Genetic Model Research Articles

Conceptual Model of Graph-based Individual Tree and Its Utilization in Digital Twin and Metaverse of Urban Forest

Abstract. 3D city models are an important cornerstone in the development of digital twin cities, allowing for various analyses and simulations. CityGML, as an open standard for 3D city models, emphasizes five main aspects: scale or level of detail (LoD), semantics, geometry, topology, and appearance. One of the important elements in CityGML 3D city models is representation of vegetation. Vegetation in CityGML, especially individual trees, is still limited in terms of detail and resolution, reducing its effectiveness for specific applications. This paper proposes a graph-based conceptual model for individual trees that conforms to the CityGML v2.0 specification. The model refers to the morphological structure of a tree consisting of roots, trunk, and crown (including branches, twigs, and leaves), and considers the five main aspects of CityGML. By enhancing semantic information and geometric details, the model aims to provide an information-rich and realistic representation of individual trees in a 3D city environment. The 3D tree model created based on this conceptual model may be applicable in the development of digital twin urban forests and virtual forest simulations that utilize immersive technologies such as the metaverse. This research opens up new opportunities in the development of solitary vegetation objects through CityGML ADE by including more detailed semantic and topological information.

Detectability of Varied Hybridization Scenarios Using Genome-Scale Hybrid Detection Methods

Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to patterns of genetic heritability that are unexpected under traditional, bifurcating models of species trees. This phenomenon has led to the development of methods to infer these varied hybridization events, both methods that reconstruct networks directly, as well as summary methods that predict individual hybridization events from a subset of taxa. However, a lack of empirical comparisons between methods – especially those pertaining to large networks with varied hybridization scenarios – hinders their practical use. Here, we provide a comprehensive review of popular summary methods: TICR, MSCquartets, HyDe, Patterson’s D-Statistic (ABBA-BABA), D3, and Dp. TICR and MSCquartets are based on quartet concordance factors gathered from gene tree topologies and HyDe, Patterson’s D-Statistic, D3, and Dp use site pattern frequencies to identify hybridization events between sets of three taxa. We then use simulated data to address questions of method accuracy and ideal use scenarios by testing methods against complex networks which depict gene flow events that differ in depth (timing), quantity (single vs. multiple, overlapping hybridizations), and rate of gene flow (γ). We find that deeper or multiple hybridization events may introduce noise and weaken the signal of hybridization, leading to higher relative false negative rates across all methods. Despite some forms of hybridization eluding quartet-based detection methods, MSCquartets displays high precision in most scenarios. While HyDe results in high false negative rates when tested on hybridizations involving extinct or unsampled ghost lineages, HyDe is the only method able to identify the direction of hybridization, distinguishing the source parental lineages from recipient hybrid lineages. Lastly, we test the methods on a dataset of ultraconserved elements from the bee subfamily Nomiinae, finding possible hybridization events between clades which correspond to regions of poor support in the species tree estimated in a previous study.

Glucose metabolism controls monocyte homeostasis and migration but has no impact on atherosclerosis development in mice

Monocytes directly contribute to atherosclerosis development by their recruitment to plaques in which they differentiate into macrophages. In the present study, we ask how modulating monocyte glucose metabolism could affect their homeostasis and their impact on atherosclerosis. Here we investigate how circulating metabolites control monocyte behavior in blood, bone marrow and peripheral tissues of mice. We find that serum glucose concentrations correlate with monocyte numbers. In diet-restricted mice, monocytes fail to metabolically reprogram from glycolysis to fatty acid oxidation, leading to reduced monocyte numbers in the blood. Mechanistically, Glut1-dependent glucose metabolism helps maintain CD115 membrane expression on monocytes and their progenitors, and regulates monocyte migratory capacity by modulating CCR2 expression. Results from genetic models and pharmacological inhibitors further depict the relative contribution of different metabolic pathways to the regulation of CD115 and CCR2 expression. Meanwhile, Glut1 inhibition does not impact atherosclerotic plaque development in mouse models despite dramatically reducing blood monocyte numbers, potentially due to the remaining monocytes having increased migratory capacity. Together, these data emphasize the role of glucose uptake and intracellular glucose metabolism in controlling monocyte homeostasis and functions.

