Molecular approaches to the study of ecdysozoan evolution

The Ecdysozoa is a large clade of animals comprising the vast majority of living species and some of the most studied invertebrate models, including fruitflies and nematodes. Some of the relationships between major ecdysozoan groups remain uncertain, however, undermining comparative studies and impairing our understanding of their evolution. One hotly debated problem is the position of myriapods which have been recently grouped according to molecules with chelicerates and not with insects and crustaceans as predicted by morphological evidence. Other disputed problems are the position of tardigrades, the position of hexapods within the crustaceans as well as the mutual affinities of the nematodes and priapulid worms. Molecular systematics of the ecdysozoans is complicated by rapid divergence of the main lineages (possibly evidenced in the Cambrian explosion) followed by a subsequent long period of evolution. This may have resulted in a dilution of the historical phylogenetic signal and an increased likelihood of encountering systematic errors of tree reconstruction. This problem is exacerbated by many lineages being poorly represented in current molecular datasets, as sequencing efforts have been biased toward lab models and economically relevant species. In order to overcome problems of systematic error, I have assembled various large mitochondrial and phylogenomic datasets, including new data from undersampled tardigrades, onychophorans and especially myriapods. I analysed these datasets using the most recent evolutionary models. I have developed two new models in order to describe the evolutionary processes of metazoan mitochondrial proteins more accurately. My analyses of multiple datasets suggest that the grouping of myriapods plus chelicerates found by previous authors is likely to be the result of systematic errors; I find support for a closer relationships between myriapods and a group of insects plus crustaceans (the Mandibulata hypothesis). My analyses also support a paraphyletic origin of Cycloenuralia (nematodes and priapulids) and a sister group relationships between tardigrades, onychophorans and euarthropods in accordance with a single origin of legged ecdysozoans, the Panarthropoda. Finally, results support a monophyletic group of hemimetabolan insects. The majority of the results reconcile molecules and morphology, while others shade new light onto arthropod systematics. The evolutionary implications of these systematic findings as well as methodological advances are discussed

Superfluidity of metastable bulk glass para-hydrogen at low temperature

Molecular para-hydrogen has been proposed theoretically as a possible candidate for superfluidity, but the eventual superfluid transition is hindered by its crystallization. In this work, we study a metastable non crystalline phase of bulk p-H2 by means of the Path Integral Monte Carlo method in order to investigate at which temperature this system can support superfluidity. By choosing accurately the initial configuration and using a non commensurate simulation box, we have been able to frustrate the formation of the crystal in the simulated system and to calculate the temperature dependence of the one-body density matrix and of the superfluid fraction. We observe a transition to a superfluid phase at temperatures around 1 K. The limit of zero temperature is also studied using the diffusion Monte Carlo method. Results for the energy, condensate fraction, and structure of the metastable liquid phase at T=0 are reported and compared with the ones obtained for the stable solid phase.Comment: 10 pages, accepted for publication in Phys. Rev.

Spitzer's Identity and the Algebraic Birkhoff Decomposition in pQFT

In this article we continue to explore the notion of Rota-Baxter algebras in the context of the Hopf algebraic approach to renormalization theory in perturbative quantum field theory. We show in very simple algebraic terms that the solutions of the recursively defined formulae for the Birkhoff factorization of regularized Hopf algebra characters, i.e. Feynman rules, naturally give a non-commutative generalization of the well-known Spitzer's identity. The underlying abstract algebraic structure is analyzed in terms of complete filtered Rota-Baxter algebras.Comment: 19 pages, 2 figure

Microscopic origins of the ferromagnetic exchange coupling in oxoverdazyl-based Cu(II) complex

The exchange channels governing the experimentally reported coupling constant Jexpt=6 cm−1 value in the verdazyl-ligand based Cu II complex Cu hfac 2 imvdz are inspected using wave function-based difference dedicated configuration interaction calculations. The interaction between the two spin 1/2 holders is summed up in a unique coupling constant J. Nevertheless, by gradually increasing the level of calculation, different mechanisms of interaction are turned on step by step. In the present system, the calculated exchange interaction then appears alternatively ferromagnetic/ antiferromagnetic/ferromagnetic. Our analysis demonstrates the tremendously importance of some specific exchange mechanisms. It is actually shown that both parts of the imvdz ligand simultaneously influence the ferromagnetic behavior which ultimately reaches Jcalc=6.3 cm−1, in very good agreement with the experimental value. In accordance with the alternation of J, it is shown that the nature of the magnetic behavior results from competing channels. First, an antiferromagnetic contribution can be essentially attributed to single excitations involving the network localized on the verdazyl part. In contrast, the ligand-to-metal charge transfer LMCT involving the imidazole moiety affords a ferromagnetic contribution. The distinct nature / of the mechanisms is responsible for the net ferromagnetic behavior. The intuitively innocent part of the verdazyl-based ligands is deeply reconsidered and opens new routes into the rational design of magnetic object

Shape Consistent 2D Keypoint Estimation under Domain Shift

Recent unsupervised domain adaptation methods based on deep architectures have shown remarkable performance not only in traditional classification tasks but also in more complex problems involving structured predictions (e.g. semantic segmentation, depth estimation). Following this trend, in this paper we present a novel deep adaptation framework for estimating keypoints under domain shift}, i.e. when the training (source) and the test (target) images significantly differ in terms of visual appearance. Our method seamlessly combines three different components: feature alignment, adversarial training and self-supervision. Specifically, our deep architecture leverages from domain-specific distribution alignment layers to perform target adaptation at the feature level. Furthermore, a novel loss is proposed which combines an adversarial term for ensuring aligned predictions in the output space and a geometric consistency term which guarantees coherent predictions between a target sample and its perturbed version. Our extensive experimental evaluation conducted on three publicly available benchmarks shows that our approach outperforms state-of-the-art domain adaptation methods in the 2D keypoint prediction task

