Wild Genotype Research Articles

Relation of CXCL10 and CXCR3 Gene Polymorphisms with COVID-19 Severity and its Serum Biochemical Markers

CXCL10 (rs201830102) is a chemokine involved in immune cell recruitment, while its receptor, CXCR3 (rs779120264), mediates immune responses through the activation of T cells. These genes are critical in the immune response to viral infections, including COVID-19. The study aimed to explore the relationship between polymorphisms in the CXCL10 gene and CXCR3 receptor with disease severity in COVID-19 patients. In this cross-sectional analytical study, 100 COVID-19 patients were enrolled after ethical approval, and written informed consent was obtained from each participant. Polymorphisms in CXCL10 and CXCR3 were analyzed by sequencing, while biochemical and hematological parameters were assessed using appropriate methods. Descriptive and inferential statistics were employed to analyze continuous and categorical data. Significant associations were observed between severe COVID-19 cases and elevated levels of serum D-dimer, ferritin, random blood sugar (RBS), neutrophils, and erythrocyte sedimentation rate (ESR), along with reduced hemoglobin levels. Lymphocyte and platelet counts were significantly lower with increased disease severity. The wild genotype of CXCL10 was notably associated with elevated ferritin levels, suggesting that certain gene variants may offer protective effects. However, no significant correlation was found between CXCR3 and CXCL10 polymorphisms and other serum biomarkers. Our study confirmed a significant rise in serum D-dimer, ferritin, RBS, neutrophils, and ESR, along with a reduction in hemoglobin, lymphocyte, and platelet counts in severe COVID-19 cases compared to mild ones. Notably, mutations in the CXCL10 gene were linked to less severe COVID-19 outcomes.

Abstract 4115801: Assessing Prevalence of Cardiac Amyloidosis at the Time of Spinal Laminectomy for Spinal Stenosis

Introduction: Cardiac amyloidosis (CA) involves deposition of amyloid fibrils within cardiac myocardium, resulting in heart failure. Recent studies have shown an association between amyloid deposition in the ligamentum flavum (LF) and development of CA. Our study aims to investigate the prevalence of CA in patients identified with amyloid deposition in their LF at the time of spinal laminectomy for spinal stenosis, employing a comprehensive approach integrating multi-modality imaging and laboratory testing. Methods: This is a retrospective study of patients age >50 years old who underwent spinal laminectomy for non-congenital spinal stenosis or spondyloarthropathy. LF tissue samples obtained during surgery were examined histologically for amyloid deposition. Patients with positive findings underwent testing, including serum markers, echocardiography, and 99mtechnetium pyrophosphate (99mTcPYP) scintigraphy. Additionally, cardiac magnetic resonance imaging (cMRI) was obtained when clinically appropriate to assess for CA. Results: Among the 197 enrolled patients, 39 (19.3%) exhibited amyloid deposition in LF tissue. Patient demographics and clinical characteristics did not significantly differ between the positive and negative groups (Table 1). Of the 39 amyloid positive specimens, subtyping using mass spectrometry identified 1 (3%) light-chain, 28 (72%) transthyretin (TTR), and 10 (25%) were unable to be subtyped. Of the 28 TTR positive patients, 8 were of the wild type genotype. Furthermore, 18 of the 28 TTR patients underwent 99mTcPYP scintigraphy, of which none had cardiac uptake consistent with TTR amyloidosis; the other 10 declined work up. Of the 10 untyped patients, 6 had 99mTcPYP scintigraphy with none of the patients having cardiac uptake. Adjunctive cMRI in select positive patients showed findings inconsistent with amyloid deposition. Serum NT-proBNP, Troponin T, and serum pre-albumin levels were similar between groups. Conclusion: Amyloid deposition in LF tissue did not correlate with cardiac manifestations of amyloidosis at the time of surgery. Longitudinal investigation is ongoing to better understand the relationship between amyloid deposition in LF tissue and the development of CA over time.

Response of the tomato leaf miner Phthorimaea absoluta to wild and domesticated tomato genotypes.

