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A dual cytogenetic and molecular analysis was performed in four species of Cyclocepala (Coleoptera: Scarabaeidae: Dynastinae) from Lesser Antilles (Martinique, Dominica and Guadeloupe). Two species/sub-species, C. mafaffa grandis and C. insulicola, are endemic to Guadeloupe. They have their own non-polymorphic karyotype and a fairly homogeneous haplotype of the COI gene. C. melanocephala rubiginosa has a distinct karyotype. Its COI haplotype is homogeneous in Guadeloupe and heterogeneous in Martinique. Finally, C. tridentata has highly different karyotypes and haplotypes in the three islands. In Martinique, its karyotype, composed of metacentrics, is monomorphic while its haplotype is fairly heterogeneous. Both are close to those of other Cyclocephala and Dynastinae species, thus fairly ancestral. In Guadeloupe, its karyotype is highly polymorphic, with many acrocentrics, and its haplotype fairly homogeneous. Both are highly derived. In Dominica, both the karyotype and the haplotype represent intermediate stages between those of Martinique and Guadeloupe. We conclude that several independent colonization episodes have occurred, which excludes that C. insulicola is a vicariant form of C. tridentata in Guadeloupe. Both chromosome and COI gene polymorphisms clearly indicate a recent colonization with a northward direction for C. tridentata. [ABSTRACT FROM PUBLISHER]

Codling moth Cydia pomonella L. (Lepidoptera: Tortricidae) is the most important insect pest of apple production in Europe. Despite the economic importance of this pest, there is not information about the genetic structure of its population in Greece and the patterns of gene-flow which might affect the success of control programs. In this study, we analysed nine samples from apple, pear and walnut from various regions of mainland Greece using 11 microsatellite loci. Six samples from the aforementioned hosts from southern France were also examined for comparison. Bayesian clustering and genetic distance analyses separated the codling moth samples in two genetic clusters. The first cluster consisted mainly of the individuals from Greece, and the second of those from France, although admixture and miss-classified individuals were also observed. The low genetic differentiation among samples within each country was also revealed by FST statistics (0.009 among Greek samples and 0.0150 among French samples compared to 0.050 global value among all samples and 0.032 the mean of the pair-wise values between the two countries). These FST values suggest little structuring at large geographical scales in agreement with previous published studies. The host species and local factors (climatic conditions, topography, pest control programs) did not affect the genetic structure of codling moth populations within each country. The results are discussed in relation to human-made activities that promote gene-flow even at large geographic distances. Possible factors for the genetic differentiation between the two genetic clusters are also discussed. [ABSTRACT FROM AUTHOR]

In cockchafers of the genus Melolontha, there is a marked intraspecific polymorphism for morphological characters, making some specimens of one species resemble another. A cytogenetic and molecular (mitochondrial COI gene sequence) study of typical and atypical forms of M. melolontha and M. hippocastani, captured at the same period and area, was performed. Karyotypes and haplotypes clearly characterize each taxon, placing atypical specimens in one or the other species unambiguously. This formally discards the role of hybridization in phenotypic resemblance, as usually proposed. Karyotypes and haplotypes were compared to those of M. pectoralis and Phyllophaga pleei, a more distantly related Melolonthinae, and some Dynastinae species, to reconstruct their ancestral karyotype. The karyotype of M. melolontha is the most derivative and that of P. pleei the most conserved among the Melolonthinae studied, which fits with the phylogeny established by COI gene analysis. Both karyotypes and COI haplotypes demonstrate the proximity of M. pectoralis and M. melolontha. The karyotype of M. melolontha is polymorphic, without relationship with morphological variations. Finally, the existence of similar morphological variations in different Melolontha species and chromosomal polymorphism in M. melolontha is discussed in relation with a network (reticulated) mode of speciation. [ABSTRACT FROM PUBLISHER]

