A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees.

Retrophylogenomics makes use of genome-wide retrotransposon presence/absence insertion patterns to resolve questions in phylogeny and population genetics. In the genomics era, evaluating high-throughput data requires the associated development of appropriately powerful statistical tools. The currently used KKSC 3-lineage statistical test for estimating the significance of retrophylogenomic data is limited by the number of possible tree topologies it can assess in one step. To improve on this, we have extended the analysis to simultaneously compare four lineages, enabling us to evaluate ten distinct presence/absence insertion patterns for 26 possible tree topologies plus 129 trees with different incidences of hybridization or introgression. The new tool provides statistics for cases involving multiple ancestral hybridizations/introgressions, ancestral incomplete lineage sorting, bifurcation, and polytomy. The test is embedded in a user-friendly web R application (http://retrogenomics.uni-muenster.de:3838/hammlet/) and is available for use by the scientific community. [ancestral hybridization/introgression; ancestral incomplete lineage sorting (ILS); empirical distribution; KKSC-statistics; 4-lineage (4-LIN) insertion polymorphism; polytomy; retrophylogenomics.].

CHARACTERISTICS OF 'NOTCH' IN RETINOPATHY OF PREMATURITY FOLLOWING INTRAVITREAL RANIBIZUMAB MONOTHERAPY.

PURPOSE: To explore the clinical features and significance of "notch" in reactivation of retinopathy of prematurity (ROP) post-intravitreal ranibizumab (IVR) monotherapy. METHODS: Ninety-six infants (173 eyes) with type 1 or aggressive ROP (A-ROP) post-IVR monotherapy were retrospectively analyzed; 51 eyes were notch (+) and 122 eyes were notch (-). General demographics and clinical outcomes were compared by notch status for type 1 and A-ROP. RESULTS: The notch primarily appeared in stage 2 ROP (84.4 and 78.9%) at the junction of zones I and II (68.8 and 63.2%) on the temporal side in type 1 ROP and A-ROP. Notch was present in the type 1 ROP group before first IVR but post-treatment in the A-ROP group. A significantly higher reactivation rate, longer follow-up duration, and postmenstrual age at last follow-up were seen in the notch (+) versus the notch (-) group. In the notch (+) ROP group, the mean gestational age (28.34±0.93 vs. 29.94±1.48 weeks) was significantly lower in reactivated versus regressed eyes. CONCLUSION: Notches appeared at different times but similar locations in type 1 ROP and A-ROP. The reactivation rate after IVR was increased in ROP with notches. Notch may be a useful biomarker for reactivation after IVR in ROP.

Identification and Validation of Lipid Metabolism Gene FASN-Associated miRNA in Wilms Tumor.

miRNA has been a research hotspot in recent years and its scope of action is very wide, involving the regulation of cell proliferation, differentiation, apoptosis, and other biological behaviors. This study intends to explore the role of miRNA in the lipid metabolism and development of Wilms tumor (WT) by detecting and analyzing the differences in the expression profiles of miRNAs between the tumor and adjacent normal tissue. Gene detection was performed in tumor tissues and adjacent normal tissues of three cases of WT to screen differentially expressed miRNAs (DEMs). According to our previous research, FASN, which participates in the lipid metabolism pathway, may be a target of WT. The starBase database was used to predict FASN-targeted miRNAs. The above two groups of miRNAs were intersected to obtain FASN-targeted DEMs and then GO Ontology (GO) functional enrichment analysis of FASN-targeted DEMs was performed. Finally, the FASN-targeted DEMs were compared and further verified by qRT‒PCR. Through gene sequencing and differential analysis, 287 DEMs were obtained, including 132 upregulated and 155 downregulated miRNAs. The top ten DEMs were all downregulated. Fourteen miRNAs targeted by the lipid metabolism-related gene FASN were predicted by starBase. After intersection with the DEMs, three miRNAs were finally obtained, namely, miR-107, miR-27a-3p, and miR-335-5p. GO enrichment analysis was mainly concentrated in the Parkin-FBXW7-Cul1 ubiquitin ligase complex and response to prostaglandin E. Further experimental verification showed that miR-27a-3p was significantly correlated with WT (P = 0.0018). Imbalanced expression of miRNAs may be involved in the occurrence and development of WT through lipid metabolism. The expression of miR-27a-3p is related to the malignant degree of WT, and it may become the target of diagnosis, prognosis, and treatment of WT in the later stage.