Phthorimaea absoluta, a highly destructive invasive pest, poses a significant threat to tomato production globally. Exploring alternative control methods, such as host plant resistance can contribute to diminish reliance on insecticides and promote sustainable integrated pest management (IPM) practices. Thus, the identification of new P. absoluta-resistant tomato cultivars and potential wild sources for breeding programmes remains imperative. We evaluated the effect of 19 tomato genotypes, comprising 16 domesticated varieties and three wild tomato species, on oviposition output of female P. absoluta, as well as on larval performance under no-choice conditions using detached leaves. We also characterized and quantified glandular and nonglandular trichomes, exploring their potential correlation with the response of P. absoluta to the tomato plants. Generally, fewer eggs were oviposited on domesticated plants, whereas the wild tomatoes Solanum arcanum and S. neorickii and the domesticated tomato Corona F1 impaired larval development. The pest larvae consumed a limited area of leaflets from S. arcanum and S. neorickii compared to other genotypes, leading to the lowest weights in both male and female pupae. All tomato plants exhibited a prevalence of nonglandular over glandular trichomes, except for S. arcanum, which exhibited a higher abundance of glandular trichomes. Although higher trichome density correlated with longer larval settlement on the leaflets, it did not influence female oviposition. Our findings demonstrate that the wild tomatoes S. arcanum and S. neorickii could be considered as potential sources for breeding programmes, and the domesticated Corona F1 could offer IPM options against P. absoluta. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The Phenology of Coffea arabica var. Esperanza L4A5 Under Different Agroforestry Associations and Fertilization Conditions in the Caribbean Region of Costa Rica

This study focused on the phenology of Coffea arabica var. Esperanza L4A5, an F1 interspecific hybrid obtained by crossing commercial varieties with wild genotypes from Ethiopia and Sudan. Most phenological studies on C. arabica have been conducted in traditional high-altitude regions, leaving a gap in the understanding of its behavior in non-traditional areas such as the Caribbean region of Costa Rica. To establish a baseline on the phenological behavior of the Esperanza L4A5 hybrid in this region, we conducted a four-year study examining the effects of different agroforestry associations: (1) Albizia saman; (2) Hymenaea courbaril and Erythrina poeppigiana; (3) Anacardium excelsum and Erythrina poeppigiana; and coffee plots under full sun. Additionally, the phenology of the coffee plants was evaluated under differentiated fertilizations (physical, chemical, and without fertilization), considering meteorological factors such as temperature, humidity, and rainfall. The observed variables included the development of floral nodes, pre-anthesis, anthesis, and fruiting stages. To analyze the relationships between environmental factors, tree cover, fertilization, and the phenological stages, we employed multiple linear regression (MLR), which revealed that both tree cover and physical and chemical fertilizations had significant effects on the presence of developed floral nodes and, consequently, on fruit production. Furthermore, the random forest (RF) model was applied to capture complex interactions between variables and to rank the importance of meteorological factors, tree cover, and fertilization practices. These analyses demonstrated that the Esperanza L4A5 hybrid exhibited viable phenological development under the atypical conditions of the Caribbean region of Costa Rica, suggesting its potential to adapt and thrive in non-traditional coffee-growing areas.

Diagnostic Implications of CD63 and CD64 Expression Levels and FcγRIIIA 158 V/F Gene Polymorphism in Primary Immune Thrombocytopenia Adult Patients.

Immune thrombocytopenic purpura (ITP) is an acquired autoimmune disease characterized by reduced platelet counts due to immune system dysregulation caused by many factors, including genetics, autoimmune diseases, infections, and inflammations. Therefore, the current study aimed to evaluate immunological markers such as the expression level of lysosomal associated membrane protein 3 (LAMP-3), also known as CD63, and the expression level of Fc-gamma receptor I (FcγRI), also known as CD64 and also investigate the association of Fc-gamma receptor IIIA (FcγRIIIA) 158 V/F polymorphism to the risk of ITP. A total of 180 subjects; 60 ITP patients, 60 patients with thrombocytopenia of other causes and 60 controls were enrolled into our study. The expression level of CD63 was done using reverse transcription quantitative PCR (RTqPCR), while CD64 expression level was done by flow cytometry. The polymorphism of FcγRIIIA 158 V/F gene was analyzed by polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) analysis. Finally, CD63 and CD64 protein-protein interactions were done by using the STRING online database. The expression of CD63 was significantly elevated in ITP patients than thrombocytopenia patients and healthy control. Also there was high expression level of CD64 on granulocytes and monocytes from ITP patients than other groups. Receiver operating characteristic curve (ROC curve) analysis of CD63 showed an area under the curve (AUC) revealed of 1.00, sensitivity of 100% and specificity of 100%; while for CD64 on granulocytes, AUC of 0.998 as well as a sensitivity of 96.66% and specificity of 93.33%. Regarding FcγRIIIa 158 V/F polymorphism, all patients and healthy volunteers included in this study showed the wild FF genotype. The expression of both CD63 and CD64 were significantly increased in ITP patients and could be good biomarkers to diagnose ITP. Additionally, there is no association between FcγRIIIa 158 V/F polymorphism and the risk of ITP disease.