Retinal pigment epithelium-specific ablation of GPx4 in adult mice recapitulates key features of geographic atrophy in age-related macular degeneration.

Age-related macular degeneration (AMD) is a leading cause of irreversible vision loss in the elderly population, particularly the late-stage of dry AMD known as geographic atrophy (GA), lacks effective treatment options. Genetic mouse models of AMD have revealed the significance of impaired lipid metabolism and anti-oxidative capacity in early/intermediate stage of AMD, but remains unclear in GA that severely damages visual function. Here, to investigate the potential relevance of peroxidized lipids in RPE for late-stage dry AMD, GPx4fl/fl mice underwent subretinal injections of RPE-specific AAV-Cre vector or control AAV vector. RPE-specific GPx4 deficiency led to rapid RPE degeneration resembling key features of late-stage dry AMD, including preceding loss of RPE cell polarity, accumulation of acrolein, malondialdehyde, and 4-hydroxynonenal, photoreceptor loss, lipofuscin-laden subretinal melanophage infiltration, and complement activation. Treatment with α-tocopherol and ferrostatin-1 mitigated RPE degeneration, and shrunk mitochondria were observed in GPx4 deficient mice, suggesting involvement of ferroptosis. Unexpectedly, necrostatin-1s, an inhibitor of necroptosis, also ameliorated RPE degeneration, and activation of RIP3 and MLKL along with inactivation of caspase-8 was observed, indicating crosstalk between ferroptosis and necroptosis pathways. Our findings shed light on the intricate mechanisms underlying RPE degeneration in AMD and highlight GPx4/lipid peroxidation as potential therapeutic targets. RPE-specific ablation of GPx4 in mice provides a valuable tool for further elucidating the interplay between lipid peroxidation, cell death pathways, and AMD pathogenesis, offering new insights for preclinical research and therapeutic development targeting GA.

Association between 5-HTR1A gene C-1019G polymorphism and antidepressant response in patients with major depressive disorder: A meta-analysis.

Major depressive disorder (MDD) is a substantial global health concern, and its treatment is complicated by the variability in individual response to antidepressants. To consolidate research and clarify the impact of genetic variation on MDD treatment outcomes. Adhering to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, a systematic search across PubMed, EMBASE, Web of Science, and the Cochrane Library was conducted without date restrictions, utilizing key terms related to MDD, serotonin 1A receptor polymorphism (5-HTR1A), C-1019G polymorphism, and antidepressant response. Studies meeting inclusion criteria were thoroughly screened, and quality assessed using the Newcastle-Ottawa Scale. Statistical analyses, including χ 2 and I² values, were used to evaluate heterogeneity and fixed-effect or random-effect models were applied accordingly. The initial search yielded 1216 articles, with 11 studies meeting criteria for inclusion. Analysis of various genetic models showed no significant association between the 5-HTR1A C-1019G polymorphism and antidepressant efficacy. The heterogeneity was low to moderate, and no publication bias was detected through funnel plot symmetry and Egger's and Begg's tests. This meta-analysis does not support a significant association between the 5-HTR1A C-1019G polymorphism and the efficacy of antidepressant treatment in MDD. The findings call for further research with larger cohorts to substantiate these results and enhance the understanding of antidepressant pharmacogenetics.

Impact of Heat Stress on Milk Yield, Milk Fat-to-Protein Ratio, and Conception Rate in Thai-Holstein Dairy Cattle: A Phenotypic and Genetic Perspective.

