Protein Polymorphisms Research Articles

Effect of the Rs2923234 and Rs1049112 Single Nucleotide Polymorphisms of Salivary Acidic Proline-rich Protein on Dental Caries in Young Children: An Analytical Cross-sectional Molecular Study

Introduction: We aimed to use polymerase chain reaction (PCR) on genomic deoxyribonucleic acid (DNA) to detect the Db allele and the rs2923234 and rs1049112 single nucleotide polymorphisms (SNPs) of the salivary acidic proline-rich proteins (PRPs) to determine their relationship with dental caries in young children. Methods: DNA was extracted from saliva samples of preschool children aged 3 to 5 years. PCR primers designed around exon 3 of the PRH1 locus yielded a 416-base product representing Db for gel electrophoresis and a 519-base product representing the rs2923234 and rs1049112 SNPs for Sanger sequencing. The data were analyzed using a logistic regression model and a multilayer perceptron artificial neural network. Results: Forty children with severe caries and 40 caries-free children completed the study. The frequency of the Db gene was 16.3% in the entire study group. The rs2923234 SNP was a marginally significant (P = 0.053) predictor for the dependent variable (caries-free or severe caries). However, the rs1049112 (P = 0.407) and the Db allele (P = 0.442) were not significant predictors. Conclusion: The rs29232334 SNP could be considered a potential genetic predictor for caries susceptibility.

Whole Genome Sequencing and Comparative Genomic Analysis of Chlamydia gallinacea Field Strains Isolated from Poultry in Poland.

Chlamydia gallinacea is an intracellular bacterium belonging to the Chlamydiaceae family. Poultry is considered to be the major reservoir of this agent, which has worldwide distribution and a particularly consistent worldwide occurrence in chicken flocks. The bacterium has been linked to respiratory disease in humans but without definitive confirmation; nevertheless, while it has not been proved to be the cause of human respiratory disease, a recent report from Italy verified its bird-to-human transmission. This aspect being significant for public health, more research is needed to gain insight into the infection biology of C. gallinacea. In this study, the genomes of eleven novel C. gallinacea field strains from different regions of Poland were analyzed comparatively. It was confirmed that C. gallinacea strains are closely related, with at least 99.46% sequence identity. They possess a conservative genome structure involving the plasticity zone with a complete cytotoxin, the type three secretion system, inclusion membrane proteins, polymorphic membrane proteins, hctA and hctB histone-like proteins, and the chlamydial protease-like activating factor exoenzyme, as well as plasmids. Genetic diversity seems to be restricted. However, some genetic loci, such as ompA and multi-locus sequence typing target genes, are diverse enough to enable high-resolution genotyping and epidemiological tracing.

The 84-bp Indel Polymorphism of The Sterol Regulatory Element-Binding Protein 1 (SREBP1) Gene in Several Cattle Breeds in Indonesia

Sterol regulatory element-binding protein 1 (SREBP1) gene is a gene that encodes SREBP1, a family of transcription factors that have a key role in lipid homeostasis as well as fatty acid metabolisms. The present study aimed to detect the 84-bp indel polymorphism in the intron 5 of the SREBP1 gene (84-bp indel) in several cattle breeds in Indonesia. A total of 740 cattle of six breeds (Limousin, Simmental, Holstein-Friesian, Bali, Sumbawa, and Pasundan) from two National Artificial Insemination Centers (NAICs) and smallholder farmers were used in this study. The detection of 84-bp indel polymorphism was performed using the polymerase chain reaction (PCR) method and visualized through a gel agarose electrophoresis system. The study showed that the L allele (insertion-type) was common and is fixed in Holstein-Friesian, Bali, and Sumbawa cattle (1.00). Meanwhile, the S allele (deletion-type) was found in Limousin, Simmental, and Pasundan cattle with a frequency of 0.24, 0.16, and 0.01, respectively. The presence of the S allele in Pasundan cattle was only found in the form of the heterozygous LS genotype (0.03). In conclusion, the 84-bp indel of the SREBP1 gene was found to be polymorphic in Limousin, Simmental, and Pasundan cattle, but monomorphic in Holstein-Friesian, Bali, and Sumbawa cattle.

