scholarly journals Variation in type two taste receptor genes is associated with bitter tasting phenylthiocarbamide consumption in mature Targhee and Rambouillet rams

2021 ◽  
Vol 5 (3) ◽  
Author(s):  
Kimberly M Davenport ◽  
J Bret Taylor ◽  
Dillan Henslee ◽  
Claire Southerland ◽  
Joel Yelich ◽  
...  
Keyword(s):  
Bitter Taste ◽  
Taste Receptor ◽  
Rangeland Management ◽  
Taste Perception ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Oxford Nanopore ◽  
Long Read ◽  
Functional Consequences ◽  
Grazing Systems

Abstract Bitter taste perception in sheep can lead to avoidance of specific types of forage, such as sagebrush, which is present on many rangeland grazing systems in the Intermountain West. In humans, bitter taste perception is influenced by variation in several TAS2R genes, including more extensively studied TAS2R38 and TAS2R16. We hypothesize that variation in taste receptor genes in sheep is associated with bitter taste. Therefore, the objective of this study was to examine variation in TAS2R genes in relation to consumption of a bitter tasting compound phenylthiocarbamide (PTC) which determines bitter “taster” and “non-taster” status in humans. Rambouillet and Targhee rams (n = 26) were offered various concentrations of PTC solution (0.2–12.29 mM) and water in a side-by-side presentation during two experiments. Blood was collected for DNA isolation and sequencing. Nineteen TAS2R genes were amplified and sequenced with long read Oxford Nanopore MinION technology. A total of 1,049 single nucleotide polymorphisms (SNPs) and 26 haplotypes were identified in these genes. Of these, 24 SNPs and 11 haplotypes were significantly (P < 0.05) associated with PTC consumption in TAS2R3, TAS2R5, TAS2R8, TAS2R9, TAS2R16, TAS2R31-like, TAS2R38, TAS2R39, and TAS2R42-like. Over 50% of the SNPs resulted in a change in amino acid sequence and several resided in potential regulatory regions, which could have downstream functional consequences and influence bitter taste perception in sheep. Further research is needed to validate these associations and elucidate the mechanisms that link variation in TAS2R genes to bitter taste perception in sheep. This may enable producers to select sheep more likely to consume bitter forage such as sagebrush as a flock and rangeland management strategy.

scholarly journals 1202. Multimodal Sequencing of a Clonal Case Cluster of Carbapenem-Resistant Citrobacter Reveals Unexpectedly Rapid Dynamics of KPC3-Containing Plasmids

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S364-S364
Author(s):  
Roby Bhattacharyya ◽  
Alejandro Pironti ◽  
Bruce J Walker ◽  
Abigail Manson ◽  
Virginia Pierce ◽  
...  
Keyword(s):  
Point Mutations ◽  
Illumina Miseq ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Carbapenem Resistant ◽  
Oxford Nanopore ◽  
Close Relationship ◽  
Long Read ◽  
Carbapenem Resistant Enterobacteriaceae

Abstract Background Carbapenem-resistant Enterobacteriaceae (CRE) are a major public health threat. We report four clonally related Citrobacter freundii isolates harboring the blaKPC-3 carbapenemase in April–May 2017 that are nearly identical to a strain from 2014 at the same institution. Despite differing by ≤5 single nucleotide polymorphisms (SNPs), these isolates exhibited dramatic differences in carbapenemase plasmid architecture. Methods We sequenced four carbapenem-resistant C. freundii isolates from 2017 and compared them with an ongoing CRE surveillance project at our institution. SNPs were identified from Illumina MiSeq data aligned to a reference genome using the variant caller Pilon. Plasmids were assembled from Illumina and Oxford Nanopore sequencing data using Unicycler. Results The four 2017 isolates differed from one another by 0–5 chromosomal SNPs; two were identical. With one exception, these isolates differed by >38,000 SNPs from 25 C. freundii isolates sequenced from 2013 to 2017 at the same institution for CRE surveillance. The exception was a 2014 isolate that differed by 13–16 SNPs from each 2017 isolate, with 13 SNPs common to all four. Each C. freundii isolate harbored wild-type blaKPC-3. Despite the close relationship among the 2017 cluster, the plasmids harboring the blaKPC-3 genes differed dramatically: the carbapenemase occurred in one of the two different plasmids, with rearrangements between these plasmids across isolates. The related 2014 isolate harbored both plasmids, each with a separate copy of blaKPC-3. No transmission chains were found between any of the affected patients. Conclusion WGS confirmed clonality among four contemporaneous blaKPC-3-containing C. freundii isolates, and marked similarity with a 2014 isolate, within an institution. That only 13–16 SNPs varied between the 2014 and 2017 isolates suggests durable persistence of the blaKPC-3 gene within this lineage in a hospital ecosystem. The plasmids harboring these carbapenemase genes proved remarkably plastic, with plasmid loss and rearrangements occurring on the same time scale as two to three chromosomal point mutations. Combining short and long-read sequencing in a case cluster uniquely revealed unexpectedly rapid dynamics of carbapenemase plasmids, providing critical insight into their manner of spread. Disclosures M. J. Ferraro, SeLux Diagnostics: Scientific Advisor and Shareholder, Consulting fee. D. C. Hooper, SeLux Diagnostics: Scientific Advisor, Consulting fee.