The multicomparative 2-n-way genome suite.

To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and comparing inserted elements among various genomes. The suite comprises two user-friendly web-based modules. The 2-way module generates pairwise whole-genome alignments of target and query species. The resulting genome coordinates of blocks (matching sequences) and gaps (missing sequences) from multiple 2-ways are then transferred to the n-way module and sorted into projects, in which user-defined coordinates from reference species are projected to the block/gap coordinates of orthologous loci in query species to provide comparative information about presence (blocks) or absence (gaps) patterns of targeted elements over many entire genomes and phylogroups. Thus, the 2-n-way software suite is ideal for performing multidirectional, non-ascertainment-biased screenings to extract all possible presence/absence data of user-relevant elements in orthologous sequences. To highlight its applicability and versatility, we used 2-n-way to expose approximately 100 lost introns in vertebrates, analyzed thousands of potential phylogenetically informative bat and whale retrotransposons, and novel human exons as well as thousands of human polymorphic retrotransposons.

ExoPLOT: Representation of alternative splicing in human tissues and developmental stages with transposed element (TE) involvement.

Advances in RNA high-throughput sequencing and large-scale functional assays yield new insights into the multifaceted activities of transposed elements (TE) and many other previously undiscovered sequence elements. Currently, no tool for easy access, analysis, quantification, and visualization of alternatively spliced exons across multiple tissues or developmental stages is available. Also, analysis pipelines demand computational skills or hardware requirements, which often are hard to meet by wet-lab scientists. We developed ExoPLOT to enable simplified access to massive RNA high throughput sequencing datasets to facilitate the analysis of alternative splicing across many biological samples. To demonstrate the functonality of ExoPLOT, we analyzed the contributon of exonized TEs to human coding sequences (CDS). mRNA splice variants containing the TE-derived exon were quantified and compared to expression levels of TE-free splice variants. For analysis, we utilized 313 human cerebrum, cerebellum, heart, kidney, liver, ovary, and testis transcriptomes, representing various pre- and postnatal developmental stages. ExoPLOT visualizes the relative expression levels of alternative transcripts, e.g., caused by the insertion of new TE-derived exons, across different developmental stages of and among multiple tissues. This tool also provides a unique link between evolution and function during exonization (gain of a new exon) and exaptation (recruitment/co-optation) of a new exon. As input for analysis, we derived a database of 1151 repeat-masked, exonized TEs, representing all prominent families of transposons in the human genome and the collection of human consensus coding sequences (CCDS). ExoPLOT screened preprocessed RNA high-throughput sequencing datasets from seven human tissues to quantify and visualize the dynamics in RNA splicing for these 1151 TE-derived exons during the entire human organ development. In addition, we successfully mapped and analyzed 993 recently described exonized sequences from the human frontal cortex onto these 313 transcriptome libraries. ExoPLOT's approach to preprocessing RNA deep sequencing datasets facilitates alternative splicing analysis and significantly reduces processing times. In addition, ExoPLOT's design allows studying alternative RNA isoforms other than TE-derived in a customized - coordinate-based manner and is available at http://retrogenomics3.uni-muenster.de:3838/exz-plot-d/.

Genome Duplication Increases Meiotic Recombination Frequency: A Saccharomyces cerevisiae Model.

