Gene Frequencies Research Articles

Interactions between ABC gene polymorphisms and processing speed in predicting depression severity

BackgroundABC family genes encode ATP-binding cassette proteins, which are involved in the transport of various substances and are associated with major depressive disorder (MDD); however, their clinical significance in MDD remains unclear. Therefore, this study aimed to investigate whether ABC family genes are associated with cognitive function, and the combined effects of genes and cognitive function on the severity of depression.MethodLinear models or logistic regression models were used to investigate the associations of ABC family gene variants with clinical symptoms and cognitive function in 805 MDD patients (12–65 years old) and 1493 age-matched healthy controls (HCs). Seven single nucleotide polymorphisms (rs28401781, rs4148739, rs3747802, rs1109866, rs1109867, rs3731885, and rs3755047) of ABCB1 and ABCB6 were selected. The cognitive function was assessed by the Wisconsin Card Sorting Test (WCST), Tower of Hanoi Test (TOH), Trail Making Test (TMT), and Verbal Fluency Test (VF).ResultsSignificant differences in gene frequency and genotype frequency were observed at the rs1109866 (X2 = 8.22, p = 0.004; X2 = 9.82, p = 0.007) and rs1109867 (X2 = 7.35, p = 0.007; X2 = 9.15, p = 0.010) between MDD patients and HCs, even after correction. While rs28401781 (t = 2.78, p = 0.006) and rs4148739 (t = 3.08, p = 0.003) were associated with the TOH test. And both rs1109866 and rs1109867 interacted with TMT results to influence depression severity in MDD patients.ConclusionThe results suggest that ABC family genes influence the severity of depression through cognitive functioning, providing possible evidence for genetic markers in MDD patients.

A Boundary Value Problem for Algebraically Accelerated Frequency of Mutations Governed by Fisher–Kolmogorov–Petrovskii–Piskunov Equation

A new generalized Fisher–Kolmogorov–Petrovskii–Piskunov equation [Formula: see text] is introduced and subjected to Lie’s Classical Method to establish the existence of the traveling waves. Indeed, exact expressions for both the solution [Formula: see text], with [Formula: see text] and the wave speed [Formula: see text] are subsequently derived by the regular perturbation method and are shown to contain both the reports of Ablowitz and Zeppetella [Explicit solutions of fisher’s equation for a special wave speed, Bulletin of Mathematical Biology 41(6) (1979) 835–840] when [Formula: see text] and Kaliappan [An exact solution for the traveling waves of [Formula: see text], Physica D: Nonlinear Phenomena 11(3) (1984) 368–374] when [Formula: see text], respectively. Remarkably, the generalized Huxley equation is a special case of our model equation. The form of the traveling waves for the Fisher–Kolmogorov–Petrovskii–Piskunov equations is identified with the regular perturbation method and the Binomial series. Our study is in agreement with the conclusion of Fisher [The wave of advance of advantageous genes, Annals of Eugenics 7(4) (1937) 355–369] that the increase of frequency of mutant genes results in the diffusion of the mutant genes into the long range.

Role of CRISPR-Cas System on Virulence traits and Carbapenem Resistance in Clinical Klebsiella pneumoniae Isolates

