Genes In Genome Research Articles

A novel approach for efficient co-expression of two foreign genes based on the reverse genetic system of Newcastle disease virus

Newcastle disease virus (NDV) is an ideal model for exploring the mechanisms of the virus; it is also an optimal vector for developing vector vaccines and for cancer therapy. A reverse genetic system of NDV Mukteswar strain controlled by eukaryotic cellular RNA polymerase II promoter was established by reverse genetics technology. Based on the reverse genetic system, an open reading frame of the enhanced green fluorescent protein (EGFP) gene be inserted between the P and M genes of the viral genome and flanked with the gene start (GS) sequence and gene end (GE) sequence to form an independent transcription unit. The rescued virus was amplified in specific pathogen-free (SPF) chicken embryos for 10 generations, and the results showed that the recombinant virus could stably express the exogenous gene for at least 10 generations. Efficient expression of two exogenous genes synchronously is essential for the development of NDV-based multivalent vaccine candidates. Explore the possibility of simultaneous and efficient expression of two exogenous genes based on NDV vector. In the present study, a recombinant virus with co-expression of EGFP and cherry fluorescent protein (CFP) inserted between the intergenic regions of the P/M gene as two independent transcription units was successfully rescued. The results showed that the two exogenous genes could be expressed synchronously and efficiently. The results of biological analysis of the expression efficiency of exogenous genes showed that the EGFP in recombinant viruses with two exogenous genes was slightly lower than that of recombinant viruses with one exogenous gene, but the expression efficiency of CFP in recombinant viruses with two exogenous genes was higher than EGFP in both viruses. These recombinant viruses have similar growth kinetics but with a little attenuation in virulence compared with parental viruses. In conclusion, these data indicated that this study successfully established the reverse genetic system of the NDV Mukteswar strain and achieved the purpose of efficient expression of two exogenous genes synchronously in a novel approach, laying the foundation for the development of multivalent vaccines or tumor therapeutics using NDV as a vector.

Aging-Related Gene-Based Prognostic Model for Lung Adenocarcinoma: Insights into Tumor Microenvironment and Therapeutic Implications

Lung cancer remains the leading cause of cancer-related mortality globally, with a poor prognosis primarily due to late diagnosis and limited treatment options. This research highlights the critical demand for advanced prognostic tools by creating a model centered on aging-related genes (ARGs) to improve prediction and treatment strategies for lung adenocarcinoma (LUAD). By leveraging datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), we developed a prognostic model that integrates 14 ARGs using the least absolute shrinkage and selection operator (LASSO) alongside Cox regression analyses. The model exhibited strong predictive performance, achieving area under the curve (AUC) values greater than 0.8 for one-year survival in both internal and external validation cohorts. The risk scores generated by our model were significantly correlated with critical features of the tumor microenvironment, including the presence of cancer-associated fibroblasts (CAFs) and markers of immune evasion, such as T-cell dysfunction and exclusion. Higher risk scores correlated with a more tumor-promoting microenvironment and increased immune suppression, highlighting the model’s relevance in understanding LUAD progression. Additionally, XRCC6, a protein involved in DNA repair and cellular senescence, was found to be upregulated in LUAD. Functional assays demonstrated that the knockdown of XRCC6 led to decreased cell proliferation, whereas its overexpression alleviated DNA damage, highlighting its significance in tumor biology and its potential therapeutic applications. This study provides a novel ARG-based prognostic model for LUAD, offering valuable insights into tumor dynamics and the tumor microenvironment, which may guide the development of targeted therapies and improve patient outcomes.

Exploring Beta-sitosterol’s Role in Breast Cancer Treatment via Integrated Network Pharmacological Analysis and In Vitro Validation

