Expression of Elafin and CD200 as Immune Checkpoint Molecules Involved in Celiac Disease.

We comprehensively evaluated the expression of therapeutically targetable immune checkpoint molecules involved in celiac disease (CD). We have focused on the alteration of the CD200/CD200R pathway and Elafin expression in celiac disease and discussed their roles in regulating the immune response. There are limited data related to the expression or function of these molecules in celiac disease. This finding could significantly contribute to the understanding of the clinical manifestation of CD. CD200, CD200R and Elafin distributions were determined by ELISA and immunohistochemistry analyses in serum and biopsies of CD patients. Analyses of Th1 and Th17 cytokines were determined. PCR amplification of a fragment of the PI3 gene was carried out using genomic DNA isolated from whole blood samples of the study subjects. Different aliquots of the PCR reaction product were subjected to RFLP analysis for SNP genotyping and detection. We characterized the expression and function of the CD200-CD200R axis and PI3 in celiac disease. A significantly higher level of soluble CD200 and CD200R and lower expression of PI3 in serum of CD patients was observed compared to healthy controls. Consistent with our results, CD200 expression is regulated by IFN-gamma. Interaction of CD200/CD200R leads to production of type-Th1 and -Th17 cytokines. Regarding the PI3 genotype, the CT genotype proportion SNP rs1733103 and the GG genotype SNP rs41282752 were predominant in CD patients. SNP rs1733103 showed a significant association between the SNP variables and CD. In celiac disease the immune checkpoint is compromised or dysregulated, which can contribute to inflammation and the autoimmunity process. The study of these checkpoint points will lead to the development of targeted therapies aimed at restoring immunological balance in CD. Specific coding regions of the PI3 gene-splice variants predispose the Elafin protein, both at the transcriptional and post-translational levels, to modify its expression and function, resulting in reduced differential functional protein levels in patients with active celiac disease.

Sex-biased gene content is associated with sex chromosome turnover in Danaini butterflies.

Sex chromosomes play an outsized role in adaptation and speciation, and thus deserve particular attention in evolutionary genomics. In particular, fusions between sex chromosomes and autosomes can produce neo-sex chromosomes, which offer important insights into the evolutionary dynamics of sex chromosomes. Here, we investigate the evolutionary origin of the previously reported Danaus neo-sex chromosome within the tribe Danaini. We assembled and annotated genomes of Tirumala septentrionis (subtribe Danaina), Ideopsis similis (Amaurina), Idea leuconoe (Euploeina) and Lycorea halia (Itunina) and identified their Z-linked scaffolds. We found that the Danaus neo-sex chromosome resulting from the fusion between a Z chromosome and an autosome corresponding to the Melitaea cinxia chromosome (McChr) 21 arose in a common ancestor of Danaina, Amaurina and Euploina. We also identified two additional fusions as the W chromosome further fused with the synteny block McChr31 in I. similis and independent fusion occurred between ancestral Z chromosome and McChr12 in L. halia. We further tested a possible role of sexually antagonistic selection in sex chromosome turnover by analysing the genomic distribution of sex-biased genes in I. leuconoe and L. halia. The autosomes corresponding to McChr21 and McChr31 involved in the fusions are significantly enriched in female- and male-biased genes, respectively, which could have hypothetically facilitated fixation of the neo-sex chromosomes. This suggests a role of sexual antagonism in sex chromosome turnover in Lepidoptera. The neo-Z chromosomes of both I. leuconoe and L. halia appear fully compensated in somatic tissues, but the extent of dosage compensation for the ancestral Z varies across tissues and species.

Exploring horizontal transfer of mariner transposable elements among ants and aphids.