Genetic recombination characterized by reciprocal exchange of genes on paired homologous chromosomes is the most prominent event in meiosis of almost all sexually reproductive organisms. It contributes to genome stability by ensuring the balanced segregation of paired homologs in meiosis, and it is also the major driving factor in generating genetic variation for natural and artificial selection. Meiotic recombination is subjected to the control of a highly stringent and complex regulating process and meiotic recombination frequency (MRF) may be affected by biological and abiotic factors such as sex, gene density, nucleotide content, and chemical/temperature treatments, having motivated tremendous researches for artificially manipulating MRF. Whether genome polyploidization would lead to a significant change in MRF has attracted both historical and recent research interests; however, tackling this fundamental question is methodologically challenging due to the lack of appropriate methods for tetrasomic genetic analysis, thus has led to controversial conclusions in the literature. This article presents a comprehensive and rigorous survey of genome duplication-mediated change in MRF using Saccharomyces cerevisiae as a eukaryotic model. It demonstrates that genome duplication can lead to consistently significant increase in MRF and rate of crossovers across all 16 chromosomes of S. cerevisiae, including both cold and hot spots of MRF. This ploidy-driven change in MRF is associated with weakened recombination interference, enhanced double-strand break density, and loosened chromatin histone occupation. The study illuminates a significant evolutionary feature of genome duplication and opens an opportunity to accelerate response to artificial and natural selection through polyploidization.

A tetrasomic inheritance model and likelihood-based method for mapping quantitative trait loci in autotetraploid species.

Dissecting the genetic architecture of quantitative traits in autotetraploid species is a methodologically challenging task, but a pivotally important goal for breeding globally important food crops, including potato and blueberry, and ornamental species such as rose. Mapping quantitative trait loci (QTLs) is now a routine practice in diploid species but is far less advanced in autotetraploids, largely due to a lack of analytical methods that account for the complexities of tetrasomic inheritance. We present a novel likelihood-based method for QTL mapping in outbred segregating populations of autotetraploid species. The method accounts properly for sophisticated features of gene segregation and recombination in an autotetraploid meiosis. It may model and analyse molecular marker data with or without allele dosage information, such as that from microarray or sequencing experiments. The method developed outperforms existing bivalent-based methods, which may fail to model and analyse the full spectrum of experimental data, in the statistical power of QTL detection, and accuracy of QTL location, as demonstrated by an intensive simulation study and analysis of data sets collected from a segregating population of potato (Solanum tuberosum). The study enables QTL mapping analysis to be conducted in autotetraploid species under a rigorous tetrasomic inheritance model.

Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species.

Dissecting the genetic architecture of quantitative traits is a crucial goal for efficient breeding of polyploid plants, including autotetraploid crop species, such as potato and coffee, and ornamentals such as rose. To meet this goal, a quantitative genetic model is needed to link the genetic effects of genes or genotypes at quantitative trait loci (QTL) to the phenotype of quantitative traits. We present a statistically tractable quantitative genetic model for autotetraploids based on orthogonal contrast comparisons in the general linear model. The new methods are suitable for autotetraploid species with any population genetic structure and take full account of the essential features of autotetrasomic inheritance. The statistical properties of the new methods are explored and compared to an alternative method in the literature by simulation studies. We have shown how these methods can be applied for quantitative genetic analysis in autotetraploids by analysing trait phenotype data from an autotetraploid potato segregating population. Using trait segregation analysis, we showed that both highly heritable traits of flowering time and plant height were under the control of major QTL. The orthogonal model directly dissects genetic variance into independent components and gives consistent estimates of genetic effects provided that tetrasomic gene segregation is considered.

Fenofibrate ameliorates diabetic retinopathy by modulating Nrf2 signaling and NLRP3 inflammasome activation.

