Elucidating the Role of OXPHOS Variants in Asthenozoospermia: Insights from Whole Genome Sequencing and an In Silico Analysis

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.

Feature Papers in Population and Evolutionary Genetics and Genomics 2023: Unraveling Population Dynamics, Diversity, and Evolutionary Paths

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

Understanding Circular RNAs in Health, Welfare, and Productive Traits of Cattle, Goats, and Sheep

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.

MassArray Genotyping as a Selection Tool for Extending the Shelf-Life of Fresh Gilthead Sea Bream and European Seabass

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.

Unveiling the Genetic Complexity of Teratozoospermia: Integrated Genomic Analysis Reveals Novel Insights into lncRNAs' Role in Male Infertility

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.

Circular RNAs and Their Role in Male Infertility: A Systematic Review

Male infertility is a global health problem that is on the rise. Today, many noncoding RNAs (ncRNAs) are associated with male infertility. Circular RNAs (circRNAs) have recently drawn attention, but a comprehensive understanding of the role of circRNAs in male infertility is limited. This systematic review investigates the differential expression of circRNAs in male infertility or circRNAs that could serve as candidate biomarkers. The PRISMA guidelines were used to search PubMed and Web of Science on 11 January 2023. Inclusion criteria were human participants, experimental studies aiming to associate circRNAs with male infertility reporting differentially expressed circRNAs, and the English language. A total of 156 articles were found, and after the screening and eligibility stages, 13 studies were included in the final sample. Many circRNAs are deregulated in male infertility, and their interactions with miRNAs play an important role in affecting cellular processes and pathways. CircRNAs could also be used as biomarkers to screen patients before sperm retrieval. However, most studies focus on the role of circRNAs in azoospermia, and there is a knowledge gap regarding other subtypes of male infertility. Future research is needed to explore the exact mechanism of action of circRNAs and investigate their use as biomarkers.

Male Infertility: From Genes to Genomes 2022

Infertility is defined as the inability to conceive after at least 12 months of regular, unprotected sexual intercourse and it is considered an alarming global health issue [...].

Gene-by-Sex Interactions: Genome-Wide Association Study Reveals Five SNPs Associated with Obesity and Overweight in a Male Population

Obesity is a chronic health problem associated with severe complications and with an increasing prevalence in the Western world. Body-fat composition and distribution are closely associated with obesity, but the human body’s composition is a sexually dimorphic trait, as differences between the two sexes are evident even from fetal life. The effect of sex hormones contributes to this phenomenon. However, studies investigating gene-by-sex interactions for obesity are limited. Therefore, the aim of the present study was to identify single-nucleotide polymorphisms (SNPs) associated with obesity and overweight in a male population. A genome-wide association study (GWAS) that included 104 control, 125 overweight, and 61 obese subjects revealed four SNPs associated with overweight (rs7818910, rs7863750, rs1554116, and rs7500401) and one SNP (rs114252547) associated with obesity in males. An in silico functional annotation was subsequently used to further investigate their role. Most of the SNPs were found in genes regulating energy metabolism and homeostasis, and some of them were expression quantitative trait loci (eQTL). These findings contribute to the understanding of the molecular mechanisms underlying obesity-related traits, especially in males, and pave the road for future research toward the improvement of the diagnosis and therapy of obese individuals.

West Nile virus-associated HLA-DRB1 alleles in the Greek population: A structural perspective

The HLA system plays a significant role via the regulation of the immune system and contributes to the progression and protection of many diseases. In our previous study, several HLA-DRB1 alleles were found to have a susceptible or protective role toward infection and neuroinvasion of West Nile Virus (WNV) in the Greek population. As expected, the majority of polymorphic positions are located in the peptide-binding region of the molecule. In the present work, the structure of these alleles was studied in silico, to examine the effect of polymorphism on the conformation of DRB1 proteins, with the aspect of WNV association. More specifically, molecular dynamics simulations were used for structural prediction of 23 available alleles. These modeled alleles were evaluated using root-mean-square deviation (RMSD) and root-mean-square fluctuation analysis. Low RMSD values indicate that different alleles have similar structures. Furthermore, low fluctuation was observed in the peptide-binding region between alleles with the higher and the lowest RMSD values. These findings indicate that probably variable residues do not affect the behavior of DRB1 alleles in WNV disease, by causing structural differences between them.

Genetic diversity and thermotolerance in Holstein cows: Pathway analysis and marker development using whole-genome sequencing

Heat stress causes extensive losses in the dairy sector, due to negative effects on milk production and reproduction. Cows have evolved a series of protective mechanisms, (physiological, biochemical, behavioural) to cope with the thermostressing environments, which have allowed the preservation of productive and reproductive potential of specific animals during summer; these animals are considered thermotolerant and could be used to design programs of selective breeding. These programs, targeting the generations of a population of heat-resistant animals, would increase the frequency of the desired phenotypes, tackling the financial losses on one hand and reducing the carbon footprints of the dairy sector on the other. The development of genomics techniques has enabled genome wide variant calling, to detect SNPs associated with the desired phenotypes. In this study, we used a comparative genomics approach to detect genetic variation associated with thermotolerance and to design molecular markers for characterizing the animals as tolerant/sensitive. A total of 40 cows from each group were split in four sequencing pools and a whole-genome sequencing approach was used. Results and conclusion: Genome-wide genetic variation between groups was characterized and enrichment analysis revealed specific pathways which participate in the adaptive mechanisms of thermotolerance, implicated into systemic and cellular responses, including the immune system functionality, Heat Stress and Unfolded Protein Response. The markers made a promising set of results, as specific SNPs in five genes encoding for Heat Shock Proteins were significantly associated with thermotolerance.

