scholarly journals Amy2B copy number variation reveals starch diet adaptations in ancient European dogs

2016 ◽  
Vol 3 (11) ◽  
pp. 160449 ◽  
Author(s):  
Morgane Ollivier ◽  
Anne Tresset ◽  
Fabiola Bastian ◽  
Laetitia Lagoutte ◽  
Erik Axelsson ◽  
...  
Keyword(s):  
Copy Number ◽  
Quantitative Polymerase Chain Reaction ◽  
Copy Numbers ◽  
Gene Coding ◽  
Number Variation ◽  
Early Farming ◽  
Polymerase Chain ◽  
Selection For ◽  
Dog Domestication ◽  
Selection Of

Extant dog and wolf DNA indicates that dog domestication was accompanied by the selection of a series of duplications on the Amy2B gene coding for pancreatic amylase. In this study, we used a palaeogenetic approach to investigate the timing and expansion of the Amy2B gene in the ancient dog populations of Western and Eastern Europe and Southwest Asia. Quantitative polymerase chain reaction was used to estimate the copy numbers of this gene for 13 ancient dog samples, dated to between 15 000 and 4000 years before present (cal. BP). This evidenced an increase of Amy2B copies in ancient dogs from as early as the 7th millennium cal. BP in Southeastern Europe. We found that the gene expansion was not fixed across all dogs within this early farming context, with ancient dogs bearing between 2 and 20 diploid copies of the gene. The results also suggested that selection for the increased Amy2B copy number started 7000 years cal. BP, at the latest. This expansion reflects a local adaptation that allowed dogs to thrive on a starch rich diet, especially within early farming societies, and suggests a biocultural coevolution of dog genes and human culture.

scholarly journals Copy Number Variation of TLR-7 Gene and its Association with the Development of Systemic Lupus Erythematosus in Female Patients from Yucatan Mexico

2014 ◽  
Vol 6 ◽  
pp. GEG.S16707 ◽  
Author(s):  
Guillermo Valencia Pacheco ◽  
Darig Cámara Cruz ◽  
Lizbeth J. González Herrera ◽  
Gerardo J. Pérez Mendoza ◽  
Guadalupe I. Adrián Amaro ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Copy Number Variation ◽  
Lupus Erythematosus ◽  
Copy Number ◽  
Target Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
Systemic Autoimmune Disease ◽  
Systemic Lupus ◽  
Number Variation ◽  
Polymerase Chain

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by the production of autoantibodies against self-antigens, which occurs most often in women between 15 and 40 years of age. The innate immunity is involved in the pathogenesis of SLE through TLR-7. Genetic factors such as copy number variation (CNV) of target genes may contribute to disease development, but this possible risk has not yet been studied in SLE patients from Yucatan, Mexico. The CNV of TLR-7 gene was determined by quantitative polymerase chain reaction assay using TaqMan probes in 80 SLE women and 150 control subjects. The results showed that 10% of SLE patients exhibited more than two copies of TLR-7 gene, whereas no mRNA overexpression was detected. These data suggested that increased CNV of the TLR-7 gene in Yucatan SLE women can be a risk factor for this disease.

scholarly journals CCL3L3-null status is associated with susceptibility to systemic lupus erythematosus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Young-Ho Kim ◽  
Eunyoung Emily Lee ◽  
Hye-Won Sim ◽  
Eun-Kyung Kang ◽  
Yoon-Ho Won ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Polymerase Chain Reaction ◽  
Lupus Erythematosus ◽  
Copy Number ◽  
Systemic Lupus ◽  
Chain Reaction ◽  
Competitive Polymerase Chain Reaction ◽  
Copy Numbers ◽  
Number Variation ◽  
Polymerase Chain

AbstractThe correlation between copy number variation (CNV) and the susceptibility to systemic lupus erythematosus (SLE) has been reported for various immunity-related genes. However, the contribution of CNVs to SLE susceptibility awaits more investigation. To evaluate the copy numbers in immunity-related genes such as TNFAIP3, TNIP1, IL12B, TBX21 (T-bet), TLR7, C4A, C4B, CCL3L1, and CCL3L3, the modified real competitive polymerase chain reaction (mrcPCR) assay was employed, and the association between the copy numbers and SLE susceptibility was analyzed in 334 SLE patients and 338 controls. CCL3L3-null status was significantly associated with SLE susceptibility (OR > 18, P < 0.0001), which remained significant by Bonferroni’s correction (corrected P = 0.0007). However, the significant association between C4B low-copy status and SLE susceptibility (OR = 1.6051, P = 0.0331) became non-significant by Bonferroni’s correction (corrected P = 0.3938). Except for these results, no other significant association between SLE susceptibility and copy number status in other genes was observed. The CCL3L3-null status may be a significant factor for SLE susceptibility.

scholarly journals Genomic Copy Number Variation Study of Nine Macaca Species Provides New Insights into Their Genetic Divergence, Adaptation, and Biomedical Application

2020 ◽  
Vol 12 (12) ◽  
pp. 2211-2230
Author(s):  
Jing Li ◽  
Zhenxin Fan ◽  
Feichen Shen ◽  
Amanda L Pendleton ◽  
Yang Song ◽  
...  
Keyword(s):  
Drug Metabolism ◽  
Copy Number Variation ◽  
Copy Number ◽  
Energy Homeostasis ◽  
Biomedical Application ◽  
Quantitative Polymerase Chain Reaction ◽  
Drug Study ◽  
Barbary Macaque ◽  
Number Variation

