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Nutrients Aug 2023Chronic pain is a prevalent and debilitating condition with significant impacts on individuals and society. While the role of diet in chronic pain is well-known, the...
Chronic pain is a prevalent and debilitating condition with significant impacts on individuals and society. While the role of diet in chronic pain is well-known, the relationship between special dietary choices and chronic pain remains unclear. This study investigates the causal associations between 20 dietary habits and chronic pain using a Mendelian randomization (MR) approach. Publicly available genome-wide association study data from the UK Biobank dataset were utilized for secondary analysis, and genetic instrumental variables strongly correlated with 20 different dietary habits were selected. Multisite chronic pain (MCP) scores were used as the primary outcome, with site-specific chronic pain (SSCP) including back pain, headache, knee pain, neck pain, and hip pain as secondary outcomes. The inverse-variance-weighted (IVW) method was the primary method used in the MR. The weighted median (WM) and Mendelian randomization pleiotropy residual sum and outlier test (MR-PRESSO) methods were used as sensitivity analyses. This study identified causal associations between specific dietary habits and chronic pain. A high intake of cheese, cereal, dried fruits, and fresh fruits was associated with lower MCP scores. Conversely, high alcohol, salt, pork, and poultry intakes were associated with higher MCP scores. Similar associations between special dietary habits and some types of SSCP, such as back and neck pain, were also observed. The findings were consistent across different statistical methods, and sensitivity analyses confirmed the reliability of the results. In conclusion, our study provides evidence of a causal relationship between various dietary habits and different types of chronic pain based on secondary analysis of the UK Biobank dataset. Adhering to an anti-inflammatory diet, including increased consumption of fruits and cereal while reducing salt and pork intake, may potentially alleviate chronic pain symptoms.
Topics: Humans; Chronic Pain; Neck Pain; Genome-Wide Association Study; Mendelian Randomization Analysis; Reproducibility of Results; Edible Grain
PubMed: 37686741
DOI: 10.3390/nu15173709 -
Molecular Biology Reports Apr 2021PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This... (Review)
Review
PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This paper will discuss the experimental details, limitations and sensitivity of the PCR Single-Strand Conformation Polymorphism method in relation to all existing literature available to us until today. Genomic DNA extraction, PCR amplification and Single-Strand Conformation Polymorphism conditions (concentration of polyacrylamide slab gel electrophoresis, dissociation treatment of double- stranded DNA) and comparison with PCR Restriction Fragment Length Polymorphism are presented. Since its discovery in 1989, there have been many variations, innovations, and modifications of the method, which makes it very easy, safe, fast and for this reason widely applied in clinical diagnostic, forensic medicine, biochemical, veterinary, microbiological, food and environmental laboratories. One of the possible applications of the method is the diagnosis and identification of mutations in new strains of coronaviruses, because science needs more tools to tackle the problem of this pandemic. The PCR Single-Strand Conformation Polymorphism method can be applied in many cases provided that control samples are available and the required conditions of the method are achieved.
Topics: Animals; Coronavirus; Humans; Molecular Typing; Pathology, Molecular; Polymerase Chain Reaction; Polymorphism, Restriction Fragment Length; Polymorphism, Single-Stranded Conformational; Sequence Analysis
PubMed: 33893925
DOI: 10.1007/s11033-021-06349-2 -
African Health Sciences Dec 2022Increasing trend of breast cancer incidence worldwide is a known fact. This curable disease may become fatal if drug resistance is developed leading to metastatic... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Increasing trend of breast cancer incidence worldwide is a known fact. This curable disease may become fatal if drug resistance is developed leading to metastatic cancerous tissue.
OBJECTIVE
This is a two parts study; a meta-analysis exploring association of drug resistance (mdr1 and ABCG2) genes with breast cancer and mutational association with molecular subtypes of cancer. Methods: PCR-SSCP for genomic polymorphisms and RT-PCR for expression analysis were performed.
RESULTS
C3435T polymorphism of mdr1 gene was most commonly studied mutation with contradictory results. Association of ABCG2 gene mutations with untreated breast cancer was reported only by one study so far. Regarding current genomic analysis of mdr1 gene, three novel mutations were found in exon 12 and 2 mutations were found in exon 26. In ABCG2 gene, addition of C and T were found in intron 8 at the intron-exon junction. A positive correlation was observed between these mutations and tumor grade. Levels of mRNA expression revealed that they were over expressed in cancerous tissues compared with controls.
CONCLUSION
These findings suggest that these genes are associated with breast cancer.