The Role of Long Noncoding RNAs on Male Infertility: A Systematic Review and In Silico Analysis

Male infertility is a complex disorder affecting many couples worldwide. Long noncoding RNAs (lncRNAs) regulate important cellular processes; however, a comprehensive understanding of their role in male infertility is limited. This systematic review investigates the differential expressions of lncRNAs in male infertility or variations in lncRNA regions associated with it. The PRISMA guidelines were used to search Pubmed and Web of Science (1 June 2022). Inclusion criteria were human participants, patients diagnosed with male infertility, and English language speakers. We also performed an in silico analysis investigating lncRNAs that are reported in many subtypes of male infertility. A total of 625 articles were found, and after the screening and eligibility stages, 20 studies were included in the final sample. Many lncRNAs are deregulated in male infertility, and interactions between lncRNAs and miRNAs play an important role. However, there is a knowledge gap regarding the impact of variants found in lncRNA regions. Furthermore, eight lncRNAs were identified as differentially expressed in many subtypes of male infertility. After in silico analysis, gene ontology (GO) and KEGG enrichment analysis of the genes targeted by them revealed their association with bladder and prostate cancer. However, pathways involved in general in tumorigenesis and cancer development of all types, such as p53 pathways, apoptosis, and cell death, were also enriched, indicating a link between cancer and male infertility. This evidence, however, is preliminary. Future research is needed to explore the exact mechanism of action of the identified lncRNAs and investigate the association between male infertility and cancer.

Male infertility and the impact of lifestyle in the Greek population: A case–control study

Background and Aims

Collection of epidemiological data has become a crucial step in every fertility evaluation, especially regarding idiopathic male infertility. Information on data such as tobacco smoking, alcohol intake, and body mass index can provide crucial information regarding the dynamics between fertility status and everyday practices. We aim to set the base for epidemiological studies on male infertility in the Greek population.

Methods

Four hundred and fourteen Greek volunteers were asked to fill in a questionnaire regarding their characteristics and lifestyle preferences, followed by a seminogram. Depending on their answers, they were divided into groups and data were analyzed for correlation with seminogram parameters using Spearman's rank correlation test.

Results

Our results indicate that a high body mass index (BMI) is negatively correlated with all three seminogram parameters (number, motility, and morphology) and exposure to radiation or chemicals is negatively correlated with sperm motility, with a p < 0.01.

Conclusions

These findings indicate negative correlations of BMI and exposure to radiation/chemicals with semen parameters in the Greek population. Such information can be used to plan a diagnostic approach or even therapeutic interventions.

P-007 Unraveling the genetic basis of Idiopathic Azoospermia: Α transcriptome profiling analyses in a Greek Population

Study question

Are there differentially expressed genes (DEGs), in the testicular tissue of azoospermic males which could uncover tissue specific gene expression signatures, associated with idiopathic azoospermia?

Summary answer

The current findings link for the first time the pathophysiology of idiopathic azoospermia to the immune system and open a new era for further investigation

What is known already

Azoospermia is the most severe form of male infertility and affects 10% of the infertile men and 1% of the general male population which equals to several million men all over the world. A causal genetic factor is established in only 25% of the cases while in the remaining 75% there is no diagnosis and is termed idiopathic. Published data demonstrate that in idiopathic azoospermia heterogeneous genetic factors are the underlying cause. Clarifying the genetic basis of azoospermia will immensely improve our current clinical and treatment approaches for patient care at the levels of diagnosis, therapy, treatment, and safety

Study design, size, duration

During June 2020 and June 2021 testicular samples from 26 consented IVF patients were included in this study. The samples were divided in 7 pools based on the presence of testicular spermatozoa found. In particular, Pools 1-3 included testicular samples with high, average and very low presence of spermatozoa, Pools 4 & 5 samples with no spermatozoa found, and Pools 6-7 included only CF carriers. Pools 6 &7 were used as controls.

Participants/materials, setting, methods

Total RNA was isolated using the RΝeasy plus universal mini kit (Qiagen) and quantified using a photometer. Next, RNA sequencing was performed by Novogene, using the Illumina NovaSeq platform and the DEGs that were identified were processed using Gene Ontology (GO) functional enrichment analysis, pathway enrichment analysis and protein-protein interaction (PPI) network reconstruction using the Gene Ontology Resource, the KEGG database and the STRING database respectively.