Background and Objective(s)The bacterial adaptive immune system known as CRISPR-Cas (clustered regularly interspersed short palindromic repeats-CRISPR-associated protein) is engaged in defense against various mobile genetic elements (MGEs) such as plasmids and bacteriophages. The purpose of this study was to characterize the CRISPR-Cas systems in carbapenem-resistant Klebsiella pneumoniae isolates and assess any possible correlation between these systems with antibiotic susceptibility, biofilm formation, and bacterial virulence. Materials and MethodsA total of 156 CRKP isolates were collected from different specimens of the inpatients. Biofilm formation and antibiotic susceptibility testing were evaluated using standard methods. Furthermore, the CRISPR-Cas system subtype genes, 11 carbapenemase genes, and 17 virulence genes were identified using separate standard PCR reactions. The diversity of the isolates was determined by random amplified polymorphic DNA (RAPD)-PCR. ResultsThe development of biofilms and antibiotic susceptibility of several CRKP isolates were significantly correlated with the absence or presence of the CRISPR-Cas system. PCR analysis of carbapenemase genes revealed that the frequency of the blaNDM-1 gene was significantly higher in the isolates with the subtype I-E CRISPR-Cas system. Moreover, the isolates with the subtype I-E CRISPR-Cas system exhibited a propensity to possess more virulence genes such as allS, k2A, wcaG, aerobactin, rmpA, iroN, magA, rmpA2, kfu, iutA, iucB, ybtS, repA, and terW. ConclusionCRISPR-Cas systems could affect the antibiotic susceptibility, capacity for biofilm formation, and virulence of Klebsiella pneumoniae. Our findings showed that the isolates containing the CRISPR-Cas system were moderate or strong biofilm producers and had a higher frequency of virulence genes.

Genomic landscape study of esophago-gastric adenocarcinoma (EGAC) in young patients under the age of 30 years.

480 Background: Despite recent advances in treatment of EGAC, prognosis continues to be poor with reported 5-year survival of less than 30%. EGAC is more frequently diagnosed at an old age with the median age at diagnosis around 65 years. However, approximately 10% of EGAC are diagnosed at a younger age of less than 50 years and those patients present with more advanced stages resulting in worse prognosis. Our study investigated the genomic landscape of EGAC diagnosed under the age of 30 years to better understand the characteristics of EGAC occurring in very young population. Methods: 8,001 cases of clinically advanced EGAC who underwent comprehensive genomic profiling (CGP) from 2012 to 2024 were included in the study. Patients aged less than 30 years were classified as ‘EGAC-young’ and patients aged 50 and older were classified as ‘EGAC-old’. All classes of genomic alterations (GA), microsatellite instability high (MSI-high) status, tumor mutation burden (TMB), genomic ancestry, genomic signature, and homologous recombination defect signature (HRDSig) were determined from the sequencing data. PD-L1 was measured by IHC using the Dako 22C3 tumor proportional score (TPS) system. Comparisons utilized the Fisher Exact method with the Benjamini-Hochberg adjustment to reduce the false discovery rate. Results: Out of 8,001 cases, 7389 (92.4%) were classified as ‘EGAC-old’ and 26 (0.3%) as ‘EGAC-young’. Both groups had a higher frequency of male patients but there was no significant difference between the two groups (86.4% vs 76.9%; NS). Median GA per tumor was 6 in both groups. The ‘EGAC-old’ featured a significantly higher frequency of EUR ancestry (92.0% vs 73.1%; P=0.026). There were no significant differences in clinically important GA between both groups, including similar ERBB2 GA (21.2% vs 30.8%; NS) and FGFR3 GA (1.2% vs 7.7%; NS). There was a trend of more frequent GA of AKT2, CCNE1, and KEAP1 noted in ‘EGAC-young’ (0.9% vs 11.5%, 8.5% vs 26.9%, 1.3% vs 11.5%, respectively; P=0.071). MSI-high status was 3.1% in the ‘EGAC-old’ but not detected in the ‘EGAC-young’ (NS). The median TMB was higher in the ‘EGAC-old’ vs ‘EGAC young’ (3.8 mutations/Mb vs 1.9 mutations/Mb; P=.003). The frequencies of a positive HRDSig were similar in both groups (5.6% vs 8.0%; NS). There were no significant differences in COSMIC trinucleotide signatures. PD-L1 expression was identified in greater than 20% of the ‘EGAC-old’ but was not measured in the ‘EGAC-young’. Conclusions: Clinically advanced EGAC in young patients under the age of 30 years features a genomic landscape that differs from EGAC identified in older patients, including lower TMB and a trend of increased GA frequency of genes related to poor prognosis in other types of cancer. Further studies are warranted to utilize CGP findings in identifying potential implications for treatment and prognostication in these rare cases of EGAC occurring in very young patients.

