Genotype frequency of ATP7A and ATP7B mutation-related copper-associated hepatitis in a Japanese guide dog Labrador retriever population

The incidence of copper-associated hepatitis in Labrador retriever in Japan has not been examined. This study examined the genotype frequencies of ATP7B:c.4358G>A, a mutation responsible for copper-associated hepatitis, and ATP7A:c.980C>T, a modifier of this disease, in Labrador retrievers of guide dog associations in Japan. Genetic material was collected by buccal swabs from 253 Labrador retrievers and genotyping was performed for the ATP7B and ATP7A mutations. The gene frequency was 0.107 for ATP7B:c.4358A. For ATP7A:c.980C, the gene frequencies were 0.703 in females and 0.368 in males. In this study, we established genotyping methods for the ATP7B:c.4358G>A and ATP7A:c.980C>T mutations. Based on the genotyping results, the risk of copper-associated hepatitis in the study population was 0.80% in males and 1.05% in females.

Effect of Protein Genotypes on Physicochemical Properties and Protein Functionality of Bovine Milk: A Review

Milk protein comprises caseins (CNs) and whey proteins, each of which has different genetic variants. Several studies have reported the frequencies of these genetic variants and the effects of variants on milk physicochemical properties and functionality. For example, the C variant and the BC haplotype of αS1-casein (αS1-CN), β-casein (β-CN) B and A1 variants, and κ-casein (κ-CN) B variant, are favourable for rennet coagulation, as well as the B variant of β-lactoglobulin (β-lg). κ-CN is reported to be the only protein influencing acid gel formation, with the AA variant contributing to a firmer acid curd. For heat stability, κ-CN B variant improves the heat resistance of milk at natural pH, and the order of heat stability between phenotypes is BB > AB > AA. The A2 variant of β-CN is more efficient in emulsion formation, but the emulsion stability is lower than the A1 and B variants. Foaming properties of milk with β-lg variant B are better than A, but the differences between β-CN A1 and A2 variants are controversial. Genetic variants of milk proteins also influence milk yield, composition, quality and processability; thus, study of such relationships offers guidance for the selection of targeted genetic variants.

Leading Enterovirus Genotypes Causing Hand, Foot, and Mouth Disease in Guangzhou, China: Relationship with Climate and Vaccination against EV71

(1) Background: Assignment of pathogens to the correct genus, species, and type is vital for controlling infectious epidemics. However, the role of different enteroviruses during hand, foot, and mouth disease (HFMD) epidemics and the major contributing factors remain unknown. (2) Methods: HFMD cases from 2016 to 2018 in Guangzhou, China were collected. The relationship between HFMD cases and genotype frequency, as well as the association between genotype frequency and climate factors, were studied using general linear models. We transformed the genotype frequency to the isometric log-ratio (ILR) components included in the model. Additionally, vaccination rates were adjusted in the climate-driven models. (3) Results: We observed seasonal trends in HFMD cases, genotype frequency, and climate factors. The model regressing case numbers on genotype frequency revealed negative associations with both the ILRs of CAV16 (RR = 0.725, p < 0.001) and EV71 (RR = 0.421, p < 0.001). The model regressing genotype frequency on driven factors showed that the trends for EV71 proportions were inversely related to vaccination rate (%, β = -0.152, p = 0.098) and temperature (°C, β = -0.065, p = 0.004). Additionally, the trends for CVA16 proportions were inversely related to vaccination rate (%, β = -0.461, p = 0.004) and temperature (°C, β = -0.068, p = 0.031). The overall trends for genotype frequency showed that EV71 decreased significantly, while the trends for CVA16 increased annually. (4) Conclusions: Our findings suggest a potential pathway for climate factors, genotype frequency, and HFMD cases. Our study is practical and useful for targeted prevention and control, and provides environmental-based evidence.

A laboratory simulation study on suppression of resistance genes by differential exposures to an insecticide in Anopheles stephensi Liston population

Background & objectives

: Insecticide applied at optimum dosage and coverage delays the development of resistance in disease vectors. The study was aimed to test the hypothesis whether decrease in exposure to insecticide leads to decrease in selection of insecticide resistance in mosquitoes. The mosquitoes were variably exposed to insecticide in the laboratory by simulating the variations in insecticide sprays applied in the field.

