Search Results (92)

This review synthesizes advances in livestock genomics by examining the interplay between candidate genes, molecular markers (MMs), signatures of selection (SSs), and quantitative trait loci (QTLs) in shaping economically vital traits across livestock species. By integrating advances in genomics, bioinformatics, and precision breeding, the study elucidates genetic mechanisms underlying productivity, reproduction, meat quality, milk yield, fibre characteristics, disease resistance, and climate resilience traits pivotal to meeting the projected 70% surge in global animal product demand by 2050. A critical synthesis of 1455 peer-reviewed studies reveals that targeted genetic markers (e.g., SNPs, Indels) and QTL regions (e.g., IGF2 for muscle development, DGAT1 for milk composition) enable precise selection for superior phenotypes. SSs, identified through genome-wide scans and haplotype-based analyses, provide insights into domestication history, adaptive evolution, and breed-specific traits, such as heat tolerance in tropical cattle or parasite resistance in sheep. Functional candidate genes, including leptin (LEP) for feed efficiency and myostatin (MSTN) for double-muscling, are highlighted as drivers of genetic gain in breeding programs. The review underscores the transformative role of high-throughput sequencing, genome-wide association studies (GWASs), and CRISPR-based editing in accelerating trait discovery and validation. However, challenges persist, such as gene interactions, genotype–environment interactions, and ethical concerns over genetic diversity loss. By advocating for a multidisciplinary framework that merges genomic data with phenomics, metabolomics, and advanced biostatistics, this work serves as a guide for researchers, breeders, and policymakers. For example, incorporating DGAT1 markers into dairy cattle programs could elevate milk fat content by 15-20%, directly improving farm profitability. The current analysis underscores the need to harmonize high-yield breeding with ethical practices, such as conserving heat-tolerant cattle breeds, like Sahiwal. Full article

Background: Polycystic ovary syndrome (PCOS) is a complex and multifactorial disorder affecting reproductive, endocrine, and metabolic functions in women of reproductive age. While environmental and lifestyle factors play a role, increasing evidence highlights the contribution of genetic and epigenetic mechanisms to its pathogenesis. Objective: This narrative review aims to provide an updated overview of the current evidence regarding the role of genetic variants, gene expression patterns, and epigenetic modifications in the etiopathogenesis of PCOS, with a focus on their impact on ovarian function, fertility, and systemic alterations. Methods: A comprehensive search was conducted across MEDLINE, EMBASE, PubMed, Web of Science, and the Cochrane Library using MeSH terms including “PCOS”, “Genes involved in PCOS”, and “Etiopathogenesis of PCOS” from January 2015 to June 2025. The selection process followed the SANRA quality criteria for narrative reviews. Seventeen studies published in English were included, focusing on original data regarding gene expression, polymorphisms, and epigenetic changes associated with PCOS. Results: The studies analyzed revealed a wide array of molecular alterations in PCOS, including the dysregulation of SIRT and estrogen receptor genes, altered transcriptome profiles in cumulus cells, and the involvement of long non-coding RNAs and circular RNAs in granulosa cell function and endometrial receptivity. Epigenetic mechanisms such as the DNA methylation of TGF-β1 and inflammation-related signaling pathways (e.g., TLR4/NF-κB/NLRP3) were also implicated. Some genetic variants—particularly in DENND1A, THADA, and MTNR1B—exhibit signs of positive evolutionary selection, suggesting possible ancestral adaptive roles. Conclusions: PCOS is increasingly recognized as a syndrome with a strong genetic and epigenetic background. The identification of specific molecular signatures holds promise for the development of personalized diagnostic markers and therapeutic targets. Future research should focus on large-scale genomic studies and functional validation to better understand gene–environment interactions and their influence on phenotypic variability in PCOS. Full article

Approximately 70% of people will experience a traumatic event in their lifetime, but post-traumatic stress disorder (PTSD) will only develop in 3.9% and complex post-traumatic stress disorder (CPTSD) in 1–8% of the population worldwide, although in some countries (e.g., Poland and Northern Ireland) it will develop in a much higher percentage. Stress-related disorders have a complex pathogenesis involving neurophysiological, genetic, epigenetic, neuroendocrine and environmental factors. This article reviews the current state of knowledge on the molecular aspects of selected PTSD symptoms: hypervigilance, re-experiencing, emotion dysregulation and dissociation, i.e., the symptoms with strong neurobiological components. Among analysed susceptibility factors are specific gene polymorphisms (e.g., FKBP5, COMT, CHRNA5, CRHR1, 5-HTTLPR, ADCY8 and DRD2) and their interactions with the environment, changes in the HPA axis, adrenergic hyperactivity and disturbances in the activity of selected anatomical structures (including the amygdala, prefrontal cortex, corpus callosum, anterior cingulate gyrus and hippocampus). It is worth noting that therapeutic methods with proven effectiveness in PTSD (TF-CBT and EMDR) have a substantial neurobiological rationale. Molecular aspects seem crucial when searching for effective screening/diagnostic methods and new potential therapeutic options. Full article