Proximal bronchiolar adenoma with malignant transformation to invasive mucinous adenocarcinoma with 4 years follow-up: a case report and literature review

BackgroundBronchiolar adenoma (BA) is a rare benign tumor originating in the bronchial mucosal epithelium and occurring primarily in the periphery of the lung. The most prominent histopathological feature of BA is a double-layer bronchial epithelium containing continuous basal cell layers. However, due to the high mutation frequency of the driver gene, there is still debate as to whether BA has the potential for malignant transformation. In frozen sections, basal cells are difficult to identify under the microscope, which makes it difficult to distinguish from mucinous adenocarcinoma, especially when BA malignancies transform into invasive mucinous adenocarcinoma (IMA), which can only be distinguished by histomorphological criteria, greatly increasing the difficulty of diagnosis.Case summaryIn this paper, we present a case study of a 59-year-old man whose chest computed tomography (CT) revealed a progressively enlarging, high-density nodule over a four-year period in the outer basal segment of the right lower lobe. Consequently, he underwent thoracoscopic wedge resection of the right lower lobe. The postoperative pathological diagnosis revealed BA with mucous gland structure formation combined with partial basal cell loss, raising the possibility of malignant transformation into IMA. Regular postoperative follow-up showed no recurrence or metastasis. Hybridization Capture-based next-generation sequencing (NGS) analysis detected driver gene mutations in Kirsten Rat Sarcoma viral oncogene homolog (KRAS) and Cyclin-Dependent Kinases (CDK) 6 in the case, thereby inferring the malignant transformation of BA into IMA.ConclusionIn this case, the detection of driver gene KRAS mutation and loss of continuity in the basal cell layer within the mucous glandular structures of the nodule suggests the malignant transformation of BA into IMA, inferring the malignant potential of BA.

Antimicrobial Resistance, Virulence Gene Profiling, and Spa Typing of Staphylococcus aureus Isolated from Retail Chicken Meat in Alabama, USA

Antibiotic-resistant Staphylococcus aureus (S. aureus) in retail meat poses a public health threat requiring continuous surveillance. This study investigated the frequency of isolation, toxin genes, and antibiotic resistance profile of S. aureus recovered from retail poultry meat samples and presented results beneficial to public health interventions. Of 200 samples collected, 16% (32/200) tested positive for S. aureus, and these were recovered from thigh 37.5% (12/32), wing 34.4% (11/32), gizzard (15.6% (5/32), and liver 12.5% (4/32) samples. Findings of spa typing analysis revealed that 68.8% (22/32), 18.8% (6/32), 9.4% (3/32), and 3.0% (1/32) of the isolates belonged to the spa types t267, t160, t548, and t008, respectively. For antibiotic susceptibility testing, 12.5% (4/32) of the isolates were resistant to only penicillin, but one isolate (1/32; 3%) showed resistance to the antibiotics penicillin, erythromycin, ampicillin, and oxacillin. PCR analysis revealed that 9.4% (3/32) of the isolates carried the mecA gene associated with methicillin-resistant Staphylococcus aureus (MRSA) isolates. One MRSA isolate was identified as a t008 spa type, and harbored a 26,974 bp-sized plasmid, which was the source of its resistance to penicillin, ampicillin, erythromycin, and oxacillin. The staphylococcal enterotoxin (SE) genes seg, sei, sek, seb, selm, and seln were also identified among the isolates, and mostly the antimicrobial and enterotoxin genes were carried on plasmids of the isolates. This study raises awareness on the continuous circulation of pathogenic microbes like S. aureus in retail poultry meat.