scholarly journals The Relationship between Single Nucleotide Polymorphisms in Taste Receptor Genes, Taste Function and Dietary Intake in Preschool-Aged Children and Adults in the Guelph Family Health Study

Nutrients ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 990 ◽  
Author(s):  
Elie Chamoun ◽  
Nicholas Carroll ◽  
Lisa Duizer ◽  
Wenjuan Qi ◽  
Zeny Feng ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Receptor Gene ◽  
Taste Receptor ◽  
Family Health ◽  
Sweet Taste ◽  
Taste Perception ◽  
Health Study ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Salt Taste

Taste is a fundamental determinant of food selection, and inter-individual variations in taste perception may be important risk factors for poor eating habits and obesity. Characterizing differences in taste perception and their influences on dietary intake may lead to an improved understanding of obesity risk and a potential to develop personalized nutrition recommendations. This study explored associations between 93 single nucleotide polymorphisms (SNPs) in sweet, fat, bitter, salt, sour, and umami taste receptors and psychophysical measures of taste. Forty-four families from the Guelph Family Health Study participated, including 60 children and 65 adults. Saliva was collected for genetic analysis and parents completed a three-day food record for their children. Parents underwent a test for suprathreshold sensitivity (ST) and taste preference (PR) for sweet, fat, salt, umami, and sour as well as a phenylthiocarbamide (PTC) taste status test. Children underwent PR tests and a PTC taste status test. Analysis of SNPs and psychophysical measures of taste yielded 23 significant associations in parents and 11 in children. After adjusting for multiple hypothesis testing, the rs713598 in the TAS2R38 bitter taste receptor gene and rs236514 in the KCNJ2 sour taste-associated gene remained significantly associated with PTC ST and sour PR in parents, respectively. In children, rs173135 in KCNJ2 and rs4790522 in the TRPV1 salt taste-associated gene remained significantly associated with sour and salt taste PRs, respectively. A multiple trait analysis of PR and nutrient composition of diet in the children revealed that rs9701796 in the TAS1R2 sweet taste receptor gene was associated with both sweet PR and percent energy from added sugar in the diet. These findings provide evidence that for bitter, sour, salt, and sweet taste, certain genetic variants are associated with taste function and may be implicated in eating patterns. (Support was provided by the Ontario Ministry of Agriculture, Food, and Rural Affairs).

scholarly journals Genetic Variation in Taste Receptor Genes (SCNN1B, TRPV1) and Its Correlation with the Perception of Saltiness in Normotensive and Hypertensive Adults

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Pradtana Tapanee ◽  
Diane K. Tidwell ◽  
M. Wes Schilling ◽  
Daniel G. Peterson ◽  
Terezie Tolar-Peterson
Keyword(s):  
Taste Receptor ◽  
Recognition Threshold ◽  
Taste Perception ◽  
Taste Sensitivity ◽  
Nucleotide Polymorphisms ◽  
Cross Sectional ◽  
Single Nucleotide ◽  
Salt Taste ◽  
Hypertensive Group ◽  
Age Range

