Hardy-Weinberg Research Articles

Genetic Diversity of Philippine Native Pigs (Sus scrofa L.) from Quezon and Marinduque Based on Morphological and Microsatellite Markers

Nine microsatellite markers recommended by the Food and Agriculture Organization were used to measure the genetic diversity of Quezon and Marinduque native pig populations – with a total of 37 and 40 individuals, respectively. All markers were discovered to be polymorphic, with a mean number of alleles per locus of 10. Marinduque native pigs were found to have a mean effective number of alleles (EA), mean observed heterozygosity (HO), mean expected heterozygosity (HE), and mean polymorphic information content (PIC) of 5.005 ± 0.547, 0.673 ± 0.040, 0.780 ± 0.024, and 0.76 ± 0.03, respectively. By contrast, Quezon native pigs had mean EA, mean HO, mean HE, and mean PIC values of 5.280 ± 0.787, 0.634 ± 0.044, 0.773 ± 0.035, and 0.75 ± 0.04, respectively. Between the two populations, the heterozygosity (HE > HO) and positive values of FIS (0.1714) and FIT (0.1868) indicated a low number of heterozygotes, suggesting the possibility of inbreeding. The test of Hardy-Weinberg equilibrium (HWE) showed that three loci each in the Quezon and Marinduque native pig populations deviated from HWE. Although morphological analysis revealed significant differences in snout shape, head profile, ear type, and all morphometric traits, a low level of genetic differentiation between the two populations was observed (FST = 0.0186; Nei genetic distance = 0.130; Nei unbiased genetic distance = 0.082). Overall, these findings imply that further studies on the genetic improvement and conservation of Philippine native pigs are required for the development of signature pig breeds across the country.

Association of LPAR1 Gene Variants with Type 2 Diabetes in Local Population

Type 2 diabetes mellitus (T2DM) is the most prevailing worldwide health challenge of the 21st century and the 5th leading cause of death worldwide. About 90% of diabetic patients are diagnosed as having T2DM. LPAR1 gene codes LPA protein that is involved in the regulation of many biological processes. In this study, we have investigated the association of single nucleotide polymorphism (SNP) of LPAR1 gene variants rs494605 and rs558347 with T2DM in our local population. This association was analyzed by amplification of the target gene through Tetra ARMS PCR. The study involved 200 participants with equal ration of cases and controls. Both genetic variants of LPAR1 rs494605 and rs558347 have allelic origin T/C. The allelic frequency of LPAR1 was calculated through the Hardy Weinberg Equilibrium. re found that in LPAR1 rs494605 mutant allele, C was 47% in cases compared to controls (39%) and in LPAR1 rs558347, heterozygosity allele (TC) was 46% compared to mutant allele C (13%), while wild T allele was 17% in cases. Many demographic and lifestyle risk factors were significantly associated with LPAR1 gene variants. The heterogeneity of genetic variants with T2DM also showed a strong correlation with obesity, hormonal imbalance, and depression with p-value of 0.001, and 95% confidence interval. Smoking and alcohol consumption are major risk factors of T2DM. Variations in LPAR1 can be used as a biomarker and diagnostic tool for T2DM.

ABCB9 polymorphism rs61955196 is associated with schizophrenia in a Chinese Han population.