Neutrophil Elastase Activates Macrophage Calpain as a Mechanism for Phagocytic Failure.

Neutrophil elastase (NE), elevated in the cystic fibrosis (CF) airway, causes macrophage phagocytic failure. We previously reported that NE increases the release of protease Calpain-2 in macrophages. We hypothesized that NE mediates macrophage failure through activation of Calpains. We demonstrate that Calpain inhibition rescued NE induced macrophage phagocytic failure in murine alveolar macrophages in both cftr-null and wild type genotypes. We then sought to determine how NE regulates Calpain-2. Human monocyte derived macrophages (hMDM) from persons with CF (PwCF) and non-CF subjects, were treated with NE or control vehicle and cell lysates prepared to evaluate Calpain-2 protein abundance by Western, and Calpain activity by a specific activity kit. Calpain is activated by intracellular calcium and inactivated by an endogenous inhibitor, Calpastatin. Human MDM were thus treated with NE or control vehicle and cell lysates were analyzed for increased intracellular calcium by Fluo-4 assay and for Calpastatin protein abundance by Western. NE increased Calpain-2 protein and activity, degraded Calpastatin, and increased intracellular calcium in macrophages. At baseline there are no differences in Calpain activity, Calpain-2 and Calpastatin expression, and intracellular calcium between CF and non-CF macrophages. NE increased macrophage Calpain-2 protein and Calpain activity by two potential mechanisms: degradation of Calpastatin, and/or increased intracellular calcium. In summary, Calpain inhibition restored NE-induced macrophage phagocytic failure suggesting a potential CFTR-independent target for phagocytic failure in the CF airway.

Unlocking nature’s drought resilience: a focus on the parsimonious root phenotype and specialised root metabolism in wild Medicago populations

Abstract Background and aims Crop wild relatives, exposed to strong natural selection, exhibit effective tolerance traits against stresses. While an aggressive root proliferation phenotype has long been considered advantageous for a range of stresses, it appears to be counterproductive under drought due to its high metabolic cost. Recently, a parsimonious root phenotype, metabolically more efficient, has been suggested to be better adapted to semiarid environments, although it is not clear that this phenotype is a trait exhibited by crop wild relatives. Methods Firstly, we analysed the root phenotype and carbon metabolism in four Medicago crop wild relatives adapted to a semiarid environment and compared them with the cultivated M. truncatula Jemalong (A17). Secondly, we exposed the cultivated (probably the least adapted genotype to aridity) and the wild (the most common one in arid zones) M. truncatula genotypes to water deficit. The carbon metabolism response in different parts of their roots was analysed. Results A reduced carbon investment per unit of root length was a common trait in the four wild genotypes, indicative of an evolution towards a parsimonious root phenotype. During the water deficit experiment, the wild M. truncatula showed higher tolerance to drought, along with a superior ability of its taproot to partition sucrose and enhanced capacity of its fibrous roots to maintain sugar homeostasis. Conclusion A parsimonious root phenotype and the spatial specialization of root carbon metabolism represent two important drought tolerance traits. This work provides relevant findings to understand the response of Medicago species roots to water deficit.