Methods

: The study was carried out on DDT resistant adults of Anopheles stephensi. Mosquitoes were differentially exposed to impregnated papers of DDT (4%), that were differentially masked to 25, 50, and 75% area with an unimpregnated Whatman No.1 filter paper, and to a positive control without any masking, i.e. 100% exposure area. The study was conducted for five generations and at each generation mosquitoes were exposed to differentially masked impregnated papers, and percent mortality was calculated.

Results

: The observed survival rate in differential exposures was more with the increase in heterozygous genotype resistance-susuceptible (RS) frequency. Resistant gene frequency with differential exposures (25 to 75%) was in the range of 0.38-0.54 for the F₀ generation, which increased to 0.84-0.93 for the F₄ generation. In 100% exposure it was 0.18 in F₀ generation, which increased to 0.58 in the F₄ generation. The resistant gene frequencies in the population showed increasing trend with decrease in exposure in contrast to complete exposure.

Interpretation & conclusion

: Variable simulated exposures resulted in precipitation of increased resistance while complete exposure resulted in lower levels of resistance, signifying the importance of optimum dosage and coverage in the indoor residual spray in delaying/avoiding the development of insecticide resistance in the disease vectors.

TBX3 and ASIP genotypes reveal discrepancies in officially recorded coat colors of Hucul horses

Although only a few specific pigmentation types are allowed within the Hucul horse registry, accurate determination of particular coat colors can be uncertain due to the presence of variation in color shades and segregation of multiple dun dilution variants. Herein, we genotyped the previously identified polymorphisms within two coat color loci TBX3 (T-box 3) and ASIP (Agouti Signaling Protein) in 462 Hucul individuals and compared the genotype predicted phenotypes with observed pigmentation types provided in the Polish Horse Breeders Association database. We identified disagreement between the predicted and recorded coat color in 157 horses (34%). The most common error was misclassification of horses with the nd1/nd1 and nd1/nd2 genotypes, what may be related with the occurrence of some 'intermediate' dilution phenotypes in such individuals. We have also proven that the frequency of the dominant dun dilution allele (D) (0.30) is higher than previously predicted by available studbooks. The D allele(s) is easily 'hidden' in various phenotypic groups including dark bay and black, therefore we hypothesized that the dun dilution effect itself is not as strongly epistatic in the Hucul horse as described in other horse breeds. This may be the result of an additional genetic modifier suppressing D allele phenotypic effect.

Physiological and Evolutionary Changes in a Biological Control Agent During Prey Shifts Over Several Generations

Biological control agents usually suffer from a shortage of target prey or hosts in their post-release stage. Some predatory agents turn to attacking other prey organisms, which may induce physiological and evolutionary changes. In this study, we investigated life history traits, gene expression and genotype frequency in the predatory ladybird beetle Cryptolaemus montrouzieri during experimental prey shifts. C. montrouzieri were either continuously fed on aphids Megoura japonica as an alternative prey for four generations or were shifted back to the initial prey mealybugs Planococcus citri in each generation. In general, the utilization of aphids resulted in reduced performance and severe physiological adjustments, indicated by significant changes in development and fecundity traits and a large number of differentially expressed genes between the two offering setup prey treatments. Within the aphid-fed lines, performance regarding the developmental time, the adult weight and the survival rate recovered to some level in subsequent generations, possibly as a result of adaptive evolution. In particular, we found that a shift back to mealybugs caused a gradual increase in fecundity. Accordingly, a genotype of the fecundity-related gene vitellogenin, of which there were several minor alleles in the initial population, became the main genotype within four generations. The present study explored the short-term experimental evolution of a so-call specialist predator under prey shift conditions. This potential rapid adaptation of biological control agents to novel prey will increase environmental risks associated with non-target effects.

IL-10(-592A/C) gene variant a predictor of postoperative atrial fibrillation in the north Indian population

BACKGROUND

There is an accumulating body of evidence indicating a strong association between inflammation and the pathogenesis of atrial fibrillation (AF) in different ethnicities across the globe. AF increases the risk of stroke and heart failure. Despite various researches on IL-10 response, there is limited clinical evidence present, which demonstrate a role of these immunity regulators in AF. Therefore, this study was designed to decipher the role of IL-10(-592A/C) polymorphism in the development of postoperative AF (post-OP AF).