BACKGROUNDSchizophrenia (SCZ) is a complex disease which can be affected by both genetic and environmental factors. Prenatal famine exposure may cause changes in DNA methylation levels of genes. Meanwhile, maternal nutrition during pregnancy is a pivotal environmental factor in the development of SCZ. DNA methylation may be an intermediate factor mediating exposure to famine during pregnancy and SCZ, and DNA methylation quantitative trait loci might serve as a promising tool for linking SCZ and prenatal famine. AIMTo analyze the association between prenatal famine exposure and SCZ risk in Northeast Han Chinese through analysis of DNA methylation related loci.METHODSA total of 954 Han Chinese from Northeast China were recruited, including 443 patients with SCZ and 511 healthy controls. The participants were further divided into famine (born in 1960-1962) and non-famine (born in 1963-1965) groups to investigate the effect of prenatal famine exposure. Four single-nucleotide polymorphisms (SNPs) selected according to the relevant literature were genotyped, namely, rs11917047 in PTPRG, rs2239681 in IGF2, rs3842756 in INSIGF, and rs61955196 in ABCB9. DNA were extracted from peripheral blood samples, and the genotypes of these SNP loci were detected using the improved Multiple Ligase Detection Reaction multiple SNP typing technique. The associations of the DNA methylation related SNPs with SCZ risk and prenatal famine, and their interactions were analyzed using logistic regression analysis and generalized multifactor dimensionality reduction (GMDR) software.RESULTSBased on the sequencing data, genotype distributions and allele frequencies of the four selected SNPs were determined. All genotype frequencies of the four SNPs in the healthy control group were tested for deviation from Hardy-Weinberg equilibrium (P > 0.05). Logistic regression analysis showed that rs61955196 was significantly associated with SCZ risk in the log-additive model [odds ratio (OR): 1.22; 95% confidence interval (CI): 1.01-1.48; P = 0.040]. We also found that the rs61955196 allele was related with an enhanced risk of SCZ (G>C, OR: 1.22; 95%CI: 1.01-1.47; P = 0.042). However, no associations were observed between rs11917047, rs2239681, or rs3842756 and SCZ risk. Under the optimal genetic model, no significant association of famine with the four SNPs was seen. Though the gene–gene interactions between rs2239681 and rs61955196 were found in GMDR analysis, none of the gene-gene interactions and gene-famine interactions were associated with the risk of SCZ.CONCLUSIONOur study suggested that rs61955196 in ABCB9 is associated with SCZ susceptibility in Northeast Han Chinese, providing insight into genetic effects on SCZ.

Matrix metalloproteinase-9 (MMP-9) promoter -1562C/T functional polymorphism is associated with an increased risk to develop micropapillary thyroid carcinoma.

Matrix metalloproteinase-9 (MMP-9) is an important mediator of tumor initiation and progression. The MMP-9 promoter -1562C/T functional polymorphism increases gene expression and was identified as a susceptibility factor for various cancers. To evaluate the influence of the MMP-9 promoter genotype on the risk of developing papillary thyroid cancer (PTC) and to correlate cancer patient genotype with the clinical and pathological phenotype. We evaluated 236 patients with nodular thyroid disease pre-thyroidectomy (119 benign disease, 117 PTC). Genomic DNA was isolated from whole blood and the MMP-9 -1562C/T genotype was evaluated by PCR-RFLP analysis. Genotype frequencies were in Hardy-Weinberg equilibrium for all groups. The T allele was significantly more frequent in cancer compared to benign disease (17.5% vs 10.1%), p= 0.019. Patients with the CT or CT+TT genotype had an increased risk of developing PTC, specifically micropapillary thyroid carcinoma (MPTC) (CT genotype: OR = 6.467, p= 0.00006; CT+TT: OR = 6.859, p= 0.00002), but not more advanced stages (CT: p= 0.094; CT+TT: p= 0.157). The -1562C/T genotype did not significantly correlate with tumor histological subtype, invasion or TNM stage. The MMP-9 -1562C/T functional polymorphism may indicate susceptibility to develop thyroid cancer, specifically intrathyroidal clinically non-relevant MPTC. This suggests that although this genotype might be a predisposing factor, other genetic/epigenetic events are needed for cancer progression.

The Conceptual Analysis of Disciplinary Evidence (CADE) framework as a guide for evidentiary reasoning: A practical implementation in a Hardy-Weinberg Equilibrium (HWE) laboratory investigation