Association between lipoprotein-associated phospholipase A2 gene Val279Phe homozygous genotypes and variant angina in Japanese women

Abstract Background The role of the lipoprotein-associated phospholipase A2 gene (PLA2G7) in the pathogenesis of cardiovascular diseases remains controversial. The PLA2G7 gene normally produces a protein called "plasma platelet activating factor-acetylhydrolase"(PAF-AH). Homozygotes of rs76863441, which is PLA2G7 Val279Phe polymorphism, produce none of PAF-AH, and heterozygotes produce less than half of the normal levels. This polymorphism is rare outside of Asia and is particularly common in Japan, where homozygous mutations account for 4% of the population. The association between rs76863441 and risk of myocardial infarction was significant in ethnicity for Japanese population, but not in other countries. Variant angina is a severe case of coronary artery spasm (CSA) and causes an acute myocardial infarction. It is widely accepted that variant angina is more common in Japanese than in other races. Purpose The aim of this study was to examine the possible association between rs76863441 and variant angina. Methods rs76863441 was analyzed by direct sequencing in 62 patients with variant angina (43 men and 19 women with a mean age of 60.0±11.6 years). In all patients, ST segment elevation was recorded on ECG and coronary angiography was performed. Acetylcholine provocation test was performed in 31 patients. We compared genotypes of rs76863441 between variant angina patients and 872 healthy volunteers without a history of heart diseases living in the same area, who participated in the Iwaki Health Promotion Project, which has been conducted by the Hirosaki University School of Medicine since 2005. These volunteers had undergone Japonica Arrays, which is the SNP array for the Japanese population. Results Homozygotes genotype for rs76863441, heterozygotes genotype, and wild genotype were present in 4 (6.5%), 22 (35.5%), and 36 (58.1%) of the variant angina group, respectively, and in 30 (3.4%), 246 (28.2%), and 596 (68.3%) of the control group, respectively. Statistically, there were no significant differences in genotypes between the variant angina group and the control group. Next, males and females were analyzed separately. In males, there were no significant differences in homozygous mutations (1 out of 43 patients (2.3%) in the variant angina group vs. 11 out of 327 patients (3.4%) in the control group, P=1.00). However, in females, there was a significant difference in homozygous mutations (3 out of 19 (15.8%) in the variant angina group vs. 19 out of 545 (3.4%) in the control group, P=0.033). Conclusions These findings indicate that homozygotes of rs76863441, which has PAF-AH deficiency, may be associated with the pathogenesis of variant angina in Japanese women. Further functional analyses of this mutation are of great interest.Genotypes of rs76863441Gender disparities of rs76863441

GJA4 gene inhibition may represent a potential target for novel antithrombotic therapies

Abstract The GJA4 gene encodes a protein called connexin 37, a component of gap junctions in vascular endothelial cells, crucial in regulating endothelial function and influencing inflammation, platelet adhesion and thrombus formation. This gene deletion in mice diminished thrombus formation in vitro in human blood. In these circumstances, connexin inhibition with pharmacological agents may represent potential avenues for developing novel antithrombotic agents. Aim To investigate whether the GJA4 rs618675 T>C variant is a risk factor for progressing atherosclerosis and cardiovascular (CV) events in an asymptomatic free of apparent CAD from a Portuguese population. Methods A prospective study was performed with 1421 individuals without apparent CV disease (73.6% male, aged 52.2±8.3 years) followed during an extended period of 7.2±5.1 years). GJA4 rs618675 T>C variant was genotyped by TaqMan real-time PCR technique (Applied Biosystems). Conventional, anthropometric, biochemical and clinical risk factors were studied. Bivariate analysis and multivariate Cox regression adjusted for age, gender, traditional risk factors, biochemical markers, and the genotypes under study was performed to determine which variables were, significantly and independently, associated with CV events. Kaplan-Meier's estimate assessed the prognosis. Results Bivariate analysis showed that 50.6% of wild genotype (TT) carriers had CV events vs. 66.2% without events. Of the risk genotype (CC) carriers, 10.1% had CV events, and 3.4% did not. After the Kaplan-Meier analysis, the TT carriers had 90% CV event-free survival time and the CC risk carriers had only 64% of event-free survival. Finally, after adjustment, CC genotype remained in the equation with an HR of 3.1 (p=0.003) and CT heterozygous with HR of 1.6 (p=0.043), together with Hypertension (HR 3.0; p<0.0001), Smoking habits (HR 2.3; p=0.001) and Diabetes (HR 1.9; p=0.015). Conclusion: The CC risk genotype of the GJA4 rs618675 represented an independent risk factor for progressing atherosclerosis and CV events in a Portuguese Population. Thrombus formation often begins with the adhesion of platelets to the endothelium, and connexin 37 may influence this process. The inhibition of connexin 37 emerges as a promising candidate for future cardiovascular prevention as well as for the development of new antithrombotic drugs.

