Polymorphism Analysis Research Articles

Unraveling relationship between the genetic polymorphism CYP2A13 and nicotine metabolism of male smokers in Medan, Indonesia

BackgroundNicotine metabolism significantly influences the levels of harmful nicotine metabolites in smokers. CYP2A13, a key enzyme in nicotine and xenobiotic metabolism, is implicated in tobacco smoke-related lung cancer.AimThis study investigated the association between CYP2A13 genetic polymorphism and nicotine metabolism in male smokers in Medan, Indonesia.Materials and methodsThis cross-sectional study included 66 male smokers (aged 20–65 years) who met pre-defined inclusion and exclusion criteria. Nicotine metabolite levels were quantified in urine samples using high-performance liquid chromatography (HPLC). CYP2A13 polymorphism was determined using polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) analysis of venous blood samples. Logistic regression analysis (Epi Info-7) assessed the association between CYP2A13 genotype and nicotine metabolism.ResultsNo significant association (p > 0.05) was found between CYP2A13 genotype and nicotine metabolism. The CC genotype was most prevalent. The majority of participants exhibited rapid nicotine metabolism.ConclusionFurther research with larger sample sizes and diverse populations is needed to elucidate the relationship between CYP2A13 genetic polymorphism and nicotine metabolism.

Subspecies delineation of Ziziphora clinopodioides complex (Lamiaceae) based on morphological, sequence-related amplified polymorphism and essential oils analyses

Ziziphora clinopodioides (Lamiaceae) is recognized as a native Iranian herb used for the treatment of diarrhea, intestinal gas, nausea, and vomiting. There is lack of consensus among some authors on its taxonomic boundaries at the subspecific level. To resolve this issue, the present study aimed to employ a combination of morphological, molecular, and phytochemical analyses. Firstly, 90 vegetative and floral characteristics were measured from 90 specimens of this species followed by conducting multivariate analyses on the 46 significantly discriminating morphological traits. Additionally, molecular markers (SRAP) were utilized generating 601 total loci of which 593 (98.31%) were polymorphic. The SRAP markers proved to be efficient, as demonstrated by the principal component analysis plot, which grouped all individuals according to their morphotypes, regardless of geographical location. According to the analysis of molecular variance (AMOVA), 10.69% of the total variations were associated with within-populations, while 89.31% were observed among populations. Furthermore, chemical analysis of essential oils (EOs) revealed the presence of Pulegone, 1,8-Cineole, and P-Mentha-3-n-8-ol as the major (>10%) EOs constituents in Z. clinopodioides. Notably, eight EOs compounds (Menthone, B-Pinene, Terpinen-4-ol, Minth-furanone, a-Thujene, Tricyclene, Caryophyllene-oxide, and Germacrene-d) identified in this study, show reliable yields with chemotaxonomic significance within the complex. A high correlation between the genetic markers and EOs content (Pearson’s correlation coefficient, r = 0.6) suggests that genetic markers may be linked to the EOs constituents. Overall, our results obtained from a combination of morphological, molecular, and chemical analyses indicate that nine subspecies of the Z. clinopodioides complex could be decreased to four subspecies.

Manipulation of the brown glume and internode 1 gene leads to alterations in the colouration of lignified tissues, lignin content and pathogen resistance in wheat.

Lignin is a crucial component of the cell wall, providing mechanical support and protection against biotic and abiotic stresses. However, little is known about wheat lignin-related mutants and their roles in pathogen defence. Here, we identified an ethyl methanesulfonate (EMS)-derived Aegilops tauschii mutant named brown glume and internode 1 (bgi1), which exhibits reddish-brown pigmentation in various tissues, including internodes, spikes and glumes. Using map-based cloning and single nucleotide polymorphism (SNP) analysis, we identified AET6Gv20438400 (BGI1) as the leading candidate gene, encoding the TaCAD1 protein. The mutation occurred in the splice acceptor site of the first intron, resulting in a premature stop codon in BGI1. We validated the function of BGI1 using loss-of-function EMS and gene editing knockout mutants, both of which displayed reddish-brown pigmentation in lignified tissues. BGI1 knockout mutants exhibited reduced lignin content and shearing force relative to wild type, while BGI1 overexpression transgenic plants showed increased lignin content and enhanced disease resistance against common root rot and Fusarium crown rot. We confirmed that BGI1 exhibits CAD activity both in vitro and in vivo, playing an important role in lignin biosynthesis. BGI1 was highly expressed in the stem and spike, with its localisation observed in the cytoplasm. Transcriptome analysis revealed the regulatory networks associated with BGI1. Finally, we demonstrated that BGI1 interacts with TaPYL-1D, potentially involved in the abscisic acid signalling pathway. The identification and functional characterisation of BGI1 significantly advance our understanding of CAD proteins in lignin biosynthesis and plant defence against pathogen infection in wheat.