Topics: Humans; Female; ATP Binding Cassette Transporter, Subfamily B; ATP Binding Cassette Transporter, Subfamily B, Member 1; Genes, MDR; Genotype; Breast Neoplasms; Case-Control Studies
PubMed: 37092084
DOI: 10.4314/ahs.v22i4.2 -
Frontiers in Microbiology 2021Dictyostelid social amoebae are a highly diverse group of eukaryotic soil microbes that are valuable resources for biological research. Genetic diversity study of these...
Dictyostelid social amoebae are a highly diverse group of eukaryotic soil microbes that are valuable resources for biological research. Genetic diversity study of these organisms solely relies on molecular phylogenetics of the gene, which is not ideal for large-scale genetic diversity study. Here, we designed a set of PCR-single-strand conformation polymorphism (SSCP) primers and optimized the SSCP fingerprint method for the screening of dictyostelids. The optimized SSCP condition required gel purification of the SSCP amplicons followed by electrophoresis using a 9% polyacrylamide gel under 4°C. We also tested the optimized SSCP procedure with 73 Thai isolates of dictyostelid that had the gene sequences published. The SSCP fingerprint patterns were related to the genus-level taxonomy of dictyostelids, but the fingerprint dendrogram did not reflect the deep phylogeny. This method is rapid, cost-effective, and suitable for large-scale sample screening as compared with the phylogenetic analysis of the gene sequences.
PubMed: 34512585
DOI: 10.3389/fmicb.2021.708685 -
Genes Oct 2022Endothelial PAS domain protein 1 gene () is a member of the HIF gene family. This gene encodes a transcription factor subunit that is involved in the induction of...
Endothelial PAS domain protein 1 gene () is a member of the HIF gene family. This gene encodes a transcription factor subunit that is involved in the induction of oxygen-regulated genes. Several studies have demonstrated that a mutation in could affect oxygen sensing, polycythemia, and hemoglobin level. However, whether mutation affects sheep oxygen metabolism is still unknown. Therefore, we explored the relationship between the variation of and oxygen metabolism in sheep. In this study, variations in ovine exon 15 were investigated in 332 Tibetan sheep and 339 Hu sheep by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. In addition, we studied the effect of these variations on blood gas in 176 Tibetan sheep and 231 Hu sheep. Finally, the mRNA expression of in six tissues of Hu sheep and Tibetan sheep living at different altitudes (2500 m, 3500 m, and 4500 m) was analyzed by real-time quantitative PCR (RT-qPCR). Four alleles (, , , and ) were detected, and their distributions highly differed between Tibetan sheep and Hu sheep. In Tibetan sheep, was the dominant allele, and and alleles were rare, whereas all four alleles were common in Hu sheep. Six single nucleotide polymorphisms (SNPs) were identified between the four alleles and one of them was non-synonymous (p.F606L). While studying the blood gas levels in Tibetan sheep and Hu sheep, one variant region was found to be associated with an elevated O and sO, which suggested that variations in are associated with oxygen metabolism in sheep. RT-qPCR results showed that was expressed in the six tissues of Hu sheep and Tibetan sheep at different altitudes. In addition, the expression of in four tissues (heart, liver, spleen, and longissimus dorsi muscle) of Hu sheep was lower than that in Tibetan sheep from three different altitudes, and the expression of was positively correlated with the altitude. These results indicate that the variations and expression of is closely related to oxygen metabolism.
Topics: Sheep; Animals; Altitude; Alleles; Hemoglobins; Oxygen; RNA, Messenger
PubMed: 36292756
DOI: 10.3390/genes13101871 -
Pathogens (Basel, Switzerland) Oct 2022The ikeda and chitose genotypes of , which for many years were thought to be benign, cause a disease that results in significant economic losses in the cattle industry....
The ikeda and chitose genotypes of , which for many years were thought to be benign, cause a disease that results in significant economic losses in the cattle industry. This study was carried out in order to determine the genotypes of in cattle in Kyrgyzstan, and 149 archived DNA samples known to be were analyzed by the PCR amplification of the major piroplasm surface protein (MPSP) gene region. Single-Strand Conformation Polymorphism (SSCP) analysis was performed to uncover the nucleotide changes in the archived DNA samples, and 15 samples showing different band profiles were subjected to sequence analysis. As a result of the sequence analysis, it was seen that the samples belonged to the buffeli and chitose A genotypes. In order to identify mixed genotypes, PCR was performed using primers specific for these genotypes, and buffeli (type 3), chitose (type 1) and buffeli+chitose were found to be positive in 26.2%, 2% and 71.8% of samples, respectively. As a result of this study, we showed the presence of buffeli (type 3) and chitose (type 1) genotypes of in cattle in Kyrgyzstan. Comprehensive epidemiological studies are needed to understand the clinical infections caused by the pathogenic chitose A and to determine the geographical distribution and different genotypes of .