ABSTRACT Recent emphasis on learning biology through scientific investigations has focused instruction on understanding and using scientific evidence. To unpack the complexities of evidentiary reasoning, here we present a novel laboratory investigation for teaching the Hardy Weinberg Equilibrium (HWE) in an introductory biology laboratory course that was informed by the Conceptual Analysis of Disciplinary Evidence (CADE) framework. This HWE laboratory investigation highlights evidentiary reasoning with scaffolding questions to target reasoning with and about scientific evidence and it provides students with detailed disciplinary knowledge underpinning their investigation and evidentiary reasoning. To indicate how CADE influenced instruction on evidentiary reasoning during the investigation, changes in one instructor’s laboratory discussion questions before and after implementing CADE are provided. Also, our CADE-informed HWE laboratory investigation is compared to other published activities for engaging students with HWE. Findings show that with CADE, the instructor implemented more scaffolds for directing students to consider multiple aspects of evidentiary reasoning and encouraged students’ epistemic considerations about the nature, scope and quality of scientific evidence. These changes suggest that CADE can be a practical pedagogical tool to inform improvements in HWE laboratory investigations and to help instructors develop and implement scaffolds to guide students’ evidentiary reasoning during a scientific investigation.

Microsatellite markers for 24 loci developed for genotyping eastern woodrats, Neotoma floridana

Population declines have been documented in many species within the genus Neotoma. Eastern woodrat, Neotoma floridana, recovery efforts in the Shawnee National Forest (SNF), Illinois USA provided an opportunity to study the long-term population-level genetic changes following an augmentation and reintroduction. We developed 24 microsatellite markers using QDD and genotyped 32 eastern woodrats from a single population. Number of alleles per locus ranged from 3 to 14 (mean = 7). Observed heterozygosity ranged from 0.375 to 0.969 per locus and expected heterozygosity from 0.485 to 0.854. Two loci showed significant deviation from Hardy–Weinberg equilibrium following Bonferroni sequential corrections. These markers will provide valuable information useful for studying population dynamics of eastern woodrats and closely-related species.

Asociación del polimorfismo rs5186 del gen AGTR1 con disminución de la TFGe en pacientes con diabetes tipo 2 de la Ciudad de México

BackgroundEarly biomarkers search for Diabetic Kidney Disease (DKD) in patients with Type 2 Diabetes Mellitus (T2DM), as genetic markers to identify vulnerable carriers of the disease even before Glomerular Filtration Rate (GFR) decline or microalbuminuria development, has been relevant during the last few years.The rs5186 (A116C) polymorphism of the Angiotensin II Receptor Type I gene (AGTR1), has been associated to multiple effects of renal injury risk, commonly detected in patients with Diabetes Mellitus (DM). It has been described that rs5186 could have an effect in stability proteins that assemble Angiotensin II Receptor Type I (AT1), modifying its action, which is why it should be considered as a risk factor for Chronic Kidney Disease (CKD), characterized by a GFR progressive reduction. Even though, the association between rs5186 AGTR1 gene polymorphism and DKD in patients with T2DM has been controversial, inconclusive, and even absent. This disputable issue might be as a result of association studies in which many and varied clinical phenotypes included are contemplated as CKD inductors and enhancers. Although, the sample sizes studied in patients with T2DM are undersized and did not have a strict inclusion criteria, lacking of biochemical markers or KDOQI classification, which have hindered its examination. ObjectiveThe aim of our study was to establish an association between rs5186 AGTR1 gene polymorphism and GFR depletion, assessed as a risk factor to DKD development in patients with T2DM. MethodsWe analyzed 297 not related patients with T2DM, divided into 221 controls (KDOQI 1) and 76 cases (KDOQI 2). Arterial pressure, anthropometric and biochemical parameters were measured. rs5186 of AGTR1 genotyping was performed by TaqMan assay real-time PCR method. Allele and genotype frequencies, and Hardy-Weinberg equilibrium were measured. Normality test for data distribution was analyzed by Shapiro-Wilk test, variable comparison by Student's t-test for continuous variables, and Chi-squared test for categorical variables; ANOVA test was used for mean comparison of more than two groups. Effect of rs5186 to DKD was estimated by multiple heritability adjustment models for risk variables of DKD. Statistical significance was indicated by p<0.05. Data was analyzed using Statistical Package STATA v11 software. ResultsDominant and Over-dominant models showed a likelihood ratio to GFR depletion of 1.89 (1.05-3.39, p = 0.031) and 2.01 (1.08-3.73, p = 0.023) in patients with T2DM. Risk factor increased to 2.54 (1.10-5.89) in women in Over-dominant model. ConclusiónIn clinical practice, most of nephropathies progress at a slow pace into a total breakdown of renal function, even asymptomatic. This is the first study, reporting that rs5186 polymorphism of AGTR1 gene contribution to GFR depletion, and this could be evaluated as a predisposing factor for DKD in patients with T2DM.