Antioxidant Genetic Variants Modify Echocardiography Indices in Long COVID.

Although disturbance of redox homeostasis might be responsible for COVID-19 cardiac complications, this molecular mechanism has not been addressed yet. We have proposed modifying the effects of antioxidant proteins polymorphisms (superoxide dismutase 2 (SOD2), glutathione peroxidase 1 (GPX1), glutathione peroxidase 3 (GPX3) and nuclear factor erythroid 2-related factor 2, (Nrf2)) in individual susceptibility towards the development of cardiac manifestations of long COVID-19. The presence of subclinical cardiac dysfunction was assessed via echocardiography and cardiac magnetic resonance imaging in 174 convalescent COVID-19 patients. SOD2, GPX1, GPX3 and Nrf2 polymorphisms were determined via the appropriate PCR methods. No significant association of the investigated polymorphisms with the risk of arrhythmia development was found. However, the carriers of variant GPX1*T, GPX3*C or Nrf2*A alleles were more than twice less prone for dyspnea development in comparison with the carriers of the referent ones. These findings were even more potentiated in the carriers of any two variant alleles of these genes (OR = 0.273, and p = 0.016). The variant GPX alleles were significantly associated with left atrial and right ventricular echocardiographic parameters, specifically LAVI, RFAC and RV-EF (p = 0.025, p = 0.009, and p = 0.007, respectively). Based on the relation between the variant SOD2*T allele and higher levels of LV echocardiographic parameters, EDD, LVMI and GLS, as well as troponin T (p = 0.038), it can be proposed that recovered COVID-19 patients, who are the carriers of this genetic variant, might have subtle left ventricular systolic dysfunction. No significant association between the investigated polymorphisms and cardiac disfunction was observed when cardiac magnetic resonance imaging was performed. Our results on the association between antioxidant genetic variants and long COVID cardiological manifestations highlight the involvement of genetic propensity in both acute and long COVID clinical manifestations.

Host CCR5 and HIV-1 env/pol polymorphisms: Role in transmission and virulence in the Kenyan population


 INTRODUCTION 
 HIV-1 env protein and host cluster of differentiation antigen 4 (CD4) and wild-CC chemokine receptor 5 (CCR5) proteins are responsible for the attachment and entry of HIV-1 into T lymphocytes, hence influencing its infectivity. However, information on the flow, distribution, ARVs resistance patterns and co-infections of the HIV-1 sub-types is limited. An up-to-date comprehensive review on the role of CCR5/CD4 and env/pol protein polymorphisms in the susceptibility to HIV-1 infection, virulence, transmission, disease progression and discordance in the Kenyan population is lacking. This study aimed to review the role of CCR5/CD4 and HIV-1 env/pol protein polymorphisms in the transmission and virulence of HIV-1 in the Kenyan population. 
 METHODOLOGY 
 Data was sourced by literature search on Google Scholar, PubMed, and ScienceDirect. Grey literature articles were manually reviewed. Study selection was based on relevance to the role of CCR5/CD4 and env/pol protein polymorphisms in the transmission and virulence of HIV-1 were included in the review. Data were extracted from individual studies or articles. Data were synthesized regarding the information on the role of CCR5/CD4 and env/pol protein polymorphisms in the transmission and virulence of HIV-1 is synchronized under the headings; introduction, molecular characterization of HIV-1, HIV-1 treatment and antiretrovirals (ARVs) resistance, influence of host genes on HIV-1 disease progression, CD4 as HIV-1 receptors, and characterization of genetic/antigenic variants circulating in a given population. 
 RESULTS 
 A total of 74 articles were screened and 66 eligible articles were reviewed, four (4) of them touching on the origin and evolutionary mechanisms of the human immunodeficiency virus (HIV), while 21 articles addressed molecular characterization of the HIV-1. A total of 11 articles addressed HIV-1 treatment and ARVs resistance whereas 13 articles addressed the influence of host genes on HIV/AIDS disease progression. Eleven (11) and 8 articles addressed the CD4 as HIV-1 receptors and characterization of HIV-1 genetic/antigenic variants circulating in a given population, respectively. 
 CONCLUSION 
 There are many HIV-1 subtypes in circulation in Kenya with uneven distribution and it is difficult to accurately predict future metamorphosis and determine and monitor the flow and ARVs resistance patterns of the sub-types. mutant allele of the β-chemokine receptor gene CCR5 prevents cell invasion and homozygotes for this mutation are resistant to infection with heterozygosity at this gene correlating with slowed HIV/AIDS disease progression. The C868T single nucleotide polymorphism (SNP) in CD4 increases the risk of HIV-1 acquisition. 
 RECOMMENDATIONS 
 There is a need for accurate prediction of the future metamorphosis and regular evaluation and monitoring of the flow, distribution, ARVs resistance patterns and co-infections of the HIV-1 sub-types and their variation over time. Detailed assessment of the role of CCR5/CD4 and env/pol protein polymorphisms in the susceptibility to HIV-1 infection, virulence, disease progression and discordance in some couples in the Kenyan population is important.

