scholarly journals The impact of CUP1 gene copy-number and XVI-VIII/XV-XVI translocations on copper and sulfite tolerance in vineyard Saccharomyces cerevisiae strain populations

2020 ◽  
Vol 20 (4) ◽  
Author(s):  
Giulia Crosato ◽  
Chiara Nadai ◽  
Milena Carlot ◽  
Juliano Garavaglia ◽  
Denise Righetto Ziegler ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Copy Number ◽  
Gene Copy Number ◽  
Copper Tolerance ◽  
Gene Copy ◽  
Wine Yeasts ◽  
Gene Encoding ◽  
Wine Production ◽  
Cup1 Gene ◽  
The Impact

ABSTRACT In wine production, sulfites are widely used as antimicrobials and antioxidants, whereas copper is associated with fungicides and wine fining treatments. Therefore, wine yeasts are constantly exposed to these agents. Copper tolerance is related to the copy number of the CUP1 gene, encoding for a metallothionein involved in copper detoxification. In wine yeasts, sulfite resistance mainly depends on the presence of the translocation t(XVI;VIII) in the promoter region of the SSU1 gene. This gene encodes for a plasma membrane sulfite pump involved in sulfite metabolism and detoxification. Recently, a new translocation, t(XVI;VIII), was identified. In this work, 253 Saccharomyces cerevisiae strains, representing three vineyard populations from two different continents, were analyzed, along with 20 industrial starters. Copper and sulfites tolerance as well as distribution of CUP1 gene copy-number, t(XVI;VIII)and t(XVI;XV) of SSU1 gene were studied to evaluate the impact of these genomic variations on population phenotypes. The CUP1 gene copy-number was found to be highly variable, ranging from zero to 79 per strain. Moreover it differently impacted the copper tolerance in the populations of the two continents. The diffusion of t(XVI;VIII) and, for the first time, t(XVI;XV) was determined in the three vineyard populations. The correlation between the presence of the translocation and strain sulfite tolerance levels was significant only for the t(XVI;VIII).

scholarly journals Isolation and analysis of rereplicated DNA by Rerep-Seq

2020 ◽  
Vol 48 (10) ◽  
pp. e58-e58 ◽  
Author(s):  
Johannes Menzel ◽  
Philip Tatman ◽  
Joshua C Black
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genomic Instability ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Adaptive Potential ◽  
Developmental Abnormalities ◽  
Origin Licensing ◽  
Multiple Replication ◽  
Dna Rereplication

Abstract Changes in gene copy number contribute to genomic instability, the onset and progression of cancer, developmental abnormalities and adaptive potential. The origins of gene amplifications have remained elusive; however, DNA rereplication has been implicated as a source of gene amplifications. The inability to determine which sequences are rereplicated and under what conditions have made it difficult to determine the validity of the proposed models. Here we present Rerep-Seq, a technique that selectively enriches for rereplicated DNA in preparation for analysis by DNA sequencing that can be applied to any species. We validated Rerep-Seq by simulating DNA rereplication in yeast and human cells. Using Rerep-Seq, we demonstrate that rereplication induced in Saccharomyces cerevisiae by deregulated origin licensing is non-random and defined by broad domains that span multiple replication origins and topological boundaries.

scholarly journals A model for the impact of FFPE section thickness on gene copy number measurement by FISH

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jiyan Yu ◽  
Qi Wang ◽  
Pu Xue ◽  
Li Zheng ◽  
Juanfen Mo ◽  
...  
Keyword(s):  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Section Thickness ◽  
Copy Number Measurement ◽  
The Impact ◽  
Ffpe Section

Intron–exon structure and gene copy number of a gene encoding for a membrane-intrinsic light-harvesting polypeptide of the red alga Galdieria sulphuraria

Gene ◽  
2000 ◽  
Vol 255 (2) ◽  
pp. 257-265 ◽  
Author(s):  
Jürgen Marquardt ◽  
Stefan Wans ◽  
Erhard Rhiel ◽  
Anke Randolf ◽  
Wolfgang E. Krumbein
Keyword(s):  
Copy Number ◽  
Light Harvesting ◽  
Gene Copy Number ◽  
Red Alga ◽  
Gene Copy ◽  
Galdieria Sulphuraria ◽  
Gene Encoding ◽  
Exon Structure

scholarly journals Ethnic-specific association of amylase gene copy number with adiposity traits in a large Middle Eastern biobank