Main results and the role of chance

In total RNA from up to 39.664 genes was detected and significant differences in gene expression (DEGs, log2fold change≥2, p-value &lt; 0.05) were identified in the 7 pools analyzed. The top 10% of the protein coding DEGs from each comparison was further analyzed. Up to 1.900 protein coding genes were found to be common in at least two comparisons and exhibit consistent expression profiles. In particular, 920 genes were overexpressed in the “good quality” testicular samples (high & average presence of spermatozoa) while 940 genes were overexpressed in the “low quality” testicular samples (rare or no spermatozoa found). GO analysis revealed that the sexual reproduction, male gamete generation spermatogenesis, cilium movement and fertilization biological processes were enriched in the “good quality” testicular pools while the biological processes response to stimulus, response to stress, response to cytokine and defense response were overrepresented in the “low quality” testicular samples. The PPI network of the DEGs was reconstructed and hub proteins with a putative key role in the pathogenesis of azoospermia were identified.

Limitations, reasons for caution

While transcriptomics analysis is becoming a powerful analysis tool there are still technical limitations which may impact the accurate representation of the DEGs profiles found. The data obtained in this study represent the whole testicular tissue samples analyzed and they are not cell-type specific

Wider implications of the findings

The findings of this study demonstrate that in the “low quality” testicular samples, there is a significant under-expression of testis-specific genes directly involved in spermatogenesis and fertilization processes, an over-expression of the genes involved in the body’s immune defense system and advance our understanding in the pathophysiology of idiopathic azoospermia.

Trial registration number

Τ1EDK-02787

Meta-analysis of gene expression data in adipose tissue reveals new obesity associated genes

High-throughput transcriptomic and proteomic data like microarray data are deposited in public databases such as Gene Expression Omnibus (GEO). Omics data integration and processing from different and independent studies is achieved by using efficient and effective computational tools through meta-analysis. Meta-analysis is a statistical powerful tool combining data from numerous studies, minimizes bias and increases statistical power by increasing sample size compared to individual studies. Therefore, we performed a meta-analysis of gene expression data in adipose tissue to identify genes that are differentially expressed between obese and non-obese subjects as well as to detect gene expression signatures, pathways and networks associated with obesity. We identified 821 differentially expressed genes (DEGs) in adipose tissue of obese subjects compared to non-obese. A protein-protein interactions (PPIs) network was reconstructed consisting of 168 proteins. Functional enrichment analysis in the network revealed proteins involved in RNA and energy metabolism. The KEGG pathway analysis revealed 15 enriched pathway terms. Furthermore, multiple testing correction methods identified five statistically significant obesity associated genes (NDUFA12, SFI1, SSB, FAR2 and LACE1) that require further investigation.

The Effects of Heat Shock Protein 70 Addition in the Culture Medium on the Development and Quality of In Vitro Produced Heat Shocked Bovine Embryos

The aims of the present study were to examine the effects of HSP70 addition in the in vitro culture medium of day 3 embryos on their developmental competence and quality. Bovine oocytes (n = 1442) were in vitro matured, inseminated and cultured for the first two days according to standardized methods. The presumptive zygotes were randomly allocated in three experimental groups: Control, C (embryos cultured at 39 °C throughout the culture period), group C41 (temperature was raised to 41 °C from the 48th to 72nd h post insemination (p.i.) and then it returned at 39 °C for the remaining culture period), and group H41 (the temperature modification was the same as in C41 and during heat exposure, HSP70 was added in the culture medium). Cleavage and embryo yield were assessed 48 h p.i. and on days 7, 8, 9, respectively and gene expression in day 7 blastocysts was assessed by RT-PCR. Blastocyst yield was the highest in group C39; and higher in group H41 compared to group C41. From the gene expression analyses, altered expression of 11 genes was detected among groups. The analysis of the orchestrated patterns of gene expression differed between groups. The results of this study confirm the devastating effects of heat stress on embryo development and provide evidence that HSP70 addition at the critical stages can partly counterbalance, without neutralizing, the negative effects of the heat insult on embryos, acting mainly through mechanisms related to energy deployment.

HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action

BACKGROUND

HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR).

METHODS

For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used.

RESULTS

All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found.

CONCLUSIONS

Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.

Developmental competence of heat stressed oocytes from Holstein and Limousine cows matured in vitro

The negative effects of heat stress on dairy cattle's fertility have been extensively studied, but the relevant knowledge for beef cattle is rather limited. The aims of this study were to investigate the effects of HS during in vitro maturation on the developmental potential of oocytes derived from Limousine and Holstein cows and to estimate the effect of the differential gene expression of important genes in oocytes, cumulus cells and blastocysts in the growth competence between the breeds. In seven replicates, cumulus oocyte complexes from Holstein and Limousine cows were matured for 24 hr at 39°C (controls C; Hol_39, Lim_39) or at 41°C from hour 2 to hour 8 of IVM (treated T; Hol_41, Lim_41), fertilized, and presumptive zygotes were cultured for 9 days at 39°C. Cleavage and embryo formation rates were evaluated 48 hr post-insemination and on days 7, 8 and 9, respectively. From all groups, subsets of cumulus cells, oocytes and blastocysts were analysed for the relative expression of genes related to metabolism, stress, apoptosis and placentation. No difference was detected in cleavage rate or in blastocyst formation rate among the control groups. In both breeds, heat stress reduced blastocyst yield, but at all days the suppression was higher in Limousines. In Holsteins, altered gene expression was detected in cumulus cells (G6PD, GLUT1) and blastocysts (PLAC8), while in Limousines, differences were found in oocytes (G6PD, HSP90AA1), in cumulus cells (CPT1B, HSP90AA1, SOD2) and blastocysts (DNMT, HSP90AA1, SOD2). It appears that Holstein COCs are more tolerant than Limousine COCs, possibly due to compulsory, production driven selection.