The major histocompatability complex (MHC) is a multigene family of receptors that bind and present antigenic peptides to T-cells. Genes of the MHC are characterized by an outstanding genetic polymorphism, which is considered to be maintained by positive selection. Sites involved in peptide binding form binding pockets (P) that are collectively termed the peptide-binding region (PBR). In this study, we examined the level of MHC genetic diversity within and among natural populations of brown hare ( Lepus europaeus) from Europe and Anatolia choosing for analysis of the second exon of the DQA locus, one of the most polymorphic class II loci. We aimed at an integrated population genetic analysis of L. europeaus by (i) correlating MHC polymorphism to genetic variability and phylogenetic status estimated previously from maternally (mtDNA) and biparentally (allozymes, microsatellites) inherited loci; and (ii) comparing full-length exon amino acid polymorphism with functional polymorphism in the PBR and the binding pockets P1, P6 and P9. A substantial level of DQA exon 2 polymorphism was detected with two completely different set of alleles between the Anatolian and European populations. However, the phylogeny of full-length exon 2 Leeu-DQA alleles did not show a strong phylogeographic signal. The presence of balancing selection was supported by a statistically significant excess of nonsynonymous substitutions over synonymous in the PBR and a trans-species pattern of evolution detected after phylogenetic reconstruction. The differentiating patterns detected between genetic and functional polymorphism, i.e. the number and the distribution of pocket variants within and among populations, indicated a hierarchical action of selection pressures. [ABSTRACT FROM AUTHOR]

Analysis of the genetic structure of the Norway lobster (Nephrops norvegicus), a marine crustacean with high commercial value, was undertaken to gain information regarding the differentiation of Atlantic from Mediterranean populations of marine invertebrates. Restriction fragment length polymorphism analysis of two mitochondrial DNA segments, 3.6 kilobases in total, was performed. Twelve populations from the North Sea, Irish Sea, Portuguese coast and Aegean Sea were analysed. Low levels of differentiation were found among them (FST = 0.018, P < 0.001) and there were no signs of an Atlantic-Mediterranean divide or of an isolation-by-distance scheme of differentiation. Possible reasons for these low levels of differentiation can be found in the recent expansion of N. norvegicus populations. This is supported by the mismatch distribution of pairwise haplotype differences, as well as by the high mean haplotype diversity (h = 0.93) combined with medium nucleotide diversity (π = 0.0057) (in comparison to values for marine crustaceans or teleosts) found in this study. This combination of high levels of haplotype diversity with moderate to low levels of nucleotide diversity has also been frequently attributed to a recent time of divergence for various marine species. No evidence was found for a Mediterranean refugium during glaciation periods, separate from the Atlantic, as has been reported for some marine species. The Irish Sea population was the most differentiated as a result of reduced levels of diversity. Results are also discussed in the light of future management of N. norvegicus stocks. [ABSTRACT FROM AUTHOR]

To assess genetic markers able to distinguish between five Greek breeds of horses, the random amplified polymorphic DNA (RAPD) technique was used. A total of 40 primers were initially screened in all breeds to identify primers that consistently revealed well-amplified, polymorphic bands. Despite the variability that was found within breeds, no specific RAPD marker for the discrimination of the breeds was detected. This is probably due to the extensive cross-breeding that has taken place over the years, resulting in a mixing of breeds. The high phenotypic divergence of the pony of Skyros from all the other Greek breeds of horses could be explained in terms of micro-evolutionary processes, such as natural selection owing to differential fitness. In addition, to determine the genetic affinities between breeds, all samples were screened with five primers. These primers produced a total of 93 bands, 51 of which were polymorphic. Data analysis for genetic polymorphism revealed a degree of divergence between breeds. According to the discriminant analysis (DA) classification, 100% of the individuals examined in this study could be classified correctly into their breeds. The results of this study show that RAPDs could be a powerful tool for the classification testing of individual horses, as well as for the determination of the genetic variation found among breeds, which is important for a proper management policy designed to protect this species. [ABSTRACT FROM AUTHOR]

The new allele DRB1*11:192 exon 2 differs from the DRB1*11:01:01:01 by three substitutions. [ABSTRACT FROM AUTHOR]