Background Beta-sitosterol, a phytosterol similar to cholesterol, is found in various plants and is recognized for its potential anticancer properties; still, the mechanism of breast cancer (BC) remains elusive. Purpose This study investigates the potential targets of beta-sitosterol in BC using network pharmacological analysis and in vitro validation. Methods Targets of beta-sitosterol and BC were identified from online databases, including Swiss Target Prediction, SuperPred, GeneCards, and DisGeNET. Protein–protein interactions of common targets were analyzed using STRING version 11.0, and network construction and core target screening were performed with Cytoscape 3.8.0. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and gene ontology (GO) annotation were conducted using the ShinyGO web tool. Molecular docking analysis was done with AutoDock Vina and the in vitro validation, including cell viability, apoptosis, and gene expression analysis was done using MTT assay, acridine orange/ethidium bromide staining, and polymerase chain reaction (PCR), respectively. Results Sixty-eight common targets for beta-sitosterol and BC were identified from 209 beta-sitosterol targets and 1,350 BC-related genes. Five core targets (HIF1A, ESR1, STAT3, TNF, and MAPK3) were identified. GO analysis linked common targets to biological processes, cellular components, and molecular functions. KEGG pathway analysis showed enrichment in pathways such as central carbon metabolism in cancer, vascular endothelial growth factor signaling, and prolactin signaling. Beta-sitosterol’s impact on MCF7 cell viability was assessed via MTT assay, and its molecular effects were explored through PCR. Results demonstrated beta-sitosterol’s ability to hinder tumor progression by modulating genes involved in ESR1, mitogen-activated protein kinase, and tumor necrosis factor signaling pathways. Conclusion These findings highlight beta-sitosterol’s potential as an anticancer agent, offering new perspectives for clinical investigations through the modulation of key signaling pathways in BC.

Lipid metabolism subtypes reflects the prognosis and immune profiles of bladder cancer patients by NMF clustering and building related signature

BackgroundLipid metabolism is crucial in tumor formation and progression. However, the role of lipid metabolism genes (LMGs) in bladder cancer (BLCA) are unknown. The purpose of this study was to construct a LMGs-related subtypes that predicted the treatment and prognosis of BLCA patients.MethodsThe Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used for this study. The gene set enrichment analysis (GSEA) was utilized to distinguish functional differences between high-risk (HR) and low-risk (LR) groups. Single-sample GSEA (ssGSEA) was employed to determine potential associations between prognostic outcomes and immune status.ResultsFirst, BLCA patients were divided into two subtypes by non-negative matrix factorization (NMF) clustering, and there were substantial variations in survival status, immune cell infiltration and immune classification between the two subtypes. Next, a prognostic signature involving 8 LMGs was identified (AKR1B1, SCD, CYP27B1, UGCG, SGPL1, FASN, TNFAIP8L3, PLA2G2A). HR patients exhibited worse outcome than LR patients. Multivariate Cox regression analysis confirmed that LMGs-related signature was an independent prognostic indicator of BLCA patients’ survival. Compared with clinicopathological variables, LMGs-related signature showed higher prognostic predictive ability, with an area under curve of 0.720 at 5 years of follow-up. Through immunotherapy analysis, drug sensitivity analysis, TIDE score and immune cell infiltration characteristics, LMGs-related signature was confirmed to accurately predict the prognosis and treatment response of BLCA patients.ConclusionOur newly established prognostic signature, which involved eight LMGs, can give prognostic distinction for BLCA and may eventually lead to novel targets for treatment.

Analysis of transcriptomic data reveals the landscape of cholesterol metabolism in prostate cancer and impact of related signature on survival

BackgroundCholesterol metabolism is essential for the development and progression of prostate cancer (PCa). Our previous study provided a new insight of cholesterol metabolism in the systematic management of PCa. However, the comprehensive role of cholesterol metabolism in PCa remains unclear.MethodsUsing the cholesterol metabolism related genes (CMRGs) downloaded from the MSigDB database, and gene expression data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), we constructed a cholesterol risk index by the least absolute shrinkage and selection operator (LASSO) model, and correlated the risk index with prognosis, tumor mutation burden (TMB), tumor microenvironment (TME) infiltration and response to chemotherapy and immunotherapy. RT-qPCR, western blot, immunohistochemistry, cell proliferation assays by CCK-8 and EdU assays, and cell apoptosis assays by flow cytometry analysis were also performed.ResultsWe found PCa was tightly correlated with the cholesterol metabolism pathways. The cholesterol risk index was an excellent and independent predictor of prognosis for PCa. A nomogram involving the risk index and other clinical factors (age, T stage) was established to explore the clinical value of risk index. We found high-risk index group was associated with worse prognosis, higher TMB, lower infiltration level of CD8+ T cells and a worse response to chemotherapy and immunotherapy. RT-qPCR, western blot and immunohistochemical staining validated the expression level of important CMRGs in PCa. In vitro experiments revealed downregulation of cholesterol metabolism could inhibit the proliferation of PCa cells and promoted their apoptosis.ConclusionsWe demonstrated the comprehensive role of cholesterol metabolism in PCa. Using the risk index, we could predict the prognosis, TME infiltration and response to chemotherapy/immunotherapy of PCa. Better understanding and evaluating the cholesterol metabolism could aid in precision medicine and promoting prognosis of PCa.

