A single‐nucleotide polymorphism of miR‐146a and psoriasis: an association and functional study

Epidermal growth factor receptor (EGFR), which is overexpressed in psoriatic lesions, has been proven to contribute to the hyperproliferation of keratinocytes in psoriasis. Single nucleotide polymorphisms (SNPs) involved in miRNAs that can regulate the expression of EGFR could potentially influence the development of psoriasis. The present study investigated the association between a functional SNP of rs2910164 in miR‐146a and the risk of psoriasis in the Chinese Han population. A total of 521 Han Chinese patients with psoriasis and 582 healthy controls were recruited in this study. The miR‐146a rs2910164 SNP was genotyped by polymerase chain reaction‐restriction fragment length polymorphism. Overall, a significantly increased risk of psoriasis was associated with the rs2910164 miR‐146a CG and GG genotypes (adjusted OR, 1.38; 95% CI, 1.06–1.80). Furthermore, the rs2910164G allele in miR‐146a attenuated its inhibitory regulation on the expression of EGFR as well as the proliferation of human keratinocytes, and lowered the level of miR‐146a in the psoriatic lesions. These findings indicate that the rs2910164G allele in miR‐146a weakens its suppression on the proliferation of keratinocytes probably through the decreased inhibition of the target gene, EGFR, which may account for the increased risk of psoriasis in this study population.     

A single‐nucleotide polymorphism of miR‐196a‐2 and vitiligo: an association study and functional analysis in a Han Chinese population

Recent evidence indicates that oxidative stress and genetic factors play an important role in the pathogenesis of vitiligo. SNPs in miRNAs involved in oxidative stress could potentially influence the development of vitiligo. In this case–control study, we investigated the association of a functional SNP of rs11614913 in miR‐196a‐2 with risk of vitiligo. A significantly lower risk of vitiligo was associated with the rs11614913 miR‐196a‐2 CC genotype (adjusted OR, 0.77; CI, 0.60–0.98). In addition, TYRP1 gene expression was considerably down‐regulated by the rs11614913 C allele in miR‐196a‐2, which lowered the levels of intracellular reactive oxygen species (ROS) and reduced the proportion of early apoptosis in human melanocytes in response to H₂O₂ treatment. Our data suggest that the rs11614913 C allele in miR‐196a‐2 confers potential protection against oxidative effects on human melanocytes through the modulation of the target gene, TYRP1, which may account for the decreased risk of vitiligo in this study population.     

High‐throughput genotyping of single‐nucleotide polymorphisms in ace‐1 gene of mosquitoes using MALDI‐TOF mass spectrometry

Abstract Acetylcholinesterase (AChE) plays a vital role in the nervous system of insects and other animal species and serves as the target for many chemical agents such as organophosphate and carbamate insecticides. The mosquito, Culex pipiens complex, a vector of human disease, has evolved to be resistant to insecticides by a limited number of amino acid substitutions in AChE1, which is encoded by the ace‐1 gene. The aims of this study are to identify single nucleotide polymorphism (SNP) sites in the ace‐1 gene of the C. pipiens complex and explore an economical high‐throughput method to differentiate the genotypes of these sites in mosquitoes collected in the field. We identified 22 SNP sites in exon regions of the ace‐1 gene. Four of them led to non‐synonymous mutations, that is, Y163C, G247S, C677S and T682A. We used matrix‐assisted laser desorption ionization – time‐of‐flight mass spectrometry for genotyping at these four sites and another site F416V, which was relevant to insecticide resistance, in 150 mosquitoes collected from 15 field populations. We were able to synchronize analysis of the five SNP sites in each well of a 384‐well plate for each individual mosquito, thus decreasing the cost to one‐fifth of the routine analysis. Heterozygous genotypes at Y163C and G247S sites were observed in one mosquito. The possible influence of the five SNP sites on the activity or function of the enzyme is discussed based on the predicted tertiary structure of the enzyme.     

Validation of a single‐nucleotide polymorphism panel for parentage testing of farmed red deer

Red deer behaviour prevents the accurate physical matching of dams to fawns and, therefore, breeders have to rely on DNA‐based parentage testing. A panel consisting of 100 single nucleotide polymorphism markers, with an average minor allele frequency of 0.25, was able to resolve 92% of fawns to both parents. In comparison, an existing 12‐marker microsatellite panel was able to resolve 68% of fawns to both parents. When excluding dam DNA information, the single nucleotide polymorphism panel matched 81% of the fawns to their sires and the microsatellite panel 71%.     