Automated Analysis of PD1 and PDL1 Expression in Lymph Nodes and the Microenvironment of Transmissible Tumors in Tasmanian Devils

ABSTRACT The wild Tasmanian devil (Sarcophilus harrisii) population has suffered a devastating decline due to two clonal transmissible cancers. The first devil facial tumor 1 (DFT1) was observed in 1996, followed by a second genetically distinct transmissible tumor, the devil facial tumor 2 (DFT2), in 2014. DFT1/2 frequently metastasize, with lymph nodes being common metastatic sites. MHC-I downregulation by DFT1 cells is a primary means of evading allograft immunity aimed at polymorphic MHC-I proteins. DFT2 cells constitutively express MHC-I, and MHC-I is upregulated on DFT1/2 cells by interferon gamma, suggesting other immune evasion mechanisms may contribute to overcoming allograft and anti-tumor immunity. Human clinical trials have demonstrated PD1/PDL1 blockade effectively treats patients showing increased expression of PD1 in tumor draining lymph nodes, and PDL1 on peritumoral immune cells and tumor cells. The effects of DFT1/2 on systemic immunity remain largely uncharacterized. This study applied the open-access software QuPath to develop a semiautomated pipeline for whole slide analysis of stained tissue sections to quantify PD1/PDL1 expression in devil lymph nodes. The QuPath protocol provided strong correlations to manual counting. PD-1 expression was approximately 10-fold higher than PD-L1 expression in lymph nodes and was primarily expressed in germinal centers, whereas PD-L1 expression was more widely distributed throughout the lymph nodes. The density of PD1 positive cells was increased in lymph nodes containing DFT2 metastases, compared to DFT1. This suggests PD1/PDL1 exploitation may contribute to the poorly immunogenic nature of transmissible tumors in some devils and could be targeted in therapeutic or prophylactic treatments. Abbreviations: PD1: programmed cell death protein 1; PDL1: programmed death ligand 1; DFT1: devil facial tumor 1; DFT2: devil facial tumor 2; DFTD: devil facial tumor disease; MCC: Matthew’s correlation coefficient; DAB: diaminobenzidine; ROI: region of interest

Structural and genomic analysis of single nucleotide polymorphisms in human host factor endothelial protein C receptor (EPCR) reveals complex interplay with malaria parasites.

