scholarly journals High Olfactory Receptor-Rich 11q11 Copy Number in Girls and African American Children

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1943
Author(s):  
Megan Phillips ◽  
Vaithinathan Selvaraju ◽  
Anna Fouty ◽  
Jeganathan Ramesh Babu ◽  
Maninder Sandey ◽  
...  

Copy number variants (CNVs) provide numerous genetic differences between individuals, and they have been linked with multiple human diseases. Obesity is one of the highly heritable complex disorders, which is associated with copy number variance (CNV). A recent report shows that the 11q11 gene, a novel olfactory receptor, and its copy number variants are involved in the early onset of obesity. In the current study, we analyzed the 11q11 gene copy number variance (CNV) based on gender in White/European American (EA) and African American (AA) normal weight and overweight/obese children. Sixty-nine boys and fifty-eight girls between the ages of 6 and 10 years belonging to either EA or AA ethnicity were involved in this study. As per World Health Organization (WHO) guidelines, each participant’s body weight and height were recorded. DNA was extracted from saliva, and the copy number variants for the 11q11 gene were measured using digital PCR. The descriptive analysis of the 11q11 copy number showed significantly more copies in girls compared to boys; similarly, AA participants had significantly increased CNV compared to EA. The normal weight (NW) and overweight/obese (OW/OB) girls were significantly less likely to belong to the low copy number variant (LCNV) group of 11q11 compared to boys; similarly, NW and OW/OB AA children were significantly less likely to belong to the LCNV group. The AA girls in LCNV had significantly higher BMI z-scores. Our findings suggest that the 11q11 copy number in children is race and gender-specific.

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Fang Huang ◽  
Biraj Shrestha ◽  
Hui Liu ◽  
Lin-Hua Tang ◽  
Shui-Sen Zhou ◽  
...  

Abstract Background The emergence and spread of artemisinin resistance in Plasmodium falciparum poses a threat to malaria eradication, including China’s plan to eliminate malaria by 2020. Piperaquine (PPQ) resistance has emerged in Cambodia, compromising an important partner drug that is widely used in China in the form of dihydroartemisinin (DHA)-PPQ. Several mutations in a P. falciparum gene encoding a kelch protein on chromosome 13 (k13) are associated with artemisinin resistance and have arisen spread in the Great Mekong subregion, including the China–Myanmar border. Multiple copies of the plasmepsin II/III (pm2/3) genes, located on chromosome 14, have been shown to be associated with PPQ resistance. Methods The therapeutic efficacy of DHA-PPQ for the treatment of uncomplicated P. falciparum was evaluated along the China–Myanmar border from 2010 to 2014. The dry blood spots samples collected in the efficacy study prior DHA-PPQ treatment and from the local hospital by passive detection were used to amplify k13 and pm2. Polymorphisms within k13 were genotyped by capillary sequencing and pm2 copy number was quantified by relative-quantitative real-time polymerase chain reaction. Treatment outcome was evaluated with the World Health Organization protocol. A linear regression model was used to estimate the association between the day 3 positive rate and k13 mutation and the relationship of the pm2 copy number variants and k13 mutations. Results DHA-PPQ was effective for uncomplicated P. falciparum infection in Yunnan Province with cure rates > 95%. Twelve non synonymous mutations in the k13 domain were observed among the 268 samples with the prevalence of 44.0% and the predominant mutation was F446I with a prevalence of 32.8%. Only one sample was observed with multi-copies of pm2, including parasites with and without k13 mutations. The therapeutic efficacy of DHA-PPQ was > 95% along the China–Myanmar border, consistent with the lack of amplification of pm2. Conclusion DHA-PPQ for uncomplicated P. falciparum infection still showed efficacy in an area with artemisinin-resistant malaria along the China–Myanmar border. There was no evidence to show PPQ resistance by clinical study and molecular markers survey. Continued monitoring of the parasite population using molecular markers will be important to track emergence and spread of resistance in this region.


Nutrients ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1379 ◽  
Author(s):  
Chandra Venkatapoorna ◽  
Priscilla Ayine ◽  
Emily Parra ◽  
Taylor Koenigs ◽  
Megan Phillips ◽  
...  