Heat stress severely affects dairy cattle production and reproduction performances in tropical regions. Genetic selection to maintain adequate yield and reproductive performance while enhancing their ability to withstand heat is essential for improving the genetics of dairy cows. Therefore, in this study, we aimed to estimate genetic parameters affecting production and reproduction performances under heat stress conditions in dairy cattle and to investigate the threshold point of heat stress for milk yield (MY), milk fat-to-protein ratio (FPR), and conception rate (CR) in Thai-Holstein dairy cattle. The data included 168,124 records related to MY and milk FPR and 21,278 records of CR in Thai-Holstein dairy cattle, covering the period from 1990 to 2007. A multiple-trait threshold-linear random regression model based on a Bayesian approach via Gibbs sampling was used to estimate variance components, genetic parameters (heritability values, and genetic correlations), and decline rates for each studied trait. The threshold point of heat stress was identified as a temperature and humidity index (THI) of 76. At THI76, a decline was observed in the MY, milk FPR, and CR of Thai dairy cattle. The heritability estimates for MY, milk FPR and CR were 0.347 ± 0.032, 0.293 ± 0.021, and 0.032 ± 0.001, respectively. The genetic correlation between MY and milk FPR and MY and CR were -0.24 and -0.53, respectively, whereas those between milk FPR and heat tolerance as well as between CR and heat tolerance were -0.48 and -0.49, respectively. In addition, the decline rates in MY, milk FPR, and CR were found to be associated with a high percentage of Holstein genetics. In conclusion, the results obtained in this study reveal that the simultaneous consideration of the MY, milk FPR, CR, and heat tolerance traits of Thai-Holstein dairy cattle is possible. In addition, developing a genetic model that incorporates THI is essential for sustainably addressing heat stress problems.

Toll-like receptors ligand immunomodulators for the treatment congenital diaphragmatic hernia

BackgroundCongenital diaphragmatic hernia (CDH) is a rare disease that affects the development of the diaphragm, leading to abnormal lung development. Unfortunately, there is no established therapy for CDH. Retinoic acid pathways are implicated in the ethology of CDH and macrophages are known to play a role in repairing organ damage.MethodsWe have analyzed the effect of several Toll like receptor (TLR) ligands in the nitrofen-induced CDH model in pregnant rats widely used to study this disease and in the G2-GATA4Cre;Wt1fl/fl CDH genetic mice model. Morphometric and histological studies were carried out. Immune cell infiltration was assayed by immunochemistry and immunofluorescence and retinoic pathway gene expression analyzed in vivo and in vitro in macrophages.ResultsWe found that administering a single dose of atypical TLR2/4 ligands (CS1 or CS2), 3 days after nitrofen, cured diaphragmatic hernia in 73% of the fetuses and repaired the lesion with complete diaphragm closure being on the other hand nontoxic for the mothers or pups. Moreover, these immunomodulators also improved pulmonary hypoplasia and alveolar maturation and vessel hypertrophy, enhancing pulmonary maturity of fetuses. We also found that CS1 treatment rescued the CDH phenotype in the G2-GATA4Cre;Wt1fl/fl CDH genetic mice model. Only 1 out of 11 mutant embryos showed CDH after CS1 administration, whereas CDH prevalence was 70% in untreated mutant embryos. Mechanistically, CS1 stimulated the infiltration of repairing M2 macrophages (CD206+ and Arg1+) into the damaged diaphragm and reduced T cell infiltration. Additionally, those TLR ligands induced retinol pathway genes, including RBP1, RALDH2, RARα, and RARβ, in the affected lungs and the diaphragm and in macrophages in vitro.ConclusionsOur research has shown that TLR ligand immunomodulators that influence anti-inflammatory macrophage activation can be effective in treating CDH, being nontoxic for the mothers or pups suggesting that those TLR ligands are a promising solution for CDH leading to orphan drug designation for CS1. The immune system of the fetus would be responsible for repairing the damage and closure of the hernia in the diaphragm and enhanced proper lung development after CS1 treatment.