Role of PAX7 Gene rs766325 and rs4920520 Polymorphisms in the Etiology of Non-syndromic Cleft Lip and Palate: A Genetic Study.

Non-syndromic cleft lip and palate (NSCLP) is one of the most common birth defects in humans with an overall prevalence of ∼1 in 700 live births around the world. The etiology of NSCLP is complex involving multiple genes, environmental factors, and gene-to-gene interactions. Several genome-wide associations (GWA) studies have shown the association of the paired box 7 ( PAX7 ) gene in the etiology of cleft lip and palate in different populations worldwide. However, there are no reported studies on the association between the rs766325 and rs4920520 polymorphisms and the risk of developing NSCLP in the Indian population. Hence, the present study aimed to test for the probable association between rs766325 and rs4920520 polymorphisms among NSCLP Indian population using a case-parent trio design. Forty case-parent trios were selected from the cleft lip and palate center based on the inclusion and exclusion criteria. Genomic DNA was isolated from the cases and their parents. The rs766325 and rs4920520 polymorphisms of the PAX7 gene were analyzed for their association using the MassARRAY analysis. The statistical analysis was done using the PLINK software. The rs766325 and rs4920520 polymorphisms were tested for the Hardy–Weinberg equilibrium. None of the polymorphisms showed any statistical significance. Hence, the rs766325 and rs4920520 polymorphisms of the PAX7 gene were found to be not associated with NSCLP in the Indian case-parent trios.

UGT1A1 gene mutations in Chinese Dong neonates in Sanjiang, Guangxi

To study the characteristics of UGT1A1 gene mutations in Dong neonates in Sanjiang County of Liuzhou and its association with the pathogenesis of hyperbilirubinemia in Dong neonates. A prospective analysis was performed on 84 neonates who were diagnosed with unexplained hyperbilirubinemia in the Department of Neonatology, Sanjiang County People's Hospital, from January 2021 to January 2022. Sixty healthy neonates born during the same period were enrolled as the control group. Peripheral blood genomic DNA was extracted for both groups, and UGT1A1 exon 1 was amplified by PCR and sequenced. In the case group, 33 neonates were found to have G71R missense mutation, with a mutation rate of 39%. The case group had a significantly higher frequency of A allele than the healthy control group (21% vs 10%, P<0.05). The risk of hyperbilirubinemia in Dong neonates carrying G71R missense mutation was 2.588 times as high as that in healthy neonates carrying wild-type UGT1A1 gene (P<0.05). Hardy-Weinberg equilibrium testing showed that the UGT1A1 G71R locus was in genetic equilibrium in both groups (P>0.05). UGT1A1 G71R mutation is a high-frequency gene mutation type in Dong neonates in Sanjiang County, and G71R missense mutation is associated with hyperbilirubinemia in Dong neonates.

Polymorphisms of genes associated with psycho-emotional deviations in a sample of healthy male conscripts

The prevalence of candidate gene polymorphic alleles associated with personality disorders was studied in a sample of healthy male Military Innovation Technopolis ERA recruits, science mouth operators of Caucasian race aged 2327 (median age 24). Genotyping of 10 studied polymorphic variants of genes was carried out using polymerase chain reaction in real time. According to the results, the distribution of genotypes in the studied group of single nucleotide polymorphisms corresponded to HardyWeinberg equilibrium, except for the C677T MTHFR variant (rs1801133). The occurrence of minor alleles was as follows: 0.500 for A1438G and 0.310 for C102T (HTRA2); 0.175 for G-6A (CNTF); 0.508 for C T (UCP2); 0.270 for A1298C and 0.325C677T (MTHFR); 0.278A2756G (MTR); 0.571A66G (MTRR); 0.381Alu Ins/Del (ACE); 0.294G1444A (PPARGC1A). In the studied sample, the frequency of occurrence of minor alleles of 10 genetic markers correlated with data collected on people of European descent. The greatest statistical deviation was observed by comparison with data on people of African descent. Statistically significant concordances with different populations and studies conducted in them are the basis for including the selected polymorphisms in a candidate list of psycho-emotional and neurological pathologies influencing the occupational fitness of servicepersons. However, reliable data on the association between mental disorders and the development of degenerative disorders are not available simultaneously in all populations; therefore, additional research is required on this subject.