Identification of a 3.7-Mb region for a marbling QTL on bovine chromosome 4 by identical-by-descent and association analysis

QTL mapping for growth and carcass traits was performed using a paternal half-sib family composed of 325 Japanese Black cattle offspring. Nine QTL were detected at the 1% chromosome-wise significance level at a false discovery rate of less than 0.1. These included two QTL for marbling on BTA 4 and 18, two QTL for carcass weight on BTA 14 and 24, two QTL for longissimus muscle area on BTA 1 and 4, two QTL for subcutaneous fat thickness on BTA 1 and 15 and one QTL for rib thickness on BTA 6. Although the marbling QTL on BTA 4 has been replicated with significant linkages in two Japanese Black cattle sires, the three Q (more marbling) haplotypes, each inherited maternally, were apparently different. To compare the three Q haplotypes in more detail, high-density microsatellite markers for the overlapping regions were developed within the 95% CIs (65 markers in 44–78 cM). A detailed haplotype comparison indicated that a small region (<3.7 Mb) around 46 cM was shared between the Qs of the two sires, whose dams were related. An association of this region with marbling was shown by a regression analysis using the local population, in which the two sires were produced and this was confirmed by an association study using a population collected throughout Japan. These results strongly suggest that the marbling QTL on BTA 4 is located in the 3.7-Mb region at around 46 cM.     

Distribution of single‐nucleotide variants on protein–protein interaction sites and its relationship with minor allele frequency

Recent advances in DNA sequencing techniques have identified rare single‐nucleotide variants with less than 1% minor allele frequency. Despite the growing interest and physiological importance of rare variants in genome sciences, less attention has been paid to the allele frequency of variants in protein sciences. To elucidate the characteristics of genetic variants on protein interaction sites, from the viewpoints of the allele frequency and the structural position of variants, we mapped about 20,000 human SNVs onto protein complexes. We found that variants are less abundant in protein interfaces, and specifically the core regions of interfaces. The tendency to “avoid” the interfacial core is stronger among common variants than rare variants. As amino acid substitutions, the trend of mutating amino acids among rare variants is consistent in different interfacial regions, reflecting the fact that rare variants result from random mutations in DNA sequences, whereas amino acid changes of common variants vary between the interfacial core and rim regions, possibly due to functional constraints on proteins. This study illustrated how the allele frequency of variants relates to the protein structural regions and the functional sites in general and will lead to deeper understanding of the potential deleteriousness of rare variants at the structural level. Exceptional cases of the observed trends will shed light on the limitations of structural approaches to evaluate the functional impacts of variants.     

Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis

For pedigree-based quantitative trait loci (QTL) association analysis, a range of methods utilizing within-family variation such as transmission-disequilibrium test (TDT)-based methods have been developed. In scenarios where stratification is not a concern, methods exploiting between-family variation in addition to within-family variation, such as the measured genotype (MG) approach, have greater power. Application of MG methods can be computationally demanding (especially for large pedigrees), making genomewide scans practically infeasible. Here we suggest a novel approach for genomewide pedigree-based quantitative trait loci (QTL) association analysis: genomewide rapid association using mixed model and regression (GRAMMAR). The method first obtains residuals adjusted for family effects and subsequently analyzes the association between these residuals and genetic polymorphisms using rapid least-squares methods. At the final step, the selected polymorphisms may be followed up with the full measured genotype (MG) analysis. In a simulation study, we compared type 1 error, power, and operational characteristics of the proposed method with those of MG and TDT-based approaches. For moderately heritable (30%) traits in human pedigrees the power of the GRAMMAR and the MG approaches is similar and is much higher than that of TDT-based approaches. When using tabulated thresholds, the proposed method is less powerful than MG for very high heritabilities and pedigrees including large sibships like those observed in livestock pedigrees. However, there is little or no difference in empirical power of MG and the proposed method. In any scenario, GRAMMAR is much faster than MG and enables rapid analysis of hundreds of thousands of markers.     