Plasmodium parasites responsible for malaria follow a complex life cycle of which half takes place inside the human host. Parasites present diverse antigens at different stages of their life cycle and interact with many surface molecules to attach to and enter host cells. The CIDRα1 domain of Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) in infected erythrocytes adheres to one such vascular receptor endothelial protein C receptor (EPCR). EPCR is implicated in the pathogenesis of severe malaria as preferential binding of CIDRα1 to endothelium results in widespread sequestration of infected erythrocytes leading to endothelium inflammation and severe disease. A single EPCR variant S219G is clinically reported to provide protection from severe malaria. In this work, we have collated all single nucleotide polymorphisms (SNPs) in EPCR from dbSNP. We structurally mapped the SNPs on the three-dimensional complex of EPCR and PfEMP1 CIDRα1. Analysis shows that most EPCR mutations lie on the receptor surface and are non-conservative. Of the 11 mutations in the CIDRα1-interaction region of EPCR, S88P, L96V/I, and R98L/H/P/C are seen with comparably higher occurrences in diverse populations. Our structural analysis details a framework of the interactions between the parasite ligand and host factor EPCR. These structural glimpses provide a blueprint for designing both field-based variant sequencing studies and vaccine development.

Genomic analysis of 61 Chlamydia psittaci strains reveals extensive divergence associated with host preference

BackgroundChlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains, 47 of which carrying a 7.6-kbp plasmid.ResultsFollowing clean-up, reassembly and polishing of poorly assembled genomes from public databases, phylogenetic analyses using C. psittaci whole-genome sequence alignment revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Strains from different non-psittacine hosts clustered in Clades 2– 4. We found that clade membership correlates with typing schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin MOMP can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps).ConclusionsOur study identified a number of genomic features that can be correlated with the phylogeny and host preference of C. psittaci strains. Our data show that intra-species genomic divergence is associated with past host change and includes deletions in the plasticity zone, structural variations in immunogenic domains and distinct repertoires of virulence factors.

Proteogenomic Features of the Highly Polymorphic Histidine-rich Glycoprotein Arose Late in Evolution

Histidine-rich glycoprotein (HRG) is a liver-produced protein circulating in human serum at high concentrations of around 125 μg/ml. HRG belongs to the family of type-3 cystatins and has been implicated in a plethora of biological processes, albeit that its precise function is still not well understood. Human HRG is a highly polymorphic protein, with at least five variants with minor allele frequencies of more than 10%, variable in populations from different parts of the world. Considering these five mutations we can theoretically expect 35 = 243 possible genetic HRG variants in the population. Here, we purified HRG from serum of 44 individual donors and investigated by proteomics the occurrence of different allotypes, each being either homozygote or heterozygote for each of the five mutation sites. We observed that some mutational combinations in HRG were highly favored, while others were apparently missing, although they ought to be present based on the independent assembly of these five mutation sites. To further explore this behavior, we extracted data from the 1000 genome project (n ∼ 2500 genomes) and assessed the frequency of different HRG mutants in this larger dataset, observing a prevailing agreement with our proteomics data. From all the proteogenomic data we conclude that the five different mutation sites in HRG are not occurring independently, but several mutations at different sites are fully mutually exclusive, whereas others are highly intwined. Specific mutations do also affect HRG glycosylation. As the levels of HRG have been suggested as a protein biomarker in a variety of biological processes (e.g., aging, COVID-19 severity, severity of bacterial infections), we here conclude that the highly polymorphic nature of the protein needs to be considered in such proteomics evaluations, as these mutations may affect HRG’s abundance, structure, posttranslational modifications, and function.

Relationship between Milk Protein Polymorphism and Selected Cows' Reproductive Indices.