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Niccolo’ Rossi ◽  
Elbay Aliyev ◽  
Alessia Visconti ◽  
Ammira S. A. Akil ◽  
Najeeb Syed ◽  
...  
Keyword(s):  
Copy Number ◽  
Middle Eastern ◽  
Large Population ◽  
Gene Copy Number ◽  
Negative Association ◽  
Gene Copy ◽  
Fat Percentage ◽  
Amylase Gene ◽  
Amylase Genes ◽  
The Impact

AbstractStudies assessing the impact of amylase genes copy number (CN) on adiposity report conflicting findings in different global populations, likely reflecting the impact of ancestral and ethnic-specific environment and lifestyle on selection at the amylase loci. Here, we leverage population size and detailed adiposity measures from a large population biobank to resolve confounding effects and determine the relationship between salivary (AMY1) and pancreatic (AMY2A) amylase genes CN and adiposity in 2935 Qatari individuals who underwent whole-genome sequencing (WGS) as part of the Qatar Genome Programme. We observe a negative association between AMY1 CNs and trunk fat percentage in the Qatari population (P = 7.50 × 10−3) and show that Qataris of Arab descent have significantly lower CN at AMY1 (P = 1.32 × 10−10) as well as less favorable adiposity and metabolic profiles (P < 1.34 × 10−8) than Qataris with Persian ancestry. Indeed, lower AMY1 CN was associated with increased total and trunk fat percentages in Arabs (P < 4.60 × 10−3) but not in Persians. Notably, overweight and obese Persians reported a significant trend towards dietary restraint following weight gain compared to Arabs (P = 4.29 × 10−5), with AMY1 CN showing negative association with dietary self-restraint (P = 3.22 × 10−3). This study reports an association between amylase gene CN and adiposity traits in a large Middle Eastern population. Importantly, we leverage rich biobank data to demonstrate that the strength of this association varies with ethnicity, and may be influenced by population-specific behaviors that also contribute to adiposity traits.

The Impact of Pharmacogenomics on Postoperative Nausea and Vomiting

2005 ◽  
Vol 102 (3) ◽  
pp. 543-549 ◽  
Author(s):  
Keith A. Candiotti ◽  
David J. Birnbach ◽  
David A. Lubarsky ◽  
Fani Nhuch ◽  
Aimee Kamat ◽  
...  
Keyword(s):  
Postoperative Nausea ◽  
Copy Number ◽  
Polymerase Chain Reaction Amplification ◽  
Gene Copy Number ◽  
Postoperative Nausea And Vomiting ◽  
Nausea And Vomiting ◽  
Gene Copy ◽  
Cyp2d6 Gene ◽  
Ultrarapid Metabolizers ◽  
The Impact

Background Some patients treated with ondansetron for postoperative nausea and vomiting do not respond to therapy. One possible mechanism for this failure is ultrarapid drug metabolism via the cytochrome P-450 system, specifically the enzyme 2D6 (CYP2D6). Ultrarapid metabolism is seen in patients with multiple functional copies (&gt;/= 3) of the CYP2D6 allele. This study was designed to determine whether patients who were given prophylactic ondansetron and had multiple CYP2D6 alleles had an increased rate of postoperative nausea and vomiting. Methods Two hundred fifty female patients undergoing standardized general anesthesia were given 4 mg ondansetron 30 min before extubation. Patients were observed for symptoms of nausea and vomiting. DNA was extracted from blood in all patients and was analyzed by using a gene-specific probe to determine the CYP2D6 gene copy number and genotyped by polymerase chain reaction amplification with a custom oligonucleotide microarray to determine the specific CYP2D6 genotypes. Results Eighty-eight patients experienced nausea, and 37 of those patients also had vomiting. In patients with one, two, or three CYP2D6 copies, the incidences of vomiting were 3 in 33 (27%), 27 in 198 (14%), and 7 in 23 (30%), respectively. The incidence of vomiting in subjects with three CYP2D6 copies was significantly different from those with two copies, but not from those with one copy. When analyzed by genotype, the incidences of vomiting in poor, intermediate, extensive, and ultrarapid metabolizers were 1 in 12 (8%), 5 in 30 (17%), 26 in 176 (15%), and 5 in 11 (45%), respectively (P &lt; 0.01 vs. all other groups). There were no differences between groups in the incidence of nausea based on CYP2D6 copy number or genotype. Conclusions Patients with three copies of the CYP2D6 gene, a genotype consistent with ultrarapid metabolism, or both have an increased incidence of ondansetron failure for the prevention of postoperative vomiting but not nausea.

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