Analysis of phylogenetic relationships in Macadamia shows evidence of extensive reticulate evolution.

The genus Macadamia in the Proteaceae family includes four species native to Australia. Two of the four species, M. integrifolia and M. tetraphylla, have recently been utilized to generate domesticated macadamia varieties, grown for their edible nuts. To explore diversity in macadamia genetic resources, a total of 166 wild genotypes, representing all four species, were sequenced. The four species were clearly distinguished as four separate clades in a phylogenetic analysis of the nuclear genome (based upon concatenated nuclear gene CDS and SNPs). The two larger species (M. integrifolia and M. tetraphylla) formed a clade, that had diverged from a clade including the smaller species (M. ternifolia and M. jansenii). The greatest diversity in nuclear and chloroplast genomes was found in the more widely distributed M. integrifolia while the rare M. jansenii showed little diversity. The chloroplast phylogeny revealed a much more complex evolutionary history. Multiple chloroplast capture events have resulted in chloroplast genome clades, including genotypes from different species. This suggests extensive reticulate evolution in Macadamia despite the emergence of the four distinct species that are supported by the analysis of their nuclear genomes. The chloroplast genomes showed strong associations with geographical distribution reflecting limited maternal gene movement in these species that have large seeds. The nuclear genomes showed lesser geographical differences, probably reflecting the longer distance pollen movement. This improved understanding of the distribution of diversity in Macadamia will aid in the conservation of these rare species now found in highly fragmented rainforest remnants.

Seasonal distribution and correlation between IL-10 and IL-13 gene polymorphism and their expression in scabies-infected patients.

Scabies is a significant concern in global health. It is more prevalent in individuals who have poor hygiene and live in crowded conditions, hence, it is seasonal distribution and immunological response in Erbil population is the aim of the present study. In the Erbil Dermatology Education Centre in Erbil, Iraq, 154 patients were recruited for the research between April 2022 and March 2023. If a patient has a suspicious skin lesion and itching for a minimum of one week, scabies may be considered. Blood samples were collected from each participant in the study to evaluate serum levels of IL-10 and IL-13, then the DNA was isolated to study the gene polymorphism for the mentioned cytokines. Results showed that female 60.3% were more infected than male 39.6%. The median age of participants was (10 - >51) years, among infested, adolescents aged 10-20 years displayed the highest rate (31.8%). The carriers of GA genotype of IL-10 were protective against the infection, OR:0.61. while the TT carriers of IL-13 were susceptible to scabies infection with OR:2.14. IL-10 GA genotype was more prevalent in male patients OR:2.14 whereas the AA genotype was most protective in females OR:0.32. the IL-13 CT genotype was protective for males with OR:0.52. Both of IL-10 and IL-13 serum levels were increased significantly with infection and highest levels were found in wild homozygous genotypes (GG and CC) and lowest ratio was found in mutant homozygous genotypes of IL-10 and IL-13 respectively. Point mutation in IL-10 GA was protective and wild TT genotype of IL-13 was susceptible to the scabies infection. Double mutation in IL-10 AA was protective to females and single mutation of IL-13 CT was protective to males.