Characterization of a 320-kb region containing the HEXA gene on bovine chromosome 10 and analysis of its association with BSE susceptibility

Bovine spongiform encephalopathy (BSE) belongs to a group of neurodegenerative diseases known as transmissible prion diseases. Recently, variants in the promoter region of the prion protein ( PRNP ) gene have been shown to have a considerable effect on the susceptibility to BSE. However, a previous genome scan revealed other putative BSE-susceptibility loci. Here, we analysed such a region on BTA10, which contains the functional candidate gene HEXA . Three hundred and twenty kilobases that, besides HEXA , also contain ARIH1 , BRUNOL6 and PARP6 were characterized and screened for polymorphisms. Genotyping of 38 SNPs in Holstein–Friesian animals from the UK (350 diseased and 270 controls) revealed two intronic SNPs that were associated with BSE incidence, with experiment-wise P -values of 3.5 × 10⁻³ and 7.7 × 10⁻³ respectively. Both SNPs were in strong linkage disequilibrium and the rare alleles had a protective effect. These alleles were contained in a haplotype dubbed 'UK-protective' that was significantly overrepresented in the controls with a permuted P -value of 2 × 10⁻³. An association study in German Holstein animals (73 diseased and 627 controls) revealed an opposite effect of the 'UK-protective' haplotype in this population, i.e. it was overrepresented in the diseased animals, although not significant after correction for multiple testing. These findings indicate a causal variant for BSE susceptibility on BTA10 in linkage disequilibrium with the markers studied. Candidate gene analyses of the surrounding region and additional association studies will help to clarify the origin of the protective effects and to identify causal variants for BSE susceptibility on BTA10.     

Genetic‐based dissection of arsenic accumulation in maize using a genome‐wide association analysis method

Understanding the mechanism of arsenic (As) accumulation in plants is important in reducing As's toxicity to plants and its potential risks to human health. Here, we performed a genome‐wide association study to dissect the genetic basis of the As contents of different maize tissues in Xixian, which was irrigated with As‐rich surface water, and Changge using an association population consisting of 230 representative maize inbred lines. Phenotypic data revealed a wide normal distribution and high repeatability for the As contents in maize tissues. The As concentrations in maize tissues followed the same trend in the two locations: kernels < axes < stems < bracts < leaves. In total, 15, 16 and 15 non‐redundant quantitative trait loci (QTL s) associated with As concentrations were identified (P  ≤ 2.04 × 10^?6) in five tissues from Xixian, Changge, and the combination of the locations, respectively, explaining 9.70%–24.65% of the phenotypic variation for each QTL , on average. Additionally, four QTL s [involving 15 single nucleotide polymorphisms (SNP s)] were detected in the single and the combined locations, indicating that these loci/SNP s might be stable across different environments. The candidate genes associated with these four loci were predicted. In addition, four non‐redundant QTL s (6 SNP s), including a QTL that was detected in multiple locations according to the genome‐wide association study, were found to co‐localize with four previously reported QTL intervals. These results are valuable to understand the genetic architecture of As mechanism in maize and facilitate the genetic improvement of varieties without As toxicity.     

Identification of genes related to intramuscular fat independent of backfat thickness in Duroc pigs using single‐step genome‐wide association

Intramuscular fat (IMF) is an important meat‐quality trait of pigs, which influences pork’s shearing force, hydraulics, tenderness and juicy flavor. However, to achieve a higher percentage of lean meat, pigs with lower backfat thickness (BF) are intensively selected for, which may lead to a reduction in pork quality. Therefore, the objective of this study was to locate loci that affect IMF without changing BF. A single‐step GWAS was performed on 950 Duroc pigs genotyped by a 50K SNP chip in order to detect genomic variants relevant to IMF and BF. The significant SNPs detected were afterwards divided into a BF subset (seven SNPs), an IMF subset (11 SNPs) and a subset of both traits (12 SNPs), according to their P‐value and LD. After SNP and QTL annotation, our results indicated that SSC1: 167938652, 166363826, 164829874 and 167171587 might be associated with IMF without changing BF. In the subset of both traits, we found that the combined effect of ALGA0006602 (SSC1: 159538854) and 12784636 (SSC1: 160773437) might improve the IMF without changing BF. Our gene annotation result showed that TLE3, ITGA11, SMAD6, PAQR5 and [RNF152^A/G × MC4R^A/A] genes might affect IMF independently of BF. We believe that the SNPs and genes identified in this study will be valuable for the future molecular breeding of IMF in Duroc pigs.     