Sex disparities in the association between rare earth elements exposure and genetic mutation frequencies in lung cancer patients

The ubiquitous use of rare earth elements (REEs) in modern living environments raised concern about their impact on human health. With the detrimental and beneficial effects of REEs reported by different studies, the genuine role of REEs in the human body remains a mystery. This study explored the association between REEs and genetic mutations in patients with lung adenocarcinoma (LUAD). A cohort of 53 LUAD patients underwent tumor DNA sequencing (1123 cancer-related genes) and plasma REE (lanthanum (La), cerium (Ce), praseodymium (Pr), neodymium (Nd), and yttrium (Y)) quantification. We found divergent relationships between plasma REE levels and mutation load between sexes. Specifically, Ce levels and mutation load were positively correlated in males but negatively correlated in females, while La exposure exhibited opposite associations in the two sexes. This observation was validated using the Bayesian Kernel Machine Regression (BKMR) model. Additionally, plasma REE levels was associated with specific mutation types and variant allele frequencies (VAFs) of particular genes in a sex-dependent manner. Mutational signature analysis revealed sex-specific associations of La with indel signatures. These findings highlight the intricate interplay between plasma REE levels and genetic mutations in LUAD, emphasizing the need for a personalized, sex-oriented approach to understand and treat this disease.

Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.

The pangenome of a species is the set of all genes carried by at least one member of the species. In bacteria, pangenomes can be much larger than the set of genes carried by a single organism. Many questions remain unanswered regarding the evolutionary forces shaping the patterns of the presence/absence of genes in pangenomes of a given species. We introduce a new model for bacterial pangenome evolution along a species phylogeny that explicitly describes the timing of appearance of each gene in the species and accounts for three generic types of gene evolutionary dynamics: persistent genes that are present in the ancestral genome, private genes that are specific to a given clade, and mobile genes that are imported once into the gene pool and then undergo frequent horizontal gene transfers. We call this model the Persistent-Private-Mobile (PPM) model. We develop an algorithm fitting the PPM model and apply it to a dataset of 902 Salmonella enterica genomes. We show that the best fitting model is able to reproduce the global pattern of some multivariate statistics like the gene frequency spectrum and the parsimony vs. frequency plot. Moreover, the gene classification induced by the PPM model allows us to study the position of accessory genes on the chromosome depending on their category, as well as the gene functions that are most present in each category. This work paves the way for a mechanistic understanding of pangenome evolution, and the PPM model developed here could be used for dynamics-aware gene classification.

Frequency of cry-like genes in Bacillus thuringiensis strains of the Crimean microorganism collection

The entomopathogenic strains of Bacillus thuringiensis are used in the development of new-generation biopreparations against leaf-eating insects. The present study was aimed at analyzing the frequency of cry-like genes in the strains and at identifying a promising strain for the development of an entomopathogenic biopreparation on its basis. The study materials included the entomopathogenic strains of Bacillus thuringiensis obtained from the Crimean microorganism collection of the Crimean Agricultural Research Institute. The entomopathogenic effect of promising strains was studied in laboratory experiments on Coleoptera and Lepidoptera larvae. The following strains of Bacillus thuringiensis were identified as the most promising, i.e., containing at least four toxin genes: 708 (cry1, thuE, cry7-8, cry11), 942 (cry1, thuE, cry11, vip), 949 (cry1, thuE, cry4, cry7-8), 989 (cry1, thuE, cry11, vip), 0162 (cry1, thuE, cry11, vip), 0307 (cry1, thuE, cry4, cry7-8), 0308 (cry1, thuE, cry4, cry7-8), 0363 (cry1, thuE, cry5, cry11) и 0371 (cry1, thuE, cry9, cry11). The isolated strains of Bacillus thuringiensis 0162, 0307, 0363, and 0371 were found to have a high entomopathogenic effect on the larvae of the Colorado potato beetle and elm-leaf beetle (88.3–100%), as well as the caterpillars of ermine moth, cabbage moth, brown-tail moth, and fall webworm (92.3–100%). It is shown that Bacillus thuringiensis strain 0371 goes through all traditional stages of development and exhibits complete release of crystals and spores from the sporangium within 45–48 h. Thus, strain 0371 can be used to develop specifications for manufacturing a plant protection biopreparation.

