A Molecular Phylogeny of Bivalve Mollusks: Ancient Radiations and Divergences as Revealed by Mitochondrial Genes

Background: Bivalves are very ancient and successful conchiferan mollusks (both in terms of species number and geographical distribution). Despite their importance in marine biota, their deep phylogenetic relationships were scarcely investigated from a molecular perspective, whereas much valuable work has been done on taxonomy, as well as phylogeny, of lower taxa. Methodology/Principal Findings: Here we present a class-level bivalve phylogeny with a broad sample of 122 ingroup taxa, using four mitochondrial markers (MT-RNR1, MT-RNR2, MT-CO1, MT-CYB). Rigorous techniques have been exploited to set up the dataset, analyze phylogenetic signal, and infer a single final tree. In this study, we show the basal position of Opponobranchia to all Autobranchia, as well as of Palaeoheterodonta to the remaining Autobranchia, which we here propose to call Amarsipobranchia. Anomalodesmata were retrieved as monophyletic and basal to (Heterodonta + Pteriomorphia). Conclusions/Significance: Bivalve morphological characters were traced onto the phylogenetic trees obtained from the molecular analysis; our analysis suggests that eulamellibranch gills and heterodont hinge are ancestral characters for all Autobranchia. This conclusion would entail a re-evaluation of bivalve symplesiomorphies

Clues of in vivo nuclear gene regulation by mitochondrial short non-coding RNAs.

Gene expression involves multiple processes, from transcription to translation to the mature, functional peptide, and it is regulated at multiple levels. Small RNA molecules are known to bind RNA messengers affecting their fate in the cytoplasm (a process generically termed \u2018RNA interference\u2019). Such small regulatory RNAs are well-known to be originated from the nuclear genome, while the role of mitochondrial genome in RNA interference was largely overlooked. However, evidence is growing that mitochondrial DNA does provide the cell a source of interfering RNAs. Small mitochondrial highly transcribed RNAs (smithRNAs) have been proposed to be transcribed from the mitochondrion and predicted to regulate nuclear genes. Here, for the first time, we show in vivo clues of the activity of two smithRNAs in the Manila clam, Ruditapes philippinarum. Moreover, we show that smithRNAs are present and can be annotated in representatives of the three main bilaterian lineages; in some cases, they were already described and assigned to a small RNA category (e.g., piRNAs) given their biogenesis, while in other cases their biogenesis remains unclear. If mitochondria may affect nuclear gene expression through RNA interference, this opens a plethora of new possibilities for them to interact with the nucleus and makes metazoan mitochondrial DNA a much more complex genome than previously thought

A 1 m3^3 Gas Time Projection Chamber with Optical Readout for Directional Dark Matter Searches: the CYGNO Experiment

The aim of the CYGNO project is the construction and operation of a 1~m$^3$ gas TPC for directional dark matter searches and coherent neutrino scattering measurements, as a prototype toward the 100-1000~m$^3$ (0.15-1.5 tons) CYGNUS network of underground experiments. In such a TPC, electrons produced by dark-matter- or neutrino-induced nuclear recoils will drift toward and will be multiplied by a three-layer GEM structure, and the light produced in the avalanche processes will be readout by a sCMOS camera, providing a 2D image of the event with a resolution of a few hundred micrometers. Photomultipliers will also provide a simultaneous fast readout of the time profile of the light production, giving information about the third coordinate and hence allowing a 3D reconstruction of the event, from which the direction of the nuclear recoil and consequently the direction of the incoming particle can be inferred. Such a detailed reconstruction of the event topology will also allow a pure and efficient signal to background discrimination. These two features are the key to reach and overcome the solar neutrino background that will ultimately limit non-directional dark matter searches.Comment: 5 page, 7 figures, contribution to the Conference Records of 2018 IEEE NSS/MI

The IGS-ETS in Bacillus (Insecta Phasmida): molecular characterization and the relevance of sex in ribosomal DNA evolution

