1,720,985 research outputs found
A glimpse into the past : phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebrates
Full text linkBackground The group XIV of C-type lectin domain-containing proteins (CTLDcps) is one of the seventeen groups of CTLDcps discovered in mammals and composed by four members: CD93, Clec14A, CD248 and Thrombomodulin, which have shown to be important players in cancer and vascular biology. Although these proteins belong to the same family, their phylogenetic relationship has never been dissected. To resolve their evolution and characterize their protein domain composition we investigated CTLDcp genes in gnathostomes and cyclostomes and, by means of phylogenetic approaches as well as synteny analyses, we inferred an evolutionary scheme that attempts to unravel their evolution in modern vertebrates. Results Here, we evidenced the paralogy of the group XIV of CTLDcps in gnathostomes and discovered that a gene loss of CD248 and Clec14A occurred in different vertebrate groups, with CD248 being lost due to chromosome disruption in birds, while Clec14A loss in monotremes and marsupials did not involve chromosome rearrangements. Moreover, employing genome annotations of different lampreys as well as one hagfish species, we investigated the origin and evolution of modern group XIV of CTLDcps. Furthermore, we carefully retrieved and annotated gnathostome CTLDcp domains, pointed out important differences in domain composition between gnathostome classes, and assessed codon substitution rate of each domain by analyzing nonsynonymous (Ka) over synonymous (Ks) substitutions using one representative species per gnathostome order. Conclusions CTLDcps appeared with the advent of early vertebrates after a whole genome duplication followed by a sporadic tandem duplication. These duplication events gave rise to three CTLDcps in the ancestral vertebrate that underwent further duplications caused by the independent polyploidizations that characterized the evolution of cyclostomes and gnathostomes. Importantly, our analyses of CTLDcps in gnathostomes revealed critical inter-class differences in both extracellular and intracellular domains, which might help the interpretation of experimental results and the understanding of differences between animal models
De novo genome assembly of the endemic Italian springtail Orchesella dallaii (Collembola: Orchesellidae)
Full text linkSpringtails (Collembola) constitute one of the most diverse and ecologically important groups of basal hexapods, yet remain significantly underrepresented in genomic databases. In this study, we present the first genome assembly of Orchesella dallaii, an Italian endemic species, representing a crucial advancement in expanding genomic resources for Collembola. Utilizing PacBio HiFi sequencing combined with an ultra-low input library preparation, we generated a highly contiguous genome assembly (223 contigs covering 304 Mb) that ranks among the most complete ones within the group. Genome annotation, supported by short-read RNA-seq data, predicted 31,769 genes with high completeness. The analysis of repeated sequences revealed a comparatively low abundance of annotated transposable elements. Additionally, the entire mitochondrial genome was assembled and annotated, confirming the gene order characteristic of the Entomobryomorpha lineage. This genomic resource provides a valuable reference for an often-overlooked taxonomic group and offers a basis for future research in comparative genomics, species delimitation, and conservation genetics of Mediterranean soil ecosystems
ALDH1A1 confers resistance to RAF/MEK inhibitors in melanoma cells by maintaining stemness phenotype and activating PI3K/AKT signaling
Full text linkThe mitogen-activated protein kinase (MAPK/ERK) pathway is pivotal in controlling the proliferation and survival of melanoma cells. Several mutations, including those in BRAF, exhibit an oncogenic effect leading to increased cellular proliferation. As a result, the combination therapy of a MEK inhibitor with a BRAF inhibitor demonstrated higher efficacy and lower toxicity than BRAF inhibitor alone. This combination has become the preferred standard of care for tumors driven by BRAF mutations. Aldehyde dehydrogenase 1A1 (ALDH1A1) is a known marker of stemness involved in drug resistance in several type of tumors, including melanoma. This study demonstrates that melanoma cells overexpressing ALDH1A1 displayed resistance to vemurafenib and trametinib through the activation of PI3K/AKT signaling instead of MAPK axis. Inhibition of PI3K/AKT signaling partially rescued sensitivity to the drugs. Consistently, pharmacological inhibition of ALDH1A1 activity downregulated the activation of AKT and partially recovered responsiveness to vemurafenib and trametinib. We propose ALDH1A1 as a new potential target for treating melanoma resistant to MAPK/ERK inhibitors
The complete mitochondrial genome of the shining leaf chafer Mimela junii (Duftschmidt, 1805) (Coleoptera: Scarabaeidae)
Full text linkThe complete mitochondrial genome of the shining leaf chafer Mimela junii was sequenced and is herein described. The mitogenome consists of a circular molecule of 16,805 bp, with an overall AT content of 75.7%. It encodes for 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and contains a non-coding Control Region (CR) characterized by the presence of tandem repeats. The gene order corresponds to the ancestral Pancrustacea model and mitogenome characteristics are congruous with those of hexapods. In the phylogenetic analysis, M. junii is nested within a paraphyletic Anomala with high support, and is herein associated with Anomala corpulenta with medium/low support
Bacterial and fungal diversity in the gut of polystyrene-fed Alphitobius diaperinus (Insecta: Coleoptera)