METHOD

The study was designed for north Indian patients. The study included 90 patients with AF and 126 controls in sinus rhythm undergoing surgery at Department of Cardiovascular and thoracic surgery, SGPGIMS, Lucknow, India. DNA samples were genotyped for common single nucleotide polymorphism (SNP) in gene IL-10(-592A/C). The PCR-based RFLP technique was used to assess the genotype frequencies. The multivariable logistic regression analysis was performed to study the association of other risk factors with AF.

RESULTS

The distribution of IL-10(-592A/C) genotypes (CC, AC, and AA) was found to be 48.41%, 47.61%, and 3.98% in controls and 41.11%, 45.55%, and 13.34% in cases, respectively (P = .0385). The frequency of allele A in cases was significantly higher than the control group (36.11% vs 27.77%, P = .0654). Compared with CC, AA genotype had increased risk of AF in both unadjusted and adjusted analyses.

CONCLUSIONS

This study suggests that IL-10(-592A/C) polymorphism may have significant association with post-OP AF development in north Indian patients.

Temporal and spatial distribution of insecticide-resistance mutations in the green peach aphid Myzus persicae (Hemiptera: Aphididae) on primary and secondary host plants in central Chile

BACKGROUND

The aphid Myzus persicae develops insensitivity to almost all classes of insecticides through target site mutations. The aim of this study was to assess the temporal and spatial distribution of resistant aphids that grow on peach trees and weeds, and establish the role of the secondary hosts as a reservoir of resistant genotypes.

RESULTS

The frequency of genotypes (RR, RS, and SS) was affected by the host plant, mainly for knock-down resistance (kdr) and modified acetylcholinesterase (MACE) mutations (P < 0.05). A higher frequency of RS and RR was observed in aphids found on peach trees than on weeds. The frequency of the R allele was significantly higher (P < 0.01) than expected in autumn and on weeds for the kdr and MACE mutations, while the frequency of the S allele was high in all seasons for all insecticide-resistance mutations (P < 0.01). The most abundant multilocus genotype was characterized as being RS for the kdr mutation and SS for both super-kdr and MACE.

CONCLUSION

This study provides farm-scale evidence that weeds are not an important reservoir of the R allele, but they are for the S allele. Hence, the presence of heterozygous genotypes on peach trees is most likely attributable to weeds. © 2017 Society of Chemical Industry.

Study on the association of the polymorphism of HLA-II gene with leukemia

We explored the association between the HLA-II gene polymorphisms and the occurrence of leukemia. For this study, we selected 53 patients with leukemia treated at Zhongnan Hospital of Wuhan University from February 2014 to September 2015 and 46 healthy patients as the control group. We used polymerase chain reaction with sequence specific primers for DNA typing which was carried out to analyze the patients HLA-A/B gene polymorphism. We also used enzyme-linked immunosorbent assay and western blotting method to measure the protein expression of different genotypes and activity. Compared to the control group, HLA-A04, B08 gene frequencies were significantly lower than those of HLA-A04, B08 gene frequencies of the observation group; results were statistically significant (χ²=16.28, P<0.05; χ²=16.47, P<0.05). However, in the control group, the frequency of HLA-A09 gene was significantly higher than that of the observation group; there was a significant difference between the two groups (χ²=15.28, P<0.05). Through the measurement of the protein expression levels of the different genotypes in the control group and the observation group, it was found that in the observation group, HLA-A04, B08 protein contents (4.6 and 3.2 µg/l) were significantly higher than those of the control group (0.13 and 0.1 µg/l). While the control group HLA-A09 genotype protein content (3.7 µg/l) was significantly higher than that of the observation group (0.2 µg/l); there were significant differences between both (P<0.05). Therefore, there is a significant correlation between HLA-II gene polymorphism and leukemia that is higher than HLA-A04 and B08 gene frequency and can help promote the occurrence of leukemia. The higher frequency of HLA-A09 gene can help to suppress the occurrence of leukemia.

Simultaneous genotyping of human platelet alloantigen-1 to 28bw systems by multiplex polymerase chain reaction sequence-based typing

BACKGROUND AND OBJECTIVES

Human platelet alloantigen (HPA) genotyping is important for the diagnosis and prevention the alloimmune platelet disorders. In this study, a simultaneous genotyping method for HPA-1 to -28bw systems was established using multiplex PCR-SBT and the frequencies of genotypes and alleles of HPA-1 to -28bw systems in the Zhejiang Han population were analysed.