This research sought to determine the effect of selected milk protein polymorphisms on the reproduction parameters of 598 black and white Polish Holstein-Friesian cattle. The analyzed genes were kappa-casein (CSN3) and beta-lactoglobulin (BLG). The following reproductive indexes were selected: the age at first calving, the interpregnancy period, the calving interval, and the insemination index. The influence of the identified genotypes on the course of parturition in cows was also analyzed. Source data were collected for each cow from the beginning of the herd life and reproduction to its culling from the herd or the end of its third lactation. Data on the age at first calving, the amount of semen portions for artificial insemination (insemination index), the interpregnancy period, and the calving interval for each cow were also collected. A contingency analysis was performed through contingency tables using a Pearson's chi-squared test for each CSN3 and BLG genotype. The results show that the BB genotype of the kappa-casein gene was associated with the most favorable values of reproductive indicators. In the case of the calving interval, the values were significantly more favorable than those of other genotypes (p ≤ 0.05). No effect of beta-lactoglobulin polymorphism on the analyzed reproductive indices was observed. On the other hand, in the case of the interpregnancy period, significant statistical differences were obtained between the AA and BB genotypes. The analyzed kappa-casein and beta-lactoglobulin genotypes did not significantly influence the course of parturition in cows. To conclude, the genotype polymorphism BB CSN3 is the most favorable for the performance of the cows in the examined herd.

MDR3 rs2109505 and rs1202283 polymorphisms are associated with susceptibility to intrahepatic cholestasis of pregnancy: A meta-analysis.

Many studies have assessed the relationship between gene polymorphisms in multidrug resistance protein 3 (MDR3) and the risk of intrahepatic cholestasis of pregnancy (ICP); however, there are many conflicting narratives. This meta-analysis was conducted to assess the association between MDR3 gene polymorphisms and ICP. A multi-database search was conducted using Web of Science, Embase, PubMed, and Chinese Biomedical Literature (CBM) databases. Eleven eligible studies focusing on 4 single nucleotide polymorphisms (SNPs) in the MDR3 gene were selected for analysis. A fixedor random-effects model was utilized for allelic, dominant, recessive, and superdominant genes. The pooled results indicated a statistically significant association between MDR3 polymorphism rs2109505 and an increased risk of ICP in both the general population and the Caucasian population. No statistically significant associations were found between MDR3 polymorphism rs2109505 and ICP in Italian or Asian populations for the 4 genetic models. The MDR3 polymorphism rs1202283 was associated with susceptibility to ICP in both the general and Italian populations. The MDR3 rs2109505 and rs1202283 polymorphisms are associated with ICP susceptibility: however, they displayed no correlation with an increased risk of ICP.

Thiophene-Based Ligands: Design, Synthesis and Their Utilization for Optical Assignment of Polymorphic-Disease-Associated Protein Aggregates.

The development of ligands for detecting protein aggregates is of great interest, as these aggregated proteinaceous species are the pathological hallmarks of several devastating diseases, including Alzheimer's disease. In this regard, thiophene-based ligands have emerged as powerful tools for fluorescent assessment of these pathological entities. The intrinsic conformationally sensitive photophysical properties of poly- and oligothiophenes have allowed optical assignment of disease-associated protein aggregates in tissue sections, as well as real-time in vivo imaging of protein deposits. Herein, we recount the chemical evolution of different generations of thiophene-based ligands, and exemplify their use for the optical distinction of polymorphic protein aggregates. Furthermore, the chemical determinants for achieving a superior fluorescent thiophene-based ligand, as well as the next generation of thiophene-based ligands targeting distinct aggregated species are described. Finally, the directions for future research into the chemical design of thiophene-based ligands that can aid in resolving the scientific challenges around protein aggregation diseases are discussed.

Polymorphic nanobody crystals as long-acting intravitreal therapy for wet age-related macular degeneration.

Wet age-related macular degeneration (wet AMD) is the most common cause of blindness, and chronic intravitreal injection of anti-vascular endothelial growth factor (VEGF) proteins has been the dominant therapeutic approach. Less intravitreal injection and a prolonged inter-injection interval are the main drivers behind new wet AMD drug innovations. By rationally engineering the surface residues of a model anti-VEGF nanobody, we obtained a series of anti-VEGF nanobodies with identical protein structures and VEGF binding affinities, while drastically different crystallization propensities and crystal lattice structures. Among these nanobody crystals, the P212121 lattice appeared to be denser and released protein slower than the P1 lattice, while nanobody crystals embedding zinc coordination further slowed the protein release rate. The polymorphic protein crystals could be a potentially breakthrough strategy for chronic intravitreal administration of anti-VEGF proteins.