The association of serum level and polymorphisms of IFN-γ (rs2069705) with the susceptibility to cutaneous leishmaniasis

Leishmaniasis, a broad range of parasitic diseases, caused by Leishmania which is a flagellated intracellular protozoan parasite of the family Trypanosomatidae. The severity of leishmaniasis diseases ranges from minor cutaneous lesions to severe visceral illnesses that can be disfiguring and life-threatening. Cytokines are glycoprotein molecules produced by various cells in response to various immunological triggers. They regulate the body’s innate and adaptive immunological responses. The aim of this study was to clarify the association of serum level and polymorphisms of IFN-γ with susceptibility to cutaneous leishmaniasis (CL). The whole blood 200 samples were collected from patients and controls from Diyala Governorate/ Iraq from October 2022 to February 2023 which were used to measure IFN-γ polymorphisms using High Resolution Melting technique. Enzyme-linked immunosorbent assay was used to detect the serum level of IFN-γ. The findings of this investigation showed that the IFN-γ serum concentration elevated significantly in patients compared to controls (P < 0.01). Also, the study found that the highest mean level IFN-γ concentrations were found in adults aged 46–55 years old for patients compared with controls with significant differences (P < 0.01). While, no significant differences were observed in the rest age groups except children aged 5–15 years old. Additionally, significant differences between patients and controls were revealed by polymorphisms data in all genetic models for genotypes GA, AA, (GA + AA) and allele A with (P < 0.01) and OR > 1. However, the distribution of IFN-γ serum levels by SNP (rs2069705) demonstrated no differences between genotypes except GG genotype which has significant differences for patients comparing to the same genotype in controls. Taking together, the SNP for IFN-γ (rs2069705) could be a risk factor for susceptibility infection with CL. Also, considered the mutant allele A as a risk allele and genotype AA in codominant genetic model as more risk factor than the genotype GA.

Meta-analysis of interleukin-10gene polymorphisms and tuberculosis susceptibility: Insights from recent studies.

Tuberculosis (TB) remains a universal health problem with significant morbidity and mortality. Understanding the genetic factors affecting TB susceptibility is crucial for effective prevention and treatment. Interleukin-10 (IL-10), a regulatory cytokine, may influence TB pathogenesis through genetic variations. The PubMed, Embase, and Google Scholar databases were searched to find studies on the relationship between IL-10gene variants and tuberculosis. Relevant studies from 2016 to 2024 were identified through database searches. The selected case-control studies met the inclusion criteria. Software such as Review Manager was used to analyze quantitative data, with statistical significance set at p< 0.05. We calculated odds ratios and their respective confidence intervals to evaluate the associations. Nine studies examined IL-10 gene polymorphisms (rs1800871 and rs1800872) in TB susceptibility. The present study did not show a notable association between IL-10 gene polymorphisms and TB among all genetic models (allelic, homozygote, heterozygote, dominant, and recessive). The obtained p-value > 0.05 indicates an insignificant association between both gene polymorphisms of IL-10. An OR-1.13; 95% CI-0.85, 1.50 was obtained for the SNP rs1800871, whereas an OR-1.02; 95% CI-0.75, 1.40 was obtained for the SNP rs1800872. Our meta-analysis revealed no significant association between IL-10 gene polymorphisms and TB susceptibility, suggesting that these variations may not significantly contribute to TB susceptibility. Further research with a larger sample size and diverse ethnicities is needed to explore additional genetic variations and their implications in TB pathogenesis.

Data-driven Strategies for Affordable Housing: A Hybrid Genetic Algorithm-Machine Learning Optimization Model in the Melbourne Metropolitan Area