Background. Different taste preferences correlated with genetic variations may lead to food consumption patterns that contribute to nutrient-related health outcomes such as hypertension. Objectives. The aim of this study was to determine whether single nucleotide polymorphisms (SNPs) in the salt taste receptor genes SCNN1B and TRPV1 affect salt taste perception among normotensive and hypertensive people. Materials and Methods. We conducted a cross-sectional case control study by design consisting of a normotensive and hypertensive group. Participants were 253 adults with age range of 20–82 residing in Mississippi, USA. For each of 128 normotensives and 125 hypertensives, the salt taste recognition threshold and salt taste receptor genotype were determined. Results. The hypertensive group had a higher salt taste recognition threshold than the normotensive group ( P < 0.001 ). The polymorphism of TRPV1, rs4790522, with the AA genotype was associated with a higher salt recognition threshold (lower salt taste sensitivity) in people with hypertension and obesity. Moreover, the polymorphism of TRPV1, rs8065080, and SCNN1B, rs239345, genes were associated with a risk of hypertension ( P = 0.016 and P = 0.024 ). Conclusion. Correlations between SNPs, salt taste sensitivity, and hypertension risk were observed. People with hypertension had a higher salt taste threshold than those with normotension.

scholarly journals Role of the TAS2R38 Bitter Taste Receptor Gene Single Nucleotide Polymorphism in Patients With Taste Disorders

2021 ◽  
Vol 64 (11) ◽  
pp. 800-805
Author(s):  
Byung-Jun Kang ◽  
Jin-Woo Park ◽  
Sang-Yen Geum ◽  
Un-Kyung Kim ◽  
Seung-Heon Shin ◽  
...  
Keyword(s):  
Bitter Taste ◽  
Receptor Gene ◽  
Strong Association ◽  
Taste Receptor ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Normal Volunteers ◽  
Taste Disorder ◽  
Taste Disorders ◽  
Tas2r38 Gene

Background and Objectives Several studies have shown that three single nucleotide polymorphisms (SNPs) in the TAS2R38 gene demonstrate a strong association with the ability to sense the bitter taste of phenylthiocarbamide (PTC) in. We have previously reported about TAS2R38 genotypes in normal volunteers. The aim of this study was to investigate the role TAS2R38 gene plays in taste disorder by examining SNPs in the TAS2R38 gene in taste disorder patients.Subjects and Method Ninety-four patients with taste dysfunction from multiple etiologies were enrolled. The genotypes were defined by identifying SNPs on the TAS2R38 gene. The proportion of different TAS2R38 genotypes in the group was compared with that in the normal volunteers of our previous study. The whole mouth taste threshold tests were performed and the thresholds were compared among the three different genotypic groups.Results The proportion of each diplotype in taste disorder patients were as follows: PAV/ PAV 36.2% (34/94), PAV/AVI 34.0% (32/94), and AVI/AVI 29.8% (28/94). The proportion of AVI/AVI type was higher in the group than in the normal volunteers (p=0.031). The detection and recognition thresholds of all four basic tastes were increased in the order of PAV/PAV, PAV/AVI, and AVI/AVI genotypes.Conclusion The proportion of AVI/AVI homozygous was significantly higher in taste disorder patients than in the normal volunteers. Our findings suggest that the genotypes of TAS2R38 may represent one of the risk factors responsible for the development of taste disorders.

Taste perception and expression in stomach of bitter taste receptor tas2r38 in obese and lean subjects

Appetite ◽  
2021 ◽  
pp. 105595
Author(s):  
Antonietta Robino ◽  
Natalia Rosso ◽  
Martina Guerra ◽  
Pio Corleone ◽  
Biagio Casagranda ◽  
...  
Keyword(s):  
Bitter Taste ◽  
Taste Receptor ◽  
Taste Perception ◽  
Bitter Taste Receptor

scholarly journals TNF-αPolymorphisms in Juvenile Idiopathic Arthritis: Which Potential Clinical Implications?

2012 ◽  
Vol 2012 ◽  
pp. 1-16 ◽  
Author(s):  
A. Scardapane ◽  
L. Breda ◽  
M. Lucantoni ◽  
F. Chiarelli
Keyword(s):  
Juvenile Idiopathic Arthritis ◽  
Large Scale ◽  
Nucleotide Polymorphisms ◽  
Necrosis Factor Alpha ◽  
Single Nucleotide ◽  
Adult Rheumatoid Arthritis ◽  
Functional Consequences ◽  
Factor Alpha ◽  
Necrosis Factor ◽  
Important Cytokine

