MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models.

We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate species, including representatives of 5 previously unsampled phyla, and 6 mammal species.

New Insights on the Male and Female Reproductive Organs of (Acanthocephala), Intestinal Parasite of Birds of Prey.

Acanthocephalans are dioecious parasites that gain sexual maturity in the alimentary canal of their definitive hosts (gnathostome vertebrates). This initial survey by light and transmission electron microscopy was conducted on the functional organization of the ovarian balls and uterine bell in mature females and on Saefftigen's pouch and the copulatory bursa in males. We studied these structures via the example of (Palaeacanthocephala) in and , from the Province of Ferrara (Northern Italy).

The human sperm proteome-Toward a panel for male fertility testing.

Background: Although male factor accounts for 40%-50% of unintended childlessness, we are far from fully understanding the detailed causes. Usually, affected men cannot even be provided with a molecular diagnosis.

Objectives: We aimed at a higher resolution of the human sperm proteome for better understanding of the molecular causes of male infertility.

Genome-Wide Association Screening Determines Peripheral Players in Male Fertility Maintenance.

Deciphering the functional relationships of genes resulting from genome-wide screens for polymorphisms that are associated with phenotypic variations can be challenging. However, given the common association with certain phenotypes, a functional link should exist. We have tested this prediction in newly sequenced exomes of altogether 100 men representing different states of fertility.

Host-dependent impairment of parasite development and reproduction in the acanthocephalan model.

Background: A central question in parasitology is why parasites mature and reproduce in some host species but not in others. Yet, a better understanding of the inability of parasites to complete their life cycles in less suitable hosts may hold clues for their control. To shed light on the molecular basis of parasite (non-)maturation, we analyzed transcriptomes of thorny-headed worms (Acanthocephala: Pomphorhynchus laevis), and compared developmentally arrested worms excised from European eel (Anguilla anguilla) to developmentally unrestricted worms from barbel (Barbus barbus).

Protein speciation is likely to increase the chance of proteins to be determined in 2-DE/MS.

Multiple spotting due to protein speciation might increase a protein's chance of being captured in a random selection of 2-DE spots. We tested this expectation in new (PXD015649) and previously published 2-DE/MS data of porcine and human tissues. For comparison, we included bottom-up proteomics studies (BU-LC/MS) of corresponding biological materials.

Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host.

Background: Seisonidea (also Seisonacea or Seisonidae) is a group of small animals living on marine crustaceans (Nebalia spec.) with only four species described so far. Its monophyletic origin with mostly free-living wheel animals (Monogononta, Bdelloidea) and endoparasitic thorny-headed worms (Acanthocephala) is widely accepted.

Fertility Relevance Probability Analysis Shortlists Genetic Markers for Male Fertility Impairment.

Impairment of male fertility is one of the major public health issues worldwide. Nevertheless, genetic causes of male sub- and infertility can often only be suspected due to the lack of reliable and easy-to-use routine tests. Yet, the development of a marker panel is complicated by the large quantity of potentially predictive markers.

Intra-Protein Coevolution Is Increasingly Functional with Greater Proximity to Fertilization.

Intramolecular coevolution of amino acid sites has repeatedly been studied to improve predictions on protein structure and function. Thereby, the focus was on bacterial proteins with available crystallographic data. However, intramolecular coevolution has not yet been compared between protein sets along a gradient of functional proximity to fertilization.

The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala).

Thorny-headed worms (Acanthocephala) are endoparasites exploiting Mandibulata (Arthropoda) and Gnathostomata (Vertebrata). Despite their world-wide occurrence and economic relevance as a pest, genome and transcriptome assemblies have not been published before. However, such data might hold clues for a sustainable control of acanthocephalans in animal production.

Description of Acanthocephalus anguillae balkanicus subsp. n. (Acanthocephala: Echinorhynchidae) from Proteus anguinus Laurenti (Amphibia: Proteidae) and the cave ecomorph of Asellus aquaticus (Crustacea: Asellidae) in Slovenia.

Acanthocephalus balkanicus Batchvarov et Combes, 1974 was incompletely described from the northern crested newt, Triturus cristatus (Laurenti) (Amphibia: Salamandridae), a possible synonym of the Balkan crested newt, Triturus ivanbureschi Arntzen et Wielstra, from a pond in village of Pesnopoy, southern Bulgaria. We provide a full description of adult males and females of the same taxon from the olm, Proteus anguinus Laurenti (Amphibia: Proteidae), the only exclusively aquatic cave-dwelling vertebrate in Europe, captured in Postojna-Planina Cave System in Slovenia. Cystacanths were also collected from the cave ecomorph of Asellus aquaticus (Linnaeus) (Crustacea: Asellidae) in the same location.

Impact of biotic interactions on the survival of emerging pathogen Acinetobacter baumannii in aquatic media.

Acinetobacter baumannii is an opportunistic pathogen causing infections in immunocompromised patients. Recent studies recorded its persistence in a variety of abiotic conditions, but data regarding the biotic interactions with other microorganisms are limited. The aim was to assess the interaction of clinically relevant A.

Correlates of evolutionary rates in the murine sperm proteome.