Emergence of multi-drug-resistant, vancomycin-resistant, and multi-virulent Enterococcus species from chicken, dairy, and human samples in Egypt.

The present study aimed to detect the frequency of vancomycin resistance and virulence genes' profiles of multi-drug-resistant (MDR) enterococcal isolates from different sources and to investigate the sequence heterogeneity between the esp genes of MDR and vancomycin-resistant Enterococcus faecalis isolates from chicken and human sources. Conventional phenotypic methods identified 91 isolates (60.7%) as Enterococcus species, and these isolates were retrieved from dairy (37/52), chicken (35/54), and human (19/44) origins. Enterococcal isolates were frequently resistant to rifampin (67%), and 38.5% of the isolates were MDR. Of the 22 vancomycin-resistant enterococci (VRE) detected isolates, 11 (50%), 9 (41%), 1 (4.5%), and 1 (4.5%) isolate were identified as E. faecium, E. faecalis, E. casseliflavus, and un-specified Enterococcus spp., respectively. Moreover, 22 (100%) and 19 (86.4%) isolates harbored vanA and vanB genes, respectively. Of note, gelE and asa1 genes were more prevalent among the tested isolates (95.5% each), and the multi-virulence criteria were detected among 68.2% of the examined isolates. The sequences of esp genes of E. faecalis from the chicken breast meat and human urine samples were 100% identical with other esp genes and pathogenicity islands on GeneBank, which is undesirable. Our findings require strict hygienic measures during the processing of chickens and their by-products to minimize the possibility of transmission of virulent enterococcal strains. Furthermore, the use of antimicrobials in poultry and animal production in developing countries should be controlled to minimize the prevalence of MDR and VRE isolates in humans.

Variation in haplotype frequencies of the TAS2R38 gene, associated with the perception of bitter taste

Introduction: Bitter taste perception is a genetic trait that influences food preferences and alcohol consumption behavior. This study investigates the variation in haplotype frequencies of the TAS2R38 gene, associated with sensitivity to bitter compounds, in 26 populations from diverse geographic regions. Three single nucleotide polymorphisms (SNPs) are analyzed: rs713598, rs1726866 and rs10246939, which determine haplotypes such as PAV and AVI. Objectives: The objective is to analyze the variation in haplotype frequencies of the TAS2R38 gene, which is associated with bitter taste perception, in 26 populations.Methods: Data from the 1000 Genomes Project were used, analyzing 5,008 genotyped chromosomes from 26 populations grouped into five macro-populations: African, American, East Asian, European and South Asian. Haplotype and diplotype frequencies were calculated, assessing Hardy-Weinberg equilibrium by Chi-square test (p<0.05) using R software.Results: The results showed that the overall frequency of TAS2R38 diplotypes is 32% for PAV/PAV, 44% for PAV/AVI and 24% for AVI/AVI. African populations presented a high frequency of PAV/AVI (46.4%), while European populations showed a higher prevalence of AVI/AVI (31.5%). Significant deviations in observed versus expected frequencies were identified.Conclusions: The variation in haplotype frequencies of the TAS2R38 gene reflects evolutionary adaptation to different dietary environments. These findings suggest that bitter taste genetics may influence food preferences and consumption behavior

Antibiotic Resistance Profile of Enterovirulent E. coli Isolates Harboring Broad-Spectrum Beta-Lactamase Genes in Cancer Patients at the Laquintinie Hospital in Douala, Littoral Region, Cameroon.