Replicating a GWAS: two novel candidate markers for oligospermia in Greek population

Genome-wide association studies have paved the way for the discovery of new markers regarding many diseases, including male infertility. A previous study on Caucasians highlighted 172 polymorphisms for their putative association with male infertility and we attempted to replicate these findings on our dataset comprising of Greek male individuals (n = 360). We retrieved 59 out of 172 polymorphisms and tested for all association models on 278 normospermic men and 82 patients with an abnormal seminogram, later separated into oligozoospermic and asthenozoospermic groups. Our findings indicate that two SNPs (rs2296225 in KIF17, rs7224496 in SMYD4) are associated with male infertility in the Greek population and have not been recorded in literature as of yet. These novel markers need further validation via additional studies and an increased individual number. All in all, replication studies, possess the power to validate existing polymorphisms found across all population and thus increase both statistical significance as well as identify novel potentially diagnostic markers.

MLST-Based Analysis and Antimicrobial Resistance of Staphylococcus epidermidis from Cases of Sheep Mastitis in Greece

Staphylococcus epidermidis is an important causal agent of ovine mastitis. A literature search indicated a lack of systematic studies of causal agents of the infection by using multi-locus sequence typing (MLST). The objectives were to analyse MLST-based data and evaluate the antimicrobial resistance of S. epidermidis isolates from ovine mastitis in Greece. The database included 1593 isolates from 46 countries: 1215 of human, 195 of environmental and 134 of animal origin, distributed into 949 sequence types (STs) and cumulatively with 450 alleles therein. Among mastitis isolates, bovine isolates were distributed into 36 different STs and ovine ones into 15 STs. The 33 isolates from ovine mastitis in Greece were in 15 different STs, 6 of these (ST677, ST678, ST700, ST 709, ST710, ST711) assigned for the first time; in addition, 5 alleles (65 for arcC, 59 for aroE, 56 and 57 for gtr and 48 for tpiA) were identified for the first time. The spanning tree of these isolates included 15 nodes and 14 edges (i.e., branches). Among these isolates, 19 showed resistance to antimicrobial agents (tetracycline, penicillin, fucidic adic, erythromycin, clindamycin, cefoxitin). Resistance-related genes (tetK, tetT, msrA, tetM, tetS, ermC, mecA) were detected. There was no association between STs and resistance to antimicrobial agents. Isolates with antimicrobial resistance were recovered more often from flocks where hand-milking was practised.

Genome-wide association study identifies candidate markers related to lincRNAs associated with male infertility in the Greek population

BACKGROUND

Male infertility is currently one of the most common problems faced by couples worldwide. We performed a GWAS on Greek population and gathered statistically significant SNPs in order to investigate whether they lie within or near lncRNA regions.

OBJECTIVES

The aim of this study was to investigate whether polymorphisms on or near lncRNAs affect interactions with miRNAs and can cause male infertility.

MATERIALS AND METHODS

In the present study, a GWAS was conducted, using samples from 159 individuals (83 normozoospermic individuals and 76 patients of known fertility issues). Standard procedures for quality controls and association testing were followed, based on case-control testing.

RESULTS

We detected six lncRNAs (LINC02231, LINC00347, LINC02134, NCRNA00157, LINC02493, Lnc-CASK-1) that are associated with male infertility through their interaction with miRNAs. Furthermore, we identified the genes targeted by those miRNAs and highlighted their functions in spermatogenesis and the fertilization process.

DISCUSSION AND CONCLUSION

lncRNAs are involved in spermatogenesis through their interaction with miRNAs. Thus, their study is very important, and it may contribute to the understanding of the molecular mechanisms underlying male infertility.