Emergence of Multidrug-Resistant NDM-5-Producing ST307 Klebsiella pneumoniae in Uruguay, 2023.

Carbapenem and colistin-resistant Klebsiella pneumoniae pose a significant threat to public health, particularly in intensive care units, due to high morbidity and mortality rates. This study aimed to analyze five NDM carbapenemase-producing multidrug-resistant K. pneumoniae isolates from different hospitals. Antimicrobial susceptibility testing, hypermucoviscosity analysis, biofilm production assessment, MLST, PCR, and whole-genome sequencing were conducted. All isolates harbored NDM-5 metallo-β-lactamase, belonging to MLST 307, were biofilm producers and exhibited a stop codon (Q30) along MgrB. Genomic analysis revealed multiple-replicon plasmids carrying resistance genes, notably blaNDM-5, blaCTX-M-15, rmtB, and qnrB1, with complex genetic structures encoding several mobile genetic elements, including the Tn3 family and IS26. All isolates harbored wzi173 (capsule-locus KL102), iutA (a siderophore-associated gene), and the type 3 fimbriae mrkABCDFHIJ operon. The core genome single nucleotide polymorphisms (SNPs) analysis suggests the circulation of two strains of ST307 clone (SNPs range differences 4-77). These findings highlight the potential plasticity of the high-risk ST307 clone and the urgent need for surveillance and intervention strategies to combat antimicrobial resistance. To our knowledge, this is the first report of K. pneumoniae ST307 carrying blaNDM-5 and the first description of ST307 in Uruguay. The presence of blaNDM-5 and pan-aminoglycoside resistance rmtB genes are identified for the first time in Uruguay.

Decoding the anomalies: a genome-based analysis of Bacillus cereus group strains closely related to Bacillus anthracis

IntroductionThe Bacillus cereus group encompasses a complex group of closely related pathogenic and non-pathogenic bacterial species. Key members include B. anthracis, B. cereus, and B. thuringiensis organisms that, despite genetic proximity, diverge significantly in morphology and pathogenic potential. Taxonomic challenges persist due to inconsistent classification methods, particularly for B. cereus isolates that resemble B. anthracis in genetic clustering.MethodsThis study investigated B. cereus group isolates from blood smears of animal carcasses in Kruger National Park, uncovering an unusual isolate with B. cereus features based on classical microbiological tests yet B. anthracis-like genomic similarities with an Average Nucleotide Identity (ANI) of ≥95%. Using comparative genomics, pan-genomics and whole genome Single Nucleotide Polymorphism (wgSNP) analysis, a total of 103 B. cereus group genomes were analyzed, including nine newly sequenced isolates from South Africa and a collection of isolates that showed some classification discrepancies, thus classified as “anomalous.”Results and discussionOf the 36 strains identified as B. anthracis in GenBank, 26 clustered phylogenetically with the four confirmed B. anthracis isolates from South Africa and shared 99% ANI. Isolates with less than 99% ANI alignment to B. anthracis exhibited characteristics consistent with B. cereus and/or B. thuringiensis, possessing diverse genetic profiles, insertion elements, resistance genes, and virulence genes features, contrasting with the genetic uniformity of typical B. anthracis. The findings underscore a recurrent acquisition of mobile genetic elements within B. cereus and B. thuringiensis, a process infrequent in B. anthracis.ConclusionThis study highlights the pressing need for standardized taxonomic criteria in B. cereus group classification, especially as anomalous isolates emerge. This study supports the existing nomenclature framework which offers an effective solution for classifying species into genomospecies groups. We recommend isolates with ANI ≥99% to standard reference B. anthracis be designated as typical B. anthracis in GenBank to maintain taxonomic clarity and precision.