Cases of antibiotic-resistant Escherichia coli (E. coli) infections are becoming increasingly frequent and represent a major threat to our ability to treat cancer patients. The emergence of antimicrobial resistance threatens the treatment of E. coli infections. In this study, the antimicrobial profiles, virulent genes, and the frequency of extended-spectrum beta-lactamase (ESBL) gene carriage in fecal E. coli isolates from cancer patients at the Laquintinie Hospital in Douala (Cameroon) were determined. 507 participants were recruited from October 2021 to March 2023, of whom 307 (60.55%) had cancer and 200 (39.45%) did not. Two hundred and two E. coli were isolated from fecal samples of one hundred and fifteen cancer patients and 47 (87) noncancer patients using EMB LEVINE agar. The antimicrobial resistance profile of the isolates was determined using the Kirby-Bauer disk diffusion method. Virulence and resistance genes were detected by simplex polymerase chain reaction (PCR). E. coli showed significant rates of resistance to amoxicillin, cefotaxime, ceftazidime, piperacillin, tetracycline, and ciprofloxacin in cancer patients compared to noncancer patients. The rate of multidrug resistance (MDR) was significantly (p < 0.05) higher in cancer patients than in noncancer patients. Fifty-five enterovirulent E. coli were identified, of which 24 (43.63%) were EPEC, 13 (23.63%) were EAEC, 6 (10.90%) were ETEC, 10 (18.18%) were STEC, and 2 (3.63%) were EIEC. The frequency of beta-lactamase genes in the 55 ESBL-producing enterovirulent E. coli isolates was determined, and 94.54% harbored at least one ESBL gene, distributed as follows: 80.00% for bla TEM, 67.27% for bla CTX-M, 24.63 for bla OXA, and 36.36% for bla SHV genes. Several associations were observed between virulence factors, resistance genes, and the antimicrobial resistance phenotype. This study revealed the real existence of fecal carriage of ESBL-producing enterovirulent E. coli isolates from cancer patients with a high rate of MDR in the latter.

Determination of &lt;i&gt;MCR-1&lt;/i&gt; Gene and Antibiotic-Resistant &lt;i&gt;Escherichia coli&lt;/i&gt; Isolates from Clinical and Non-clinical Samples

Background: In recent years, resistant infections and antibiotic resistance in livestock have been increasing, and it seems that these issues will cause more problems in the future. Objectives: This study investigates the association between the pattern of Escherichia coli antibiotic resistance (ECAR) and the identification of the mobilized colistin resistance (mcr-1 gene) among clinical and non-clinical samples. Methods: In this study, 265 samples were collected from clinical (human urine, N = 79) and non-clinical sources (animal feces from poultry and livestock farms, N = 186). All samples were processed, and E. coli bacteria were isolated and identified. The agar dilution method was used to evaluate colistin resistance, and the presence of the mcr-1 gene was characterized among E. coli isolates. Results: Out of 265 samples (clinical and fecal), 37.97% (30/79) of clinical samples and 37.63% (70/186) of animal feces showed growth of E. coli. The highest number of E. coli isolates was found in feces from livestock farms (71.48%; 50/70). Antimicrobial susceptibility testing (AST) of E. coli isolated from clinical samples showed that the highest resistance (46.66%) was to ciprofloxacin, and the lowest resistance (16.66%) was to colistin. Analysis of polymerase chain reaction (PCR) data also showed that 60% of colistin-resistant isolates from clinical urine samples and 70% from animal feces samples were positive for the plasmid-mediated mcr-1 gene. Conclusions: The findings indicate that the high frequency of the mcr-1 gene among both clinical and animal-collected isolates may be a significant factor in the development of colistin resistance among circulating E. coli isolates.

Occurrence of virulence genes in multidrug-resistant Escherichia coli isolates from humans, animals, and the environment: One health perspective.