The Tibetan goat (Capra hircus) exhibits remarkable adaptations to high-altitude hypoxia, yet the molecular mechanisms remain unclear. This study integrates RNA-seq, WGCNA, and machine learning to explore gene-environment interactions (G × E) in hypoxia adaptation. Fibroblasts from the Tibetan goat and Yunling goat were cultured under hypoxic (1% O₂) and normoxic (21% O₂) conditions, respectively. This identified 68 breed-specific (G), 100 oxygen-responsive (E), and 620 interaction-driven (I) Differentially Expressed Genes (DEGs). The notably higher number of interaction-driven DEGs compared to other effects highlights transcriptional plasticity. We defined two gene sets: Environmental Stress Genes (n = 632, E ∪ I) and Genetic Adaptation Genes (n = 659, G ∪ I). The former were significantly enriched in pathways related to oxidative stress defense and metabolic adaptation, while the latter showed prominent enrichment in pathways associated with vascular remodeling and transcriptional regulation. CTNNB1 emerged as a key regulatory factor in both gene sets, interacting with CASP3 and MMP2 to form the core of the protein–protein interaction (PPI) network. Machine learning identified MAP3K5, TGFBR2, RSPO1 and ITGB5 as critical genes. WGCNA identified key modules in hypoxia adaptation, where FOXO3, HEXIM1, and PPARD promote the stabilization of HIF-1α and metabolic adaptation through the HIF-1 signaling pathway and glycolysis. These findings underscore the pivotal role of gene–environment interactions in hypoxic adaptation, offering novel perspectives for both livestock breeding programs and biomedical research initiatives. Full article

This article methodically reveals how, in woody plants (poplar), the interaction between N and P coordinates root structure and nutrient absorption through a complex hormone signaling network. This study bridges a significant gap in our knowledge of nutrient interaction networks. The results demonstrate that NO₃⁻ significantly enhances the gene expression and enzymatic activity of organic acid synthases (MDH, PEPC) and APs. Furthermore, it synergizes with IAA/ABA signals to refine root structure, enhancing the surface area for P absorption. In low Pi availability environments, NO₃⁻ further promotes P recycling by simultaneously boosting the levels of Pi transport proteins (notably, the PHO family), facilitating myo-inositol phosphate metabolism (via IMP3/ITPK1-mediated PP-InsPs degradation), and augmenting IAA/SA signals. Pi induces the activity of N assimilation enzymes (GS/GOGAT/GDH), facilitating nitrogen metabolism. However, in the absence of N, it leads to a metabolic imbalance characterized by high enzymatic activity but low efficiency. Alternatively, adequate N availability allows Pi to improve root robustness and N assimilation efficiency, mediated by IAA/GA accumulation and ABA signaling (e.g., SNRK2/ABF). We propose the existence of an intricate network in poplar, orchestrated by transcriptional cascades, metabolic regulation, and hormonal synergism. Key modules such as SPX-PHR, NLA, HHO2, and MYB59 are likely central to this network’s function. These findings offer a foundational framework for the development of molecular breeding and precise fertilization strategies, enhancing the efficient use of N and P in forestry. Full article

Micro/nanoplastics (M/NPs) have become prevalent in aquatic environments due to their widespread applications. Likewise, ubiquitous ecological macromolecules can adsorb onto M/NPs to form an “eco-corona”, which significantly alters their environmental behaviors including aggregation dynamics, adsorption/desorption, and bioavailability. Therefore, it is necessary to analyze the role of eco-corona in assessing the environmental risks of M/NPs. This review systematically summarizes the formation mechanisms of eco-corona and evaluates its regulatory effects on the stability and ecotoxicity of M/NPs. Compared with other ecological macromolecules (e.g., natural organic matter and extracellular polymeric substances), humic acid (HA) tightly binds to M/NPs through electrostatic and hydrophobic interactions, significantly affecting their hetero-aggregation behavior and colloidal stability. In terms of bioavailability, the various functional groups on the HA surface can regulate the surface charge and hydrophobicity of M/NPs, thereby affecting their bioaccumulation and “Trojan horse” effect. Notably, the HA corona alleviates M/NPs-induced growth inhibition and oxidative stress. Genotoxicity assessment further showed that HA corona can regulate the expression of genes related to oxidative stress response and detoxification pathways. Future studies should focus on the synergistic effects between eco-corona and co-existing pollutants in complex aquatic environments to elucidate the long-term ecological risks associated with eco-corona formation. Full article