Comparative analysis of Hymenasplenium (Aspleniaceae) chloroplast genomes from China

Hymenasplenium is one of the two genera in the large fern family Aspleniaceae. A previous study explored the molecular phylogeny of this genus using several chloroplast DNA fragments and identified three major clades, one of which is the monophyletic Old World clade with southwestern China as its diversity center. To date, there were only a few studies conducted on chloroplast genomes in Hymenasplenium or Aspleniaceae, limiting the understanding of the plastome features and its role in evolution of this group. Here, we studied the complete chloroplast genomes of 12 Hymenasplenium species covering all four subclades of the Old World clade distributed in China. The length of the Hymenasplenium plastomes ranged from 151,617 to 151,930 bp, and contained 129 genes in total, comprising 87 protein-coding, 34 tRNA, and eight rRNA genes. The GC content ranged from 41.8% to 42.1%. Comparative analyses of the Hymenasplenium chloroplast genomes displayed conserved genomic structure and identical gene arrangement. A total of 1,375 simple sequence repeats and 1,639 large repeats were detected. In addition, we detailed hypervariable regions that can be helpful for further phylogenetic research and species delimitation in Hymenasplenium. Furthermore, we supported phylogenetic relationships among major groups as well as possible cryptic speciation found in previous research in the genus. Our study provides new insights into evolutionary history and basic resources for phylogenetic and taxonomic studies of the genus Hymenasplenium.

Unraveling the causal relationship and potential mechanisms between osteoarthritis and breast cancer: insights from mendelian randomization and bioinformatics analysis

ObjectiveTo investigate the effect of osteoarthritis (OA) on the development of breast cancer (BC), and reveal the potential mechanisms underlying the association between them.MethodsA two-step, multivariable Mendelian Randomization (MR) analysis was performed, using statistics from genome-wide association studies (GWAS), to determine the effect of OA on BC and explore the role of major depressive disorder (MDD) in mediating it. Furthermore, transcriptomic analysis based on the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were utilized to establish a prognostic model and explore the underlying mechanisms. Additionally, BC cells and nude mice were used to verify the role of RTN4 in BC.ResultsThe two-sample MR analysis implied a causal relationship between OA and BC at the genetic level, and the mediating MR analysis identified that MDD may play a potential role in mediating it, accounting for approximately 12.20%. Then, we constructed a prognostic model (OA-score) with six genes screened out from datasets and selected RTN4 as the representative gene for validation study. It was demonstrated that high OA-score was an independent risk factor for breast cancer, and patients with low OA-score were more likely to have better OS, higher infiltration level of DC and CD 4 + T cells, and higher expression of some immune checkpoints. Moreover, the knockdown of RTN4 inhibited breast cancer cell proliferation, migration and invasion.ConclusionOur study identified the causal influence of OA on BC mediated by MDD at the genetic level. OA-Score may potentially serve as a new prognostic biomarker for OA related BC patients.

Mitochondrial-related drug resistance lncRNAs as prognostic biomarkers in laryngeal squamous cell carcinoma

Laryngeal squamous cell carcinoma (LSCC) is a common malignant tumor of the head and neck that significantly impacts patients' quality of life, with chemotherapy resistance notably affecting prognosis. This study aims to identify prognostic biomarkers to optimize treatment strategies for LSCC. Using data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), combined with mitochondrial gene database analysis, we identified mitochondrial lncRNAs associated with drug resistance genes. Key long non-coding RNAs (lncRNAs) were selected through univariate Cox regression and Lasso regression, and a multivariate Cox regression model was constructed to predict prognosis. We further analyzed the differences in immune function and biological pathway enrichment between high- and low-risk groups, developed a nomogram, and compared drug sensitivity. Results showed that the prognostic model based on seven mitochondrial lncRNAs could serve as an independent prognostic factor, with Area Under the Curve (AUC) values of 0.746, 0.827, and 0.771 at 1, 3, and 5 years, respectively, outperforming some existing models, demonstrating high predictive performance. Significant differences were observed in immune function and drug sensitivity between the high- and low-risk groups. The risk prediction model incorporating seven drug resistance-related mitochondrial lncRNAs can accurately and independently predict the prognosis of LSCC patients.