Oxidative stress and neuroinflammation contribute significantly to the development and progression of diabetic retinopathy. Fenofibrate has received great attention as it benefits diabetic patients by reducing retinal laser requirement. Nuclear factor erythroid-2-related factor 2 (Nrf2) is a master regulator of anti-oxidative defense. Activation of nucleotide binding domain, leucine-rich repeat-containing receptor (NLR), pyrin domain-containing 3 (NLRP3) inflammasome plays a pivotal role in neuroinflammation. The purpose of this study is to determine whether fenofibrate protects retinas from oxidative damage and neuroinflammation via modulating the Nrf2 pathway and blocking NLRP3 inflammasome activation during diabetes. Diabetes is induced by intraperitoneal injection of streptozotocin in mice. Fenofibrate was given to mice in rodent chow. Upregulation of Nrf2 and NLRP3 inflammasome, enhanced ROS formation, and increased leukostasis and vascular leakage were observed in diabetic mouse retinas. Notably, Nrf2 and Caspase-1 were mainly colocalized with glutamine synthetase, one of the Mȕller cell markers. Fenofibrate further increased the expression of Nrf2 and its target gene NQO-1 and HO-1 and reduced ROS formation in diabetic retinas. In addition, retinal expression of NLRP3, Caspase-1 p20, IL-1ß p17, and ICAM-1 were dramatically increased in vehicle-treated diabetic mice, which were abolished by fenofibrate intervention. Moreover, fenofibrate treatment also attenuated diabetes-induced retinal leukostasis and vascular leakage in mice. Taken together, fenofibrate attenuates oxidative stress and neuroinflammation in diabetic retinas, which is at least partially through modulating Nrf2 expression and NLRP3 inflammasome activation.

Thermally activated persulfate oxidation of NAPL chlorinated organic compounds: effect of soil composition on oxidant demand in different soil-persulfate systems.

This study investigates the interaction of persulfate with soil components and chlorinated volatile organic compounds (CVOCs), using thermally activated persulfate oxidation in three soil types: high sand content; high clay content; and paddy field soil. The effect of soil composition on the available oxidant demand and CVOC removal rate was evaluated. Results suggest that the treatment efficiency of CVOCs in soil can be ranked as follows: cis-1,2-dichloroethene > trichloroethylene > 1,2-dichloroethane > 1,1,1-trichloroethane. The reactions of soil components with persulfate, shown by the reduction in soil phase natural organics and mineral content, occurred in parallel with persulfate oxidation of CVOCs. Natural oxidant demand from the reaction of soil components with persulfate exerted a large relative contribution to the total oxidant demand. The main influencing factor in oxidant demand in paddy-soil-persulfate systems was natural organics, rather than mineral content as seen with sand and clay soil types exposed to the persulfate system. The competition between CVOCs and soil components for oxidation by persulfate indicates that soil composition exhibits a considerable influence on the available oxidant demand and CVOC removal efficiency. Therefore, soil composition of natural organics and mineral content is a critical factor in estimating the oxidation efficiency of in-situ remediation systems.

A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations.

KEY MESSAGE: This optimized approach provides both a computational tool and a library construction protocol, which can maximize the number of genomic sequence reads that uniformly cover a plant genome and minimize the number of sequence reads representing chloroplast DNA and rRNA genes. One can implement the developed computational tool to feasibly design their own RAD-seq experiment to achieve expected coverage of sequence variant markers for large plant populations using information of the genome sequence and ideally, though not necessarily, information of the sequence polymorphism distribution in the genome. Advent of the next generation sequencing techniques motivates recent interest in developing sequence-based identification and genotyping of genome-wide genetic variants in large populations, with RAD-seq being a typical example. Without taking proper account for the fact that chloroplast and rRNA genes may occupy up to 60 % of the resulting sequence reads, the current RAD-seq design could be very inefficient for plant and crop species. We presented here a generic computational tool to optimize RAD-seq design in any plant species and experimentally tested the optimized design by implementing it to screen for and genotype sequence variants in four plant populations of diploid and autotetraploid Arabidopsis and potato Solanum tuberosum. Sequence data from the optimized RAD-seq experiments shows that the undesirable chloroplast and rRNA contributed sequence reads can be controlled at 3-10 %. Additionally, the optimized RAD-seq method enables pre-design of the required uniformity and density in coverage of the high quality sequence polymorphic markers over the genome of interest and genotyping of large plant or crop populations at a competitive cost in comparison to other mainstream rivals in the literature.