Phylogenetic relationships between genera Dorcadion, Lamia, Morimus, Herophila and some other Lamiinae (Coleoptera: Cerambycidae) based on chromosome and CO1 gene sequence comparison

A dual molecular and cytogenetic study was performed with the aim to improve the controversial systematic classification of some species of Lamiinae (Coleoptera: Cerambycidae). The karyotypes of species belonging to genera Morimus, Herophila, Dorcadion, Neodorcadion and Lamia share a number of characters, which differentiate them from other species, belonging to genera Phytoecia, Parmena and Monochamus. The karyotypes of the last three species comprise 20 chromosomes, mostly metacentric or sub-metacentric, as in the presumed Cerambycidae ancestors. The karyotypes of the former species share many characters derived from the Lamiinae ancestors by a number of chromosome fissions and inversions indicating their monophyly. Comparisons of the CO1 gene sequence also show the monophyly of Morimus, Lamia, Herophila and Dorcadion and their distant relationship with others. These convergent results allow us to propose a phylogenetic classification of these genera, which places the monospecific genus Lamia close to Dorcadion, clearly separates Dorcadion and Neodorcadion and places Herophila closer to Morimus than to Dorcadion/Lamia. The genus Morimus is the most derived. CO1 mutations loosely separate the forms M. asper and M. funereus, which have similar karyotypes and behaviour and copulate in captivity. The form M. ganglebaueri may have a funereus X asper hybrid origin.

Phylogenetic Analysis of Bird-Virulent West Nile Virus Strain, Greece

We report the full polyprotein genomic sequence of a West Nile virus strain isolated from Eurasian magpies dying with neurologic signs in Greece. Our findings demonstrate the local genetic evolution of the West Nile virus strain responsible for a human disease outbreak in the country that began in 2010.

Curcumin mediates attenuation of pro-inflammatory interferon γ and interleukin 17 cytokine responses in psoriatic disease, strengthening its role as a dietary immunosuppressant

Curcumin exhibits anti-inflammatory properties and has been used for centuries in traditional medicine and as dietary supplement. Data from clinical trials has strengthened the notion that curcumin may exert an anti-inflammatory and immunosuppressive role in patients with psoriatic disease, but its mode of action has remained elusive. We hypothesized that curcumin could inhibit interferon (IFN)-γ and interleukin (IL)-17 production in peripheral blood mononuclear cells from patients with psoriasis and psoriatic arthritis (PsA). To this end, we assessed the in vitro effect of curcumin on IFN-γ production by cluster differentiation (CD)4(+), CD8(+) T cells, natural killer (NK) and NKT cells and on IL-17 production by CD4(+) T cells from 34 patients with psoriatic disease (22 with psoriasis and 12 with PsA); 15 normal subjects were included as healthy controls. We also assessed the effect of curcumin on signal transducer and activator of transcription (STAT)3 activation. Curcumin significantly decreased, in a dose dependent manner, IFNγ-production by CD4(+) and CD8(+) T cells, and NK and NKT cells in patients with psoriatic disease and healthy controls. It also decreased IL-17 production by CD4(+) T cells (Th17). At the molecular level, curcumin increased STAT3 serine 727 phosphorylation intensity and p-STAT3(+) CD4(+) T cells in patients with PsA and psoriasis. In conclusion, curcumin in vitro inhibits pro-inflammatory IFN-γ and IL-17 production in psoriatic disease, and this may strengthen its role as a dietary immunosuppressant in patients with this disease.

Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective

Previous studies in hares and jackrabbits have indicated that positive selection has shaped the genetic diversity of mitochondrial genes involved in oxidative phosphorylation, which may affect cellular energy production and cause regional adaptation to different environmental (climatic) pressures. In the present study, we sequenced the NADH dehydrogenase subunit 6 (MT-ND6) gene of 267 brown hares (L. europaeus) from Europe and Asia Minor and tested for positive selection and adaptations acting on amino acid sequences (protein variants). Molecular diversity indices and spatial clustering were assessed by DnaSP, Network, and Geneland, while the presence of selection signals was tested by codeml in PAML, and by using the Datamonkey Adaptive Evolution web server. The SPSS software was used to run multinomial regression models to test for possible effects of climate parameters on the currently obtained protein variants. Fifty-eight haplotypes were revealed with a haplotype diversity of 0.817, coding for 17 different protein variants. The MT-ND6 phylogeographic pattern as determined by the nucleotide sequences followed the earlier found model based on the neutrally evolving D-loop sequences, and reflected the earlier found phylogeographic Late Pleistocene scenario. Based on several selection tests, only one codon position consistently proved to be under positive selection. It did occur exclusively in the evolutionarily younger hares from Europe and it gave rise to several protein variants from the southeastern and south-central Balkans. The occurrence of several of those variants was significantly favored under certain precipitation conditions, as proved by our multinomial regression models. Possibly, the great altitudinal variation in the Balkans may have lead to bigger changes in precipitation across that region and this may have imposed an evolutionarily novel selective pressure on the protein variants and could have led to regional adaptation.

Islands and hybrid zones: combining the knowledge from "Natural Laboratories" to explain phylogeographic patterns of the European brown hare

Background

The aim of the study was to use hybrid populations as well as island populations of the European brown hare (Lepus europaeus) to explore the effect of evolutionary events, such as the post-deglaciation translocations, spontaneous and human-mediated, local adaptation and the genetic drift in the shaping of the phylogeographic patterns of the species. For this purpose, we used molecular markers, both nuclear and mitochondrial, that are indicative for local adaptation as well as neutral markers to elucidate the patterns of population differentiation based on geographic isolation and the clade of origin. To broaden our analysis, we included data from our previous studies concerning mainland populations, to explore the genetic differentiation in the base of the geographic origin (mainland/island) of the populations.