Salivary amylase (AMY1) is the most abundant enzyme in human saliva, responsible for the hydrolysis of α-1,4 glycosidic linkages that aids in the digestion of starch. Recently studies have shown that the copy number of AMY1 is associated with obesity; however, the data varies with location. One-third of children are overweight/obese in Alabama. In this study, we aim to determine the relationship between the copy number of AMY1 gene and obesity measurements in children from Alabama. One hundred twenty-seven children aged between 6 to 10 years participated in this study. Anthropometric measurements were measured using WHO recommendations. Genomic DNA was extracted from saliva, and the copy number of the AMY1 gene was estimated by digital PCR. The association between AMY1 copy number and obesity measurements was analyzed by linear regression. The mean AMY1 copy number significantly decreased in overweight/obese (6.21 ± 1.48) compared to normal weight (7.97 ± 2.35) children. AMY1 copy number inversely associated with the obesity measurements. African Americans had a stronger association between low AMY1 copy number and obesity compared to white/European Americans. Our findings suggest that overweight/obese children have a low AMY1 copy number and the effect is more prominent in African Americans.


2021 ◽  
Author(s):  
Xiuqin Bao ◽  
Danqing Qin ◽  
Jian Ma ◽  
Xiangcheng Zhou ◽  
Jicheng Wang ◽  
...  

Abstract Background: α-thalassemia, with carrier rates of 11.31% and 17.55% respectively in Guangdong and Guangxi province, is a highly prevalent disease in Southern China and tropical and subtropical regions and is mainly caused by deletion in α-globin gene (HBA1 and HBA2). The clinical manifestation of α-thalassemia is highly correlated with the copy number of α-globin gene. The decrease of copy number results in α-thalassemia, while duplication or triplication compounded with β-thalassemia may aggravate the clinical manifestation. However, the usual methods we used to measure the copy number variants can only detect the three common types: --SEA, -α3.7 and − α4.2, which may easily miss the rare deletional type and duplication or triplication cases. Therefore, it is essential to establish a new method which allows detection of different copy number variants in α-globin genes, including deletion, duplication and triplication simultaneously and accurately.Methods: 428 peripheral blood and fetal chorionic villus or amniotic fluid samples were recruited in this study. We used a pair of primers and two probes to perform droplet digital PCR.Results: By performing only two reactions, we accurately detected the copy number variants in α-globin genes, including the common form α-thalassemia, triplications such as αααanti4.2 and trisomy 16. The accuracy rate for detecting the copy number of α-globin genes can up to 100%.Conclusions: In conclusion, droplet digital PCR served as an accurate and rapid method for copy number variation detection in clinical screening for α-thalassemia.


2014 ◽  
Vol 74 (17) ◽  
pp. 4853-4863 ◽  
Author(s):  
David Endesfelder ◽  
Rebecca A. Burrell ◽  
Nnennaya Kanu ◽  
Nicholas McGranahan ◽  
Mike Howell ◽  
...  

2011 ◽  
Vol 8 (5) ◽  
pp. 682-692 ◽  
Author(s):  
Daniel Arvidsson ◽  
Mark Fitch ◽  
Mark L. Hudes ◽  
Catrine Tudor-Locke ◽  
Sharon E. Fleming

Background:Different movement efficiency in overweight children may affect accelerometer output data. The purpose was to investigate the ability of accelerometers to assess physical activity intensity and number of steps in normal-weight compared with overweight children.Methods:Eleven normal-weight and 14 overweight African American children walked at 2, 4, 5, and 6 km/h on a treadmill wearing Lifecorder, ActiGraph, RT3, and Biotrainer. Oxygen uptake was measured and steps manually counted. Fat free mass (FFM) was assessed from bioelectrical impedance analysis. Accelerometer counts and the individual linear regression lines of accelerometer counts versus VO2/FFM were evaluated, together with steps recorded by Lifecorder and Actigraph.Results:Correlations between accelerometer counts and VO2/FFM for all monitors were r ≥ .95 (P < .01). The accelerometer counts and their relationship to VO2/FFM did not generally differ significantly by body weight status. Lifecorder and Actigraph underestimated steps at 4, 5, and 6 km/h by less than 9%, but the error was up to −95% at 2 km/h.Conclusions:All 4 accelerometers show high ability to assess physical activity intensity, and can be used to compare physical activity between normal-weight and overweight children. The Lifecorder and the ActiGraph showed high accuracy in assessing steps, providing speed of movement exceeded 2 km/h.