Cytogenetic observations on two ovarian carcinomas with double minutes, one with a 6q- marker chromosome

A high number of structurally altered marker chromosomes was found in two cases of ovarian carcinoma. Even by the application of different staining methods it was not possible to identify all the chromosomes. No evidence for the existence of a translocation between chromosomes 6 and 14 was found, which seems to be a specific abnormality characteristic of papillary serous cystadenocarcinomas of the ovary. It is of interest that double minutes were present in both cases. This offers further evidence for the assumption that double minutes are not infrequent in carcinomas. Their orthodox mitotic behaviour leads to high karyotype variability (number of double minutes/cell), and may be of particular importance for tumour biology. The methodological and cytogenetic implications of the results are discussed.     

A domesticated transposon mediates the effects of a single‐nucleotide polymorphism responsible for enhanced muscle growth

Single‐nucleotide polymorphisms (SNPs) in the regulatory regions of the genome can have a profound impact on phenotype. The G3072A polymorphism in intron 3 of insulin‐like growth factor 2 (IGF2) is implicated in higher muscle content and reduced fat in European pigs and is bound by a putative repressor. Here, we identify this repressor—which we call muscle growth regulator (MGR)—by using a DNA protein interaction screen based on quantitative mass spectrometry. MGR has a bipartite nuclear localization signal, two BED‐type zinc fingers and is highly conserved between placental mammals. Surprisingly, the gene is located in an intron and belongs to the hobo‐Ac‐Tam3 transposase superfamily, suggesting regulatory use of a formerly parasitic element. In transactivation assays, MGR differentially represses the expression of the two SNP variants. Knockdown of MGR in C2C12 myoblast cells upregulates Igf2 expression and mild overexpression retards growth. Thus, MGR is the repressor responsible for enhanced muscle growth in the IGF2 G3072A polymorphism in commercially bred pigs.     

Rapid,economical single‐nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non‐model organism: a case study of Atlantic cod Gadus morhua

By combining next‐generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single‐nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non‐model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small‐scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small‐scale next‐generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.     

Large‐scale culture of a megakaryocytic progenitor cell line with a single‐use bioreactor system

The increasing application of regenerative medicine has generated a growing demand for stem cells and their derivatives. Single‐use bioreactors offer an attractive platform for stem cell expansion owing to their scalability for large‐scale production and feasibility of meeting clinical‐grade standards. The current work evaluated the capacity of a single‐use bioreactor system (1 L working volume) for expanding Meg01 cells, a megakaryocytic (MK) progenitor cell line. Oxygen supply was provided by surface aeration to minimize foaming and orbital shaking was used to promote oxygen transfer. Oxygen transfer rates (k_La) of shaking speeds 50, 100, and 125 rpm were estimated to be 0.39, 1.12, and 10.45 h^?1, respectively. Shaking speed was a critical factor for optimizing cell growth. At 50 rpm, Meg01 cells exhibited restricted growth due to insufficient mixing. A negative effect occurred when the shaking speed was increased to 125 rpm, likely caused by high hydrodynamic shear stress. The bioreactor culture achieved the highest growth profile when shaken at 100 rpm, achieving a total expansion rate up to 5.7‐fold with a total cell number of 1.2 ± 0.2 × 10⁹ cells L^?1. In addition, cells expanded using the bioreactor system could maintain their potency to differentiate following the MK lineage, as analyzed from specific surface protein and morphological similarity with the cells grown in the conventional culturing system. Our study reports the impact of operational variables such as shaking speed for growth profile and MK differentiation potential of a progenitor cell line in a single‐use bioreactor. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:362–369, 2018     

Linkage analysis of the human HMG14 gene on chromosome 21 using a GT dinucleotide repeat as polymorphic marker

A (GT)n repeat in intron 4 of the functional human HMG14 gene on chromosome 21 was used as polymorphic marker to map this gene relative to the genetic linkage map of human chromosome 21. Variation in the length of the (GT)n repeat was detected by electrophoresis on polyacrylamide gels of DNA amplified by the polymerase chain reaction using primers flanking the repeat. The observed heterozygosity of this polymorphism in 40 CEPH families was 58% with six different alleles. Linkage analysis localized the HMG14 gene close to the ETS2 gene and locus D21S3 in chromosomal band 21q22.3.