Escherichia coli is one of the critical One Health pathogens due to its vast array of virulence and antimicrobial resistance genes. This study used multiplex PCR to determine the occurrence of virulence genes bfp, ompA, traT, eaeA, and stx1 among 50 multidrug-resistant (MDR) E. coli isolates from humans (n = 15), animals (n = 29), and the environment (n = 6) in Dar es Salaam, Tanzania. Their association with antimicrobial-resistant genes (ARGs) was determined using Principal Component Analysis (PCA). All 50/50 (100%) MDR E. coli isolates carried at least one virulence gene, with 19/50 (38%) carrying four genes, bfp + traT + eaeA + ompA. The findings showed a high occurrence of virulence genes bfp (82%), traT (82%), eaeA (78%), and ompA (72%); the study detected no stx1 in any of the isolates. In humans, the most detected virulence genes were bfp and traT 14/15 (93.3%); for poultry, it was eaeA 13/14 (92.9%); for pigs, was bfp and traT 13/15 (86.7%); while for river water, it was eaeA 6/6 (100%). The study observed no significant association between virulence genes and ARGs. PCA results show the genes ompA, traT, eaeA, and bfp contributed to the virulence of the isolates, and blaTEM, blaCTX-M, and qnrs contributed to ARGs. The PCA ellipses show that isolates from pigs had more virulence genes than those isolated from poultry, river water, and humans. The high frequency of numerous virulence genes in MDR E. coli isolates from humans, animals, and the environment indicates that these isolates have a very high potential to cause diseases that are difficult to treat because they are MDR.

Relative Frequencies of Deleterious Genes in Natural Populations of Drosophila melanogaster Originating from the Nucleoelectric Plant of Laguna Verde, Veracruz

Relative Frequencies of Deleterious Genes in Natural Populations of Drosophila melanogaster Originating from the Nucleoelectric Plant of Laguna Verde, Veracruz

Association of DNA Repair XRCC1 Gene Polymorphism with Leukemia

A group of cancerous diseases of the blood and bone marrow known as leukemias are life-threatening. It is crucial to recognize the leukemic cells lineage when making a diagnosis of leukemia because treatment for the disease depends on whether the cells are myeloid or lymphoid. As per the Observation There is total 300 blood samples in which 150 were leukemic patients and 150 were healthy person. The genotype distribution frequencies of the XRCC1 gene's SNP rs25487 results demonstrate a highly significant connection between heterozygous (GA) rs25487 of the XRCC1 gene and an increased risk of leukemia up to 2-folds (OR=2.52; 95% CI=1.51- 4.20; p=0.0004). The scenario is identical when it comes to homozygous mutant (AA), which also shown a highly significant connection with a reduced risk of leukemia and performs a protective role (OR=0.40; 95% CI=0.23-0.70; p=0.0014). The combined genotype model of mutant and hetero of rs25487 demonstrated a weakly non-significant correlation with leukemia (OR=1.14; 95% CI=0.72-1.82; p=0.5618). This study intended to look at the connection between leukemia risk regulation and XRCC1 polymorphisms, as well as the conceivable relationship between leukemia patients and the XRCC1 polymorphism (rs25487). It was determined that rs25487 was linked to a higher risk of leukemia in people

Understanding mode of gene action governing green forage yield and its component traits in pearl millet

Understanding the genetic control of forage yield and related traits can decide breeding strategies for high-biomass cultivars. In this study, generation mean analysis was used to evaluate gene effects and non-allelic interactions for forage yield and its component traits in pearl millet using two experimental crosses developed by using two high-yielding inbreds IP 18168 and IP 22419 and their six generations (P1, P2, F1, BC1, BC2 and F2) were independently evaluated during Kharif season 2022. Significant variability and the inadequacy of an additive-dominance model highlighted the role of epistasis, with additive × dominance interactions prominent for forage yield and plant height. Dominance and epistatic effects were also crucial for traits like leaf and internode number, leaf length and leaf width. These findings indicated one or two generations of selfing followed by recurrent selection in advanced generations will be useful in enhancing the frequency of genes with increasing effects on green forage yield. Our findings could be helpful in designing the forage pearl millet breeding programs in India.