Endo-lysosomal assembly variations among Human Leukocyte Antigen class I (HLA-I) allotypes

Abstract The extreme polymorphisms of HLA-I proteins enable the presentation of diverse peptides to cytotoxic T lymphocytes (CTL). The canonical endoplasmic reticulum (ER) HLA-I assembly pathway enables presentation of cytosolic peptides, but effective intracellular surveillance requires multi-compartmental antigen sampling. Endo-lysosomes are generally sites of HLA class II assembly, but human monocytes and monocyte-derived dendritic cells (moDCs) also contain significant reserves of endo-lysosomal HLA-I molecules. We hypothesized variable influences of HLA-I polymorphisms upon outcomes of endo-lysosomal trafficking, as the stabilities and peptide occupancies of cell surface HLA-I are variable. Consistent with this model, when the endo-lysosomal pH of moDCs is disrupted, HLA-B allotypes display varying propensities for reductions in surface expression, with HLA-B* 08:01 or HLA-B*35:01 being among the most resistant or sensitive respectively, among eight tested HLA-B allotypes. Perturbations of moDC endo-lysosomal pH result in redistribution of HLA-B*35:01, but not HLA-B* 08:01, to LAMP1 +compartments and increase HLA-B*35:01 peptide receptivity. These findings reveal the intersection of the vacuolar cross-presentation pathway with a constitutive assembly pathway for some HLA-B allotypes. Notably, cross-presentation of epitopes derived from two soluble antigens was also more efficient for B*35:01 compared to B*08:01, even when matched for T cell response sensitivity, and more affected by cathepsin inhibition. Thus, HLA-I polymorphisms dictate the degree of endo-lysosomal assembly, which can supplement ER assembly for constitutive HLA-I expression and increase the efficiency of cross-presentation. Supported by grants NIH R01 AI044115 T32GM008353 and T32AI007413

Iron-overload affects anti-tumor immune response in pancreatic cancer.

Abstract HFE is the most frequently mutated gene in hereditary hemochromatosis, a disease in which iron accumulates in organs leading to toxicities. Worldwide, two main polymorphisms in HFE protein have been observed, namely C282Y and H63D. Even if associated to milder iron accumulations, H63D polymorphism increases the risk of cancer development and aggressiveness. As observed in pancreatic cancer patients, a great percentage of those that underwent to surgery also present H63D polymorphism but displayed a worse survival. To better characterize how the iron accumulation affects anti-tumor response in the context of the pancreatic ductal adenocarcinoma (PDA), we crossed genetically engineered mice (GEM) that spontaneously develop PDA with mice engineered to express H67D mutation (HfeH67D), the orthologue of H63D in human. Histological analysis of GEM showed that H67D polymorphism accelerated PDA progression, increased the number of metastases, and altered the composition of infiltrating immune cells. Accordingly, these mouse models also displayed a reduced overall survival compared to controls. By exploiting OVA as a well-known antigen, we injected OVA-expressing PDA cells subcutaneously in mice carrying or not the H67D mutation to assess their ability to mount a normal memory response. OVA-expressing PDA cells grew faster in the presence of H67D polymorphism, but immunized mice displayed a reduction in tumor volume similar to the WT counterpart. HfeH67Dmice displayed an increased production of anti-OVA IgG antibodies, especially IgE, but a decreased in OVA-specific IFNγ-secreting T cells. Overall, H67D polymorphism impacts the activation of anti-tumoral immune response, which consequently worsens PDA progression. Supported by grants from AIRC (ID22234; ID26341)

Serum and genetic markers related to rapid clinical progression of coronary artery disease