Prognostic, oncogenic roles, and pharmacogenomic features of AMD1 in hepatocellular carcinoma

Background AMD1 is the gene encoding S-adenosylmethionine decarboxylase 1. How AMD1 affects the prognosis of hepatocellular carcinoma (HCC) patients is unclear.MethodsUsing the Cancer Genome Atlas (TCGA) liver hepatocellular carcinoma datasets, gene enrichment and immunological traits were compared between groups with high and low AMD1 expression. After altering AMD1 expression in HCC cells, cell viability, the clonal formation rate, and migration and invasion ability were detected. Univariate Cox regression analysis and Pearson correlation were used to screen for AMD1-related genes (ARGs). Multidimensional bioinformatic algorithms were utilized to establish a risk score model for ARGs.Results AMD1 expression was notably increased in the majority of cancer types. High AMD1 expression was associated with adverse outcomes and poorer immunotherapy response in HCC patients. AMD1 exhibited higher expression levels in HCC cell lines. The efficient inhibition of HCC cell proliferation, migration, and invasion in vitro can be achieved through the downregulation of AMD1. The AMD1-related risk score was constructed with the expression of 9 ARGs, and demonstrated high predictive efficacy in multiple validation cohorts. Patients with high risk scores exhibited greater resistance to classical chemotherapy drugs. The nomogram, which consists of age, stage, and the AMD1-related risk score, was used to calculate the probability of survival for each individual.ConclusionThe present study indicates that AMD1 functions as a potential role in HCC progression and may serve as a therapeutic target in HCC. This study constructed a novel AMD1-related scoring system for predicting the prognosis and treatment responsiveness of patients with HCC, enabling the prediction of prognosis and identification of potential treatment targets.

Prognostic and Immunologic Significance of SH2B2 in Colon Adenocarcinoma and its Relationship to Proliferation, Migration, and Invasion.

SH2B adaptor protein 2 (SH2B2, also named APS) is an adaptor protein implicated in the modulation of insulin signaling pathways and glucose metabolism. Its role in colon adenocarcinoma (COAD) is unknown. Data from The Cancer Genome Atlas and Gene Expression Omnibus database were utilized to assess SH2B2 expression and its clinical significance in COAD. We investigated the associations between SH2B2 expression with genomic instability, tumor mutational burden (TMB), DNA methylation, alternative splicing, immune infiltration, and drug sensitivity. A SH2B2 knockdown model was developed to examine its impact on COAD cellular functions. Highly expressed SH2B2 is associated with a poorer prognosis in COAD. SH2B2 expression in COAD is associated with copy number variations, microsatellite instability, methylation patterns, and alternative 5' splicing events, but not with TMB. SH2B2 is positively correlated with mostly immune cells and the expression of PD-1 and CTLA4. The IC50 values of ten drugs were significantly correlated with SH2B2 expression. BI-2536_1086 had a strong binding affinity with SH2B2. Furthermore, the knockdown of SH2B2 reduced the proliferation, migration, and invasion of COAD cells. SH2B2 appears to act as an oncogene in COAD and may serve as a pivotal prognostic and therapeutic target, deserving further exploration.

A novel nuclear RNA HSD52 scaffolding NONO/SFPQ complex modulates DNA damage repair to facilitate temozolomide resistance.

Temozolomide (TMZ) is used in the treatment of glioblastoma (GBM). However, the primary obstacle remains the emergence of TMZ chemotherapy resistance. NONO and SFPQ are multifunctional nuclear proteins involved in genome stability and gene regulation. However, the specific role of NONO and SFPQ in TMZ resistance of GBM remains to be explored. RIP-chip and RNA microarray of TMZ-resistant and parental cells were performed for the gain of HSD52. The effects of HSD52 on TMZ resistance were investigated through in vitro assays, intracranial xenograft and GBM organoid models. The underlying mechanisms were explored by DNA methylation chip, RIP, RNA pulldown assays, among others. GBM clinical samples were rolled in to investigate the clinical significance of HSD52. We identified a novel non-coding RNA, HSD52, that was highly expressed in TMZ-resistant GBM and facilitated the interaction between NONO and SFPQ. H3 ubiquitination attenuation and reduced DNMT1 recruitment increased HSD52 transcription via DNA hypo-methylation. HSD52 formed an RNA duplex with UFL1 mRNA, thereby promoting NONO/SFPQ complex binding to UFL1 mRNA and enhancing its stability, and then contributed to TMZ resistance through activating ATM signaling pathway. In vivo xenograft and GBM organoid models showed significant repression in tumor growth after HSD52 knockout with TMZ treatment. In GBM clinical samples, HSD52 was responsible for the malignant progression and TMZ resistance. Our results revealed that HSD52 could serve as a promising therapeutic target to overcome TMZ resistance, improving the clinical efficacy of TMZ chemotherapy in GBM.

