Trophic Position of the White Worm (Enchytraeus albidus) in the Context of Digestive Enzyme Genes Revealed by Transcriptomics Analysis.

To assess the impact of Enchytraeidae (potworms) on the functioning of the decomposer system, knowledge of the feeding preferences of enchytraeid species is required. Different food preferences can be explained by variations in enzymatic activities among different enchytraeid species, as there are no significant differences in the morphology or anatomy of their alimentary tracts. However, it is crucial to distinguish between the contribution of microbial enzymes and the animal's digestive capacity. Here, we computationally analyzed the endogenous digestive enzyme genes in Enchytraeus albidus. The analysis was based on RNA-Seq of COI-monohaplotype culture (PL-A strain) specimens, utilizing transcriptome profiling to determine the trophic position of the species. We also corroborated the results obtained using transcriptomics data from genetically heterogeneous freeze-tolerant strains. Our results revealed that E. albidus expresses a wide range of glycosidases, including GH9 cellulases and a specific digestive SH3b-domain-containing i-type lysozyme, previously described in the earthworm Eisenia andrei. Therefore, E. albidus combines traits of both primary decomposers (primary saprophytophages) and secondary decomposers (sapro-microphytophages/microbivores) and can be defined as an intermediate decomposer. Based on assemblies of publicly available RNA-Seq reads, we found close homologs for these cellulases and i-type lysozymes in various clitellate taxa, including Crassiclitellata and Enchytraeidae.

Discovery and characterization of the α-amylases cDNAs from Enchytraeus albidus shed light on the evolution of "Enchytraeus-Eisenia type" Amy homologs in Annelida.

Although enchytraeids have gained popularity in scientific research, fundamental questions regarding their feeding ecology and biology remain largely unexplored. This study investigates α-amylases, major digestive enzymes responsible for hydrolyzing starch and similar polysaccharides into sugars, in Enchytraeus albidus. Genetic data related to α-amylases is currently lacking for the family Enchytraeidae but also for the entire Annelida. To detect and identify coding sequences of the expressed α-amylase genes in COI-monohaplotype culture (PL-A strain) of E. albidus, we used classical "gene fishing" and transcriptomic approaches. We also compared coding sequence variants of α-amylase retrieved from transcriptomic data related to freeze-tolerant strains. Our results reveal that E. albidus possesses two distinct α-amylase genes (Amy I and Amy II) that are homologs to earthworm Eisenia fetida Ef-Amy genes. Different strains of E. albidus possess distinctive alleles of α-amylases with unique SNP patterns specific to a particular strain. Unlike Amy II, Amy I seems to be a highly polymorphic and multicopy gene. The domain architecture of the putative Amy proteins was found the same as for classical animal α-amylases with ABC-domains. A characteristic feature of Amy II is the lack of GHGA motif in the flexible loop region, similarly to many insect amylases. We identified "Enchytraeus-Eisenia type" α-amylase homologs in other clitellates and polychaetes, indicating the ancestral origin of Amy I/II proteins in Annelida. This study provides the first insight into the endogenous non-proteolytic digestive enzyme genes in potworms, discusses the evolution of Amy α-amylases in Annelida, and explores phylogenetic implications.

New reports on iron related proteins: Molecular characterization of two ferroportin genes in common carp (Cyprinus carpio L.) and its expression pattern.

Iron uptake, transport, and storage require the involvement of several proteins, including ferroportin (fpn), the sole known iron efflux transporter. Due to its critical function fpn has been studied, particularly in humans. Here, we characterized the ferroportin gene in common carp (Cyprinus carpio L.) and performed RNA-seq analysis to evaluate its constitutive transcription levels across different tissues. Our results indicate that C. carpio possesses two functional fpns with distinct expression patterns, highlighting the potential for functional divergence and expression differentiation among fpns in this species.

Ovary organization and ultrastructure in six species of Amynthas and Metaphire earthworms (Annelida, Crassiclitellata, Megascolecidae).

Ovaries in earthworms belonging to the family Megascolecidae are paired structures attached to the septum in the anterior part of the XIII segment. They are fan to rosette shaped with numerous rows of growing oocytes, known as egg strings, radiating from the ovary center towards the segmental cavity. The histological and ultrastructural ovary organization in megascolecids and the course of oogenesis remain unknown. The paper presents the results of light and electron microscopy analyses of ovaries in six megascolecid species, three from the genus Amynthas and three from Metaphire. Both parthenogenetic and sexually reproducing species were included in the study. The organization and ultrastructure of ovaries in all studied species are broadly similar. Considering the histological organization of ovaries, they could be divided into two zones. Zone I (proximal, close to the connection with the septum) is tightly packed with germline and somatic cells. Germ cells are interconnected via intercellular bridges and thin strands of the central cytoplasm (known as cytophore) and form syncytial cysts. Cysts unite oogonia, early meiotic cells (till diplotene), and clustering cells develop synchronously. During diplotene, interconnected cells lose developmental synchrony; most probably, one cell per cyst grows faster than others, detaches from the cysts, and becomes an oocyte. The remaining cells grow slightly and are still interconnected via the thin and reticular cytophore; these cells are considered nurse cells. Zone II has a form of egg strings where growing oocytes are isolated one from another by thin somatic cells and form short cords. We present the ultrastructural details of germline and somatic cells. We propose the term "Amynthas" type of ovaries for this ovary organization. We suppose that such ovaries are characteristic of other megascolecids and related families.