Introduction and objectivesPatients with clinically evident coronary artery disease differ in their rate of progression, which impacts prognosis. We aimed to characterize serum and genetic markers in patients with rapid clinical progression (RCP) of coronary artery disease vs those with long standing stable (LSS) disease. MethodsRetrospective study of cases (RCP) and controls (LSS) (1:2). Patients requiring ≥ 2 revascularizations due to atherosclerotic progression in the 10 years after a first angioplasty were considered to be RCP and those without events during the same period after the first angioplasty were considered to have LSS disease. After patient selection, we analyzed serum values, mRNA expression and genetic polymorphisms of inflammatory markers, including interleukin-6, C-reactive protein, and tumor necrosis factor (TNF)-a, and atherogenic markers consisted of proprotein convertase subtilisin/kexin type 9 (PCSK9), low-density lipoprotein receptor, sterol regulatory element binding transcription factor 2, and apolipoprotein-B. ResultsThe study included 180 patients (58 RCP and 122 LSS). Demographic characteristics, classic risk factors and the extent of coronary disease were similar in the 2 groups. Patients with RCP showed higher serum levels of interleukin-6 and PCSK9 and higher TNF mRNA expression. Interleukin-6 rs180075C, TNF rs3093664 non-G and PCSK9 rs2483205 T alleles conferred a risk of RCP (P<.05 in all cases). Among patients with RCP, 51.7% had all 3 risk alleles vs 18% of those with LSS (P<.001). ConclusionsWe suggest the existence of specific phenotypic and genotypic markers associated with RCP of coronary artery disease that could help to individualize the type and intensity of treatment.

Impacts of the A20 protein polymorphism, rs2230926, in human B cells

Abstract Patients with autoimmune diseases, such as systemic lupus erythematosus (SLE), often have skewed B cell population ratios, accumulation of autoantibodies, and an increased amount of proinflammatory cytokines aiding in disease development. Genome-wide association studies (GWAS) have strongly linked polymorphisms in A20, encoded by TNFAIP3, to autoimmune diseases including SLE. A20 functions to inhibit the activation of nuclear factor kappa B (NF-κB) through ubiquitination and deubiquitylation of key signaling proteins and has been extensively studied in epithelial cells in response to TNF. Given the role of autoantibodies in SLE and the importance of NF-κB in regulating B cell fate, the role of SLE linked polymorphisms in A20 and their effects on both the canonical and noncanonical NF-κB pathways in human B cells is poorly understood. Our lab has identified an A20 polymorphism, rs2230926 (F127C), that is enriched in a cohort of African American females with SLE. Herein, we investigate the impact of rs2230926 on B cell function. We employed CRISPR/Cas9 genome-editing and generated a TNFAIP3knockout lymphoblastoid Raji human B cell line. To determine how the polymorphism rs2230926 affects the NF-kB pathway, we re-introduced WT A20, A20-rs2230926, and a truncated version of A20 into the TNFAIP3-KO cell line. Using a combination of qRT-PCR, western blotting, and flow cytometry, we determined how rs2230926 influences the expression of proinflammatory cytokines, response to various B cell stimuli, and ultimately NF-κB activity. Dissecting A20’s role in NF-kB signaling will help to understand the dysfunction and regulation of B cells in autoimmunity. Supported by grants from NIH to CDS (R01 AI148471)

Single-Nucleotide Polymorphisms Identified within Exon 2 of Fertility-Associated Bone Morphogenetic Protein (BMP15) Gene in Three Romanian Sheep Breeds

The improvement of the reproductive traits of animals is of great interest for livestock production. Due to its positive impact on the sheep industry’s profitability, prolificacy is one of the most economically significant biological traits, showing variation between and within breeds of domestic sheep (Ovis aries). Different mutations in BMPR-1B, BMP15 and GDF9 genes coding for the transforming growth factor-β (TGFβ) superfamily have been shown to influence the ovulation rate and litter size. Numerous single-nucleotide polymorphisms (SNPs) in the bone morphogenetic protein 15 (BMP15) gene have been linked to ewe fecundity. Using targeted PCR amplification and Sanger sequencing, we were able to identify heterozygous SNPs in exon 2 of BMP15 in three sheep breeds reared in Romania: Tsigai, Cluj Merino and Tsurcana. The sequence analysis revealed three previously documented mutations, namely the missense mutation c.755T&gt;C (L252P), which is predicted to change the tertiary structure of the BMP15 protein, and two silent mutations, c.747T&gt;C (P249P) and c.1047G&gt;A (V349V). In addition, we also identified one novel silent mutation, c.825G&gt;A (S275S). Based on our findings and publicly available data, we indicate four putative mutational hotspots within exon 2 of BMP15 that could be considered for improving the indigenous sheep breeds through targeted gene editing and SNP genotyping strategies.