Porous Molybdenum Phosphide Nano-Octahedrons Derived from Confined Phosphorization in UIO-66 for Efficient Hydrogen Evolution.

Herein, a series of porous nano-structured carbocatalysts have been fused and decorated by Mo-based composites, such as Mo2 C, MoN, and MoP, to form a hybrid structures. Using the open porosity derived from the pyrolysis of metal-organic frameworks (MOFs), the highly dispersive MoO2 small nanoparticles can be deposited in porous carbon by chemical vapor deposition (CVD). Undergoing different treatments of carbonization, nitridation, and phosphorization, the Mo2 C-, MoN-, and MoP-decorated carbocatalysts can be selectively prepared with un-changed morphology. Among these Mo-based composites, the MoP@Porous carbon (MoP@PC) composites exhibited remarkable catalytic activity for the hydrogen evolution reaction (HER) in 0.5 m H2 SO4 aqueous solution versus MoO2 @PC, Mo2 C@PC, and MoN@PC. This study gives a promising family of multifunctional lab-on-a-particle architectures which shed light on energy conversion and fuel-cell catalysis.

Hollow Zn/Co ZIF Particles Derived from Core-Shell ZIF-67@ZIF-8 as Selective Catalyst for the Semi-Hydrogenation of Acetylene.

The rational design of metal-organic frameworks (MOFs) with hollow features and tunable porosity at the nanoscale can enhance their intrinsic properties and stimulates increasing attentions. In this Communication, we demonstrate that methanol can affect the coordination mode of ZIF-67 in the presence of Co(2+) and induces a mild phase transformation under solvothermal conditions. By applying this transformation process to the ZIF-67@ZIF-8 core-shell structures, a well-defined hollow Zn/Co ZIF rhombic dodecahedron can be obtained. The manufacturing of hollow MOFs enables us to prepare a noble metal@MOF yolk-shell composite with controlled spatial distribution and morphology. The enhanced gas storage and porous confinement that originate from the hollow interior and coating of ZIF-8 confers this unique catalyst with superior activity and selectivity toward the semi-hydrogenation of acetylene.

[Development of a computerized three-dimension system for displaying and analyzing mandibular helical axis pathways].

This paper is aimed to develop a computerized three dimensional system for displaying and analyzing mandibular helical axis pathways. Mandibular movements were recorded using a six-degrees-of-freedom ultrasonic jaw movement recording device. The three-dimensional digital models of the midface and the mandible were reconstructed and segmented from CT skull images. The digital models were then transformed to the coordinate system of mandibular motion data by using an optical measuring system. The system was programmed on the base of the Visualization ToolKit and Open Scene Graphics Library. According to the motion data, transformation matrices were calculated to simulate mandibular movements. Meanwhile, mandibular helical axis pathways were calculated and displayed three dimensionally by means of an eigenvalues method. The following parameters of mandibular helical axis were calculated: the rotation around instantaneous helical axis, the translation along it, its spatial orientation, its position and distance relative to any special reference point. These parameters could be exported to describe comprehensively the whole mandiblular movements. It could be concluded that our system would contribute to the study of mandiblular helical axis pathways.

Temozolomide alleviates breast carcinoma via the inhibition of EGFR/ERK/ MMP-1 pathway with induction of apoptotic events.