Abstract. The escalating rental crisis in Australia, rooted in demographic dynamics, a scarcity of lands suitable for development and the influence of interest rates and government subsidies, necessitates innovative solutions for housing affordability. One promising approach is to increase the supply of affordable rental housing. Nevertheless, these efforts must be guided by well-informed policies as they are required to cater to the diverse needs of the stakeholders involved. Accordingly, this study aims to prioritize suburbs in the Melbourne Metropolitan area for the construction of apartment/unit buildings, benefiting both builders/investors and renters. Leveraging a hybrid Genetic Algorithm-Machine Learning (GA-ML) framework, multi-objective optimization models are developed to rank 105 suburbs based on key parameters for both builders/investors and renters. The optimization process seeks to maximize economic outlook and rental yields for builders/investors while minimizing rents and commuting distances for renters, in addition to proximity to essential amenities. First, an initial optimization using GA based on six key parameters is performed considering a linear multi-objective function. Subsequently, ML-based objective functions are defined using Random Forest (RF) and extreme Gradient Boosting (XGBoost) models to refine the optimization model for suburb rankings. The evaluation reveals strong correlations between GA and GA-XGB rankings, suggesting the effectiveness of the GA-XGBoost model in prioritizing suburbs. Notably, suburbs consistently prioritized across all models include Brunswick, Coburg, Preston and Reservoir, highlighting their suitability for apartment/unit building construction. By directing attention to specific suburbs aligned with different stakeholders' needs and preferences, this study contributes to a more sustainable and equitable housing landscape.

Corticostriatal Maldevelopment in the R6/2 Mouse Model of Juvenile Huntington's Disease.

There is a growing consensus that brain development in Huntington's disease (HD) is abnormal, leading to the idea that HD is not only a neurodegenerative but also a neurodevelopmental disorder. Indeed, structural and functional abnormalities have been observed during brain development in both humans and animal models of HD. However, a concurrent study of cortical and striatal development in a genetic model of HD is still lacking. Here we report significant alterations of corticostriatal development in the R6/2 mouse model of juvenile HD. We examined wildtype (WT) and R6/2 mice at postnatal (P) days 7, 14, and 21. Morphological examination demonstrated early structural and cellular alterations reminiscent of malformations of cortical development, and ex vivo electrophysiological recordings of cortical pyramidal neurons (CPNs) demonstrated significant age- and genotype-dependent changes of intrinsic membrane and synaptic properties. In general, R6/2 CPNs had reduced cell membrane capacitance and increased input resistance (P7 and P14), along with reduced frequency of spontaneous excitatory and inhibitory synaptic events during early development (P7), suggesting delayed cortical maturation. This was confirmed by increased occurrence of GABA A receptor-mediated giant depolarizing potentials at P7. At P14, the rheobase of CPNs was significantly reduced, along with increased excitability. Altered membrane and synaptic properties of R6/2 CPNs recovered progressively, and by P21 they were similar to WT CPNs. In striatal medium-sized spiny neurons (MSNs), a different picture emerged. Intrinsic membrane properties were relatively normal throughout development, except for a transient increase in membrane capacitance at P14. The first alterations in MSNs synaptic activity were observed at P14 and consisted of significant deficits in GABAergic inputs, however, these also were normalized by P21. In contrast, excitatory inputs began to decrease at this age. We conclude that the developing HD brain is capable of compensating for early developmental abnormalities and that cortical alterations precede and are a main contributor of striatal changes. Addressing cortical maldevelopment could help prevent or delay disease manifestations.

New Plasmid Constructs for Production of Yeast Based Oral Vaccines

In order to avoid conventional vaccines, there is an urgent need to look for new ways of vaccine generation that can cut down the cost, time, and the need for special requirements during storage and distribution. The development of oral peptide/protein-based vaccines could be an ideal alternative. Five expression plasmids are designed in this work for the production of Saccharomyces cerevisiae-based oral vaccines. Therefore, in this work genetic cassette with different organizations of the required genetic components for efficient gene expression is constructed in the pYES2 plasmid. The construction of five new plasmids for surface display of heterologous recombinant proteins in S. cerevisiae would enable easy insertion of the gene of interest into an optimized genetic cassette consisting of a strong host promoter GAL1, HA-tag for detection of recombinant enzymes, GAS1 gene with/without binding sequence coded for GAS1 cell wall protein and signal sequence for directing the protein into the secretory pathway. After the construction of the genetic cassettes, E gene coded for envelope protein of Chikungunya and Dengue virus is inserted in the genetic cassettes. Genetic models pYES2HAGAS1EgeneChikungunya, pYES2HAGAS1 Egene Dengue, pYES2GAS1 Egene ChikungunyaHA, and pYES2GAS1EGeneDengueHA are constructed with different genetic organizations to display envelope protein of Chikungunya and Dengue virus in the cell surface of S. cerevisiae. In the pYES2SignalEGeneDengueHA construction, envelope protein will be secreted by S. cerevisiae into the media. The constructed vectors are specialized to regulate the expression and surface display of heterologous recombinant proteins in Saccharomyces cerevisiae and will be suitable for large-scale oral vaccine production.