CARD8 polymorphisms among bacterial meningitis patients in North-West Ethiopia

BackgroundThe severity of infectious disease outcomes is dependent on the virulence factors of the pathogen and the host immune response. CARD8 is a major regulator of the innate immune proinflammatory response and has been suggested to modulate the host response to common inflammatory diseases. In the present study, the C10X genetic polymorphism in the CARD8 gene was investigated in relation to bacterial meningitis.MethodsA total of 400 clinically suspected meningitis patients hospitalized at the University of Gondar Hospital were enrolled in the study. Cerebrospinal fluid (CSF) and blood samples were collected for laboratory investigations. The collected CSF was cultured, and all the results obtained from the culture were confirmed using direct RT‒PCR. Genotyping of whole-blood samples was performed using a TaqMan assay. The results were compared with apparently healthy controls and with PCR-negative meningitis suspected patients.ResultsOf the included patients, 57% were men and the most common clinical signs and symptoms were fever (81%), headache (80%), neck stiffness (76%), nausea (68%), and vomiting (67%). Microbiology culture identified 7 patients with bacterial meningitis caused by Neisseria meningitidis (n = 4) and Streptococcus pneumoniae (n = 3). The RT-PCR revealed 39 positive samples for N. meningitidis (n = 10) and S. pneumoniae (n = 29). A total of 332 whole-blood samples were genotyped with the following results: 151 (45.5%) C10X heterozygotes, 59 (17.7%) C10X homozygotes and 122 (36.7%) wild genotypes. The polymorphic gene carriers among laboratory confirmed, clinically diagnosed meningitis and healthy controls were 23(46%), 246(40%), and 1526(39%), respectively with OR = 1.27 (0.7–2.3) and OR = 1.34 (0.76–2.4). The presence of the C10X polymorphism in the CARD8 gene was more prevalent in suspected meningitis patients than in healthy controls (OR 1.2; 1.00-1.5). Homozygote C10X polymorphic gene carriers were more susceptible to infectious disease. The presence of viable or active bacterial infection was found to be associated with the presence of heterozygous C10X carriers.ConclusionsA greater proportion of C10X in the CARD8 gene in confirmed bacterial meningitis patients and clinically diagnosed meningitis patients than in healthy controls. Homozygote C10X polymorphic gene carriers were more susceptible to infectious disease than heterozygote gene carriers and healthy controls.

First Comprehensive Evaluation of Genetic Variability for Bacterial Blight Resistance in Wild Punica granatum L. Populations from the North-Western Himalayas

Identifying and selecting disease-resistant sources from wild germplasm pools is pivotal due to their ecological benefits and cost-effectiveness. This study encompassed the survey and collection of wild pomegranate genotypes alongside commercial cultivars, followed by screening against native pathogens. Additionally, biochemical analyses were conducted to elucidate defense mechanisms in both resistant and susceptible genotypes. Cuttings from selected germplasm across four districts were obtained, grown for one year, and assessed for pathogenicity and biochemical responses. Microscopic and molecular analyses confirmed the pathogen as Xanthomonas axonopodis pv. punicae (Xap), identified by its distinctive morphology and a 1500 bp amplicon along with phylogeny analysis. Germplasm screening via detached and attached leaf assays identified genotypes with minimal disease severity, highlighting SH-14 and SH-16 as highly resistant in the attached leaf assay. Principal component analysis categorized genotypes based on disease parameters, with PC1 explaining approximately 75% of the variability. Agglomerative hierarchical clustering further grouped genotypes into ten clusters, emphasizing clusters IX and X for their significant resistance traits. Biochemical studies revealed that the resistant genotype SH-16 exhibited higher levels of constitutive defense components like chlorophyll and vitamin C, as well as induced defense components such as phenols, flavonoids, and antioxidants, compared to the susceptible cultivar Bhagwa. These findings underscore the critical roles of both constitutive and induced defense mechanisms in conferring pomegranate resistance to Xap. The study's comprehensive approach in evaluating genetic and biochemical resistance provides valuable insights for breeding disease-resistant pomegranate varieties, marking a significant advancement in exploring pomegranate wild relatives from the Himalayan region for their resistance to bacterial blight.

Resistance and genetic divergence of wild cotton genotypes under attack by sucking pests

Resistance and genetic divergence of wild cotton genotypes under attack by sucking pests

Novel Candidate Single Nucleotide Polymorphisms of ERCC2 Gene that Influence Colorectal Cancer Susceptibility