<p>Abstract</p> <p>Background</p> <p>DNA encoding for ribosomal RNA (rDNA) is arranged in tandemly-repeated subunits, each containing ribosomal genes and non-coding spacers. Because tandemly-repeated, rDNA evolves under a balanced influence of selection and "concerted evolution", which homogenizes rDNA variants over the genome (through genomic turnover mechanisms) and the population (through sexuality).</p> <p>Results</p> <p>In this paper we analyzed the IGS-ETS of the automictic parthenogen <it>Bacillus atticus </it>and the bisexual <it>B. grandii</it>, two closely related stick-insect species. Both species share the same IGS-ETS structure and sequence, including a peculiar head-to-tail array of putative transcription enhancers, here named <it>Bag530</it>. Sequence variability of both IGS-ETS and <it>Bag530 </it>evidenced a neat geographic and subspecific clustering in <it>B. grandii</it>, while <it>B. atticus </it>shows a little but evident geographic structure. This was an unexpected result, since the parthenogen <it>B. atticus </it>should lack sequence fixation through sexuality. In <it>B. atticus </it>a new variant might spread in a given geographic area through colonization by an all-female clone, but we cannot discard the hypothesis that <it>B. atticus </it>was actually a bisexual taxon in that area at the time the new variant appeared. Moreover, a gene conversion event between two <it>Bag530 </it>variants of <it>B. grandii benazzii </it>and <it>B. grandii maretimi </it>suggested that rRNA might evolve according to the so-called "library hypothesis" model, through differential amplification of rDNA variants in different taxa.</p> <p>Conclusion</p> <p>On the whole, <it>Bacillus </it>rDNA evolution appears to be under a complex array of interacting mechanisms: homogenization may be achieved through genomic turnover that stabilizes DNA-binding protein interactions but, simultaneously, new sequence variants can be adopted, either by direct appearance of newly mutated repeats, or by competition among repeats, so that both DNA-binding proteins and repeat variants drive each other's evolution. All this, coupled with chromosome reshuffling due to sexuality (when present), might drive a quick fixation of new rDNA variants in the populations.</p

Erratum to: Evidence for somatic transcription of male-transmitted mitochondrial genome in the DUI species Ruditapes philippinarum (Bivalvia: Veneridae)

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Increased Fluctuating Asymmetry in a Naturally Occurring Hybrid Zone between the Stick Insects Bacillus Rossius Rossius and Bacillus Rossius Redtenbacheri

The impact of interracial hybridization on fluctuating asymmetry (FA) and phenotypic variability (σ2p) in a presumed natural hybrid zone between the stick insects, Bacillus rossius rossius Rossi and Bacillus rossius redtenbacheri Nasceti & Bullini (Phasmatodea: Bacillidea), found on the Italian island Sardinia was investigated. The lengths of three bilateral traits and three unilateral traits were measured, and each individual was genotyped by five microsatellite loci. The genotypic data clearly confirmed the existence of the hybrid zone on Sardinia. A significantly increased FA was found in the hybrids when compared to both parental subspecies, which this study attributes to genetic incompatibilities in the hybrids. The increase in FA was not correlated with any increase in σ2P in the hybrids, which indicates that in this case σ2p and FA originate from separate processes

Efficacy of Tixagevimab-Cilgavimab as Immunoprophylaxis in Patients With Hematologic Cancer

This cohort study compares outcomes for patients with hematologic malignant tumors who prophylactically received tixagevimab-cilgavimab against SARS-CoV-2 with those who did not

Quantitative variation of melanins in alpaca (Lama pacos L.)

The amount of melanin pigments was investigated in 95 Peruvian alpaca, representative of six different fleece colours, by means of spectrophotometric assays: SpEM (Spectrophoto­metric Eumelanin), SpPM (Spectrophotometric Pheomelanin), SpASM (Spectrophotometric Alkali Soluble Melanin), and SpTM (Spectro­photometric Total Melanin). It was found that these melanin pigments were suitable for identifying three homogeneous groups, each consisting of two closely related colours. A low, an intermediate, and a high amount of SpASM, SpTM, and SpPM characterize pinkish grey and light reddish brown, brown and reddish brown, dark reddish brown and black fleeces, respectively. SpEM and SpTM provide a further split within this latter group; higher concentrations of these pigments distinguish black fleece from dark reddish brown