Background: Breast cancer (BC), one of the most common cancers, has increased in Mexico during the past decade, along with other chronic and metabolic diseases. Methods: Herein, we analyzed 121 SNPs (85 SNPs related to BC and/or glucose-associated metabolic pathways and 36 SNP classified as ancestry markers) in 92 confirmed BC cases and 126 unaffected BC women from Northeastern Mexico. The relationship of these 121 SNPs with BC, considering BMI, menopause status, and age as cofactors, was explored using a gene–environment (G × E) interaction multi-locus model. Results: Twelve gene variants were significantly associated with BC: three located in exome (rs3856806 PPARG, rs12792229 MMP8, and rs5218 KCNJ11-ABCC8), and nine in non-coding regions, which are involved in accelerated decay of the mRNA transcripts, regulatory regions, and flanking regions (rs3917542 PON1; rs3750804 and rs3750805 TCF7L2; rs1121980 and rs3751812 FTO; rs12946618 RPTOR; rs2833483 SCAF4; rs11652805 AMZ2P1-GNA13; and rs1800955 SCT-DEAF1-DRD4). Conclusions: This study identified an association between BC and menopause, age (above 45), obesity, and overweight status with gene variants implicated in diabetes mellitus, obesity, insulin resistance, inflammation, and remodeling of the extracellular matrix. Full article

Alcohol use disorder (AUD) contributes significantly to the global burden of disease. The susceptibility for AUD is mediated through an interaction of genetic risk factors and environmental influences. These gene × environment (G × E) interactions manifest as epigenetic regulations of gene expression, among other things. Previous research suggests an association between Ganglioside Induced Differentiation Associated Protein 1 (GDAP1) DNA methylation and AUD. Here, we investigate the epigenetic dysregulation of GDAP1 in AUD through comparing DNA methylation in whole blood and saliva, as well as H3K4-trimethylation (H3K4me3) in PBMC (Peripheral Blood Mononuclear Cell) samples of AUD patients and healthy control individuals. Additionally, the effect of abstinence-based therapy was investigated. AUD patients before treatment exhibit significantly lower promoter DNA methylation levels in whole blood and saliva, as well as lower H3K4me3 near the transcription start site. GDAP1 gene expression was not significantly altered. Following treatment, H3K4me3 was significantly increased in patients and no longer differed from control individuals. There was no significant effect of treatment on DNA methylation. We conclude that GDAP1 is epigenetically dysregulated in AUD patients, and is responsive to abstinence-based therapy at the level of H3K4me3. It should be investigated further to establish its potential as a diagnostic biomarker. Full article

Complex diseases such as type 2 diabetes are influenced by both environmental and genetic risk factors, leading to a growing interest in identifying gene–environment (G × E) interactions. A three-step variable selection method for single-index varying-coefficients models was proposed in recent research. This method selects varying and constant-effect genetic predictors, as well as non-zero loading parameters, to identify genetic factors that interact linearly or nonlinearly with a mixture of environmental factors to influence disease risk. In this paper, we extend this approach to a binary response setting given that many complex human diseases are binary traits. We also establish the oracle property for our variable selection method, demonstrating that it performs as well as if the correct sub-model were known in advance. Additionally, we assess the performance of our method through finite-sample simulations with both continuous and discrete gene variables. Finally, we apply our approach to a type 2 diabetes dataset, identifying potential genetic factors that interact with a combination of environmental variables, both linearly and nonlinearly, to influence the risk of developing type 2 diabetes. Full article