Prevalence of Salmonella in Poultry Slaughterhouses of Kerman, Iran

Background: Salmonella is a prevalent infectious agent that infects several animals. Chicken is a main meal for humans, and the infectivity of the animal by bacteria threatens both human health and economic conditions. Improving our knowledge regarding the prevalence of Salmonella in chicken can help us organize new strategies to increase the quality of food in Iran. This project aimed to explore the prevalence of Salmonella infection among chickens from poultry slaughterhouses in Kerman, Iran. Methods: In this cross-sectional study, 100 samples of chicken meat from poultry slaughterhouses supplied to shopping centers in Kerman were collected for investigation. To confirm the Salmonella infection, tissues were homogenized under sterile conditions and then either cultured in differentiated media, or their bacterial DNA was extracted and tested by real-time polymerase chain reaction (RT-PCR). The infected chicken underwent a PCR test to determine the Salmonella species. The isolates of Salmonella were subjected to antibiotic susceptibility testing by the disc-diffusion method against imipenem (10 μg), and the presence of the blaNDM gene was detected by PCR. Results: The findings revealed that 50 out of 100 samples were infected by Salmonella, which was confirmed by both microbial culture and RT-PCR. The PCR test demonstrated that three samples were Salmonella Enteritidis, and two samples were Salmonella Typhimurium. Finally, 17 (34%) Salmonella isolates were resistant to imipenem, and the frequency of the blaNDM gene was 38 (76%) out of 50 samples. Conclusion: The isolation of Salmonella from the chicken’s meat may indicate a chicken’s systemic infection and failure to control the most important microbe for public health. Thus, the control measures have to be revised, and a national Salmonella control program should be put in place urgently.

Combined role of PEAR1 and GP genes in the mechanism of aspirin resistance and its clinical significance

Exploring the mechanism of aspirin resistance helps to improve the prevention and treatment of ischemic stroke diseases and reduce the interference of resistance mechanism on the therapeutic effect of aspirin. In this paper, the Affiliated Hospital of Beihua university, together with two other hospitals, was chosen as the research unit, from which 260 AIS patients were selected for aspirin resistance study. The joint role of PEAR1 gene and GP gene in the mechanism of aspirin resistance was discussed by genotyping, TEG assay, univariate analysis, and binary logistic analysis methods. Among the GP1BA genes in AIS patients, the frequency of CC-type genes was as high as 92.03%, and the risk of aspirin resistance was significantly increased in CC-type relative to TT-type. The incidence of rs5924 allele T was significantly higher in the AR group than in the AS group (OR = 1.632, p = 0.006), and there was a significant effect of diabetic conditions on aspirin resistance at the 1% level. Diabetes significantly inhibits plasma proteins in AIS patients and makes aspirin less inhibitory to platelets. Therefore, clarifying the influence of PEAR1 and GP genes in the mechanism of aspirin resistance can be used to obtain the precise loci from the gene therapy point of view to enhance the disease treatment effect of aspirin.

Linkage-based ortholog refinement in bacterial pangenomes with CLARC.

Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying genes into core and accessory clusters of orthologous groups (COGs). However, strict sequence identity cutoffs can misclassify divergent alleles as different genes, inflating accessory gene counts. CLARC (Connected Linkage and Alignment Redefinition of COGs) [https://github.com/IndraGonz/CLARC] improves pangenome analyses by condensing accessory COGs using functional annotation and linkage information. Through this approach, orthologous groups are consolidated into more practical units of selection. Analyzing 8,000+ Streptococcus pneumoniae genomes, CLARC reduced accessory gene estimates by more than 30% and improved evolutionary predictions based on accessory gene frequencies. By refining COG definitions, CLARC offers critical insights into bacterial evolution, aiding genetic studies across diverse populations.