Hypertension ◽  
2016 ◽  
Vol 68 (suppl_1) ◽  
Author(s):  
Ryousuke Satou ◽  
Akemi Katsurada ◽  
Kayoko Miyata ◽  
Andrei Derbenev ◽  
Andrea Zsombok

The intrarenal renin-angiotensin system (RAS) has been shown to play crucial roles in the development of hypertension and RAS associated kidney injury including diabetic nephropathy. Although some circulating RAS components are filtered into kidneys and contribute to the regulation of intrarenal RAS activity, evaluating expression levels of RAS components in the kidney is important to elucidate the mechanisms underlying intrarenal RAS activation. Digital PCR is a new technique that has been established to quantify absolute target gene levels, which allows for comparisons of different gene levels. Thus, this study was performed to establish profiles of absolute gene copy numbers for intrarenal RAS components in wild-type (WT) rats, WT and streptozotocin (STZ)-induced diabetic mice. Male Sprague-Dawley rats (N=5) and male C57BL/6J mice were used in this study. The mice were subjected to either control (N=5) or STZ (200 mg/kg, N=4) injection. Seven days after STZ injection, copy numbers of renal cortical angiotensinogen (AGT), angiotensin-converting enzyme (ACE), ACE2, angiotensin type 1 receptor a (AT1a), and AT2 mRNA were determined by a droplet digital PCR. Since (pro)renin proteins produced by juxtaglomerular cells are secreted to circulating system, analysis of renin mRNA was excluded from this evaluation. In the renal cortex of WT rats, the copy number of AGT was higher than other measured RAS components (AGT: 719.2±46.6, ACE: 116.0±14.9, ACE2: 183.6±21.5, AT1a: 196.0±25.2 copies in 1 ng total RNA). AT2 levels were lower than other components (0.068±0.01 copies). In WT mice, ACE exhibited the highest copy number in the components (AGT: 447.2±29.0, ACE: 1662.4±61.2, ACE2: 676.8±41.5, AT1a: 867.0±16.8, AT2: 0.049±0.01 copies). Although STZ-induced diabetes did not change ACE2 and AT1a, ACE levels were reduced (765.5±98.1 copies) and AT2 levels were augmented (0.10±0.01 copies) as previously demonstrated. Accordingly, the absolute quantification by digital PCR established precise gene profiles of intrarenal RAS components, which will provide rationales for targeting the each component in future studies. Furthermore, the results indicate that the high sensitive assay accurately quantifies rare target genes including intrarenal AT2.


2019 ◽  
Vol 22 (3) ◽  
pp. 670-671 ◽  
Author(s):  
Tracy Brandt ◽  
Laura M. Sack ◽  
Dolores Arjona ◽  
Duanjun Tan ◽  
Hui Mei ◽  
...  

2019 ◽  
Vol 22 (2) ◽  
pp. 336-344 ◽  
Author(s):  
Tracy Brandt ◽  
Laura M. Sack ◽  
Dolores Arjona ◽  
Duanjun Tan ◽  
Hui Mei ◽  
...  

2020 ◽  
Vol 87 (8) ◽  
pp. 736-744 ◽  
Author(s):  
Jin P. Szatkiewicz ◽  
Menachem Fromer ◽  
Randal J. Nonneman ◽  
NaEshia Ancalade ◽  
Jessica S. Johnson ◽  
...  

2021 ◽  
Author(s):  
Alexey Yanchukov ◽  
Zusana Hiadlovska ◽  
Zeljka Pezer ◽  
Milos Macholan ◽  
Jaroslav Pialek ◽  
...  

Hybrid zones have long been described as "windows on the evolutionary process", and studying them has become even more important since the advance in the genome analysis tools. The hybrid zone between two subspecies of the house mouse (Mus musculus musculus and Mus m. domesticus) is a unique model speciation system to study fine scale interactions of recently diverged genomes. Here, we explore the role of gene Copy Number Variation in shaping the barrier to introgression in the hybrid zone within a previously established transect in Central Europe. The CNV of seven pre-selected candidate genes was determined via droplet-digital PCR and analyzed in the context of ~500k SNPs, with the ancestral population (i.e. musculus or domesticus) of every SNP allele previously inferred in the admixed individuals (Baird et al., in prep.). The copy numbers of five genes were clearly associated with the prevalence of either musculus or domesticus genomes across the hybrid zone. In three cases, the highest and/or outlying levels of association were observed at or very close to the annotated positions of the respective gene amplicons, demonstrating the power of our approach in confirming the reference locations of copy number variants. Notably, several other reference locations were recognized as positive outliers in the association with particular CNV genes, possibly representing the extra gene copies and/or their epistatic interaction sites.


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