This study investigates Brucella ceti infection in marine mammals stranded along the Lisbon and Tagus Valley coast between 2022 and mid-2024, marking the first report of Brucella presence in Portuguese waters. Out of 59 examined marine mammals, B. ceti was isolated in three common dolphins (5.1%), a prevalence rate consistent with previous studies from other coastlines. PCR-based detection indicated a higher infection rate (23.7%), suggesting an underestimation of the prevalence of B. ceti infection in this population. Multi-locus Sequence Typing (MLST) and Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA) revealed distinct genetic profiles and close relationships to B. ceti strains from the Atlantic, supporting the hypothesis of specific host-adapted lineages in dolphins. Virulence genes, including those for host interaction (bspE, btpB) and intracellular survival (virB7, vceA), were consistent across isolates, highlighting the pathogenic potential. Additionally, antimicrobial resistance (AMR) genes, such as mprF and efflux proteins (bepC-G), were also identified. These findings underscore the need for further research and surveillance to understand B. ceti transmission, host range, and impacts on Atlantic cetaceans, as well as to develop effective diagnostic and management strategies to mitigate infection risks in marine environments. Full article

Low-temperature (LT) stress seriously affects the distribution, seedling survival, and grain yield of maize. At the seedling emergence stage, maize’s coleoptile is one of the most sensitive organs in sensing LT signaling and, in general, it can envelop young leaves to protect them from LT damage. In addition, brassinolides (BRs) have been shown to enhance LT tolerance from various species, but the effects of BRs on coleoptiles in maize seedlings under LT stress are unclear. Therefore, in this study, the pre-cultured coleoptiles of Zheng58 seedlings were treated with or without 2.0 μM 24-epibrassinolide (EBR) at 25 °C and 10 °C environments for five days to analyze their physiological and transcriptomic changes. Physiological analysis showed that a 10°C LT stress increased the content of glucose (0.43 mg g⁻¹ FW), sucrose (0.45 mg g⁻¹ FW), and starch (0.76 mg g⁻¹ FW) of Zheng58 coleoptiles compared to a 25°C environment. After the coleoptiles were exposed to a 2.0 μM EBR application under 10°C temperature for five days, the contents of these three sugars continued to increase, and reached 2.68 mg g⁻¹ FW, 4.64 mg g⁻¹ FW, and 9.27 mg g⁻¹ FW, respectively, indicating that sugar signaling and metabolism played key roles in regulating LT tolerance in the coleoptiles of maize seedlings. Meanwhile, a transcriptome analysis showed that 84 and 15 differentially expressed genes (DEGs) were enriched in the sucrose and starch metabolism and photosynthesis pathways, respectively, and multiple DEGs involved in these pathways were significantly up-regulated under LT stress and EBR stimulation. Further analysis speculated that the four DEGs responsible for sucrose-phosphate synthetase (SPS, i.e., Zm00001d048979, probable sucrose-phosphate synthase 5 and Zm00001d012036, sucrose-phosphate synthase 1), sucrose synthase (SUS, Zm00001d029091, sucrose synthase 2 and Zm00001d029087, sucrose synthase 4) were crucial nodes that could potentially link photosynthesis and other unknown pathways to form the complex interaction networks of maize LT tolerance. In conclusion, our findings provide new insights into the molecular mechanisms of exogenous EBR in enhancing LT tolerance of maize seedlings and identified potential candidate genes to be used for LT tolerance breeding in maize. Full article

Environmental forces impacting public health include exposure to toxic substances, adverse childhood experiences (ACEs), diet, and exercise. Here, we examine the first two of these forces in some detail since they may be amenable to correction through cultural, medical, and practitioner intervention. At the same time, changing people’s dietary and exercise routines are likely more resistant to these interventions and are referred to only incidentally in this review. That is, societal efforts could prevent exposure to toxicants and ACEs—not necessarily requiring cooperation by the affected individuals—whereas changing diet and exercise practices requires an individual’s discipline. Toxic substances considered in this review include endocrine disruptors, arsenics, 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), the organic solvent, Trichloroethylene (TCE), and the Benzo[a]pyrene (B[a]P) produced from incomplete combustion of tobacco and other organic materials. Exposure to each of these toxic substances may have serious adverse health effects, especially in genetically more susceptible individuals. For example, children of mothers exposed to the endocrine disruptor, Atrazine, have significantly lower birth length, weight, and head circumference. Moreover, male offspring exhibit genital abnormalities, and all of these effects may be transgenerational. However, analyses of interactions among genes, the environment, and epigenetic modifications have already revealed distinctive individual risks of adverse reactions to toxic exposure. So, interventions through precision medicine might improve the health of those exposed individuals. Adults previously exposed to more than one ACE (e.g., child abuse and inter-parental violence) are more likely to develop anxiety, cancer, and diabetes. Detecting ACE exposures in children in the general population is fraught with difficulty. Thus, the risks of ACEs to our health remain even more insidious than exposures to toxicants. Nevertheless, higher provider compassion is associated with significantly better clinical outcomes for patients with these afflictions. For all these reasons, the first major aim of this review is to recount several of the major forces contributing to or impairing public health. Our second major aim is to examine mitigating influences on these forces, including social justice and provider compassion in the setting of precision medicine. Idealistically, these mitigators might eventually lead to the development of more cooperative and compassionate cultures and societies. Full article