Construction of a prognostic model based on cuproptosis-related genes and exploration of the value of DLAT and DLST in the metastasis for non-small cell lung cancer.

To reveal the clinical value of cuproptosis-related genes on prognosis and metastasis in non-small cell lung cancer. Gene expression profiles and clinical information of non-small cell lung cancer were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases. The data were grouped into training set, internal testing set, and external testing set. A risk prognostic model was constructed by Lasso-Cox regression analysis. Hub genes were identified and evaluated using immunohistochemistry and the transwell migration assay in 50 clinical patients. A total of 17/19 cuproptosis-related genes were differentially expressed in tumors, 8 were significantly associated with prognosis, and 4 were markedly associated with metastasis. A risk model based on 2 cuproptosis-related genes was constructed and validated for predicting overall survival. The risk score was proven to be an independent risk factor for the prognosis of non-small cell lung cancer. Dihydrolipoamide S-acetyltransferase and dihydrolipoamide S-succinyltransferase, key genes in cuproptosis, were proven to be associated with non-small cell lung cancer prognosis and metastasis. Immunohistochemistry showed that their expression significantly predicted metastasis but failed to predict prognosis in non-small cell lung cancer patients. The transwell migration assay further increased the cellular reliability of our findings. The cuproptosis-related genes prognostic model effectively predicted the prognosis of non-small cell lung cancer. Dihydrolipoamide S-acetyltransferase and dihydrolipoamide S-succinyltransferase may serve as predictive markers for metastasis in non-small cell lung cancer.

Lytic Spectra of Tailed Bacteriophages: A Systematic Review and Meta-Analysis

As natural predators of bacteria, tailed bacteriophages can be used in biocontrol applications, including antimicrobial therapy. Also, phage lysis is a detrimental factor in technological processes based on bacterial growth and metabolism. The spectrum of bacteria bacteriophages interact with is known as the host range. Phage science produced a vast amount of host range data. However, there has been no attempt to analyse these data from the viewpoint of modern phage and bacterial taxonomy. Here, we performed a meta-analysis of spotting and plaquing host range data obtained on strains of production host species. The main metric of our study was the host range value calculated as a ratio of lysed strains to the number of tested bacterial strains. We found no boundary between narrow and broad host ranges in tailed phages taken as a whole. Family-level groups of strictly lytic bacteriophages had significantly different median plaquing host range values in the range from 0.18 (Drexlerviridae) to 0.70 (Herelleviridae). In Escherichia coli phages, broad host ranges were associated with decreased efficiency of plating. Bacteriophage morphology, genome size, and the number of tRNA-coding genes in phage genomes did not correlate with host range values. From the perspective of bacterial species, median plaquing host ranges varied from 0.04 in bacteriophages infecting Acinetobacter baumannii to 0.73 in Staphylococcus aureus phages. Taken together, our results imply that taxonomy of bacteriophages and their bacterial hosts can be predictive of intraspecies host ranges.

Olikomycin A–A Novel Calcium‐Dependent Lipopeptide with Antibiotic Activity Against Multidrug‐Resistant Bacteria

AbstractResearch into new antibiotics is becoming increasingly important as antibiotic resistance increases worldwide. The genus Streptomyces in particular is able to produce a wide range of antimicrobial products due to the large number of biosynthetic gene clusters (BGCs) in its genome. However, not all BGCs are expressed under laboratory conditions. In this work, deletion of the gene wblA, encoding a global regulator of natural product biosynthesis and morphogenesis in Streptomyces, led to the production of a novel natural product, olikomycin A, in Streptomyces ghanaensis ATCC 14672. Complete structure elucidation revealed that olikomycin A belongs to a class of calcium‐dependent antibiotics known as non‐ribosomal peptide synthetase (NRPS)‐encoded acidic lipopeptides. These compounds exhibit remarkable antimicrobial activity in the presence of calcium. Insights into olikomycin A biosynthesis were provided by whole genome sequencing and gene inactivation studies, while bioactivity assays showed strong inhibition of the growth of multidrug‐resistant Gram‐positive pathogens via disrupting cell membrane integrity. Olikomycin A shows an antibiotic profile similar to that of daptomycin, which is already in clinical use.