Whether tumor necrosis factor alpha (TNF-α) gene polymorphisms (SNPs) influence disease susceptibility and treatment of patients with juvenile idiopathic arthritis (JIA) is presently uncertain. TNF-αis one of the most important cytokine involved in JIA pathogenesis. Several single nucleotide polymorphisms (SNPs) have been identified within the region of the TNF-αgene but only a very small minority have proven functional consequences and have been associated with susceptibility to JIA. An association between some TNF-αSNPs and adult rheumatoid arthritis (RA) susceptibility, severity and clinical response to anti-TNF-αtreatment has been reported. The most frenquetly studied TNF-αSNP is located at −308 position, where a substitution of the G allele with the rare A allele has been found. The presence of the allele −308A is associated to JIA and to a poor prognosis. Besides, the −308G genotype has been associated with a better response to anti-TNF-αtherapy in JIA patients, confirming adult data. Psoriatic and oligoarticular arthritis are significantly associated to the −238 SNP only in some works. Studies considering other SNPs are conflicting and inconclusive. Large scale studies are required to define the contribution of TNF-αgene products to disease pathogenesis and anti-TNF-αtherapeutic efficacy in JIA.

scholarly journals Genotyping single nucleotide polymorphisms for allele-selective therapy in Huntington disease

2020 ◽  
Vol 6 (3) ◽  
pp. e430 ◽  
Author(s):  
Daniel O. Claassen ◽  
Jody Corey-Bloom ◽  
E. Ray Dorsey ◽  
Mary Edmondson ◽  
Sandra K. Kostyk ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Huntington Disease ◽  
Prospective Observational Study ◽  
Cag Repeat ◽  
Cag Repeats ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cag Repeat Expansion ◽  
Long Read ◽  
Selective Therapy

BackgroundThe huntingtin gene (HTT) pathogenic cytosine-adenine-guanine (CAG) repeat expansion responsible for Huntington disease (HD) is phased with single nucleotide polymorphisms (SNPs), providing targets for allele-selective treatments.ObjectiveThis prospective observational study defined the frequency at which rs362307 (SNP1) or rs362331 (SNP2) was found on the same allele with pathogenic CAG expansions.MethodsAcross 7 US sites, 202 individuals with HD provided blood samples that were processed centrally to determine the number and size of CAG repeats, presence and heterozygosity of SNPs, and whether SNPs were present on the mutant HTT allele using long-read sequencing and phasing.ResultsHeterozygosity of SNP1 and/or SNP2 was identified in 146 (72%) individuals. The 2 polymorphisms were associated only with the mHTT allele in 61% (95% high density interval: 55%, 67%) of individuals.ConclusionsThese results are consistent with previous reports and demonstrate the feasibility of genotyping, phasing, and targeting of HTT SNPs for personalized treatment of HD.

scholarly journals Limited genetic diversity of blaCMY-2-containing IncI1-pST12 plasmids from Enterobacteriaceae of human and broiler chicken origin in the Netherlands

2020 ◽  
Author(s):  
Evert den Drijver ◽  
Joep J.J.M. Stohr ◽  
Jaco J. Verweij ◽  
Carlo Verhulst ◽  
Francisca C. Velkers ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pan Genome ◽  
Long Read ◽  
Short Read Sequence ◽  
High Degree ◽  
Limited Genetic Diversity

AbstractDistinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1-pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1-pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNP) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1-pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1-pST12 plasmids revealed a low number of SNP differences (range of 0-9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. NGS-analysis of blaCMY--2-containing IncI1-pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.

scholarly journals LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants

2021 ◽  
Author(s):  
Jyun-Hong Lin ◽  
Liang-Chi Chen ◽  
Shu-Qi Yu ◽  
Yao-Ting Huang
Keyword(s):  
Variant Calling ◽  
Cost Effective ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Single Nucleotide ◽  
Chromosome Conformation ◽  
Long Reads ◽  
Cost Effective Approach ◽  
Long Read ◽  
Microbial Strains

AbstractLong-read phasing has been used for reconstructing diploid genomes, improving variant calling, and resolving microbial strains in metagenomics. However, the phasing blocks of existing methods are broken by large Structural Variations (SVs), and the efficiency is unsatisfactory for population-scale phasing. This paper presents an ultra-fast algorithm, LongPhase, which can simultaneously phase single nucleotide polymorphisms (SNPs) and SVs of a human genome in ∼10-20 minutes, 10x faster than the state-of-the-art WhatsHap and Margin. In particular, LongPhase produces much larger phased blocks at almost chromosome level with only long reads (N50=26Mbp). We demonstrate that LongPhase combined with Nanopore is a cost-effective approach for providing chromosome-scale phasing without the need for additional trios, chromosome-conformation, and single-cell strand-seq data.

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