Bacteria in the phylum Gemmatimonadota are globally distributed and abundant in microbial communities of various environments, playing an important role in driving biogeochemical cycling on Earth. Although high diversities in taxonomic composition and metabolic capabilities have been reported, little is known about the environmental preferences and associated functional features that facilitate adaptation among different Gemmatimonadota lineages. This study systematically analyzed the relationships between the environments, taxonomy, and functions of Gemmatimonadota lineages, by using a comparative genomics approach based on 1356 Gemmatimonadota genomes (213 high-quality and non-redundant genomes) available in a public database (NCBI). The taxonomic analysis showed that the 99.5% of the genomes belong to the class Gemmatimonadetes, and the rest of the genomes belong to the class Glassbacteria. Functional profiling revealed clear environmental preference among different lineages of Gemmatimonadota, and a marine group and two non-marine groups were identified and tested to be significantly different in functional composition. Further annotation and statistical comparison revealed a large number of functional genes (e.g., amiE, coxS, yfbK) that were significantly enriched in genomes from the marine group, supporting enhanced capabilities in energy acquisition, genetic information regulation (e.g., DNA repair), electrolyte homeostasis, and growth rate control. These genomic features are important for their survival in the marine environment, which is oligotrophic, variable, and with high salinity. The findings enhanced our understanding of the metabolic processes and environmental adaptation of Gemmatimonadota, and further advanced the understanding of the interactions of microorganisms and their habitats. Full article

Mounting evidence supports the key role of the disrupted integrity of the blood-brain barrier (BBB) in stress- and inflammation-associated depression. We assumed that variations in genes regulating the expression and coding proteins constructing and maintaining this barrier, along with those involved in inflammation, have a predisposing or protecting role in the development of depressive symptoms after experiencing severe stress. To prove this, genome-by-environment (GxE) interaction analyses were conducted on 6.26 M SNPS covering 19,296 genes on PHQ9 depression in interaction with adult traumatic events scores in the UK Biobank (n = 109,360) in a hypothesis-free setup. Among the 63 genes that were significant in stress-connected depression, 17 were associated with BBB, 23 with inflammatory processes, and 4 with neuroticism. Compared to all genes, the enrichment of significant BBB-associated hits was 3.82, and those of inflammation-associated hits were 1.59. Besides some sex differences, CSMD1 and PTPRD, encoding proteins taking part in BBB integrity, were the most significant hits in both males and females. In conclusion, the identified risk genes and their encoded proteins could provide biomarkers or new drug targets to promote BBB integrity and thus prevent or decrease stress- and inflammation-associated depressive symptoms, and possibly infection, e.g., COVID-19-associated mental and neurological symptoms. Full article

The drought response index (DRI) is an indicator of drought tolerance after adjustment for variation in flowering date and potential yield under well-watered conditions. Using a temperate japonica mapping population of 97 recombinant inbred lines from a cross between Otomemochi (OTM) and Yumenohatamochi (YHM), we evaluated DRI during the reproductive stage under very severe drought in one year and under severe drought in the next year. DRI under very severe drought (−6.4 to 15.9) and severe drought (−3.9 to 8.3) positively correlated with grain dry weight under drought. Three QTLs for DRI were identified: RM3703–RM6911–RM6379 and RM6733–RM3850 both on chromosome 2 in both years combined; and RM8120–RM2615–RM7023 on chromosome 6 in the second year. The latter collocated with putative genes for signaling and defense mechanisms (e.g., PIN1B, BZIP46) revealed by database analysis. Top DRI lines retained root dry weight and had bigger steles. QTL-by-environment interaction had a greater relative contribution than the main effects of QTLs. Comparison with three previous studies revealed that the QTLs for DRI were unique to each experiment and/or population; most of them closely colocalized with reported drought-yield QTLs. Full article