Placobdella nabeulensis sp. nov. (Hirudinea: Glossiphoniidae), a new glossiphoniiform leech from Palearctic North Africa.

BACKGROUND: Herein, we describe a new species of turtle blood-feeding leech, Placobdella nabeulensis sp. nov. from Palearctic North Africa (Tunisia and Algeria). The new species is described based on detailed morphological analyses using light and scanning electron microscopes. RESULTS: Apart from the detailed morphology of the atrium, morphological features alone do not sufficiently separate the species from congeners due to the absence of distinct diagnostic characters. Therefore, we turned to molecular data to better distinguish this new species from other members of the genus and establish a basis for its genetic separation. Four DNA fragments were successfully amplified, including mitochondrial COI and 12S rDNA, as well as nuclear 28S rDNA and histone H3. We then provided the molecular descriptor of the taxon, based on redundant diagnostic nucleotide combinations in DNA sequence alignment within the Folmer region. Results of the phylogenetic analysis and species delimitation methods (ABGD, ASAP, and bPTP) based on the COI locus support the species rank of the Tunisian-Algerian Placobdella. CONCLUSIONS: The new species is most closely related to the European species Placobdella costata (Fr. Müller, 1846) and the present study indicates that Placobdella nabeulensis sp. nov. has likely been confused with the European counterpart in several previous studies. This article is registered at www.zoobank.org under urn:lsid:zoobank.org:pub:4A4B9C1D-2556-430F-8E4B-0CE99F2012F5.

Ovary micromorphology in hormogastrid earthworms with a particular emphasis on the organization of the germline cysts.

There is a gap in our knowledge of microorganization and the functioning of ovaries in earthworms (Crassiclitellata) and allied taxa. Recent analyses of ovaries in microdriles and leech-like taxa revealed that they are composed of syncytial germline cysts accompanied by somatic cells. Although the pattern of cyst organization is conserved across Clitellata - each cell is connected via one intercellular bridge (ring canal) to the central and anuclear cytoplasmic mass termed the cytophore - this system shows high evolutionary plasticity. In Crassiclitellata, only the gross morphology of ovaries and their segmental localization is well known, whereas ultrastructural data are limited to lumbricids like Dendrobaena veneta. Here we present the first report about ovarian histology and ultrastructure in Hormogastridae, a small family of earthworms inhabiting the western parts of the Mediterranean sea basin. We analyzed three species from three different genera and showed that the pattern of ovary organization is the same within this taxon. Ovaries are cone-like, with a broad part connected to the septum and a narrow distal end forming an egg string. Ovaries are composed of numerous cysts uniting a small number of cells, eight in Carpetania matritensis. There is a gradient of cysts development along the long ovary axis, and three zones can be distinguished. In zone I, cysts develop in complete synchrony and unite oogonia and early meiotic cells (till diplotene). Then (zone II), the synchrony is lost, and one cell (prospective oocyte) grows faster than the rest (prospective nurse cells). In zone III, oocytes pass the growth phase and gather nutrients; at this time, their contact with the cytophore is lost. Nurse cells grow slightly, eventually die via apoptosis, and are removed by coelomocytes. The most characteristic feature of hormogastrid germ cysts is the inconspicuous cytophore in the form of thread-like thin cytoplasmic strands (reticular cytophore). We found that the ovary organization in studied hormogastrids is very similar to that described for D. veneta and propose the term "Dendrobaena" type of ovaries. We expect the same microorganization of ovaries will be found in other hormogastrids and lumbricids.

Local aromaticity in polyacenes manifested by individual proton and carbon shieldings: DFT mapping of aromaticity.

Exponential dependencies between locally calculated geometric and magnetic indexes of aromaticity, harmonic oscillator model of aromaticity (HOMA) and nucleus independent chemical shifts (NICS)(0), NICS(1) and NICS(1)zz, and the number of conjugated benzene rings in linear acenes, from benzene to decacene were observed at B3LYP/6-311+G** level of theory. Correlations between HOMA and NICS indexes showed exponential dependencies and were fitted with simple three-parameter function. Similar correlations between both indexes of aromaticity and proton and carbon nuclear isotropic shieldings of individual acene rings were observed. Contrary to proton data, the predicted 13 C nuclear isotropic shieldings of carbon atoms belonging to inner rings in polyacenes were less shielded, indicating lower aromaticity and therefore, higher reactivity.