MATERIALS AND METHODS

The specific primers were designed according to the nucleotide sequences of HPA-1 to 28bw systems which are located in ITGB3, GP1BA, ITGA2B, ITGA2, GP1BB and CD109, respectively. The multiplex PCR amplification systems were used, and then, the amplicons were purified and sequenced. A total of 335 healthy volunteer blood donors were detected.

RESULTS

The genotypes of ten reference samples from Platelet Immunology Workshop of ISBT were in concordance with the known genotypes. Among the 28 HPA systems, HPA a and b alleles were found in HPA-1 to 6w, HPA-15 and HPA-21w systems in the Chinese Han population, while only HPA aa genotype was detected in the other HPA systems. The frequencies of HPA-1a and HPA-1b were 0·993 and 0·007, with 0·943 and 0·057 for HPA-2a and HPA-2b, 0·527 and 0·473 for HPA-3a and HPA-3b, 0·997 and 0·003 for HPA-4a and HPA-4b, 0·991 and 0·009 for HPA-5a and HPA-5b, 0·980 and 0·020 for HPA-6wa and HPA-6wb, 0·508 and 0·492 for HPA-15a and HPA-15b and 0·994 and 0·006 for HPA-21wa and HPA-21wb.

CONCLUSIONS

One multiplex PCR-SBT method for HPAs was established and the data of the study could help to prevent and treat for alloimmune thrombocytopenia.

Genotype-Frequency Estimation from High-Throughput Sequencing Data

Rapidly improving high-throughput sequencing technologies provide unprecedented opportunities for carrying out population-genomic studies with various organisms. To take full advantage of these methods, it is essential to correctly estimate allele and genotype frequencies, and here we present a maximum-likelihood method that accomplishes these tasks. The proposed method fully accounts for uncertainties resulting from sequencing errors and biparental chromosome sampling and yields essentially unbiased estimates with minimal sampling variances with moderately high depths of coverage regardless of a mating system and structure of the population. Moreover, we have developed statistical tests for examining the significance of polymorphisms and their genotypic deviations from Hardy-Weinberg equilibrium. We examine the performance of the proposed method by computer simulations and apply it to low-coverage human data generated by high-throughput sequencing. The results show that the proposed method improves our ability to carry out population-genomic analyses in important ways. The software package of the proposed method is freely available from https://github.com/Takahiro-Maruki/Package-GFE.

[Polymorphism in the Serotonin Transporter Gene (SLC6A4) and Emotional Bipolar Disorder in Two Regional Mental Health Centers from the Eje Cafetero (Colombia)]

INTRODUCTION

The indel polymorphisms in the promoting region and the 2(nd) intron polymorphisms in the serotonin transporter gene (SLC6A4) have been associated to bipolar disorder 1 (BD1) in several population studies. The objective was to analyze the genotypic and allelic frequencies in both gene regions in a study of cases and controls with individuals from Risaralda and Quindío (Colombia) so as to establish possible associations to BD1, and compare results with previous and similar studies.

METHODS

133 patients and 120 controls were studied. L and S indel polymorphisms in the promoting region were analyzed by PCR, together with VNTR STin2.10 and STin 2.12 VNTRs polymorphisms in the 2(nd) intron of the SL-C6A4 gene

RESULTS

Genotypic and allelic frequencies for the S and L polymorphisms were similar both in cases and controls. However, the LL genotype was significantly increased both in BD1 population (OR=1.89; CI95%=1.1-3.68), and when discriminated by gender. This particular genotype in general population is OR=2.22; IC95%=1.04-5.66 for women, and OR=1.62; IC 95%=0.71-4.39 for men. No significant genotypic and allelic differences were found for VNTR STin2.10 and STin 2.12. polymorphisms.

CONCLUSIONS

No association was found between polymorphisms of 5-HTTLPR polymorphisms and the 2(nd) intron of the serotonin transporting gene in general patients with BD1, nor when compared by gender. Our results are similar to those reported for Caucasian populations and differ from those of Asian and Brazilian populations.