Results

Our results suggest that local adaptation shapes the differentiation in both genomes, favoring specific alleles in nuclear genes (e.g. DQA) or haplotypes in mtDNA (e.g. Control Region, CR). mtDNA variation was found to be in a higher level and was able to give a phylogeographic signal for the populations. Furthermore, the degree of variation was influenced not only by the geographic origin, but also by the clade of origin, since specific island populations of Anatolian origin showed a greater degree of variation compared to specific mainland populations of the European clade. Concerning the hybrid population, we confirmed the existence of both clades in the territory and we provided a possible explanation for the lack of introgression between the clades.

Conclusion

Our results indicate that the Quaternary’s climatic oscillations played a major role in the shaping of the phylogeographic patterns of the species, by isolating populations in the distinct refugia, where they adapted and differentiate in allopatry, leading to genome incompatibilities observed nowadays.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1354-y) contains supplementary material, which is available to authorized users.

Amino acid signatures in the HLA class II peptide-binding region associated with protection/susceptibility to the severe West Nile Virus disease

The MHC class II region in humans is highly polymorphic. Each MHC molecule is formed by an α and a β chain, produced by different genes, creating an antigen-binding groove. In the groove there are several pockets into which antigens anchor and fit. The affinity of this fitting determines the recognition specificity of a given peptide. Here, based on our previous results about the association of MHC class II with the WNV disease, we examined the role of the binding pockets of HLA-DPA1, -DQA1 and-DRB1 in the severe form of the disease. In HLA-DQA1, variants in all pockets 1, 6 and 9 were found to be associated with either protection and/or susceptibility to neuroinvasion caused by WNV. Similarly, pockets 7, 9 and 10 in HLA-DRB1 were associated with severe disease. Protein modeling of these molecules revealed structural and functional differences among alleles with opposite roles concerning the development of the disease. Different amino acids in positions α52 and α66 (HLA-DQA1) significantly influenced the peptide binding while DYWLR/EFA combination (HLA-DRB1) was associated with neuronal damage. Further studies could help us understand the selectivity of pocket variants in order to create suitable peptides for an effective response.

Mitogenomic analysis in European brown hare (Lepus europaeus) proposes genetic and functional differentiation between the distinct lineages

European brown hare is a small game species spreading across Europe to Asia Minor, with important economic traits. Population genetics studies using mitochondrial DNA markers have revealed the existence of two major phylogeographic lineages, the European and the Anatolian. European lineage is further divided in the European type halpogroup and south-eastern European type halpogroup, while Anatolian consists only by the Anatolian/Middle Eastern type halpogroup. All three haplogroups show a discrete geographical distribution, with an overlapping zone forming in North-East Greece and Bulgaria, forming a contact zone. Despite the existence of a contact zone, European haplotype was never detected in Anatolia and vice versa, proposing the presence of genetic barriers responsible for this phenomenon. In this study, we analyzed the whole mitochondrial genomes of specimens originating from both lineages, aiming to detect the genetic and functional differentiation of the oxidative phosphorylation complexes that are encoded by mtDNA that could lead gradually to the reproductive isolation of the lineages.

Genetic Contribution of MHC Class II Genes in Susceptibility to West Nile Virus Infection

WNV is a zoonotic neurotropic flavivirus that has recently emerged globally as a significant cause of viral encephalitis. The last five years, 624 incidents of WNV infection have been reported in Greece. The risk for severe WNV disease increases among immunosuppressed individuals implying thus the contribution of the MHC locus to the control of WNV infection. In order to investigate a possible association of MHC class II genes, especially HLA-DPA1, HLA-DQA1, HLA-DRB1, we examined 105 WNV patients, including 68 cases with neuroinvasive disease and 37 cases with mild clinical phenotype, collected during the period from 2010 to2013, and 100 control individuals selected form the Greek population. Typing was performed for exon 2 for all three genes. DQA1*01:01 was considered to be "protective" against WNV infection (25.4% vs 40.1%, P = 0.004) while DQA1*01:02 was associated with increased susceptibility (48.0% vs 32.1%, P = 0.003). Protection against neuroinvasion was associated with the presence of DRB1*11:02 (4.99% vs 0.0%, P = 0.018). DRB1*16:02 was also absent from the control cohort (P = 0.016). Three additional population control groups were used in order to validate our results. No statistically significant association with the disease was found for HLA-DPA alleles. The results of the present study provide some evidence that MHC class II is involved in the response to WNV infection, outlining infection "susceptibility" and "CNS-high-risk" candidates. Furthermore, three new alleles were identified while the frequency of all alleles in the study was compared with worldwide data. The characterization of the MHC locus could help to estimate the risk for severe WNV cases in a country.