The potential status of A1 and A2 variants of bovine beta-casein locus of some indigenous genetic resources reared in Turkey

The aim of this study was to determine the Beta-Casein gene (CSN2) polymorphism in four domestic cattle breed. The genomic DNA of 374 animals, including Anatolian Black (AB, n= 100), Eastern Anatolian Red (EAR, n= 100), Southern Anatolian Red (SAR, n= 87), Turkish Grey (TG, n= 87), were obtained, and C&gt;A polymorphism in 67th amino acid in the 7th exons of β-casein gene was determined by TaqI enzyme with PCR-RFLP with method. The A1 allele frequency were determined in AB, EAR, SAR and TG as 0.200, 0.195, 0.190 and 0.201, respectively, while the A2 allele frequency were 0.800, 0.805, 0.810 and 0.799, respectively. A1 and A2 allele frequencies were generally calculated as 0.200 and 0.800, respectively. A1A1 genotypes in AB, EAR, SAR and TG breeds were 0.020, 0.070, 0.000 and 0.020, respectively; A1A2 genotypes were 0.360, 0.250, 0.380 and 0.360, respectively; A2A2 genotypes were determined as 0.620, 0.680, 0.620 and 0.620, respectively. The A1A1 genotype frequency has not been detected in the SAR breed. AB, EAR, SAR and TG cattle breeds were calculated as 0.360, 0.250, 0.379 and 0.356 for Ho; 0.320, 0.314, 0.307 and 0.321 for He and 0.380, 0.320, 0.379 and 0.379 for PIC, respectively. EAR and SAR population were not found in Hardy-Weinberg equilibrium (P&lt;0.05). However, AB and TG populations were found in Hardy-Weinberg equilibrium in terms of β-casein gene (P&gt; 0.05).In conclusion, AB, EAR, SAR and TG cattle breeds having A2A2 genotype commonly reared in Turkey are satisfactory and could be used in selection programs as a domestic genetic resource for A2 milk production in the future.

Construction and characterization of microsatellite markers for the Neptune whelk, Neptunea cumingii

The Neptune whelk, Neptunea cumingii, is an economic gastropod endemic to the East Asia Warm Temperate Biotic Subregion. The study of the development in microsatellite markers maybe beneficial for assessing the genetic diversity and conservation of resources on this dwindling species. The microsatellite markers were constructed and characterized through Illumina high-throughput sequencing and capillary electrophoresis techniques. Eleven polymorphic microsatellite loci were screened and validated. The observed heterozygosity and expected heterozygosity of each locus showed a range from 0.0600 to 0.6508 and from 0.7380 to 0.9375, respectively. The average Shannon's information index and polymorphism information content were 2.0828 and 0.8325, respectively. Deviation from all loci was generated from Hardy-Weinberg equilibrium. The 11 microsatellite markers developed in this study show polymorphic status. These markers are expected to be highly informative for further analysis of genetic diversity in N. cumingii.

Allelic frequencies distribution and forensic parameters of 23 autosomal short tandem repeats in the population of the State of Pernambuco, Brazil