Efficacy of CLT4A variants as immunoregulatory molecules among Vitiligo patients in Saudi Arabia

Vitiligo is a skin depigmentation condition caused by the immune-mediated perdition of melanocytes. In vitiligo, cytotoxic T-lymphocytes damage melanocytes, causing skin depigmentation. The Cytotoxic T-Lymphocyte Antigen 4 (CTLA-4) gene has been reported to be related to vitiligo and other autoimmune diseases. The purpose of this study was to explore the molecular involvement of rs231775 and rs3087243 SNPs in the CTLA4 gene in vitiligo patients. The recruitment was based on the sample size calculation and based on it, we have recruited 300 Saudi individuals who were evenly divided into vitiligo cases and controls. Extracted genomic DNA was utilized to amplify rs231775 and rs3087243 SNPs in the CTLA4 gene, which were subsequently digested and verified using Sanger sequencing. The polymerase chain reaction and restriction fragment length polymorphism analysis laboratory data were stored in Excel and used for further statistical analysis. Although baseline details had no correlation (p > 0.05) between the two groups, Hardy-Weinberg Equilibrium analysis was in agreement with the vitiligo patients (p > 0.05). The genotype and allele frequencies were frequently associated (p < 0.05) with rs3087243, and rs231775 SNP showed a nominal association with GG genotype and G allele (p < 0.05). The specific relationship in vitiligo cases was revealed by MDR, GDMR, and linkage disequilibrium (p < 0.05), but not with haplotype analysis (p > 0.05). Thus, the study concluded that rs3087243 SNP was associated and rs231775 SNP showed a nominal association with vitiligo in the Saudi population.

Independent introductions and nosocomial transmission of Candida auris in Saudi Arabia ─ a genomic epidemiological study of an outbreak from a hospital in Riyadh.

Candida auris, a pathogenic yeast responsible for global healthcare-associated outbreaks, was involved in a significant outbreak at King Fahad Medical City (KFMC) in Riyadh, affecting 20 patients from August 2018 to May 2019. Our study analyzed 23 C. auris isolates from these patients, utilizing whole genome sequencing, single-nucleotide polymorphism (SNP) analysis, phylogenetic analysis, and transmission network construction. We identified four phylogeographic clades in Saudi Arabia, with two present among the KFMC isolates. The transmission network predominantly displayed two star-like patterns, indicative of super-spreader events. Resistance to various azoles was common, and one isolate was resistant to 5-flucytosine, linked to specific mutations in the ERG11 and CIT1 genes. High genetic similarity of the isolates suggested a nosocomial origin of the KFMC outbreak. The distribution of phylogeographic clades suggests at least four separate introductions into Saudi Arabia from 2017 to 2019 and two into KFMC, underscoring both direct and nosocomial transmission pathways within the hospital.IMPORTANCECandida auris is an emerging multidrug-resistant yeast that poses a significant threat in healthcare settings worldwide. This study is one of the largest genomic investigations of a Candida auris outbreak in the Middle East, focusing on a hospital in Riyadh, Saudi Arabia. By analyzing the genomes of isolates from 20 patients, we uncovered multiple independent introductions of C. auris into the region, as well as its subsequent spread within a hospital. The findings highlight the complex transmission dynamics and the challenges in controlling this pathogenic yeast in healthcare environments. This research underscores the critical need for robust genomic surveillance and accurate identification methods to prevent and manage C. auris outbreaks, which are increasingly linked to high mortality rates and limited treatment options. The insights gained from this study contribute to our understanding of C. auris transmission and resistance, offering valuable guidance for public health strategies.

CRISPR in clinical diagnostics: bridging the gap between research and practice.