YAP1 modulation of primary cilia-mediated ciliogenesis in 2D and 3D prostate cancer models.

The primary cilium, a non-motile organelle present in most human cells, plays a crucial role in detecting microenvironmental changes and regulating intracellular signaling. Its dysfunction is linked to various diseases, including cancer. We explored the role of ciliated cells in prostate cancer by using Gefitinib and Jasplakinolide compounds to induce ciliated cells in both normal and tumor-like prostate cell lines. We assessed GLI1 and IFT20 expression and investigated YAP1 protein's role, which is implicated in primary cilium regulation. Finally, we examined these compounds in 3D cell models, aiming to simulate in vivo conditions. Our study highlights YAP1 as a potential target for novel genetic models to understand the primary cilium's role in mediating resistance to anticancer treatments.

Genetic polymorphism of IL-40 in male patients with ankylosing spondylitis

Background: Ankylosing spondylitis (AS) is a kind of arthritis marked by persistent inflammation in the spine's joints, usually at the point where the spine and pelvis meet. Such a disease has different causes, including immunological causes. Therefore, it is necessary to investigate the role of the immune system in this disease to improve a potential treatment strategy. In this context, the present study examined the single nucleotide polymorphisms (SNPs) of the IL-40 gene of IL-40 in a group of Iraqi males with AS to determine their associations in AS pathogenesis. Method: The study included a total of 200 Iraqi male participants (100 with AS and 100 healthy subjects). The detection of SNPs of IL-40 was performed using polymerase chain reaction (PCR) techniques followed by the Sanger sequencing method. Multinomial logistic regression analysis was used to analyze the SNPs under five genetic models (allele, recessive, dominant, and co-dominant). Results: Detected that the heterozygous genotype (GA and AA) and alleles (G and A) of rs72896265, the heterozygous genotype (AG and GG) and alleles (A and G) of rs60316778 and both heterozygous genotype (CC) and alleles (C and T) of rs9915090 were significantly associated with AS risk (p &lt; 0.001).

Research on cargo volume prediction and personnel scheduling optimization of sorting center based on BP neural network and improved genetic algorithm

With the development of Internet technology, e-commerce has become the primary choice for consumers to shop, and the huge order transaction volume has generated logistics problems. As an important part of the logistics network, the sorting platform is essential to improve its management efficiency. To enhance the efficiency of the sorting center, the topological relationship diagram is used to show the logistics network, and the cargo volume of the sorting center in the next 30 days and every hour is predicted based on the BP neural network model. Based on the mixed integer linear programming model and the improved genetic algorithm SCAGA model, the total man-days are minimized to ensure that the cargo volume is processed. At the same time, to ensure that the actual hourly efficiency is as balanced as possible, the optimization problem of personnel scheduling is studied. To maintain the efficient operation of the logistics industry, the accurate prediction of the number of goods and the reasonable scheduling of personnel, to provide a set of efficient and economical personnel scheduling programs for the logistics company, thus improving the overall operational efficiency and service quality.

Glycerol Kinase Drives Hepatic de novo Lipogenesis and Triglyceride Synthesis in Nonalcoholic Fatty Liver by Activating SREBP-1c Transcription, Upregulating DGAT1/2 Expression, and Promoting Glycerol Metabolism.