Completion of the first 20 nucleotides of exon 2 of DPA1*03:01 allele. [ABSTRACT FROM AUTHOR]

Objective: To investigate whether idiopathic nonobstructive azoospermia (iNOA) has its own transcriptomic signature., Design: Testicular tissue biopsies were retrieved, processed, and prepared for ribonucleic acid (RNA) extraction from 26 consented patients diagnosed with iNOA. Samples were grouped into four pools based on the presence of testicular spermatozoa: two replicate pools for "No presence" (Null-spz-1 and Null-spz-2 pools), one for "High presence" (High-spz pool), and one for "Rare presence" (Rare-spz pool). A second set of replicate pools (CF-1 and CF-2) were used from patients with obstructive azoospermia (OA) and served as controls. RNA sequencing (RNA-seq) and comparative transcriptomics analysis were performed, followed by differential gene expression analysis focused on protein-coding genes only. Differentially expressed genes (DEGs) exclusively upregulated or downregulated were further analyzed using the Gene Ontology (GO), STRING, and Kyoto Encyclopedia of Genes and Genome bioinformatic platforms., Setting: Private Fertility Clinic and Public University., Patients: Males in whom iNOA was diagnosed., Exposure: Testicular biopsies from men in whom iNOA was diagnosed., Main Outcome Measures: Protein-coding DEGs., Results: A significantly altered transcriptomic profile of protein-coding genes was identified in the testicular tissues from men with iNOA. A total of 3,858 genes exhibited dysregulated expression, with 1,994 genes being exclusively downregulated and 1,734 upregulated. Biological processes such as male gamete generation (GO:0048232) and meiotic cycle (GO:0051321) were significantly enriched by the downregulated DEGs whereas the upregulated DEGs enriched BPs such as regulation of cell death (GO:0010941), regulation of cell adhesion (GO:0030155), and defense response (GO:0006952). Interactome analysis identified hub genes among the downregulated DEGs, including PCNA, PLK1, MCM4, CDK1, CCNB1, AURKA, CCNA2, and CDC6, and among the upregulated DEGs, including EGFR, RELA, CTNNB1, MYC, JUN, SMAD3, STAT3 NFKB1, TGFB1, and ACTB. In addition, Kyoto Encyclopedia of Genes and Genome analysis demonstrated that pathways such as cell cycle (hsa04110) and oocyte meiosis (hsa04114) are primarily affected by the downregulated genes, whereas the upregulated genes mainly affected pathways such as the focal adhesion (hsa04510) and the PI3-Akt signaling pathway (hsa04151)., Conclusion: A distinct messenger RNA expression profile and altered transcriptomic activity were identified in the testicular tissues of men with iNOA., Clinical Trial Registration Number: University of Thessaly 1, 15.04.2016 and the Greek National Authority 701/15.9.2017., Competing Interests: Declaration of Interests A.C. has nothing to disclose. T.S. has nothing to disclose. K. M.-A. has nothing to disclose. K.M. has nothing to disclose. M.M. has nothing to disclose. T.G. has nothing to disclose. A. P. has nothing to disclose. C.O. has nothing to disclose. G.S. has nothing to disclose. N.C. has nothing to disclose. Z.M. has nothing to disclose., (Copyright © 2024 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.)