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) has transformed molecular biology through its precise gene-editing capabilities. Beyond its initial applications in genetic modification, CRISPR has emerged as a powerful tool in diagnostics and biosensing. This review explores its transition from genome editing to innovative detection methods, including nucleic acid identification, single nucleotide polymorphism (SNP) analysis, and protein sensing. Advanced technologies such as SHERLOCK and DETECTR demonstrate CRISPR's potential for point-of-care diagnostics, enabling rapid and highly sensitive detection. The integration of chemical modifications, CRISPR-Chip technology, and enzymatic systems like Cas12a and Cas13a enhances signal amplification and detection efficiency. These advancements promise decentralized, real-time diagnostic solutions with significant implications for global healthcare. Furthermore, the fusion of CRISPR with artificial intelligence and digital health platforms is paving the way for more accessible, cost-effective, and scalable diagnostic approaches, ultimately revolutionizing precision medicine.

IL-6–174 G/C transversion might decrease male infertility risk: A case-control study

Background: Genetic predispositions have been identified as important factors in male infertility. Among the many genes related to male reproductive function, interleukin 6 (IL-6) has emerged as a key player. Despite the growing recognition of genetic factors in male infertility, the specific association between the IL-6–174 G/C genetic polymorphism and male infertility remains an area that needs further investigation.Objective: This investigation explores the correlation between the IL-6–174 G/C transversion and male infertility.Materials and Methods: In a case-control study, a total of 314 men who referred to the Kashan Infertility Center, Shahid Beheshti hospital, Kashan, Iran, were enrolled for IL-6–174 G/C polymorphism analysis. The study comprised 163 infertile participants as the case group and 151 fertile men as the control group. Following the screening, 2 ml of whole blood was collected from each participant. Cases were categorized into 3 subgroups based on World Health Organization criteria: (i) nonobstructive azoospermia (n = 42), (ii) oligozoospermia (n = 61), and (iii) asthenozoospermia (n = 60). After DNA extraction, genotypes of the samples at the -174 G/C (rs1800795) locus were determined using the polymerase chain reaction-restriction fragment length polymorphism method. Results: Our genetic investigation demonstrated a significant association between the GC genotype and male infertility. Furthermore, a correlation was observed between the heterozygous GC genotype and reduced risk of oligozoospermia and asthenospermia. Additionally, the C allele was correlated with a decreased risk of infertility and specific subgroups such as oligozoospermia and asthenospermia.Conclusion: Our findings suggest that the IL-6–174 G/C transversion could potentially serve as a protective genetic factor against male infertility.

Ayurvedic Personalized Healthcare: Integrating Genomics, Epigenomics and Traditional Wisdom

In the evolving landscape of personalized medicine, integrating Ayurvedic principles with modern genomic science presents a transformative opportunity for healthcare. This paper explores the concept of Prakriti, the unique constitution of individuals as defined in Ayurveda, and its potential correlation with genetic profiles. By merging Ayurvedic insights with genomic and epigenomic research, we propose a framework for personalized healthcare that considers both genetic predispositions and lifestyle factors. The study outlines practical approaches, including the use of Single Nucleotide Polymorphism (SNP) analysis to identify genetic variations linked to specific Prakriti types, and the role of epigenetics in understanding how lifestyle choices influence gene expression. Additionally, we discuss the implementation of Genome-Wide Association Studies (GWAS) to identify biomarkers that can enhance disease prevention and treatment strategies tailored to individual needs. By fostering collaboration between Ayurvedic practitioners and genomic researchers, we aim to promote a holistic understanding of health that bridges ancient wisdom with contemporary science. Ultimately, this integration not only enriches personalized healthcare but also paves the way for innovative treatment solutions that honor both genetic diversity and traditional knowledge.

Association of adenylate cyclase activity in vasopressor-type neurally mediated syncope based on the α2b-AR gene.