Full text linkThe use of plastics burgeoned in the last decades to become an essential component of our society. An envi-ronment friendly method to dispose of plastic waste is not available yet, to the outcome that these accumulate in landfills or are scattered as microplastics. New researches reported that some coleopteran species are able to destroy plastics thanks to their chewing mouthparts and the metabolic activity of their gut microbiota. This study shows that the lesser mealworm Alphitobius diaperinus is capable of feeding on, and apparently degrading, polystyrene. The gut microbiota of polystyrene-fed larvae was characterized using an NGS metagenomic approach, targeting both bacteria and fungi. Several microbe taxa emerged as differentially abundant between treatment and control groups (Cronobacter, Kocuria and Pseudomonas as bacteria, Aspergillus, Hyphodermella, Trichoderma as fungi). Some of them have been found in association with plastic compounds and/or have been proposed to be capable of plastic degradation. This research supports the notion that, although synthetic mol-ecules, unlike most natural compounds, do not generally enter the natural food chain to be degraded by the environmental microbiota, some microbial communities may be able to decompose plastics. We speculate that, once identified, such communities may open to the possibility of devising bioreactors for plastic degradation
First de novo transcriptome analysis of the Antarctic springtail Cryptopygus terranovus (Collembola: Isotomidae) following mid-term heat exposure
Full text linkGlobal human activities, such as greenhouse emissions and pollution, are promoting global
warming, environmental changes and biodiversity reduction. Pristine environments such as those of
Antarctica are not immune to these phenomena, as is noticeable from the increasing pace of the
temperature shift registered within the continent in recent decades. In this study, we describe the first
de novo transcriptome analysis of the endemic Antarctic springtail (= collembolan) Cryptopygus
terranovus and we evaluate its global gene expression response following a mid-term exposure of
20 days to 18°C. Expression data are compared with wild specimens sampled from their native
environment to outline the molecular mechanisms triggered by the thermal exposure. Although
individual plasticity in transcript modulation is assessed, several pathways appear to be differentially
modulated in springtails subjected to the heat treatment vs wild specimens. Through enrichment
analysis, we show that protein catabolism, fatty acid metabolism and a sexual response characterized
by spermatid development are induced, while carbohydrate consumption, lipid catabolism and tissue
development are downregulated in treated samples compared to control
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Re-evaluating the internal phylogenetic relationships of Collembola by means of mitogenome data
Full text linkCollembola are an ancient and early diverging lineage of basal hexapods that occur in virtually all terrestrial habitats on Earth. Phylogenetic relationships between the different orders of Collembola are fiercely debated. Despite a range of studies and the application of both morphological and genetic approaches (singly or in combination) to assess the evolutionary relationships of major lineages in the group, no consensus has been reached. Several mitogenome sequences have been published for key taxa of the class (and their number is increasing rapidly). Here, we describe two new Antarctic Collembola mitogenomes and compare all complete or semi-complete springtail mitogenome sequences available on GenBank in terms of both gene order and DNA sequence analyses in a genome evolution and molecular phylogenetic framework. With minor exceptions, we confirm the monophyly of Poduromorpha and Symphypleona sensu stricto (the latter placed at the most basal position in the springtail phylogenetic tree), whereas monophyly of Neelipleona and Entomobryomorpha is only supported when a handful of critical taxa in these two lineages are excluded. Finally, we review gene order models observed in the class, as well as the overall mitochondrial nucleotide composition
Molecular comparison among three Antarctic endemic springtail species and description of the mitochondrial genome of Friesea gretae (Hexapoda, Collembola)
Full text linkSpringtails and mites are the dominant groups of terrestrial arthropods in Antarctic terrestrial ecosystems. Their Antarctic diversity includes a limited number of species, which are frequently endemic to specific regions within the continent. Advances in molecular techniques, combined with the re-evaluation of morphological characters and the availability of new samples, have recently led to the identification of a number of new springtail species within previously named, but ill-defined, species entities described in the last century. One such species, the neanurid Friesea grisea, originally described from sub-Antarctic South Georgia, was for many years considered to be the only known springtail with a pan-Antarctic distribution. With the recent availability of new morphological and molecular data, it has now been firmly established that the different representatives previously referred to this taxon from the Antarctic Peninsula and Victoria Land (continental Antarctica) should no longer be considered as representing one and the same species, and three clearly distinct taxa have been recognized: F. antarctica, F. gretae and F. propria. In this study, the relationships among these three species are further explored through the sequencing of the complete mtDNA for F. gretae and the use of complete mitogenomic as well as cytochrome c oxidase I data. The data obtained provide further support that distinct species were originally hidden within the same taxon and that, despite the difficulties in obtaining reliable diagnostic morphological characters, F. gretae is genetically differentiated from F. propria (known to be present in different locations in Northern Victoria Land), as well as from F. antarctica (distributed in the Antarctic Peninsula)
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