PubMed: 36297242
DOI: 10.3390/pathogens11101185 -
Mycorrhiza Nov 2019Like the majority of land plants, liverworts regularly form intimate symbioses with arbuscular mycorrhizal fungi (Glomeromycotina). Recent phylogenetic and physiological...
Like the majority of land plants, liverworts regularly form intimate symbioses with arbuscular mycorrhizal fungi (Glomeromycotina). Recent phylogenetic and physiological studies report that they also form intimate symbioses with Mucoromycotina fungi and that some of these, like those involving Glomeromycotina, represent nutritional mutualisms. To compare these symbioses, we carried out a global analysis of Mucoromycotina fungi in liverworts and other plants using species delimitation, ancestral reconstruction, and network analyses. We found that Mucoromycotina are more common and diverse symbionts of liverworts than previously thought, globally distributed, ancestral, and often co-occur with Glomeromycotina within plants. However, our results also suggest that the associations formed by Mucoromycotina fungi are fundamentally different because, unlike Glomeromycotina, they may have evolved multiple times and their symbiotic networks are un-nested (i.e., not forming nested subsets of species). We infer that the global Mucoromycotina symbiosis is evolutionarily and ecologically distinctive.
Topics: Fungi; Glomeromycota; Hepatophyta; Mycorrhizae; Phylogeny; Symbiosis
PubMed: 31720838
DOI: 10.1007/s00572-019-00918-x -
Animals : An Open Access Journal From... Sep 2020Genes of the major histocompatibility complex (MHC) code for cell surface proteins essential for adaptive immunity. They show the most outstanding genetic diversity in...
Genes of the major histocompatibility complex (MHC) code for cell surface proteins essential for adaptive immunity. They show the most outstanding genetic diversity in vertebrates, which has been connected with various fitness traits and thus with the long-term persistence of populations. In this study, polymorphism of the MHC class II locus was investigated in chamois with Single-Strand Conformation Polymorphism (SSCP)/Sanger genotyping and Ion Torrent S5 next-generation sequencing (NGS). From eight identified variants in 28 individuals, five had already been described, and three were new, undescribed alleles. With conventional SSCP/Sanger sequencing, we were able to detect seven alleles, all of which were also detected with NGS. We found inconsistencies in the individual genotypes between the two methods, which were mainly caused by allelic dropout in the SSCP/Sanger method. Six out of 28 individuals were falsely classified as homozygous with SSCP/Sanger analysis. Overall, 25% of the individuals were identified as genotyping discrepancies between the two methods. Our results show that NGS technologies are better performing in sequencing highly variable regions such as the MHC, and they also have a higher detection capacity, thus allowing a more accurate description of the genetic composition, which is crucial for evolutionary and population genetic studies.
PubMed: 32962183
DOI: 10.3390/ani10091694 -
Molecular Biology Reports Dec 2023In recent years, strategic plans for poultry production have emphasized quantitative traits, particularly body weight and carcass traits (meat yield), in response to...
In recent years, strategic plans for poultry production have emphasized quantitative traits, particularly body weight and carcass traits (meat yield), in response to overpopulation challenges. Candidate genes such as adenylosuccinate lyase (ADSL), melanocortin-4-receptor (MC4R), and calpain 1 (CAPN1) have played vital roles in this context due to their associations with muscle growth and body composition. This study aims to investigate the influence of polymorphisms and gene expressions of the aforementioned genes on body weight (BW), growth rate (GR), breast weight (BrW), and thigh weight (TW) across four distinct chicken breeds: Fayoumi, Matrouh, Mamourah, and Leghorn. The use of PCR-SSCP analysis revealed genetic polymorphisms through the identification of various patterns (genotypes) within the three examined genes. The ADSL, MC4R, and CAPN1 genes exhibited five, three, and two different genotypes, respectively. These polymorphisms displayed promising connections with enhancing economically significant production traits, particularly BW, BrW and TW. Furthermore, gene expression analyses were conducted on breast and thigh tissues obtained from the chicken breeds at 60 days of age, where ADSL and MC4R exhibited a noteworthy up-regulation in Fayoumi and Matrouh breeds, and down-regulation in Mamourah and Leghorn. In contrast, CAPN1 expression decreased across most breeds with a slight increase noted in Fayoumi breed. In conclusion, this investigation underscores the substantial impact of ADSL, MC4R, and CAPN1 genes on economically important production traits within Egyptian domestic chicken breeds. Consequently, these genes emerge as significant molecular markers, holding potential utility in avian selection and breeding programs aimed at enhancing productive performance.
Topics: Animals; Chickens; Adenylosuccinate Lyase; Egypt; Polymorphism, Single Nucleotide; Genotype; Meat; Body Weight
PubMed: 38071695
DOI: 10.1007/s11033-023-08999-w