Glycerol kinase (GK) participates in triglyceride (TG) synthesis by catalyzing glycerol metabolism. Whether GK contributes to nonalcoholic fatty liver (NAFL) is unclear. The expression of hepatic Gk is found to be increased in diet-induced and genetic mouse models of NAFL and is positively associated with hepatic SREBP-1c expression and TG levels. Cholesterol and fatty acids stimulate GK expression in hepatocytes. In HFD-induced NAFL mice, knockdown of hepatic Gk decreases expression of SREBP-1c and its target lipogenic genes as well as DGAT1/2, increases serum glycerol levels, decreases serum TG levels, and attenuates hepatic TG accumulation. Overexpression of GK in hepatocytes in mice or in culture produces opposite results. Mechanistic studies reveal that GK stimulates SREBP-1c transcription directly by binding to its gene promoter and indirectly by binding to SREBP-1c protein, thereby increasing lipogenic gene expression and de novo lipogenesis. Studies with truncated GK and mutant GKs indicate that GK induces SREBP-1c transcription independently of its enzyme activity. GK contributes to lipid homeostasis under physiological conditions by catalyzing glycerol metabolism rather than by regulating SREBP-1c transcription. Collectively, these results demonstrate that increased hepatic GK promotes de novo lipogenesis and TG synthesis in NAFL by stimulating SREBP-1c transcription and DGAT1/2 expression and catalyzing glycerol metabolism.

Urban Street Landscape Design System Driven by Optimized Genetic Algorithm

With the acceleration of urbanization in China, urban and rural construction land continues to expand. In order to avoid “urban street view disease” in the process of urbanization, dynamic simulation of urban street view land is of great significance. The dynamic model of urban street view land can simulate the dynamic expansion process of street view concretely and effectively, and predict the distribution and form of urban street view land in the future more accurately. How to improve the accuracy of urban street view dynamic model based on geographic cellular automata has always been the direction of unremitting exploration in academic circles. In view of the limitations of the traditional genetic algorithm model, this study constructs a genetic algorithm-logistic regression model, and takes Chengdu-Chongqing Economic Zone as a case, and optimizes the best regression coefficient of the logistic regression model through genetic algorithm fitting, so as to realize the accurate simulation of the dynamic change of urban street view land.

Akkermansia muciniphila: biology, microbial ecology, host interactions and therapeutic potential.

Akkermansia muciniphila is a gut bacterium that colonizes the gut mucosa, has a role in maintaining gut health and shows promise for potential therapeutic applications. The discovery of A. muciniphila as an important member of our gut microbiome, occupying an extraordinary niche in the human gut, has led to new hypotheses on gut health, beneficial microorganisms and host-microbiota interactions. This microorganism has established a unique position in human microbiome research, similar to its role in the gut ecosystem. Its unique traits in using mucin sugars and mechanisms of action that can modify host health have made A. muciniphila a subject of enormous attention from multiple research fields. A. muciniphila is becoming a model organism studied for its ability to modulate human health and gut microbiome structure, leading to commercial products, a genetic model and possible probiotic formulations. This Review provides an overview of A. muciniphila and Akkermansia genus phylogeny, ecophysiology and diversity. Furthermore, the Review discusses perspectives on ecology, strategies for harnessing beneficial effects of A. muciniphila for human mucosal metabolic and gut health, and its potential as a biomarker for diagnostics and prognostics.

Integrating Multi-Omics Data to Uncover Prostate Tissue DNA Methylation Biomarkers and Target Genes for Prostate Cancer Risk.