SNP Identification through Transcriptome Analysis of the European Brown Hare (Lepus europaeus): Cellular Energetics and Mother's Curse

The European brown hare (Lepus europaeus, Pallas 1778) is an important small game species in Europe. Due to its size and position in the food chain, as well as its life history, phenotypic variation and the relatively recent speciation events, brown hare plays an important role in the structure of various ecosystems and has emerged as an important species for population management and evolutionary studies. In order to identify informative SNPs for such studies, heart and liver tissues of three samples from the European lineage and a three-sample pool from the Anatolian lineage were subjected to RNA-Sequencing analysis. This effort resulted in 9496 well-assembled protein-coding sequences with close homology to human. After applying very stringent filtering criteria, 66185 polymorphic sites were identified in 7665 genes/cds and 2050 of those polymorphic sites are potentially capable of distinguishing the European from the Anatolian lineage. From these distinguishing mutations we focused on those in genes that are involved in cellular energy production, namely the glycolysis, Krebs cycle and the OXPHOS machinery. A selected set of SNPs was also validated by Sanger sequencing. By simulating the three European individuals as one pool, no substantial informative-SNP identification was lost, making it a cost-efficient approach. To our knowledge this is the first attempt to correlate the differentiation in both nuclear and mitochondrial genome between the two different lineages of L. europaeus with the observed spatial partitioning of the lineages of the species, proposing a possible mechanism that is maintaining the reproductive isolation of the lineages.

Complete exon 2 sequence of the HLA-DPA1*03:01 allele by sequence-based typing

Completion of the first 20 nucleotides of exon 2 of DPA1*03:01 allele.

West Nile Virus Seroprevalence in the Greek Population in 2013: A Nationwide Cross-Sectional Survey

Cases of West Nile Virus (WNV) disease were recorded for three consecutive years in Greece following the year 2010 outbreak. A cross-sectional serologic survey was conducted to estimate the WNV seroprevalence and assess the ratio of infection to neuroinvasive disease. A stratified left-over sampling methodology was used including age and residence strata. A total of 3,962 serum samples was collected and tested for WNV Immunoglobulin G (IgG) antibodies by Enzyme–Linked Immunosorbent Assay (ELISA). All positive samples were further tested by Plaque Reduction Neutralization Test (PRNT) and WNV Immunoglobulin M (IgM) antibodies. WNV IgG antibodies were detected in 82 samples and 61 were also positive in PRNT representing a weighted seroprevalence of 2.1% (95% C.I.: 1.7–2.6) and 1.5% (95% C.I.: 1.2–2.0), respectively. Multivariable analysis showed that seroprevalence was associated with age and residence. The overall ratio of neuroinvasive disease to infected persons was estimated at 1:376 (95% C.I.: 1:421–1:338), while the elderly people had the highest ratio. This nationwide study provided valuable data regarding the epidemiology of WNV in Greece based on the fact that elderly people have higher risk of being both infected and having severe disease.

First evidence of Leishmania infection in European brown hare (Lepus europaeus) in Greece: GIS analysis and phylogenetic position within the Leishmania spp

Although the existence of a sylvatic transmission cycle of Leishmania spp., independent from the domestic cycle, has been proposed, data are scarce on Leishmania infection in wild mammals in Greece. In this study, we aimed to investigate the presence of Leishmania infection in the European brown hare in Greece, to infer the phylogenetic position of the Leishmania parasites detected in hares in Greece, and to identify any possible correlation between Leishmania infection in hares with environmental parameters, using the geographical information system (GIS). Spleen samples from 166 hares were tested by internal transcribed spacer-1 (ITS-1)-nested PCR for the detection of Leishmania DNA. Phylogenetic analysis was performed on Leishmania sequences from hares in Greece in conjunction with Leishmania sequences from dogs in Greece and 46 Leishmania sequences retrieved from GenBank. The Leishmania DNA prevalence in hares was found to be 23.49 % (95 % confidence interval (CI) 17.27-30.69). The phylogenetic analysis confirmed that the Leishmania sequences from hares in Greece belong in the Leishmania donovani complex. The widespread Leishmania infection in hares should be taken into consideration because under specific circumstances, this species can act as a reservoir host. This study suggests that the role of wild animals, including hares, in the epidemiology of Leishmania spp. in Greece deserves further elucidation.

Transient up- and down-regulation of expression of myosin light chain 2 and myostatin mRNA mark the changes from stratified hyperplasia to muscle fiber hypertrophy in larvae of gilthead sea bream (Sparus aurata L.)

Hyperplasia and hypertrophy are the two mechanisms by which muscle develops and grows. We study these two mechanisms, during the early development of white muscle in Sparus aurata, by means of histology and the expression of structural and regulatory genes. A clear stage of stratified hyperplasia was identified early in the development of gilthead sea bream but ceased by 35 dph when hypertrophy took over. Mosaic recruitment of new white fibers began as soon as 60 dph. The genes mlc2a and mlc2b were expressed at various levels during the main phases of hyperplasia and hypertrophy. The genes myog and mlc2a were significantly up-regulated during the intensive stratified formation of new fibers and their expression was significantly correlated. Expression of mstn1 and igf1 increased at 35 dph, appeared to regulate the hyperplasia-to-hypertrophy transition, and may have stimulated the expression of mlc2a, mlc2b and col1a1 at the onset of mosaic hyperplasia. The up-regulation of mstn1 at transitional phases in muscle development indicates a dual regulatory role of myostatin in fish larval muscle growth.

