalaitzis, Panagiotis
Source:
Food chemistry: X 2020 v.6 pp. 100082
ISSN:
2590-1575
Subject:
single nucleotide polymorphism,   etc   ; DNA; adulterated products; cultivars; melting; microsatellite repeats; olive oil; product authenticity; quantitative analysis; traceability;     Show all 10 Subjects
Abstract:
... A plethora of biotechnological methodologies is used to authenticate quality olive oils. Among the DNA-based approaches, SNPs and SSRs combined with high resolution melting (HRM) provide certain advantages such as speed, simplicity and reliability. SNP-HRM and SSR-HRM were used for the authentication of monovarietal olive oils as well as the quantification of varietal composition in olive oil DNA ...
DOI:
10.1016/j.fochx.2020.100082
PubMed:
32154510
PubMed Central:
PMC7058896

15. Non-linear association of serum molybdenum and linear association of serum zinc with nonalcoholic fatty liver disease: Multiple-exposure and Mendelian randomization approach

Author:
Li, Longman; Huang, Lulu; Huang, Sifang; Luo, Xiaoyu; Zhang, Haiying; Mo, Zengnan; Wu, Tangchun; Yang, Xiaobo
Source:
The Science of the total environment 2020 v.720 pp. 137655
ISSN:
0048-9697
Subject:
single nucleotide polymorphism,   etc   ; Chinese people; blood serum; dose response; fatty liver; homeostasis; longitudinal studies; men; models; molybdenum; regression analysis; zinc;     Show all 12 Subjects
Abstract:
... The homeostasis imbalance of metals is closely associated with nonalcoholic fatty liver disease (NAFLD). A total of 1594 and 566 Chinese Han men were enrolled in cross-sectional and longitudinal analyses, respectively. We measured the serum concentrations of 22 metals by ICP-MS. The traditional and the LASSO regression methods were used to construct multiple-metals models, respectively. We perform ...
DOI:
10.1016/j.scitotenv.2020.137655

16. Spatial genetic structure at the leading edge of a spruce budworm outbreak: The role of dispersal in outbreak spread

Author:
Larroque, Jeremy; Johns, Rob; Canape, Jade; Morin, Benoit; James, Patrick M.A.
Source:
Forest ecology and management 2020 v.461 pp. 117965
ISSN:
0378-1127
Subject:
single nucleotide polymorphism,   etc   ; Choristoneura fumiferana; cluster analysis; forest pests; genetic variation; genotyping; insects; larvae; population growth; Maine; New Brunswick; Quebec;     Show all 12 Subjects
Abstract:
... Outbreaking insects often undergo rapid population growth synchronously in multiple locations separated by large distances. Dispersal may play an essential role in synchronizing outbreaks over large geographic areas but its role in outbreak spread remains unclear. In our study, we used population genetics to assess how much dispersal contributes to the spread of a major forest pest, the spruce bud ...
DOI:
10.1016/j.foreco.2020.117965

17. Circulating phylloquinone, inactive Matrix Gla protein and coronary heart disease risk: A two-sample Mendelian Randomization study

Author:
Zwakenberg, Sabine R.; Burgess, Stephen; Sluijs, Ivonne; Weiderpass, Elisabete; Beulens, Joline W.J.; van der Schouw, Yvonne T.
Source:
Clinical nutrition 2020 v.39 no.4 pp. 1131-1136
ISSN:
0261-5614
Subject:
single nucleotide polymorphism,   etc   ; coronary disease; genome-wide association study; menaquinones; observational studies; phylloquinone; prospective studies; risk assessment; United Kingdom;     Show all 9 Subjects
Abstract:
... Multiple observational studies and small-scale intervention studies suggest that high vitamin K intake is associated with improved markers for cardiovascular health. Circulating phylloquinone solely represents phylloquinone (vitamin K1) intake, while dephosphorylated uncarboxylated Matrix Gla Protein (dp-ucMGP) represents both phylloquinone and menaquinone (vitamin K2) intake. This study aims to i ...
DOI:
10.1016/j.clnu.2019.04.024

18. Single nucleotide polymorphism‐based species phylogeny of greater fritillary butterflies (Lepidoptera: Nymphalidae: Speyeria) demonstrates widespread mitonuclear discordance

Author:
Campbell, Erin O.; Gage, Edward V.; Gage, Randy V.; Sperling, Felix A. H.
Source:
Systematic entomology 2020 v.45 no.2 pp. 269-280
ISSN:
0307-6970
Subject:
single nucleotide polymorphism,   etc   ; Speyeria; butterflies; genes; genetic markers; genomics; insect taxonomy; intraspecific variation; mitochondria; mitochondrial DNA; nucleotide sequences; phylogeny;     Show all 12 Subjects
Abstract:
... The systematics of Speyeria butterflies has historically been complicated by intraspecific variability that has challenged efforts to delimit species and reconstruct phylogenies. Our study presents a phylogenetic comparison of genomic single nucleotide polymorphisms (SNPs) and mitochondrial COI gene sequences, with comprehensive taxon sampling that includes 15 species and 46 subspecies. Increased ...
DOI:
10.1111/syen.12393

19. Exploring the genetics underpinning dynamic laryngeal collapse associated with poll flexion in Norwegian‐Swedish Coldblooded Trotter racehorses

Author:
Velie, B. D.; Smith, P. M.; Fjordbakk, C. T.; Solé, M.; Jäderkvist Fegraeus, K.; Rosengren, M. K.; Røed, K. H.; Ihler, C. F.; Lindgren, G.; Strand, E.
Source:
Equine veterinary journal 2020 v.52 no.2 pp. 174-180
ISSN:
0425-1644
Subject:
single nucleotide polymorphism,   etc   ; breeds; chromosomes; endoscopy; genes; genomics; genotyping; haplotypes; larynx; phenotype; racehorses; risk; sample size; veterinarians;     Show all 14 Subjects
Abstract:
... BACKGROUND: Dynamic laryngeal collapse (DLC) associated with poll flexion is the most common disorder of the upper respiratory tract (URT) in the Norwegian‐Swedish Coldblooded Trotter (NSCT). The disorder, which has also been diagnosed in other breeds of trotters and gaited horses, appears to be related to anatomic phenotypes and only occurs during poll flexion when the horse is exercised ‘on the ...
DOI:
10.1111/evj.13171

20. Is embryo abortion a post‐zygotic barrier to gene flow between Littorina ecotypes?

Author:
Johannesson, Kerstin; Zagrodzka, Zuzanna; Faria, Rui; Marie Westram, Anja; Butlin, Roger K.
Source:
Journal of evolutionary biology 2020 v.33 no.3 pp. 342-351
ISSN:
1010-061X
Subject:
single nucleotide polymorphism,   etc   ; Littorina; clutch size; ecotypes; females; gene flow; heterozygosity; hybrids; karyotyping; reproductive isolation; snails; Sweden;     Show all 12 Subjects
Abstract:
... Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection agai ...
DOI:
10.1111/jeb.13570
PubMed:
31724256
PubMed Central:
PMC7079066