Colorectal cancer (CRC) is the most common gastrointestinal malignancy and one of the top ten common cancers worldwide with approximately 2 million cases. There are multiple risk factors that could lead to CRC emergence; of which are genetic polymorphisms. Excision repair cross-complementing group 2 (ERCC2) gene encodes for ERCC2 enzyme which plays a crucial role in maintaining genomic integrity by removing DNA adducts. Several studies suggested that there could be a link between genetic polymorphisms of ERCC2 gene and the risk of CRC development. Hence the present study aims to validate the relationship between the following ERCC2 single nucleotide polymorphisms (rs13181, rs149943175, rs530662943, and rs1799790) and CRC susceptibility. A total of 121 participants were enrolled in this case control study; 72 CRC patients and 49 apparently healthy individuals. Genotyping was performed using polymerase chain reaction (PCR) followed by sequencing then the association between genetic polymorphisms and CRC susceptibility was examined. GA genotype and A allele of rs149943175 were associated with lower risk of CRC development. However, GA genotype and A allele carriers of rs530662943 had significantly increased risk compared to GG genotype. Additional stratified analyses showed that carriers of heterozygous genotype of rs149943175 who non-smokers, females or BMI figures less than 25 are less likely to develop CRC compared to wild genotype carriers. Taken together, genetic polymorphisms of ERCC2 modulate the susceptibility of CRC malignancy.

Repeat expansions inRFC1gene in Refractory Chronic Cough

IntroductionRefractory chronic cough (RCC), persisting despite addressing contributory diagnoses, is likely underpinned by neurally-mediated cough hypersensitivity.RFC1-disorders are genetic neurodegenerative conditions caused by biallelicRFC1repeat expansion sequences, commonly presenting with cough, followed by neurological features including cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS). The prevalence and identifying clinical characteristics ofRFC1repeat-expansion disorders in patients with RCC are unknown.MethodsConsecutive patients with RCC underwentRFC1genotyping, cough severity visual analogue scale (VAS), and cough-specific health status assessment (Leicester Cough Questionnaire, LCQ). Participants with biallelicRFC1repeat expansions (RFC1++) also underwent nerve conduction studies, brain imaging (MRI), and cough reflex sensitivity testing.ResultsFifty-one participants with RCC were recruited; 36 (71%) female, median (IQR) age 65 (56–70) years, duration of cough 12.8 (6.9–20.0) years. Four (8%) wereRFC1++, five (10%) monoallelic carriers (RFC1+−), and 42 (82%) of wild type genotype (RFC1−−). No difference was observed in age, sex, cough duration, spirometry, VAS or LCQ scores between RFC1++ and RFC1--subjects (p>0.05). The symptom of pins and needles was more frequent in RFC1++ (n=4, 100%) compared to RFC1−− (n=12, 33%) (p=0.01). RFC1++ participants had impaired sensory action potentials, and one had cerebellar atrophy. RFC1++ participants had heightened cough reflex sensitivity to capsaicin, similar to previous CANVAS and RCC studies.ConclusionBiallelic RFC1 repeat expansions (RFC1++) were present in 8% of RCC patients. RFC1++ participants demonstrated features of cough reflex hypersensitivity. RFC1++ chronic cough had few identifying features, although symptoms of pins and needles were more common.

Detached leaf assay-based screening of anthracnose resistant wild strawberry genotypes

Detached leaf assay-based screening of anthracnose resistant wild strawberry genotypes

Investigation of the α9-nicotinic receptor single nucleotide polymorphisms induced oncogenic properties and molecular mechanisms in breast cancer.

α9-nAChR, a subtype of nicotinic acetylcholine receptor, is significantly overexpressed in female breast cancer tumor tissues compared to normal tissues. Previous studies have proposed that specific single nucleotide polymorphisms (SNPs) in the CHRNA9 (α9-nAChR) gene are associated with an increased risk of breast cancer in interaction with smoking. The study conducted a breast cancer risk assessment of the α9-nAChR SNP rs10009228 (NM_017581.4:c.1325A > G) in the Taiwanese female population, including 308 breast cancer patients and 198 healthy controls revealed that individuals with the heterozygous A/G or A/A wild genotype have an increased susceptibility to developing breast cancer in the presence of smoking compared to carriers of the G/G variant genotype. Our investigation confirmed the presence of this missense variation, resulting in an alteration of the amino acid sequence from asparagine (N442) to serine (S442) to facilitate phosphorylation within the α9-nAchR protein. Additionally, overexpression of N442 (A/A) in breast cancer cells significantly enhanced cell survival, migration, and cancer stemness compared to S442 (G/G). Four-line triple-negative breast cancer patient-derived xenograft (TNBC-PDX) models with distinct α9-nAChR rs10009228 SNP genotypes (A/A, A/G, G/G) further demonstrated that chronic nicotine exposure accelerated tumor growth through sustained activation of the α9-nAChR downstream oncogenic AKT/ERK/STAT3 pathway, particularly in individuals with the A/G or A/A genotype. Collectively, our study established the links between genetic variations in α9-nAChR and smoking exposure in promoting breast tumor development. This emphasizes the need to consider gene-environment interactions carefully while developing effective breast cancer prevention and treatment strategies.