Abstract Copy number variation (CNV) can promote phenotypic diversification and adaptive evolution. However, the genomic architecture of CNVs among Macaca species remains scarcely reported, and the roles of CNVs in adaptation and evolution of macaques have not been well addressed. Here, we identified and characterized 1,479 genome-wide hetero-specific CNVs across nine Macaca species with bioinformatic methods, along with 26 CNV-dense regions and dozens of lineage-specific CNVs. The genes intersecting CNVs were overrepresented in nutritional metabolism, xenobiotics/drug metabolism, and immune-related pathways. Population-level transcriptome data showed that nearly 46% of CNV genes were differentially expressed across populations and also mainly consisted of metabolic and immune-related genes, which implied the role of CNVs in environmental adaptation of Macaca. Several CNVs overlapping drug metabolism genes were verified with genomic quantitative polymerase chain reaction, suggesting that these macaques may have different drug metabolism features. The CNV-dense regions, including 15 first reported here, represent unstable genomic segments in macaques where biological innovation may evolve. Twelve gains and 40 losses specific to the Barbary macaque contain genes with essential roles in energy homeostasis and immunity defense, inferring the genetic basis of its unique distribution in North Africa. Our study not only elucidated the genetic diversity across Macaca species from the perspective of structural variation but also provided suggestive evidence for the role of CNVs in adaptation and genome evolution. Additionally, our findings provide new insights into the application of diverse macaques to drug study.

scholarly journals Salivary AMY1 Copy Number Variation Modifies Age-Related Type 2 Diabetes Risk

2020 ◽  
Vol 66 (5) ◽  
pp. 718-726
Author(s):  
Yuwei Liu ◽  
Caren E Smith ◽  
Laurence D Parnell ◽  
Yu-Chi Lee ◽  
Ping An ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Copy Number Variation ◽  
Metabolic Pathway ◽  
Copy Number ◽  
Lipid Lowering ◽  
Pathway Enrichment Analysis ◽  
Copy Numbers ◽  
Number Variation ◽  
The Relationship

Abstract Background Copy number variation (CNV) in the salivary amylase gene (AMY1) modulates salivary α-amylase levels and is associated with postprandial glycemic traits. Whether AMY1-CNV plays a role in age-mediated change in insulin resistance (IR) is uncertain. Methods We measured AMY1-CNV using duplex quantitative real-time polymerase chain reaction in two studies, the Boston Puerto Rican Health Study (BPRHS, n = 749) and the Genetics of Lipid-Lowering Drug and Diet Network study (GOLDN, n = 980), and plasma metabolomic profiles in the BPRHS. We examined the interaction between AMY1-CNV and age by assessing the relationship between age with glycemic traits and type 2 diabetes (T2D) according to high or low copy numbers of the AMY1 gene. Furthermore, we investigated associations between metabolites and interacting effects of AMY1-CNV and age on T2D risk. Results We found positive associations of IR with age among subjects with low AMY1-copy-numbers in both studies. T2D was marginally correlated with age in participants with low AMY1-copy-numbers but not with high AMY1-copy-numbers in the BPRHS. Metabolic pathway enrichment analysis identified the pentose metabolic pathway based on metabolites that were associated with both IR and the interactions between AMY1-CNV and age. Moreover, in older participants, high AMY1-copy-numbers tended to be associated with lower levels of ribonic acid, erythronic acid, and arabinonic acid, all of which were positively associated with IR. Conclusions We found evidence supporting a role of AMY1-CNV in modifying the relationship between age and IR. Individuals with low AMY1-copy-numbers tend to have increased IR with advancing age.

scholarly journals A Comparison of the Vertical Transmission of High- and Low-Virulence Nucleopolyhedrovirus Strains in Lymantria Dispar L.

Insects ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 455
Author(s):  
Yuriy B. Akhanaev ◽  
Irina A. Belousova ◽  
Darya A. Lebedeva ◽  
Sergey V. Pavlushin ◽  
Vyacheslav V. Martemyanov
Keyword(s):  
Vertical Transmission ◽  
Lymantria Dispar ◽  
Quantitative Polymerase Chain Reaction ◽  
Fourth Instar ◽  
Insect Host ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Virus Survival ◽  
Virus Strains ◽  
Selection Of

Baculoviruses can persist in insect host organisms after infection and may be vertically transmitted to the next generation, in which they may be reactivated. The goal of the present study was to compare the efficiency of the vertical transmission of high- and low-virulence strains and the subsequent reactivation of Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV) in the offspring of Lymantria dispar L. adults who survived after viral infection. As a result of parental infection, the fecundity of survived females, pupae weight, and fertility were significantly different compared to the untreated insects. However, differences in these parameters between high- and low-virulence strains were not observed. The prevalence of virus strains in the offspring measured by quantitative polymerase chain reaction also did not differ. When the larvae reached the fourth instar, they were starved to activate the vertically transmitted virus. The frequency of virus activation in the experiment was not dependent on the virulence of the virus strains. These results are helpful for understanding the strategy of virus survival in nature and for the selection of the most effective strains with transgenerational effects in the years following pest treatment.

scholarly journals Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1008 ◽  
Author(s):  
Fei Ge ◽  
Congjun Jia ◽  
Min Chu ◽  
Chunnian Liang ◽  
Ping Yan
Keyword(s):  
Body Weight ◽  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Quantitative Polymerase Chain Reaction ◽  
The Body ◽  
Gene Copy ◽  
Common Source ◽  
Economic Traits ◽  
Number Variation

Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.

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