Located in the Northeast Region, the Pernambuco State is one of the 27 federative units of Brazil. Here, we determined populational data for 23 short tandem repeat (STR) markers – CSF1PO, FGA, TH01, TPOX, vWA, D1S1656, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D22S1045, PENTA D, PENTA E and SE33 — of the Pernambuco population. The sample consisted of 767 healthy, adult, unrelated individuals (437 males, 330 females) born and resident in the State of Pernambuco. STRs were amplified using three multiplex kits, according to the availability: PowerPlex® Fusion 6C System (Promega Corporation), PowerPlex® Fusion System (Promega Corporation) and GlobalFiler™ Express (Thermo Fisher Scientific). Allelic frequencies, forensic parameters and Hardy-Weinberg equilibrium determinations were estimated for all the 23 loci. No deviations from the Hardy-Weinberg equilibrium were observed for any of the markers, after Bonferroni correction. We observed that the most and less informative markers were SE33 and TPOX, respectively. The combined power of discrimination (CPD) was 0.99999999999999999999999999999, and the combined power of exclusion (CPE) was 0.99999999997. The cumulative typical paternity index was 37,919,301,869.3021. Interpopulation analyses (Nei’s genetic distance) based on the expanded CODIS core loci was performed between the Pernambuco sample and other global populations. Pernambuco was the closest Brazilian population to African group and stayed distant from the Native American group. This work contributed to show that a panel of 23 autosomal STR loci is very informative, being able for forensic applications related in this population.

Allele Frequencies and Forensic Statistical Parameters for 21 Autosomal Short Tandem Repeats (STRs) loci in Northern Thai Population

Background: Although the genetic information of STRs has been established over the entire world, the differentcharacteristics between populations influenced the STRs information. FBI’s guideline recommended to expandadditional number of STRs loci to increase power of discrimination and exclusion. Unfortunately, the currentdata of STRs in northern Thai population have not fully covered additional loci. The aim of this study is to obtainaccurate allele frequencies of STRs among northern Thai population.Methods: The genetic profiles ofunrelated individuals were characterized by Investigator 24 plex Go kit. Allelefrequencies and forensic statistical parameters were calculated within GenoProof®3and Arlequin ver 3.5.2.2.Results: The SE33 and TH01 loci represented largest and lowest number of different alleles, respectively. Therewas no significant deviation from the Hardy–Weinberg equilibrium (HWE) after Bonferroni correction in all loci(p=0.002). The SE33 locus showed the greatest PD and PE, whereas the TPOX represented the lowest PD and PE.The studied population (northern Thai) appear to be most closely related to previously reported populationscontaining of Chinese, Japanese, and Vietnamese based on allele frequency.Conclusion: Our results recommended that current autosomal STRs data extended the application of STRs typingin parentage analyses and human identification among the localized population in northern region of Thailanddue to highly informative polymorphic data.

Identifikasi Keragaman SNP Gen MSTN Pada Sapi Limousin

Abstract Limousin cattle (Bos Taurus) are beef cattle that have a large, long, body shape, with have advantages of fast body growth, high fertility and easy reproducibility. Myostatin gene is a family of TGF-β which plays a role in muscle growth and meat quality. This study aims to identify diversity of the Single Nucleotide Polymorphism (SNPs) Myostatine gene in the coding region in limousine cattle. Blood samples were taken from 15 limousine cattle from BPTU-HPT Padang Mangatas, West Sumatra Province. SNPs identification is finish by amplifying the coding region using the sequencing method. This study revealed 12 SNPs spread over 2 SNPs in exon 1 (c.400 G&gt;A, c.415 C&gt;A), 8 SNPs in exon 2 (c.2411 C&gt;T, c.2477 G&gt;A, c. .2489 G&gt;A, c.2503 G&gt;A, c.2521 G&gt;A, c.2577 C&gt;T, c.2609 G&gt;A, c.2636 G&gt;A), and in exon 3 find 2 SNPs (c .5107 C&gt;A, c.5113 T&gt;C) are polymorphic with allele frequencies in general being in Hardy-Weinberg equilibrium except for SNP c.2411 C&gt;T which is not in balance. SNPs identified in the MSTN gene of limousine cattle are expected can fungtion as candidate genetic markers, especially for the perfection of beef cattle in Indonesia. Key words: Limousin Cattle, MSTN, SNP

Association of IL-4 and IL-10 Polymorphisms With Preterm Birth Susceptibility: A Systematic Review and Meta-Analysis.