Aphids and ants are mutualistic species with a close space-time relationship, which may facilitate the occurrence of horizontal transfer events between these insect groups. Myrmar-like mariner elements were previously isolated from two ant (Myrmica ruginodis and Tapinoma ibericum) and two aphid species (Aphis fabae and Aphis hederae). The aim of this work is to determine the presence of Myrmar-like mariner elements in new ant and aphid species, as well as to analyze the likelihood of horizontal transfer events between these taxa. To accomplish this, the Myrmar-like element has been isolated from five aphid species and six ant species. Among these new analyzed species, full-length Myrmar-like mariner elements with very high sequence similarity have been isolated from the aphids Aphis nerii, Aphis spiraecola, Brachycaudus cardui, and Rhopalosiphum maidis as well as from the ants Lasius grandis and Lasius niger, even though aphids and ants belong to two insect orders (Hemiptera and Hymenoptera) that have evolved independently for at least 300 million-years. Both Lasius species establish frequent mutualistic relationships with multiple aphid species, including A. nerii, A. spiraecola, and B. cardui. The study of the putative protein encoded by them and the phylogenetic analysis suggests that they could be active transposons shared by aphids and ants through horizontal transfer events. Additionally, mariner elements with internal deletion were found in several aphids and one ant species, showing a high degree of sequence similarity among them. The characteristics of these elements with internal deletion suggest a complex origin involving various evolutionary processes, possibly including also horizontal transfer events. Myrmar-like elements have also been isolated from the other ant species, although without similarity with the aphid mariner sequences. Myrmar-like elements are also present in phylogenetically distant insect species, as well as in one crustacean species. The phylogenetic study carried out with all Myrmar-like elements suggests the probable occurrence of horizontal transfer events.

Contribution of the satellitome to the exceptionally large genome of dinoflagellates: The case of the harmful alga Alexandrium minutum.

Dinoflagellates are known to possess an exceptionally large genome organized in permanently condensed chromosomes. Focusing on the contribution of satellite DNA (satDNA) to the whole DNA content of genomes and its potential role in the architecture of the chromosomes, we present the characterization of the satellitome of Alexandriun minutum strain VGO577. To achieve this, we analyzed Illumina reads using graph-based clustering and performed complementary bioinformatic analyses. In this way, we discovered 180 satDNAs occupying 17.38 % of the genome. The 12 most abundant satDNAs represent the half of the satellitome but no satDNA is overrepresented, with the most abundant contributing ∼1.56 % of the genome. The largest repeat unit is 517 bp long but more than the half of the satDNAs (101) have repeat units shorter than 20 bp. We used FISH to map a selected set of 26 satDNAs. Although some satDNAs generate discrete hybridization signals at specific chromosomal locations (hybridization sites, HS), our cytological analysis showed that most satDNAs are dispersed throughout the genome, probably forming short arrays. Two satDNAs co-localize with the 45S rDNA. With the exception of telomeric DNA, no other satDNA yields HS on all chromosomes. In addition, we analyzed nine satDNAs yielding HS in VGO577 in four other A. minutum strains. Polymorphism at the intraspecific level was found for the presence/absence and/or abundance of some satDNAs, suggesting the amplification/deletion of these satDNAs following geographic separation or during culture maintenance of the strains. We also discuss how these results contribute to the understanding of chromosome architecture and evolution of dinoflagellate genomes.

Fast satellite DNA evolution in Nothobranchius annual killifishes.

Satellite DNA (satDNA) is a rapidly evolving class of tandem repeats, with some monomers being involved in centromere organization and function. To identify repeats associated with (peri)centromeric regions, we investigated satDNA across Southern and Coastal clades of African annual killifishes of the genus Nothobranchius. Molecular cytogenetic and bioinformatic analyses revealed that two previously identified satellites, designated here as NkadSat01-77 and NfurSat01-348, are associated with (peri)centromeres only in one lineage of the Southern clade. NfurSat01-348 was, however, additionally detected outside centromeres in three members of the Coastal clade. We also identified a novel satDNA, NrubSat01-48, associated with (peri)centromeres in N. foerschi, N. guentheri, and N. rubripinnis. Our findings revealed fast turnover of satDNA associated with (peri)centromeres and different trends in their evolution in two clades of the genus Nothobranchius.