Genetic polymorphism between the Sorani and Hawrami kurdish populations and COVID-19 outcome.

Coronavirus Disease 2019 (COVID-19) is a global pandemic, and mortality and clinical consequences vary across countries. One of the factors influencing COVID-19 outcomes is genetic polymorphism. Two Kurdish populations, Sorani and Hawrami, live in the Sulaimani province of the Kurdistan Region of Iraq. It seems Hawrami had a milder COVID-19 outcome. According to previous research conducted on various ethnic groups across the globe, single nucleotide polymorphisms (SNPs) in the interferon-induced transmembrane protein 3 (IFITM3) and interluken-6 (IL6) genes were associated with the severity of COVID-19 in those populations. We hypothesized that Hawrami may have protective SNPs. So, in this study, we used DNA sequencing to genotype three IFITM3 SNPs and nine IL6 SNPs by DNA sequencing to investigate the association of Sorani and Hawrami population polymorphisms. Genotype AA for the rs12252 SNP in IFITM3 was insignificantly more common in the Sorani group (54% vs. 44%). The Hawrami population showed a higher percentage of the CC genotype of the rs34481144 SNP in the IFITM3 gene (62% vs. 44.3%) and a higher proportion of the non-risky GG genotype of the rs1800795 SNP in the IL6 gene (53.4 vs. 43.3); however, the SNPs were insignificantly associated between the two populations. IFITM3 and IL6 SNPs have no statistically significant association between the two Kurdish populations. The decreased proportion of non-risk alleles at rs34481144 and rs1800795 in the Hawrami population may partially support the research hypothesis. However, contrary to our hypothesis, the Sorani group had an insignificantly higher protective variant of the rs12252 SNP.

Regulation of NADP-Malic Enzyme Activity in Maize (Zea mays L.) under Salinity with Reference to Light and Darkness.

We revealed the functional characterization of C4-NADP-malic enzyme (NADP-ME), extracted and partially purified from maize (Zea mays L. cv. Kaveri 50). The leaf discs were previously activated under 1000-1200 µE m-2 s-1, incubated in bicarbonate (2.0 mM) solution, and subjected to salt stress (100 mM NaCl). Initially, salt stress was evident from the accumulations of proline, chlorophyll content, carbohydrate profile, and Hill activity influencing the C4 enzyme. Primarily, in illuminated tissues, the activity of the enzyme recorded a reduced trend through salinity irrespective of light and darkness compared to the control. On illumination, the kinetic parameters such as Vmax of the enzyme increased by 1.36-fold compared to in the dark under salinity whereas Km was decreased by 20% under the same condition. The extent of light induction was proportionate to limiting (0.01 mM) and saturated (4.0 mM) malate concentrations for enzyme activity. Moreover, the catalytic properties of the enzyme were also tested on concomitant responses to activator (citrate and succinate) and inhibitor (oxalate and pyruvate) residues. The sensitivity to light and dark effects was also tested for reducing agents such as dithiothreitol, suggesting the effect of the changes in redox on the regulatory properties of the enzyme. The ratio of enzyme activity under light and darkness in the presence or absence of a reducing agent was concomitantly increased with varying malate concentrations. At the molecular level, protein polymorphism of the enzyme represented minor variations in band intensities, however, not in numbers through salinity subjected to light and darkness. Therefore, salinity-induced changes in the decarboxylation reaction, evident by NADP-ME activity, may be based on the redox property of regulatory sites and sensitivity to light and darkness.