Neurally mediated syncope (NMS) arises from a neural reflex; however, its underlying cause remains unknown. Previous research has shown that variations in the Gi-α signal transduction rate led to changes in adenylate cyclase (AC) activity levels. Thus, we hypothesized that these fluctuations in AC activity could contribute to NMS. This study aimed to investigate the receptor genes associated with glutamate (Glu) repeat polymorphism sites Glu12 and Glu9 in the α2B-AR gene. A total of 50 patients with vasodepressor-type (VT)-NMS and 20 healthy volunteers were included in this study. We assessed AC activity levels and blood pressure responses during the head-up tilt (HUT) test and conducted a Glu repeat polymorphism analysis to explore its potential association with NMS. Our findings showed significantly higher AC activity in patients with the Glu12/12 homotype than healthy volunteers across all four HUT test points. Conversely, patients with the Glu9/12 heterotype exhibited a significant difference only 10 min after the test initiation, suggesting a pronounced activation effect of the β2-AR Gs-α subunit in these individuals. Both genotypes displayed the greatest blood pressure fluctuations under 70° tilt stress, with patients with Glu12/12 showing consistent cardiac load and higher values than those with Glu9/12 at two points. Notably, the frequency of NMS onset within 20 min during the tilt test varied, with one Glu12/12 patient and seven Glu9/12 patients experiencing syncope. Additionally, patients with the Glu9/12 heterotype were found to have a higher risk of syncope after prolonged standing compared to those with the Glu12/12 homotype. These results suggest that patients with the Glu12/12 homotype exhibit elevated AC activity levels, which may help increase blood pressure to prevent syncope. This study underscores that variations in AC activity among different gene types could influence the frequency of NMS onset during standing.

Association Between the Aromatase rs2414096 Polymorphism and Prostate Cancer

Abstract Objectives The purpose of this study was to investigate association between the aromatase (CYP19A1) rs2414096 polymorphism and the risk of prostate cancer development, progression and aggressiveness in the Slovak population. Background Aromatase catalyses the final reaction of androgens aromatization to estrogens, irreversible conversion of androstenedione to estrone and testosterone to estradiol. Methods The study population consisted of 721 prostate cancer patients and 660 men in the control group. Genotyping was performed via restriction fragment length polymorphism analysis. The expression levels of CYP19A1 in prostate cancer tissues were compared with those in benign prostatic hyperplasia tissues. Results The CYP19A1 rs2414096 AA genotype and A allele were significantly associated with an increased risk of prostate cancer development. The significant association between this genotype and PSA level ≥ 10 ng/ml, Gleason score ≥ 7 and with the presence of metastases was observed. Significantly decreased relative expression of CYP19A1 was detected in prostate cancer tissues. Patients with the AA genotype presented higher relative CYP19A1 expression than did those with the GG genotype. Significantly lower circulating testosterone levels and higher serum PSA levels were detected in patients with the AA genotype. Conclusion The CYP19A1 rs2414096 polymorphism was significantly associated with prostate cancer development and aggressiveness in Slovak patients.

The relationship between probiotics and prebiotics, kidney dysfunction and mortality - Results from a longitudinal cohort study and Mendelian randomization.

The benefits of probiotics/prebiotics consumption on chronic kidney disease (CKD) and mortality remains controversial. This study investigates the association of probiotics/prebiotics consumption with chronic kidney disease (CKD) and mortality. Clinical data were retrieved from the National Health and Nutrition Examination Survey (NHANES) 2005-2016 database. Weighted multivariable logistic and liner regression models, cox proportional hazards models and stratified analysis were used to analyse the relationships between consumption of probiotics/prebiotics, renal parameters, CKD and mortality. We also conducted a two-sample Mendelian randomization (MR) analysis of single nucleotide polymorphisms (SNPs) related to different genera of gut microbiota to assess their causal relationships with CKD and mortality. 15,291 subjects were analysed (897 with consumption of probiotics/prebiotics and 14,394 without). The use of probiotics/prebiotics showed an inverse correlation with urinary albumin-to-creatinine ratio (UACR) (P<0.05). Probiotics/prebiotics use was associated with lower risk of CKD in subjects with hypertension, hyperlipidaemia and diabetes mellitus. The consumption of probiotics/prebiotics was associated with a significantly lower risk of all-cause mortality in different regression models (P<0.001, for all), but the lower risk of cardiovascular mortality did not reach statistical significance (P>0.05, for all)]. MR analysis showed negative associations between the genetically predicted genus Flavonifractor and risk of CKD and diabetic kidney disease (DKD). After multivariable regression, and cox proportional hazards analysis, we found that the use of probiotics/prebiotics was associated with improved kidney and mortality outcomes in the general population from NHANES database. The two-sample MR analysis provided further genetic evidence that a distinct genus of gut microbiota was associated with reduced risk of CKD, DKD and mortality.