Background: Protein-coding genes expressed in sperm evolve at different rates. To gain deeper insight into the factors underlying this heterogeneity we examined the relative importance of a diverse set of previously described rate correlates in determining the evolution of murine sperm proteins.

Results: Using partial rank correlations we detected several major rate indicators: Phyletic gene age, numbers of protein-protein interactions, and survival essentiality emerged as particularly important rate correlates in murine sperm proteins.

The FOXP2-Driven Network in Developmental Disorders and Neurodegeneration.

The transcription repressor FOXP2 is a crucial player in nervous system evolution and development of humans and songbirds. In order to provide an additional insight into its functional role we compared target gene expression levels between human neuroblastoma cells (SH-SY5Y) stably overexpressing cDNA of either humans or the common chimpanzee, Rhesus monkey, and marmoset, respectively. RNA-seq led to identification of 27 genes with differential regulation under the control of human , which were previously reported to have FOXP2-driven and/or songbird song-related expression regulation.

Organization and evolution of the proboscis musculature in avian parasites of the genus Apororhynchus (Acanthocephala: Apororhynchida).

The highly enlarged proboscis in adult thorny-headed worms of the genus Apororhynchus suggests that its inner organization might be specialized as well. However, what kind of changes occurred in the stem line of monogeneric Apororhynchida is widely unknown and there are different conceptions regarding the presence/absence of several muscles. To expand our knowledge on this topic, I examined ethanol-fixed specimens, whole mounts, and semi-thin sections of three Apororhynchus species using the light microscope.

Effects of different kinds of essentiality on sequence evolution of human testis proteins.

We asked if essentiality for either fertility or viability differentially affects sequence evolution of human testis proteins. Based on murine knockout data, we classified a set of 965 proteins expressed in human seminiferous tubules into three categories: proteins essential for prepubertal survival ("lethality proteins"), associated with male sub- or infertility ("male sub-/infertility proteins"), and nonessential proteins. In our testis protein dataset, lethality genes evolved significantly slower than nonessential and male sub-/infertility genes, which is in line with other authors' findings.

Evolutionary anatomy of the muscular apparatus involved in the anchoring of Acanthocephala to the intestinal wall of their vertebrate hosts.

Different conceptions exist regarding structure, function, and evolution of the muscles that move the acanthocephalan presoma, including the proboscis, i.e., the usually hooked hold-fast anchoring these endoparasites to the intestinal wall of their vertebrate definitive hosts.

Phylointeractomics reconstructs functional evolution of protein binding.

Molecular phylogenomics investigates evolutionary relationships based on genomic data. However, despite genomic sequence conservation, changes in protein interactions can occur relatively rapidly and may cause strong functional diversification. To investigate such functional evolution, we here combine phylogenomics with interaction proteomics.

Cellular Prion Protein (PrP) and Hypoxia: True to Each Other in Good Times and in Bad, in Sickness, and in Health.

The cellular prion protein (PrP) and hypoxia appear to be tightly intertwined. Beneficial effects of PrP on neuronal survival under hypoxic conditions such as focal cerebral ischemia are strongly supported. Conversely, increasing evidence indicates detrimental effects of increased PrP expression on cancer progression, another condition accompanied by low oxygen tensions.

Phylogeny of Syndermata (syn. Rotifera): Mitochondrial gene order verifies epizoic Seisonidea as sister to endoparasitic Acanthocephala within monophyletic Hemirotifera.

A monophyletic origin of endoparasitic thorny-headed worms (Acanthocephala) and wheel-animals (Rotifera) is widely accepted. However, the phylogeny inside the clade, be it called Syndermata or Rotifera, has lacked validation by mitochondrial (mt) data. Herein, we present the first mt genome of the key taxon Seison and report conflicting results of phylogenetic analyses: while mt sequence-based topologies showed monophyletic Lemniscea (Bdelloidea+Acanthocephala), gene order analyses supported monophyly of Pararotatoria (Seisonidea+Acanthocephala) and Hemirotifera (Bdelloidea+Pararotatoria).

Structural and functional similarity of amphibian constitutive androstane receptor with mammalian pregnane X receptor.

The nuclear receptors and xenosensors constitutive androstane receptor (CAR, NR1I3) and pregnane X receptor (PXR, NR1I2) induce the expression of xenobiotic metabolizing enzymes and transporters, which also affects various endobiotics. While human and mouse CAR feature a high basal activity and low induction upon ligand exposure, we recently identified two constitutive androstane receptors in Xenopus laevis (xlCARá and â) that possess PXR-like characteristics such as low basal activity and activation in response to structurally diverse compounds. Using a set of complementary computational and biochemical approaches we provide evidence for xlCARá being the structural and functional counterpart of mammalian PXR.

Platyzoan paraphyly based on phylogenomic data supports a noncoelomate ancestry of spiralia.

Based on molecular data three major clades have been recognized within Bilateria: Deuterostomia, Ecdysozoa, and Spiralia. Within Spiralia, small-sized and simply organized animals such as flatworms, gastrotrichs, and gnathostomulids have recently been grouped together as Platyzoa. However, the representation of putative platyzoans was low in the respective molecular phylogenetic studies, in terms of both, taxon number and sequence data.