Description of ovary organization and oogenesis in a phreodrilid clitellate.

Phreodrilidae is a small family uniting about 50 species of minute freshwater clitellate annelids inhabiting mainly the Southern hemisphere. Other than the male and spermathecal genitalia, their internal organization is poorly known. Here, we present results of our study of the ovaries and oogenesis in Insulodrilus bifidus, a phreodrilid from Western Australia using light and electron microscopy. The ovaries are paired and located in segment XII. They are inconspicuous and composed of several (10-12) spherical germ-line cysts loosely interconnected by flattened somatic cells. The cysts usually comprise 32 germ cells and each cell is connected via a cytoplasmic bridge (ring canal) to the central cytoplasmic mass (the cytophore). In ovaries, germ cells in a given cyst develop in full synchrony. However, there is no synchrony among cysts, so there is a developmental gradient of cysts (from oogonial to early meiotic) along the longitudinal ovary axis. Within the cysts that are located in the distal end of the ovary the synchrony is finally lost and interconnected cells diversify into two morphologically distinct categories: an oocyte and 31 nurse cells. Such cysts detach from the ovaries and further development occurs within the body cavity. The oocyte gathers nutrients, mainly in form of yolk spheres, whereas nurse cells grow slightly and do not gather yolk. Organelles such as ribosomes, mitochondria and endoplasmic reticulum pass freely through the ring canals and are present within the cytophore, which suggests cytoplasmic transfer towards the oocyte. The formation of female germ-line cysts equipped with cytophore and cells differentiated into oocyte and nurse cells matches the general pattern of oogenesis found in clitellates. In details, the ovary organization and oogenesis found in I. bifidus resembles the situation described in some representatives of Naidinae and Enchytraeidae.

Local aromaticity mapping in the vicinity of planar and nonplanar molecules.

We report on nucleus-independent magnetic shielding (NICS) scans over the centers of six- and five-membered rings in selected metal phthalocyanines (MPc) and fullerene C60 for more accurate characterization of local aromaticity in these compounds. Detailed tests were conducted on model aromatic molecules including benzene, pyrrole, indole, isoindole, and carbazole and subsequently applied to H2 Pc, ZnPc, Al(OH)Pc, and CuPc. Similar behavior of three selected magnetic probes, Bq, 3 He, and 7 Li+ , approaching perpendicularly the ring centers, was observed. For better visualization of shielding zone over the centers of aromatic rings, we introduced a simple mathematical procedure: the first and second derivatives of scan curves with respect to magnetic probe position enabled their additional examination. It allowed an easier localization of curve minimum and discrimination between areas in space varying by the magnetic field magnitude and to illustrate local aromaticity of two different kinds of rings in MPc with better resolution. Our results supported earlier reports on very low aromaticity indexes of pyrrole ring incorporated into MPc and significant aromaticity of the central macrocycle. No direct dependence between harmonic oscillator model of aromaticity and NICS was observed. Instead, a correlation between position of scan curve minimum and its magnitude were observed. In addition, the NICS values and 3 He chemical shifts in the middle of neutral C60 and C606- anion agreed well with the reported experimental NMR values for He@C60 and He@C606- .

Convergence of nuclear magnetic shieldings and one-bond 1 J(11 B1 H) indirect spin-spin coupling constants in small boron molecules.

Self-consistent field Hartree-Fock, density functional theory, and coupled-cluster calculations of the nuclear magnetic shielding constants of BH and BH3 molecules have been conducted to characterize the convergence of individual results obtained with correlation-consistent and polarization-consistent basis sets. The individual 11 B and 1 H NMR parameters were estimated in the complete basis set limit and compared with benchmark results. Only the KT3 density functional accurately reproduced 11 B shielding in BH molecule.

Method and basis set dependence of the NICS indexes of aromaticity for benzene.

The role of theory level in prediction of benzene magnetic indexes of aromaticity is analysed and compared with calculated nuclear magnetic shieldings of 3 He used as NMR probe. Three closely related nucleus-independent chemical shift (NICS) based indexes were calculated for benzene at SCF-HF, MP2, and DFT levels of theory and the impact of basis set on these quantities was studied. The changes of benzene NICS(0), NICS(1), and NICS(1)zz parameters calculated using SCF-HF, MP2 and several density functionals were within 1 to 3 ppm. Similar deviations between magnetic indexes of aromaticity were observed for values calculated with selected basis sets. Only very small effect of polar solvent on benzene aromaticity was predicted. The 3 He nuclear magnetic isotropic shielding (σ) and its zz-components (σzz ) of helium atom approaching the centre of benzene ring from above produced similar curves versus benzene-He distance to NICS parameters calculated for similarly moving Bq ghost atom. We also propose an experimental verification of NICS calculations by designing the 3 He NMR measurement for benzene saturated with helium gas or in low temperature matrices.