A cross-tissue transcriptome-wide association study identifies new susceptibility genes for insomnia.

Despite a significant genetic component to insomnia (heritability: 22%-25%), the genetic loci that modulate insomnia risk remain limited. We used the Unified Test for Molecular Markers (UTMOST) for transcriptome-wide association studies (TWAS) across various tissues, integrating summary statistics from a Genome-Wide Association Study (GWAS) of 462,341 European participants with gene expression data from the Genotype-Tissue Expression (GTEx) project. Three validation methods (FUSION, FOCUS, and MAGMA) were used to confirm important genes. Tissue and functional enrichment analyses of insomnia-related single-nucleotide polymorphisms (SNPs) were conducted with MAGMA. Conditional and joint analyses, along with fine mapping, were used to enhance our understanding of insomnia's genetic architecture. Mendelian randomization was used to assess causal associations between significant genes and insomnia. Two novel susceptibility genes, VRK2 and MMRN1, were identified as linked to insomnia risk using four TWAS approaches. Mendelian randomization analysis suggests VRK2 increases the risk of insomnia. Tissue enrichment analyses indicated that insomnia-related SNPs were enriched in specific brain regions, including the cerebellum, frontal cortex (BA9), hypothalamus, and hippocampus. Conditional and joint analyses identified two genomic regions (2p16.1 and 4q22.1). Functional enrichment analyses showed that pathways related to insomnia involve the SMAD2/3 pathway, synaptic function, and oxidative stress. This study identifies two new candidate genes, VRK2 and MMRN1, that may contribute to insomnia risk through neurodevelopment, neuroinflammation, and synaptic function, suggesting potential therapeutic targets.NEW & NOTEWORTHY This study identifies VRK2 and MMRN1 as novel susceptibility genes for insomnia through transcriptome-wide association studies (TWAS). Mendelian randomization confirms a causal link between VRK2 and insomnia. Key brain regions, including the cerebellum and frontal cortex, and critical pathways like SMAD2/3 signaling and oxidative stress are implicated. These findings provide new insights into the genetic basis of insomnia.

Association of Matrix Metalloproteinase-1 Promoter Genotypes With Endometriosis Risk.

Over-expression of matrix metalloproteinase-1 (MMP-1) has been suggested as a biomarker for endometriosis. However, the genetic influence of MMP-1 in the pathogenesis of endometriosis remains unclear, with its role yet to be fully elucidated. This study aimed to investigate the association between MMP-1 rs1799750 promoter polymorphisms and the risk of developing endometriosis. This hospital-based case-control study included 203 women diagnosed with endometriosis and 636 age-matched controls. Genotyping of the MMP-1 rs1799750 polymorphism was conducted using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Among the patients with endometriosis, the distribution of genotypes 2G/2G, 2G/1G, and 1G/1G at MMP-1 rs1799750 was 52.7%, 41.4%, and 5.9%, respectively. This distribution significantly differed from that of the control group, which exhibited frequencies of 41.3%, 48.3%, and 10.4%, respectively (p for trend=0.0092). In the dominant model, carriers of the 2G/1G and 1G/1G genotypes had a reduced prevalence in the endometriosis group compared to 2G/2G carriers [odds ratio (OR)=0.63, 95% confidence interval (95%CI)=0.46-0.87, p=0.0058]. Additionally, the 1G allele frequency in the endometriosis group was 26.6%, significantly lower than the 34.5% observed in controls (OR=0.69, 95%CI=0.54-0.88, p=0.0037). The 1G allele of MMP-1 rs1799750 is associated with reduced susceptibility to endometriosis in the Taiwanese population. These results highlight the potential of MMP-1 rs1799750 polymorphism as a protective genetic marker, warranting further investigations to explore its genotype-phenotype correlation and underlying biological mechanisms.