Background/objectives: Male infertility is a complex condition with various underlying genetic factors. microRNAs (miRNAs) play a crucial role in gene regulation, and their disruption can significantly impact fertility. This study aimed to identify variants within miRNA genes and elucidate their impact on male infertility., Methods: Whole genome sequencing was performed on blood samples from men with asthenozoospermia, oligozoospermia, and teratozoospermia, compared to normozoospermic controls. The analysis revealed a significant number of unique variants in each infertile group. We subsequently focused on variants in miRNA regions, followed by an in silico analysis to investigate the role of the identified variants and miRNAs in male infertility., Results: Focused analysis on miRNA genes identified 19 exclusive variants in teratozoospermic men, 24 in asthenozoospermic, and 27 in oligozoospermic, all mapping to pre-miRNAs or mature miRNAs. Functional analyses using Gene Ontology (GO) and KEGG pathways highlighted key biological processes and pathways disrupted by these variants and miRNA-mRNA interactions, including transcription regulation, signaling, and cancer-related pathways. Furthermore, six variants (rs17797090, rs1844035, rs7210937, rs451887, rs12233076, and rs6787734) were common across the infertile groups, suggesting their importance in male infertility or their potential as biomarkers. Common variants were also validated in another clinically relevant group of men. Some miRNAs with identified variants, such as hsa-miR-449b and hsa-miR-296, have been previously implicated in male infertility and exhibit differential expression between fertile and infertile men, according to the literature, too., Conclusion: These results provide new insights into the genetic basis of male infertility and open avenues for future research and therapeutic interventions.

Azoospermia and severe oligozoospermia represent the most extreme forms of male infertility. Despite their prevalence, the genetic foundations of these conditions are not well understood, with only a limited number of genetic factors identified so far. This study aimed to identify single-nucleotide polymorphisms (SNPs) linked to both azoospermia and severe oligozoospermia. We conducted a genome-wide association study (GWAS) involving 280 Greek males with normal semen parameters and 85 Greek males diagnosed with either azoospermia or severe oligozoospermia. Following rigorous quality control measures, our analysis identified seven SNPs associated with azoospermia/severe oligozoospermia. An in silico functional annotation was subsequently used to further investigate their role. These SNPs, found in regions not previously associated with male reproductive disorders, suggest novel genetic pathways that may contribute to these forms of infertility and pave the way for future studies. Additionally, this study sheds light on the significant role of noncoding RNAs in the pathogenesis of male infertility, with three of the identified SNPs situated in long intergenic non-coding RNAs (lincRNAs). Our findings highlight the intricate genetic landscape of azoospermia and severe oligozoospermia, underlining the necessity for more detailed studies to fully grasp the underlying mechanisms and their potential for informing diagnostic and therapeutic strategies.

Infertility is a global health challenge that affects an estimated 72.4 million people worldwide. Between 30 and 50% of these cases involve male factors, showcasing the complex nature of male infertility, which can be attributed to both environmental and genetic determinants. Asthenozoospermia, a condition characterized by reduced sperm motility, stands out as a significant contributor to male infertility. This study explores the involvement of the mitochondrial oxidative phosphorylation (OXPHOS) system, crucial for ATP production and sperm motility, in asthenozoospermia. Through whole-genome sequencing and in silico analysis, our aim was to identify and characterize OXPHOS gene variants specific to individuals with asthenozoospermia. Our analysis identified 680,099 unique variants, with 309 located within OXPHOS genes. Nine of these variants were prioritized due to their significant implications, such as potential associations with diseases, effects on gene expression, protein function, etc. Interestingly, none of these variants had been previously associated with male infertility, opening up new avenues for research. Thus, through our comprehensive approach, we provide valuable insights into the genetic factors that influence sperm motility, laying the foundation for future research in the field of male infertility.

The dialogue between population genetics and evolutionary biology, which historically followed separate paths, has now developed into a complex and interdisciplinary field of study [...].

Moderate-to-severe psoriasis (Ps) treatment includes systemic drugs and biological agents. Apremilast, a small molecule primarily metabolized by cytochrome CYP3A4, modulates the immune system by specifically inhibiting phosphodiesterase type 4 (PDE4) isoforms and is currently used for the treatment of Ps and psoriatic arthritis (PsA). Clinical trials and real-world data showed variable efficacy in response among Ps patients underlying the need for personalized therapy. This study implements a candidate-gene and a network-based approach to identify genetic markers associated with apremilast response in forty-nine Greek Ps patients. Our data revealed an association of sixty-four SNPs within or near PDE4 and CYP3A4 genes, four SNPs in ncRNAs ANRIL , LINC00941 and miR4706 , which influence the abundance or function of PDE4s, and thirty-three SNPs within fourteen genes whose protein products either interact directly with PDE4 proteins or constitute components of the cAMP signaling pathway which is modulated by PDE4s. Notably, fifty-six of the aforementioned SNPs constitute eQTLs for the respective genes in relevant to psoriasis tissues/cells implying that these variants could be causal. Our analysis provides a number of novel genetic variants that, upon validation in larger cohorts, could be utilized as predictive markers regarding the response of Ps patients to apremilast treatment.