Previous studies have indicated that specific CpG sites may be linked to the risk of prostate cancer (PCa) by regulating the expression of PCa target genes. However, most existing studies aim to identify DNA methylation (DNAm) biomarkers through blood tissue genetic instruments, which impedes the identification of relevant biomarkers in prostate tissue. To identify PCa risk-associated CpG sites in prostate tissue, we established genetic prediction models of DNAm levels using data from normal prostate samples in the GTEx (N = 108) and assessed associations between genetically predicted DNAm in prostate and PCa risk by studying 122,188 cases and 604,640 controls. We observed significant associations for 3879 CpG sites, including 926 at novel genomic loci. Among them, DNAm levels of 80 CpG sites located at novel loci are significantly associated with expression levels of 45 neighboring genes in normal prostate tissue. Of these genes, 11 further exhibit significant associations with PCa risk for their predicted expression levels in prostate tissue. Intriguingly, a total of 31 CpG sites demonstrate consistent association patterns across the methylation-gene expression-PCa risk pathway. Our findings suggest that specific CpG sites may be related to PCa risk by modulating the expression of nearby target genes.

Polymorphism Of Orosomucoid-Like 3 ORMDL3 Rs4795405 C&gt;T In Iraqi Patients with Asthma

The aim of this study was to investigate the association of polymorphism of Orosomucoid-like 3 ORMDL3 rs4795405 C/T gene to the susceptibility of asthma among Iraqi asthmatic patients. Forty-five asthmatic patients (23 males and 22 females), their age 19-70 years and 35 healthy controls( 18 males and 17 females) ,their age 18-71years were selected from Wasit Province using a convenient sampling method. Genetic polymorphism of Orosomucoid-like 3 ORMDL3 rs4795405 C&gt;T was carried out using TaqMan -PCR. both patients and control groups, the distribution frequencies of genotypes and alleles of the rs4795405 C/T gene were in Hardy-Weinberg equilibrium (P&lt;0.05) .The most common genotype in both control and asthma patients was the heterozygous genotype CT with a percentage of 67% and 66% respectively. The genotype CC was higher in the asthmatic group (20%) compared to the control group (14%). In contrast, genotype TT, the less predominant genotype, was less in the asthmatic group were less in asthmatic group (13%) compared control group (20%).The C allele was more frequent in asthma patients than in healthy controls (53.33%vs47.14%), whereas the T allele was frequent in healthy controls than in asthma patients (52.86% vs 46.67%) with no significant differences. The association analysis displayed that the individuals carrying the homozygous CC genotype were more likely to have a increased risk of asthma with OR=1.5(CI95% 0.4537to4.9593) ,P=0.5063.The heterozygous genotypes CT was not associated with asthma with OR=1.0 (CI95%0.4103 to2.6538 ),P=0.9288 . The TT genotype decreases the association with asthma OR=0.6 (CI950.1865 to2.0302), P =0.4253. These results suggested that the T allele might play a protective role against asthma whereas the C allele might consider a risk factor in asthma. The subgroup analysis revealed that the asthma risk of females with ORMDL3 CC genotype was 2.4 fold increases the risk of asthma OR=2.4889 (CI95% 0.5478to11.3081), P= 0.2377 The TC and TT genotype decreases the association with the disease with with OR = 0.8485 (CI 95% 0.2312to3.1142), P = 0.8044 and OR= 0.2121(CI95% 0.02 to2.2473)P =0.1979 respectively. Among males, ORMDL3 CT genotype ncreased asthmatic risk among patients’ males 1.3 fold, OR= 1.3333 (CI95%0.3433 to 5.1781), P=0.6777. The genotype CC decreases the association with the disease OR=0.3810 (CI95%0.0317to 4.5813), P=0.4469. While, the homozygous TT genotype was not associated with the disease OR=1.0294 (CI95% 0,2313 to4.5814), P=0.9696. The analysis of genetic model for Orosomucoid-lik 3 ORMDL3 rs4795405 showed the recessive model (CC+CT/ TT ) increased the association with the asthma OR=1.6250 P=0.4253.The Over-dominant model(CT+TT/ CC) and the dominant model(CT+TT/ CC) decreased the association with asthma OR=0.9583,P=0.9288and OR= 0.6667 ,P=0.5063 respectively.