PURPOSE: To evaluate the chemotherapeutic activity of temozolomide counter to mammary carcinoma. METHODS: In-vitro anticancer activity has been conducted on MCF7 cells, and mammary carcinoma has been induced in Wistar rats by introduction of 7, 12-Dimethylbenz(a)anthracene (DMBA), which was sustained for 24 weeks. Histopathology, immunohistochemistry, cell proliferation study and apoptosis assay via TUNEL method was conducted to evaluate an antineoplastic activity of temozolomide in rat breast tissue. RESULTS: IC50 value of temozolomide in MCF7 cell has been obtained as 103 µM, which demonstrated an initiation of apoptosis. The temozolomide treatment facilitated cell cycle arrest in G2/M and S phase dose dependently. The treatment with temozolomide suggested decrease of the hyperplastic abrasions and renovation of the typical histological features of mammary tissue. Moreover, temozolomide therapy caused the downregulation of epidermal growth factor receptor, extracellular signal-regulated kinase, and metalloproteinase-1 expression and upstream of p53 and caspase-3 proliferation to indicate an initiation of apoptotic events. CONCLUSIONS: The occurrence of mammary carcinoma has been significantly decreased by activation of apoptotic pathway and abrogation of cellular propagation that allowable for developing a suitable mechanistic pathway of temozolomide in order to facilitate chemotherapeutic approach.

Age-related differences in saccadic indices of top-down guidance via short-term memory during visual search.

Aging has been associated with significant declines in the speed and accuracy of visual search. These effects have been attributed partly to low-level (bottom-up) factors including reductions in sensory acuity and general processing speed. Aging is also associated with changes in top-down attentional control, but the impact of these on search is less well-understood. The present study investigated age-related differences in top-down attentional control by comparing the speed and accuracy of saccadic sampling in the presence and absence of top-down information about target color in young (YA) and older (OA) observers. Displays contained an equal number of red and blue Landholt stimuli. Targets were distinguished from distractors by a unique orientation, and observers reported the direction of the target's gap on each trial. Single-target cues signaled the color of the target with 100% validity. Dual-target cues indicated the target could be present in either colored subgroup. The results revealed reliable group differences in the benefits associated with top-down information on single-target cues compared to dual-target cues. On single-target searches, OA made significantly more saccades than YA to stimuli in the uncued color subset. Single-target cues also produced a smaller advantage in the time taken to fixate the target in OA compared to YA. These results support an age-related decline in observers' use of top-down information to restrict sequences of saccades to a task-relevant subset of objects during visual search. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

High-Performance Sub-10 nm Two-Dimensional SbSeBr Transistors through Transport Orientation.

Exploring two-dimensional (2D) materials with a small carrier effective mass and suitable band gap is crucial for the design of metal oxide semiconductor field effect transistors (MOSFETs). Here, the quantum transport properties of stable 2D SbSeBr are simulated on the basis of first-principles calculations. Monolayer SbSeBr proves to be a competitive channel material, offering a suitable band gap of 1.18 eV and a small electron effective mass (me*) of 0.22m0. The 2D SbSeBr field effect transistor (FET) with 8 nm channel length exhibits a high on-state current of 1869 µA/µm, low power consumption of 0.080 fJ/µm, and small delay time of 0.062 ps, which can satisfy the requirements of the International Technology Roadmap for Semiconductors for high-performance devices. Moreover, despite the monolayer SbSeBr having an isotropic me*, the asymmetrical band trends enable SbSeBr FETs to display transport orientation, which emphasizes the importance of band trends and provides valuable insights for selecting channel materials.

Causal relationship between Alzheimer's disease and cardiovascular disease: a bidirectional Mendelian randomization analysis.