Association of Vitamin D receptor gene polymorphisms (FokI, ApaI, TaqI), metabolic features and susceptibility to polycystic ovary syndrome: a preliminary single center case-control study

Research questionAre the combined genotypes and haplotypes of VDR gene polymorphisms (FokI, ApaI, TaqI) associated with PCOS susceptibility and metabolic features of the disease? DesignWe performed a case-control study, including 46 women with PCOS and 48 controls. Genotypes of VDR genes were determined using the PCR-RFLP (restriction fragment length polymorphism) method. In all women, the waist circumference, parameters of lipid and glucose metabolism were evaluated. ResultsPCOS group presented higher waist circumference and visceral adiposity index (VAI) levels compared to controls. Total cholesterol, LDL-C and triglycerides had higher values in PCOS women. VDR-FokI C/C (F/F) genotype had significantly higher odds of PCOS (adjusted OR = 6.27, 95% CI: 1.53-25.65). VDR-Apal was associated with susceptibility to PCOS in the dominant model, the variant genotype (A/C-A/A) (A/a- a/a) had higher odds of PCOS than the wild genotype C/C (A/A) (adjusted OR = 3.15, 95% CI: 1.07-9.32). Haplotype analysis revealed that T-C- T (f-A-T) haplotype was statistically associated with lower odds of PCOS (adjusted OR = 0.10, 95% CI: 0.01-0.95). PCOS women with VDR-Fokl T/T (f/f) genotype had lower fasting glucose and higher VAI levels compared to C/T (Ff) or C/C (F/F) genotype. ConclusionThe present findings suggest the association between FokI and ApaI polymorphisms and PCOS susceptibility. Moreover, T/T (f/f) genotype of VDR-FokI could be a marker of decreased fasting glucose in PCOS. TaqI polymorphism did not reveal a relationship with PCOS susceptibility in our study population.

Comparative Long Non-Coding Transcriptome Analysis of Three Contrasting Barley Varieties in Response to Aluminum Stress.

Aluminum toxicity is a major abiotic stress on acidic soils, leading to restricted root growth and reduced plant yield. Long non-coding RNAs are crucial signaling molecules regulating the expression of downstream genes, particularly under abiotic stress conditions. However, the extent to which lncRNAs participate in the response to aluminum (Al) stress in barley remains largely unknown. Here, we conducted RNA sequencing of root samples under aluminum stress and compared the lncRNA transcriptomes of two Tibetan wild barley genotypes, XZ16 (Al-tolerant) and XZ61 (Al-sensitive), as well as the aluminum-tolerant cultivar Dayton. In total, 268 lncRNAs were identified as aluminum-responsive genes on the basis of their differential expression profiles under aluminum treatment. Through target gene prediction analysis, we identified 938 candidate lncRNA-messenger RNA (mRNA) pairs that function in a cis-acting manner. Subsequently, enrichment analysis showed that the genes targeted by aluminum-responsive lncRNAs were involved in diterpenoid biosynthesis, peroxisome function, and starch/sucrose metabolism. Further analysis of genotype differences in the transcriptome led to the identification of 15 aluminum-responsive lncRNAs specifically altered by aluminum stress in XZ16. The RNA sequencing data were further validated by RT-qPCR. The functional roles of lncRNA-mRNA interactions demonstrated that these lncRNAs are involved in the signal transduction of secondary messengers, and a disease resistance protein, such as RPP13-like protein 4, is probably involved in aluminum tolerance in XZ16. The current findings significantly contribute to our understanding of the regulatory roles of lncRNAs in aluminum tolerance and extend our knowledge of their importance in plant responses to aluminum stress.