ObjectivePreterm birth (PTB) is a typical inflammatory disease with unclear pathogenesis. The studies investigating the relationship between anti-inflammatory factors IL-4 and IL-10 gene polymorphisms and PTB produced conflicting results. This systematic review and meta-analysis aimed to summarize the effects of IL-4 and IL-10 gene polymorphisms and clarify their possible association with PTB.MethodsA systematic literature review was conducted using PubMed, Web of Science, and Cochrane library (up to 02 April 2022). The MeSH terms, related entry terms, and other names in “Gene” database were used to find relevant articles. A fixed- or random-effects model was used to calculate the significance of IL-4 and IL-10 gene polymorphisms, depending on study heterogeneity. The odds ratios (OR) and 95% confidence intervals (CIs) were calculated in the allele, recessive, dominant, co-dominant, and over-dominant models. The Eggers publication bias plot was used to graphically represent the publication bias.ResultsPolymorphisms in two interleukins (IL-4-590C/T (rs2243250) = 5 and IL-10-592A/C (rs1800872), -819T/C (rs1800871) and -1082A/G (rs1800896) = 16) were found in 21 articles. Overall, only the over-dominant gene model AA + GG vs. AG revealed significant association between IL-10-1082A/G (rs1800896) and PTB (OR [95% CI] = 0.87 [0.76, 0.99], p = 0.04). However, in the allele model, recessive model, dominant model, co-dominant model, and over-dominant model, the polymorphisms for IL-4-590C/T (rs2243250), IL-10-592A/C (rs1800872), and IL-10-819T/C (rs1800871) were not found to be associated with the risk of PTB. In gene models, no statistically significant association was found between IL-4-590C/T (rs2243250), IL-10-592A/C (rs1800872), IL-10-819T/C (rs1800871), and IL-10-1082A/G (rs1800896) polymorphisms and PTB in subgroup analyses by racial or control group Hardy-Weinberg Equilibrium (HWE) p-value. Eggers’s publication bias plot and heterogeneity test (I2<50%, p = 0.05) of IL-10-1082A/G (rs1800896) suggested that the funnel asymmetry could be due to publication bias rather than heterogeneity.ConclusionThe current study suggests that the over-dominant gene model AA + GG vs. AG of IL-10-1082A/G (rs1800896) polymorphism may be associated with genetic susceptibility to PTB and may have a protective function against PTB risk. There was unclear association found between IL-4-590C/T (rs2243250), IL-10-592A/C (rs1800872) and IL-10-819T/C (rs1800871) polymorphisms and PTB. Due to the limitations of included studies and the risk of publication bias, additional research is required to confirm our findings.Systematic Review Registration https://inplasy.com/inplasy-2022-4-0044, identifier INPLASY202240044.

Investigation of TLR2 -EcoRV, NOD2- BsaHI ve IFNγ- HphI allele frequency distribution among Turkish Native Cattle Breeds

Changing climatic conditions and growing population size lead take precautions against potential risks. Researchers who study in the agricultural field, including animal production, focus on finding out variants and breeds resistant to diseases and environmental stress. Detecting gene regions that affect resistance to diseases and environmental stress might increase the performance of the selection in favor of these traits. Due to these reasons in this study, five Turkish native cattle breeds were investigated for SNPs belonging to TLR2, NOD2, and IFNγ (using EcoRV, BsaHI ve HphI enzymes, respectively) reported to be associated with paratuberculosis previously. In total, 169 animals were analyzed from Native Southern Yellow (NSY= 29), East Anatolian Red (EAR=35), Anatolian Grey (AG=36), South Anatolian Red (SAR=34), and Native Black (NB=35). The genotype and allele frequencies were calculated with the PopGene32 program, and Khi square test was performed to determine whether the populations were in Hardy-Weinberg equilibrium (HWE). While at TLR2- EcoRV and NOD2- BsaHI loci, two alleles (A and C, C and T, respectively), IFNγ- HphI locus was found to be monomorphic for the G allele. For TLR2- EcoRV locus, the C allele was found as predominant except NB breed, and the C allele was predominant for all breeds at NOD2- BsaHI locus. However, in all breeds, NOD2- BsaHI locus was at HWE, for TLR2- EcoRV NSY and SAR breeds showed derivation from HWE.