Tumour budding in cutaneous squamous cell carcinoma: A novel prognosis risk factor.

INTRODUCTION: Most cutaneous squamous cell carcinomas (cSCC) have a good prognosis, there is a small group where metastasis and death occur and the evaluation of this risk is still cause for controversy. Tumour budding is a pattern of histological invasion that is an emerging risk factor in other solid tumours. OBJECTIVE: To examine the association between tumour budding and other known high-risk predictors in cSCC. In addition, the impact of tumour budding on overall survival (OS) and disease-specific survival (DSS) was analysed. METHOD: Retrospective study. It included patients with a diagnosis of non-genital cSCC by excisional biopsy at a university hospital, between 2010 and 2020. A pathologist re-analysed their histological slides and evaluated budding. Univariate and multivariate analyses were made to study the associations. RESULTS: 156 cSCC biopsies were found, and positive tumour budding was found in 13.5%. This correlated with worse DSS and OS. On univariate analysis, budding was correlated with the diameter, thickness of the tumour, histological grade, level of invasion, perineural and lymphovascular invasion, previous radiotherapy, recurrent tumours and lymph node metastasis (LNM). Multivariate analysis: tumour budding was associated with poorly differentiated tumours, prior radiotherapy and LNM. CONCLUSION: An association was found between tumour budding and most known risk factors in cSCC. We found findings that indicate that the presence of tumour budding is associated with a worse prognosis in terms of LNM, OS and DSS. This supports the results of previous work which has suggested that budding could be related to high-risk cSCC.

Differential Spreading of Microsatellites in Holocentric Chromosomes of Chagas Disease Vectors: Genomic and Evolutionary Implications.

This study focused on analyzing the distribution of microsatellites in holocentric chromosomes of the Triatominae subfamily, insect vectors of Chagas disease. We employed a non-denaturing FISH technique to determine the chromosomal distribution of sixteen microsatellites across twenty-five triatomine species, involving five genera from the two principal tribes: Triatomini and Rhodniini. Three main hybridization patterns were identified: strong signals in specific chromosomal regions, dispersed signals dependent on microsatellite abundance and the absence of signals in certain chromosomal regions or entire chromosomes. Significant variations in hybridization patterns were observed between Rhodniini and Triatomini species. Rhodniini species displayed weak and scattered hybridization signals, indicating a low abundance of microsatellites in their genomes. In contrast, Triatomini species exhibited diverse and abundant hybridization patterns, suggesting that microsatellites are a significant repetitive component in their genomes. One particularly interesting finding was the high abundance of GATA repeats, and to a lesser extent AG repeats, in the Y chromosome of all analyzed Triatomini species. In contrast, the Y chromosome of Rhodniini species did not show enrichment in GATA and AG repeats. This suggests that the richness of GATA repeats on the Y chromosome likely represents an ancestral trait specific to the Triatomini tribe. Furthermore, this information can be used to elucidate the evolutionary relationships between Triatomini and other groups of reduviids, contributing to the understanding of the subfamily's origin. Overall, this study provides a comprehensive understanding of the composition and distribution of microsatellites within Triatominae genomes, shedding light on their significance in the evolutionary processes of these species.

The spread of satellite DNAs in euchromatin and insights into the multiple sex chromosome evolution in Hemiptera revealed by repeatome analysis of the bug Oxycarenus hyalinipennis.