Observational studies suggest that cardiovascular disease (CVD) increases the risk of developing Alzheimer's disease (AD). However, the causal relationship between the two is not clear. This study applied a two-sample bidirectional Mendelian randomization method to explore the causal relationship between CVD and AD. Genome-wide association study (GWAS) data from 46 datasets of European populations (21,982 cases of AD and 41,944 controls) were utilized to obtain genetic instrumental variables for AD. In addition, genetic instrumental variables for atrial fibrillation (AF), heart failure (HF), myocardial infarction (MI), coronary heart disease (CHD), angina pectoris (AP), and ischemic stroke (IS) (including large-artery atherosclerotic stroke [LAS] and cardioembolic stroke [CES]) were selected from GWAS data of European populations (P < 5E-8). The inverse variance weighting method was employed as the major Mendelian randomization analysis method. Genetically predicted AD odds ratios (OR) (1.06) (95% CI: 1.02-1.10, P = 0.003) were linked to higher AP analysis. A higher genetically predicted OR for CES (0.9) (95% CI 0.82-0.99, P = 0.02) was linked to a decreased AD risk. This Mendelian randomized study identified AD as a risk factor for AP. In addition, CES was related to a reduced incidence of AD. Therefore, these modifiable risk factors are crucial targets for preventing and treating AD.

Causality between heart failure and epigenetic age: a bidirectional Mendelian randomization study.

AIMS: Heart failure (HF) is a prevalent age-related cardiovascular disease with poor prognosis in the elderly population. This study aimed to establish the causal relationship between ageing and HF by conducting a bidirectional Mendelian randomization (MR) analysis on epigenetic age (a marker of ageing) and HF. METHODS AND RESULTS: Genome-wide association study data for epigenetic age (GrimAge, HorvathAge, HannumAge, and PhenoAge) and HF were collected and assessed for significant genetic variables. A bidirectional MR analysis was carried out using the random-effects inverse-variance weighted (IVW) method as the primary approach, while other methods (MR-Egger, weighted median, simple mode, and weighted mode) and multiple sensitivity analyses (heterogeneity analysis, leave-one-out sensitivity analysis, and horizontal pleiotropy analysis) were employed to evaluate the impact of epigenetic age on HF and vice versa. Bidirectional MR analysis of two samples revealed that the epigenetic PhenoAge clock increased the risk of HF [IVW odds ratio (OR) 1.015, 95% confidence interval (CI) 1.002-1.028, P = 0.028 and weighted median OR 1.020, 95% CI 1.001-1.038, P = 0.039]. Other results were not statistically significant. CONCLUSIONS: The bidirectional MR analysis demonstrated a causal link between genetically predicted epigenetic age and HF in individuals of European descent. Further research into epigenetic age in other populations and additional genetic information related to HF is warranted.

A bioinformatics approach to identifying the biomarkers and pathogenesis of major depressive disorder combined with acute myocardial infarction.

This study investigated the pathogenesis of major depressive disorder (MDD) and acute myocardial infarction (AMI) using bioinformatics. We analyzed MDD and AMI (MDD-AMI) datasets provided by the Gene Expression Omnibus (GEO) database for genes common to MDD and AMI using GEO2R and weighted gene co-expression network analysis (WGCNA). We also performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, and we used Disease Ontology (DO) analysis to identify a) the pathways through which genes function and b) comorbidities. We also created a protein-protein interaction (PPI) network using the STRING database to identify the hub genes and biomarkers. NetworkAnalyst 3.0 was used to construct a transcription factor (TF) gene regulatory network. We also identified relevant complications and potential drug candidates. The 27 genes common to MDD and AMI were enriched in the pathways regulating TFs and mediating immunity and inflammation. The hub genes in the PPI network included TLR2, HP, ICAM1, LCN2, LTF, VCAN, S100A9 and NFKBIA. Key TFs were KLF9, KLF11, ZNF24, and ZNF580. Cardiovascular, pancreatic, and skeletal diseases were common complications. Hydrocortisone, simvastatin, and estradiol were candidate treatment drugs. Identification of these genes and their pathways may provide new targets for further research on the pathogenesis, biomarkers, and treatment of MDD-AMI. Together our results suggested that TLR2 and VCAN might be the key genes associated with MDD complicated by AMI.