Circular RNAs (circRNAs) are unique noncoding RNA molecules, notable for their covalent closed-loop structures, which play a crucial role in regulating gene expression across a variety of biological processes. This review comprehensively synthesizes the existing knowledge of circRNAs in three key livestock species: Bos taurus (cattle), Ovis aries (sheep), and Capra hircus (goats). It focuses on their functional importance and emerging potential as biomarkers for disease detection, stress response, and overall physiological health. Specifically, it delves into the expression and functionality of circRNAs in these species, paying special attention to traits critical to livestock productivity such as milk production, meat quality, muscle development, wool production, immune responses, etc. We also address the current challenges faced in circRNA research, including the need for standardized methodologies and broader studies. By providing insights into the molecular mechanisms regulated by circRNAs, this review underscores their scientific and economic relevance in the livestock industry. The potential of circRNAs to improve animal health management and the quality of animal-derived products aligns with growing consumer concerns for animal welfare and sustainability. Thus, this paper aims to guide future research directions while supporting the development of innovative strategies in livestock management and breeding.

In modern aquaculture, genomics-driven breeding programs have emerged as powerful tools for optimizing fish quality. This study focused on two emblematic Mediterranean fish species, the European seabass ( Dicentrarchus labrax ) and the gilthead sea bream ( Sparus aurata ), with a primary aim of exploring the genetic basis of white muscle/fillet degradation in fresh fish following harvest. We identified 57 and 44 missense SNPs in gilthead sea bream and European seabass, respectively, located within genes encoding for endogenous proteases responsible for fillet quality. These SNPs were cherry-picked based on their strategic location within the catalytic/regulatory domains of endogenous proteases that are expressed in the white muscle. Using MassArray technology, we successfully associated differentiated enzymatic activity of those endogenous proteases post-harvest as a phenotypic trait with genetic polymorphism of six SNPs in gilthead sea bream and nine in European seabass. These findings can be valuable attributes in selective breeding programs toward the extension of freshness and shelf life of these species. The integration of MassArray technology into breeding programs offers a cost-effective strategy for harnessing the potential of these genetic variants to enhance the overall quality of the final product. Recognizing that fresh fish perishability is a challenge, extending shelf-life is pivotal in reducing losses and production costs.

Male infertility is a global health issue, affecting over 20 million men worldwide. Genetic factors are crucial in various male infertility forms, including teratozoospermia. Nonetheless, the genetic causes of male infertility remain largely unexplored. In this study, we employed whole-genome sequencing and RNA expression analysis to detect differentially expressed (DE) long-noncoding RNAs (lncRNAs) in teratozoospermia, along with mutations that are exclusive to teratozoospermic individuals within these DE lncRNAs regions. Bioinformatic tools were used to assess variants' impact on lncRNA structure, function, and lncRNA-miRNA interactions. Our analysis identified 1166 unique mutations in teratozoospermic men within DE lncRNAs, distinguishing them from normozoospermic men. Among these, 64 variants in 23 lncRNAs showed potential regulatory roles, 7 variants affected 4 lncRNA structures, while 37 variants in 17 lncRNAs caused miRNA target loss or gain. Pathway Enrichment and Gene Ontology analyses of the genes targeted by the affected miRNAs revealed dysregulated pathways in teratozoospermia and a link between male infertility and cancer. This study lists novel variants and lncRNAs associated for the first time with teratozoospermia. These findings pave the way for future studies aiming to enhance diagnosis and therapy in the field of male infertility.