Satellite DNAs (satDNAs) are highly repeated tandem sequences primarily located in heterochromatin, although their occurrence in euchromatin has been reported. Here, our aim was to advance the understanding of satDNA and multiple sex chromosome evolution in heteropterans. We combined cytogenetic and genomic approaches to study, for the first time, the satDNA composition of the genome in an Oxycarenidae bug, Oxycarenus hyalinipennis. The species exhibits a male karyotype of 2n = 19 (14A + 2 m + X1 X2 Y), with a highly differentiated Y chromosome, as demonstrated by C-banding and comparative genomic hybridization, revealing an enrichment of repeats from the male genome. Additionally, comparative analysis between males and females revealed that the 26 identified satDNA families are significantly biased towards male genome, accumulating in discrete regions in the Y chromosome. Exceptionally, the OhyaSat04-125 family was found to be distributed virtually throughout the entire extension of the Y chromosome. This suggests an important role of satDNA in Y chromosome differentiation, in comparison of other repeats, which collectively shows similar abundance between sexes, about 50%. Furthermore, chromosomal mapping of all satDNA families revealed an unexpected high spread in euchromatic regions, covering the entire extension, irrespective of their abundance. Only discrete regions of heterochromatin on the Y chromosome and of the m-chromosomes (peculiar chromosomes commonly observed in heteropterans) were enriched with satDNAs. The putative causes of the intense enrichment of satDNAs in euchromatin are discussed, including the possible existence of burst cycles similar to transposable elements and as a result of holocentricity. These data challenge the classical notion that euchromatin is not enriched with satDNAs.

Holocentric repeat landscapes: From micro-evolutionary patterns to macro-evolutionary associations with karyotype evolution.

Repetitive elements can cause large-scale chromosomal rearrangements, for example through ectopic recombination, potentially promoting reproductive isolation and speciation. Species with holocentric chromosomes, that lack a localized centromere, might be more likely to retain chromosomal rearrangements that lead to karyotype changes such as fusions and fissions. This is because chromosome segregation during cell division should be less affected than in organisms with a localized centromere. The relationships between repetitive elements and chromosomal rearrangements and how they may translate to patterns of speciation in holocentric organisms are though poorly understood. Here, we use a reference-free approach based on low-coverage short-read sequencing data to characterize the repeat landscape of two independently evolved holocentric groups: Erebia butterflies and Carex sedges. We consider both micro- and macro-evolutionary scales to investigate the repeat landscape differentiation between Erebia populations and the association between repeats and karyotype changes in a phylogenetic framework for both Erebia and Carex. At a micro-evolutionary scale, we found population differentiation in repeat landscape that increases with overall intraspecific genetic differentiation among four Erebia species. At a macro-evolutionary scale, we found indications for an association between repetitive elements and karyotype changes along both Erebia and Carex phylogenies. Altogether, our results suggest that repetitive elements are associated with the level of population differentiation and chromosomal rearrangements in holocentric clades and therefore likely play a role in adaptation and potentially species diversification.

Low-power laser manufacturing of copper tracks on 3D printed geometry using liquid polyimide coating.

Silver nanoparticle photoreduction synthesis by direct laser writing is a process that enables copper micro-track production on very specific polymers. However, some important 3D printing polymers, such as acrylonitrile butadiene styrene (ABS) and acrylates, do not accept this treatment on their surface. This work presents an approach to produce copper microcircuitry on 3D substrates from these materials by using direct laser writing at low power (32 mW CW diode laser). We show that by coating a thin layer of polyimide (PI) on a 3D-printed geometry, followed by a sequence of chemical treatments and low-power laser-induced photoreduction, copper tracks can be produced using silver as catalyst. The surface chemistry of the layer through the different stages of the process is monitored by FTIR and X-ray photoelectron spectroscopy. The copper tracks are selectively grown on the laser-patterned areas by electroless copper deposition, with conductivity (1.2 ± 0.7) × 107 S m-1 and a width as small as 28 µm. The patterns can be written on 3D structures and even inside cavities. The technique is demonstrated by integrating different circuits, including a LED circuit on 3D printed photopolymer acrylate and a perovskite solar cell on an ABS 3D curved geometry.