The genotypic profile of milk proteins in Holstein cows raised in South of Brazil

Genotyping in dairy cattle allows knowing the alleles and genotypes associated with milk proteins that affect yield and milk quality. This study aimed to verify the genotype profile for κ-casein I and II (κ-CN), α-s1-casein (α-CN) and β-lactoglobulin (β-LG), for Holstein cows raised in southern Brazil, where there is no scientific evidence on the presence of these alleles in dairy herds. Hair follicles samples from each animal were used for DNA extraction and genotyping. We calculated the allelic and genotypic frequencies for four types of milk protein variants in the population, and a chi-square test was employed to see whether the population of animals used was in Hardy-Weinberg equilibrium. Allele A and AA genotype showed the highest frequency for both κ-CN (56.77 to 80.36%). For α-s1-CN and β-LG, the B allele was the most frequent, as BB (80.26%) and AB (47.15%), respectively. Due to the presence of alleles associated with protein levels in milk, we concluded that these herd cows present milk technological properties interesting to produce dairy products.

Association of the 5HTR2C gene Ser23 variation with childhood allergic asthma

Abstract Objective: Allergic asthma is the most frequently observed subtype of individuals with asthma. The effects of serotonin plays in the pathophysiology of asthma has not been clearly determined. Thus, this study aimed to investigate the association between the 5HTR2C gene rs 6318 G&gt;C polymorphism and allergic asthma in pediatric patients in Cyprus. Methods: This study included total number of 177 individuals with 118 control and 59 pediatric patients (43 atopic and 16 non-atopic asthma patient). A skin prick test was performed for each patient to confirm asthma diagnosis and to evaluate atopic status. Genotyping for the 5HTR2C was completed by Real Time-PCR analysis. Results: The genotype distribution frequencies were not in agreement with the Hardy-Weinberg Equilibrium in the patients’ group (p&lt;0.00001). The frequency of the risk allele (allele C) was not significantly different between the patient and control groups (p=0.255). The genotypic distribution between atopic asthma and non-atopic asthma within the patientsts groups was not in agreement with the Hardy-Weinberg Equilibrium (p=0.006). However, risk allele presence showed a statistically significant association with atopy-related asthma (p=0.037). Discussion &amp; Conclusion: Overall, despite the finding of no association between the 5HTR2C rs6318 C allele and childhood asthma, the current results indicated that there is a strong association between the 5HTR2C rs6318 C variant and childhood atopic asthma.

Association Between TAB2 Gene Polymorphisms and Susceptibility to Cryptorchidism in Han Chinese Population in Southwest China

To conduct preliminary investigation into the correlation between transforming growth factor beta-activated protein kinase 1-binding protein 2 ( TAB2) gene and the incidence of cryptorchidism in Han Chinese population in Southwest China. A total of 259 patients with cryptorchidism and 355 healthy controls from Southwest China were enrolled for the study. Polymerase chain reaction-restriction fragment length polymorphism method was used to analyze the genotype of the 3 tag single nucleotide polymorphisms (SNPs) of TAB2 gene, i.e., rs237028, rs521845 and rs652921. The Chi-square test was used to analyze the relationship between the genotype frequency of the three tag SNPs and the incidence of cryptorchidism. The distribution of the 3 tag SNPs' alleles and genotypes were in agreement with the Hardy-Weinberg equilibrium, and the genotype results of polymerase chain reaction-restriction fragment length polymorphism assay were consistent with those of Sanger sequencing. The frequency of the G allele at TAB 2 rs237028 was significantly higher in the cryptorchidism group than that in the control group (30.9% vs. 25.6%, P=0.04, OR=1.31, 95% CI: 1.01-1.70). In the dominant model, the risk of cryptorchidism was significantly higher in AG/GG genotype carriers ( P=0.006, OR=1.57, 95% CI: 1.14-2.17). In the cryptorchidism group, the TC/CC genotype frequency of the rs652921 locus were significantly higher than that of the control group (75.3% vs. 67.0%, P=0.03, OR=1.50, 95% CI: 1.05-2.14). Correlation between rs521845 and susceptibility to cryptorchidism was not observed in the Han Chinese population. The AG/GG genotype of rs237028 locus and the TC/CC genotype of rs652921 locus of the TAB2 gene may be associated with increased risks of cryptorchidism in Han Chinese population in southwest China.