Predicting prognosis, immune landscape, and drug targets with a novel signature for hepatocellular carcinoma

Background Despite advances in therapeutics, hepatocellular carcinoma (HCC) remains one of the most malignant types of digestive tract cancers with a poor prognosis. Pyroptosis is a form of programmed cell death induced by inflammatory caspases. Recent studies have identified pyroptosis, a form of programmed cell death induced by inflammatory caspases, as playing a role in tumorigenesis and cancer progression. However, the functions and mechanisms of pyroptosis in HCC are barely explored. Methods Gene expression and clinical data were derived from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. A prognostic signature and nomogram were constructed by on differentially expressed genes and clinical data. Pathway enrichment and immune cell infiltration were further analyzed. Potential drugs to modulate the pathways were explored. Results In this study, a pyroptosis-related gene signature was developed and identified to be significantly correlated with the survival of HCC patients. Additionally, a nomogram on the basis of pyroptosis-related genes was constructed with distinct prognostic values. Furthermore, the pyroptosis-related gene signature might correlate with immune-related pathways and the regulation of the immune microenvironment, and several compounds (KIN001-220, TPCA-1, LY-303511, physostigmine, vemurafenib, etc.) could potentially reverse the pathogenic gene-expression patterns. Conclusions Our study provides evidence that pyroptosis is involved in HCC development, progression and immune microenvironment, which is promising in predicting the prognosis and developing targeted therapy.

Biosynthesis of Tetramate Derivatives in Penicillium crustosum Reveals the Involvement of ortho-Quinone Methide in Crosstalk of Multiple Pathways.

Genome mining and gene deletion experiments in Penicillium crustosum proved the involvement of the PKS-NRPS PemA and the trans-enoyl reductase PemB in the formation of three enantiomeric clavatol-containing tetramate pairs. Overexpression of a transcription factor significantly improved the product yields. Feeding experiments provided evidence for their formation via 1,4-Michael addition of hydroxyclavatol to two tetramates from the Pem pathway. This study provides another example of the involvement of reactive intermediates in multiple biosynthetic pathways.

Geography, Antimicrobial Resistance, and Genomics of Salmonella enterica (Serotypes Newport and Anatum) from Meat in Mexico (2021–2023)

Salmonella enterica non-typhoidal is a major contributor to diarrheal diseases, with over 2600 serovars identified across diverse environments. In Mexico, serovars Newport and Anatum have shown a marked increase, especially in foodborne disease, posing a public health problem. We conducted a cross-sectional study from 2021 to 2023 using active epidemiological surveillance to assess contamination in ground beef and pork at butcher shops nationwide. It involved isolation, phenotypic antimicrobial resistance, comparative genomics, spatial distribution, antimicrobial-resistance genes, and pangenome analysis. A total of 402 non-typhoidal S. enterica strains were isolated, including 59 Newport and 50 Anatum. After curating for redundancy, 45 Newport and 32 Anatum strains remained. We found that 75% of Newport strains exhibited multidrug resistance (MDR), compared to 25% of Anatum strains. Salmonella Newport also showed a broader distribution and stronger antibiotic-resistance capacity, particularly due to genes such as mphA and ramA. Our pangenome analysis showed a predominance of cell maintenance and survival-process genes in the accessory genome of both serotypes. Considering unique genes, Salmonella Anatum and Newport showed a notorious abundance of genes with functions related to replication, recombination, and repair. The substantial rise of Anatum and Newport strains in meat samples for human consumption presents an epidemiological alert, highlighting the critical need for stringent surveillance programs to mitigate human and ecosystem health risks.