Making the Genome Huge: The Case of Triatoma delpontei, a Triatominae Species with More than 50% of Its Genome Full of Satellite DNA.

The genome of Triatoma delpontei Romaña & Abalos 1947 is the largest within Heteroptera, approximately two to three times greater than other evaluated Heteroptera genomes. Here, the repetitive fraction of the genome was determined and compared with its sister species Triatoma infestans Klug 1834, in order to shed light on the karyotypic and genomic evolution of these species. The T. delpontei repeatome analysis showed that the most abundant component in its genome is satellite DNA, which makes up more than half of the genome. The T. delpontei satellitome includes 160 satellite DNA families, most of them also present in T. infestans. In both species, only a few satellite DNA families are overrepresented on the genome. These families are the building blocks of the C-heterochromatic regions. Two of these satellite DNA families that form the heterochromatin are the same in both species. However, there are satellite DNA families highly amplified in the heterochromatin of one species that in the other species are in low abundance and located in the euchromatin. Therefore, the present results depicted the great impact of the satellite DNA sequences in the evolution of Triatominae genomes. Within this scenario, satellitome determination and analysis led to a hypothesis that explains how satDNA sequences have grown on T. delpontei to reach its huge genome size within true bugs.

Complete Nucleotide Sequence of the Mitogenome of Tapinoma ibericum (Hymenoptera: Formicidae: Dolichoderinae), Gene Organization and Phylogenetics Implications for the Dolichoderinae Subfamily.

The ant Tapinoma ibericum Santschi, 1925 is native to the Iberian Peninsula. This species, as well as other species from the Tapinoma nigerrimum complex, could form supercolonies that make these species potentially invasive and could give rise to pests. Recently a mature colony from this species has been found in the Isle of Wight (United Kingdom). Mitogenomes have been used to study the taxonomy, biogeography and genetics of species, improving the development of strategies against pest invasion. However, the number of available mitogenomes from the subfamily Dolichoderinae is still scarce and only two of these mitogenomes belong to Tapinoma species. Herein, the complete mitogenome of T. ibericum is presented in order to increase the molecular information of the genus. The T. ibericum mitogenome, retrieved by Next-Generation Sequencing data, is 15,715 bp in length. It contains the typical set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs and the A + T-rich control region. Comparisons of the T. ibericum mitogenome with other dolichoderine mitogenomes revealed the existence of four gene rearrangements in relation with the ancestral insect mitogenome. One of these rearrangements, involving the tRNA-Ile, tRNA-Gln and tRNA-Met genes, was found in most of the analyzed ant mitogenomes. Probably this rearrangement was an ancestral or plesiomorphic character in Formicidae. Interestingly, another rearrangement that affects to tRNA-Trp, tRNA-Cys and tRNA-Tyr genes was found only in Tapinoma species. This change could be a synapomorphic character for the genus Tapinoma, and could be used as a phylogenetic marker. Additionally, a phylogenetic analysis was performed using the protein-coding gene sequences from available Dolichoderinae mitogenomes, as well as mitogenomes from representative species from other Formicidae subfamilies. Results support the monophyletic nature of the genus Tapinoma placing it within the same clade as the rest of Dolichoderinae species.

Complete mitochondrial genome of the blister beetle Hycleus scutellatus Rosenhauer, 1856 (Coleoptera, Meloidae).

In this study, we report the complete mitochondrial genome or mitogenome of the blister beetle Hycleus scutellatus, one endemic species from the Iberian Peninsula. The mitogenome was 16,035 base pairs in length, with an A + T content of 71.7%. It has 37 genes including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. To analyze the evolutionary position of H. scutellatus, we constructed a phylogenetic tree using all available mitogenomes from species of the family Meloidae. The results show that Hycleus species are very close to the genus Mylabris. We present here the mitogenome of H. scutellatus as a new resource to elucidate the phylogenetic relations among the Meloidea family, being this source very useful for future evolutionary analyses of blister beetles.