Characteristics of polymorphism of genes involved in the regulation of glucose metabolism and steroid hormone synthesis in patients with polycystic ovary syndrome

Background: Polycystic ovary syndrome is an urgent problem of gynecological endocrinology. Currently, a number of genes have been studied that control glucose metabolism and are involved in the synthesis, conversion into an active form and transport of steroid hormones, mutations in which with a certain degree of reliability can serve as a diagnostic criterion for polycystic ovary syndrome. Aim: The aim of this study was to evaluate the PPARG Pro12Ala, INS 223HphI AT, and SHBG (TAAAA)n gene polymorphisms in patients with polycystic ovary syndrome and in healthy individuals. Materials and methods: The polymerase chain reaction method and restriction fragment length polymorphism analysis were used. The frequencies of alleles and genotypes of polymorphic variants were studied in 136 women with polycystic ovary syndrome and 47 women in the control group: Pro12Ala (PPARG gene), 223HphI AT, (INS gene) and (TAAAA)n repeats (SHBG gene). Results: The distribution of the allele and genotype frequencies for the PPARG (rs1801282) and INS (rs689) genes in patients with polycystic ovary syndrome and in healthy individuals did not differ. The distribution of the genotype frequencies in the group of women with polycystic ovary syndrome differed (p = 0.02) from that in the control group for the (TAAAA)n polymorphism in the SHBG gene. In the presence of a long repeat in the SHBG gene in at least one of the homologous chromosomes, the probability of a woman having polycystic ovary syndrome increases by 2.5 times. Patients with a verified A/A genotype (INS), in the presence of an SHBG gene allele with a long repeat, have a ten-fold higher risk of developing polycystic ovary syndrome than women with SHBG gene short alleles. Conclusions: Patients with long repeats in the SHBG gene are at risk for developing polycystic ovary syndrome with phenotypes A, B, and C, especially in combination with the presence of the A/A genotype, class I (INS).

589. Late Onset Invasive Group B Streptococcal Disease Outbreak in a Neonatal Intensive Care Unit Identified Through Whole Genome Sequencing — Connecticut, 2020–2024

Abstract Background Group B Streptococcus (GBS) is a major cause of neonatal sepsis. Outbreaks of GBS late-onset disease (LOD), defined as infection during the first 7–89 days of life, are uncommon. In September 2023, 4 GBS LOD cases were reported by a neonatal intensive care unit (NICU) to the Connecticut Department of Public Health (DPH). We investigated to characterize the outbreak and guide response. Methods We identified patients with invasive (i.e., GBS isolated from a sterile site) LOD hospitalized in the NICU through review of data from DPH’s Active Bacterial Core Surveillance Program during January 2019–April 2024. We distinguished outbreak cases through whole-genome sequencing (WGS) of associated bacterial isolates. Single nucleotide polymorphism (SNP) analysis with a cutoff of ≤12 SNPs defined a case as outbreak-related. We abstracted medical records to collect case data. We performed 3 on-site assessments of infection prevention and control (IPC) practices and policies. To monitor response effectiveness, we performed weekly GBS colonization screening (aural, oropharyngeal, rectal sites) of infants admitted to the NICU during December 2023–April 2024. We performed WGS on GBS isolates associated with each colonization. Results We identified 12 outbreak-related cases during January 2020–April 2024 based on WGS. Median case interval, time between illness onset, was 85 days but ranged from three days to 458 days; 3 outbreak-patients died. Chart abstraction and on-site assessments indicated the milk room as an area for potential transmission. Variability was noted in adherence to appropriate hand hygiene, personal protective equipment use, and environmental cleaning throughout the NICU. Screening identified 7 colonized infants; GBS isolates from 3 infants matched the outbreak, and 1 colonized infant developed LOD. We recommended addressing IPC gaps and continuing GBS colonization screening to monitor for ongoing transmission. Conclusion This investigation highlights the integration of WGS with classic epidemiology to distinguish outbreak-related cases with long intervals between identification. In LOD GBS outbreaks where IPC gaps appear to contribute to transmission, colonization screening and WGS can evaluate effectiveness of implementation of protocols to address IPC gaps. Disclosures Meghan Maloney, MPH, Pfizer Global R&amp;D: Former employee, separated in 2009. I do have a retirement entitlement which I do not actively manage/no stock options. PGRD offers periodic buy outs

Integrating mitochondrial and lysosomal gene analysis for breast cancer prognosis using machine learning