Novel Genomic Regions and Gene Models Controlling Copper and Cadmium Stress Tolerance in Wheat Seedlings

Heavy metal pollution is a global issue that affects plant growth and human health. Copper and cadmium are two significant heavy metals that have become more concentrated in many soils. These metals are taken up by many plants, including wheat, and can cause various diseases in humans. The most effective way to mitigate the harmful effects of heavy metals is to grow tolerant wheat genotypes. In the current study, two different pot experiments were conducted to understand the genetic control of copper and cadmium tolerance in wheat seedlings. Two populations were used in this study, consisting of 92 genotypes for the copper experiment and 73 genotypes for the cadmium experiment. In both experiments, a replicated complete block design with three replications was used. Highly significant differences were found between the tested genotypes for all studied traits in both metals, except for root weight and the ratio between shoot weight and root weight under cadmium contamination. Single-marker analysis was performed for all significant traits, and a total of 265 and 381 markers were found to be significantly associated with seedling traits under copper and cadmium conditions, respectively. Of these markers, only eight were commonly associated with the tolerance to both metals. These markers were located within five different gene models that were functionally annotated to control heavy metal tolerance. Gene enrichment of the five identified genes revealed two key genes that significantly influenced eight biological processes, six molecular functions, and three Kyoto Ecyclopedia of Genes and Genomes (KEGG) pathways involved in heavy metal tolerance. The sources of the eight markers and their associated genes were identified in twelve genotypes, including one Egyptian and one Kazakhstani genotype, which showed superior responses to copper and cadmium, respectively. These genes and the genotypes carrying them are crucial for future breeding programs aimed at enhancing heavy metal tolerance in wheat.

Genome-wide analysis and expression profiling of the polyamine oxidase gene family in Solanum tuberosum L.

BackgroundPolyamine oxidase (PAO) is a crucial enzyme involved in the breakdown of polyamines (PAs) in plants. It not only regulates the levels of PAs, but also plays a role in the oxidative decomposition of PAs and the release of stress-related signals, contributing to the plant’s response and resistance to various adversities. While there have been numerous studies on the response of PAO to stress in other crops, there is a lack of research on this topic in potatoes, a major food crop.ResultsIn this study, we aimed to explore the biological function of the StPAO gene in potato growth and development, as well as its expression patterns under stress. Using bioinformatics methods, we identified 14 StPAO genes in the potato genome. Protein sequence comparisons revealed a high similarity between the PAO proteins of potato and Arabidopsis. Chromosomal mapping and gene structure analysis showed that the StPAO genes were not evenly distributed on the chromosome and all contained an amino-oxidase domain. Furthermore, analysis of the promoters of these genes revealed the presence of abiotic and stress-related cis-acting elements, indicating their potential role in responding to different stresses. To investigate the expression patterns of these genes under stress, we used qRT-PCR to study their response to high temperature, drought, and ABA stress. Our results showed that StPAO6 and StPAO10 were significantly up-regulated under high temperature stress, indicating that they were involved in the process of potato resistance to high temperatures. Similarly, StPAO1, StPAO3, and StPAO4 were significantly up-regulated under drought stress, indicating their potential role in potatoes’ responses to drought. After ABA treatment, the expression levels of StPAO4, StPAO5, StPAO7, and StPAO14 were significantly up-regulated, suggesting their involvement in chemical defense mechanisms. Interestingly, the expression of StPAO11–13 was inhibited by all three stresses.ConclusionsIn conclusion, our study highlights the multifunctional nature of the StPAO gene family in potatoes, which plays a crucial role in coping with various stresses. This research deepens our understanding of the potato StPAO gene family and provides a reference for future studies on its function. It also serves as a theoretical basis for breeding stress-resistant potato varieties in the future.

Inferring causal relationships among histone modifications in exon skipping event

Alternative splicing is a crucial processes of gene expression. Over 90% multi-exonic genes in human genome undergo alternative splicing. Although the splicing code has been proposed, it still couldn’t satisfactorily explain the tissue-specific alternative splicing. Results of co-transcriptional RNA processing analysis demonstrated that, except for trans- and cis-acting elements, histone modifications also play a role alternative splicing. In the present work, we analyzed the associations among 27 kinds of histone modifications in H1 human embryonic stem cell. In order to illustrate the casual relationships between histone modification and alternative splicing, we built the Bayesian network and validated its robustness by using cross validation test. In addition to the combinatorial patterns, distinct histone modification patterns were also observed in the alternative spliced exons and surrounding intron regions, indicating that histone modifications could substantially mark alternative splicing.