Polarisation of major histocompatibility complex II host genotype with pathogenesis of European Brown Hare syndrome virus

A study was conducted in order to determine the occurrence of European Brown Hare Syndrome virus (EBHSV) in Denmark and possible relation between disease pathogenesis and Major Histocompatibility Complex (MHC) host genotype. Liver samples were examined from 170 brown hares (hunted, found sick or dead), collected between 2004 and 2009. Macroscopical and histopathological findings consistent with EBHS were detected in 24 (14.1%) hares; 35 (20.6%) had liver lesions not typical of the syndrome, 50 (29.4%) had lesions in other tissues and 61 (35.9%) had no lesions. Sixty five (38.2%) of 170 samples were found to be EBHSV-positive (RT-PCR, VP60 gene). In order to investigate associations between viral pathogenesis and host genotype, variation within the exon 2 DQA gene of MHC was assessed. DQA exon 2 analysis revealed the occurrence of seven different alleles in Denmark. Consistent with other populations examined so far in Europe, observed heterozygosity of DQA (H_o = 0.1180) was lower than expected (H_e = 0.5835). The overall variation for both nucleotide and amino acid differences (2.9% and 14.9%, respectively) were lower in Denmark than those assessed in other European countries (8.3% and 16.9%, respectively). Within the peptide binding region codons the number of nonsynonymous substitutions (dN) was much higher than synonymous substitutions (dS), which would be expected for MHC alleles under balancing selection. Allele frequencies did not significantly differ between EBHSV-positive and -negative hares. However, allele Leeu-DQA*30 was detected in significantly higher (P = 0.000006) frequency among the positive hares found dead with severe histopathological lesions than among those found sick or apparently healthy. In contrast, the latter group was characterized by a higher frequency of the allele Leeu-DQA*14 as well as the proportion of heterozygous individuals (P = 0.000006 and P = 0.027). These data reveal a polarisation between EBHSV pathogenesis and MHC class II genotype within the European brown hare in Denmark.

Toll like receptor 9 (TLR9) polymorphism G520R in sheep is associated with seropositivity for Small Ruminant Lentivirus

Infectious diseases of sheep are of major economic importance causing direct and indirect losses. Among the major sheep infectious agents are Small Ruminant Lentivirus, Chlamydophila abortus and Mycobacterium avium subsp. paratuberculosis infections, mainly due to their worldwide distribution and economic impact that they cause. Based on the differential susceptibility to infectious diseases between and within breeds and on the recent findings regarding the putative involvement of TLR9 in disease susceptibility, the aim of this study was to evaluate the levels of nucleotide variation of TLR9 and its mediator MyD88 in three sheep flocks originated from different breeds and assess their possible association with seropositivity/seronegativity for different infectious agents. The analysis indicated that the change of G to R at codon 520 of TLR9 polypeptide shows a significant association with Small Ruminant Lentivirus seropositivity. This amino-acid substitution, which can result in polarity change, might influence structure and function of LRR17, interfering with ligand binding and thus could be used in studies investigating susceptibility/resistance to Small Ruminant Lentivirus infections in sheep.

Evidence for European brown hare syndrome virus introduction with translocated brown hares (Lepus europaeus): implications for management of restocking operations

Context Criticisms of wildlife restocking operations typically focus on concerns that translocations can lead to the introduction of pathogens, and risk the integrity of locally adapted genetic diversity. Restocking programs aiming to stabilise population declines of European brown hares using captive-bred individuals have been carried out in several European countries, including Greece. Aims To assess the potential for imported hares to introduce novel strains of European brown hare syndrome virus (EBHSV) during restocking operations, by (1) inferring the origin of wild Greek hares on the basis of their mitochondrial DNA (mtDNA) haplotype, (2) screening the hares to detect and characterise EBHSV, and (3) determining whether certain hare origin–EBHSV combinations occur in the wild. Methods RNA extraction, polymerase chain reaction (PCR) amplification, and sequence and phylogenetic analyses of EBHSV were performed on 53 hares. Diagnostic RFLP markers of the mtDNA were used to infer the origins of sampled hares. Key results Thirty-three hares had ‘typical’ native Greek haplotypes and 20 had mtDNA haplotypes matching those found in imported and released hares. Twelve of the latter and none of the former were positive for EBHSV. Phylogenetic analysis showed that nine virus isolates formed a single genetic lineage distinct from northern–central European ones. Three virus sequences from three imported reared-and-released hares, from Chalkidiki, were closely related to the northern–central European EBHS viruses. Conclusions Alien strains of EBHSV are co-introduced with released captive-bred animals, possibly resulting in negative impacts on populations of Greek hares that have not evolved resistance to these novel virus strains. Implications The identification of these allopatric EBHSV strains has led the authorities to ban captures and transportations of local brown hares for any restocking operation. We consider it imperative to reinforce microbiological and genetic controls before further releases of captive-bred game species in the wild in Greece.