The impact of mitochondrial and lysosomal co-dysfunction on breast cancer patient outcomes is unclear. The objective of this study is to develop a predictive machine learning (ML) model utilizing mitochondrial and lysosomal co-regulators in order to provide a foundation for future studies focused on breast cancer (BC) patients’ stratification and personalized interventions. Firstly, Differences and correlations of mitochondrial and lysosome related genes were screened and validated by differential analysis, copy number variation (CNV), single nucleotide polymorphism (SNPs) and correlation analysis. WGCNA and univariate Cox regression were employed to identify prognostic mitochondrial and lysosomal co-regulators. ML was utilized to further selected these regulators and then the coxboost + Survivor-SVM model was identified as the most suitable model for predicting outcomes in BC patients. Subsequently, the association between the immune and mlMSGs score was investigated through scRNA-seq. We found that the overall immunoinfiltration of immune cells was decreased in the high-risk group, it was specifically noted that B cell mlMSGs activity remained diminished in high-risk patients. Finally, the expression and function of the key gene SHMT2 were confirmed through in vitro experiments. This study shows that the ML model demonstrated a strong association with patient outcomes. Analysis conducted through the model has identified decreased B-cell immune infiltration and increased mlMSGs activity as significant factors influencing patient prognosis. These results may offer novel approaches for early intervention and prognostic forecasting in BC.

Exploring the impact of deleterious missense nonsynonymous single nucleotide polymorphisms in the DRD4 gene using computational approaches

Dopamine receptor D4 (DRD4) plays a vital role in regulating various physiological functions, including attention, impulse control, and sleep, as well as being associated with various neurological diseases, including attention deficit hyperactivity disorder, novelty seeking, and so on. However, a comprehensive analysis of harmful nonsynonymous single nucleotide polymorphisms (nsSNPs) of the DRD4 gene and their effects remains unexplored. The aim of this study is to uncover novel damaging missense nsSNPs and their structural and functional effects on the DRD4 receptor. From the dbSNP database, we found 677 nsSNPs, and then we analyzed their functional consequences, disease associations, and effects on protein stability with fifteen in silico tools. Five variants, including L65ICL1P (rs1459150721), V1163.33D (rs761875546), I1293.46S (rs751467198), I1564.46T (rs757732258), and F2015.47S (rs199609858), were identified as the most deleterious mutations that were also present in the conserved region and showed lower interactions with neighboring residues. To comprehensively understand their impact, we docked agonist dopamine and antagonist nemonapride at the binding site of the receptor, followed by 200 ns molecular dynamics simulations. We identified the V116D and I129S mutations as the most damaging, followed by F201S in the dopamine-bound states. Both the V116D and I129S variants demonstrated significantly high RMSD, Rg, and SASA, and low thermodynamic stability. The F201S-dopamine complex exhibited lower compactness and higher motions, along with a significant loss of hydrogen bonds and active site interactions. By contrast, while interacting with nemonapride, the impact of the I156T and L65P mutations was highly deleterious; both showed lower stability, higher flexibility, and higher motions. Additionally, nemonapride significantly lost interactions with the active site, notably in the I156T variant. We also found the V116D-nemonapride complex as structurally damaging; however, the interaction patterns of nemonapride were less altered in the MMPBSA analysis. Overall, this study revealed five novel deleterious variants along with a comprehensive understanding of their effect in the presence of an agonist and antagonist, which could be helpful for understanding disease susceptibility, precision medicine, and developing potential drugs.

Association of the SNP in akirin 2 Gene With Growth and Carcass Traits in Zavot Cattle.

Understanding the genetic factors that influence meat yield is crucial due to the economic importance of average daily live weight gain (ADWG) in livestock. This study investigates the relationship between the c.*188G>A SNP in the 3'-UTR region of the akirin 2 gene and growth traits in Zavot cattle, focusing on the gene's role in muscle development. Genotyping of the c.*188G>A SNP was conducted using polymerase chain reaction-restriction fragment length polymorphism analysis, revealing frequencies of 0.09 for AA, 0.75 for AG and 0.16 for GG genotypes, respectively. Our findings demonstrate a significant association between this SNP and ADWG, as well as percentage. These results suggest that the c.*188G>A SNP within akirin 2 could serve as a valuable DNA marker for predicting ADWG and percentage traits in Zavot cattle.