Investigating the microbial community of Cacopsylla spp. as potential factor in vector competence of phytoplasma

Phytoplasmas are obligatory intracellular bacteria that colonize the phloem of many plant species and cause hundreds of plant diseases worldwide. In nature, phytoplasmas are primarily transmitted by hemipteran vectors. While all phloem-feeding insects could in principle transmit phytoplasmas, only a limited number of species have been confirmed as vectors. Knowledge about factors that might determine the vector capacity is currently scarce. Here, we characterized the microbiomes of vector and non-vector species of apple proliferation (AP) phytoplasma ‘Candidatus Phytoplasma mali’ to investigate their potential role in the vector capacity of the host. We performed high-throughput 16S rRNA metabarcoding of the two principal AP-vectors Cacopsylla picta and Cacopsylla melanoneura and eight Cacopsylla species, which are not AP-vectors but co-occur in apple orchards. The microbiomes of all species are dominated by Carsonella, the primary endosymbiont of psyllids and a second uncharacterized Enterobacteriaceae endosymbiont. Each Cacopsylla species harboured a speciesspecific phylotype of both symbionts. Moreover, we investigated differences between the microbiomes of AP-vector versus non-vector species and identified the predominant endosymbionts but also Wolbachia and several minor taxa as potential indicator species. Our study highlights the importance of considering the microbiome in future investigations of potential factors influencing host vector competence. We investigated the potential role of symbiotic bacteria in the acquisition and transmission of phytoplasma. By comparing the two main psyillid vector species of Apple proliferation (AP) phytoplasma and eight co-occurring species, which are not able to vector AP-phytoplasma, we found differences in the microbial communities of AP-vector and non-vector species, which appear to be driven by the predominant symbionts in both vector species and Wolbachia and several minor taxa in the non-vector species. In contrast, infection with APphytoplasma did not affect microbiome composition in both vector species. Our study provides new insights into the endosymbiont diversity of Cacopsylla spp. and highlights the importance of considering the microbiome when investigating potential factors influencing host vector competenc

Genome-scaled phylogeny of Saccharomyces cerevisiae from spontaneous must fermentations

Modern winemakers commonly inoculate selected S. cerevisiae strains in must to obtain controlled fermentations and reproducible products. However, wine has been produced for thousands of years using spontaneous fermentations from wild strains, a practice that is experiencing a revival among small wine producers. Despite the widespread usage of such strains in the past, there is much to know about their ecology, evolution and functional potential. For example, the reciprocal affinities of these strains within the S. cerevisiae phylogeny have yet to be discovered, as well as the degree of their biodiversity and their impact on wine terroir. To fill this knowledge gap, we aim at characterising at strain level the S. cerevisiae present in spontaneously fermented musts sampled across Italy. We set up a protocol based on polyphenols-removing prewashes, followed by whole-genome shotgun sequencing at a depth of 5Gb of DNA per sample. We performed both an assembly-free analysis to reconstruct the strain-level phylogeny of S. cerevisiae strains using the species-specific-marker based StrainPhlAn, and the reconstruction of Metagenome-Assembled Genomes of these strains for downstream functional analyses. To plan conservation acts in a scenario of continuous climate change, we aim at isolating and maintaining strains of interest. We will present preliminary results from the analysis of spontaneous musts sampled at different fermenting stages

Tuning the optical properties of silicon quantum dots via surface functionalization with conjugated aromatic fluorophores

The authors acknowledge Karen Nygard at UWO Biotron for assistance with confocal microscopy. This work was financially supported by NSERC Canada Discovery (Charpentier).Silicon Quantum Dots (SQDs) have recently attracted great interest due to their excellent optical properties, low cytotoxicity, and ease of surface modification. The size of SQDs and type of ligand on their surface has a great influence on their optical properties which is still poorly understood. Here we report the synthesis and spectroscopic studies of three families of unreported SQDs functionalized by covalently linking to the aromatic fluorophores, 9-vinylphenanthrene, 1-vinylpyrene, and 3-vinylperylene. The results showed that the prepared functionalized SQDs had a highly-controlled diameter by HR-TEM, ranging from 1.7–2.1 nm. The photophysical measurements of the assemblies provided clear evidence for efficient energy transfer from the fluorophore to the SQD core. Fӧrster energy transfer is the likely mechanism in these assemblies. As a result of the photogenerated energy transfer process, the emission color of the SQD core could be efficiently tuned and its emission quantum efficiency enhanced. To demonstrate the potential application of the synthesized SQDs for bioimaging of cancer cells, the water-soluble perylene- and pyrene-capped SQDs were examined for fluorescent imaging of HeLa cells. The SQDs were shown to be of low cytotoxicity.Publisher PDFPeer reviewe

Curcumin and Novel Synthetic Analogs in Cell-Based Studies of Alzheimer's Disease

Alzheimer's disease (AD) is a chronic neurodegenerative disorder that is associated with the most common type of dementia and is characterized by the presence of deposits of the protein fragment amyloid beta (A\u3b2) in the brain. The natural product mixture of curcuminoids that improves certain defects in innate immune cells of AD patients may selectively enhance A\u3b2 phagocytosis by alteration of gene transcription. In this work, we evaluated the protective effects of curcuminoids in cells from AD patients by investigating the effect on NF-\u3baB and BACE1 signaling pathways. These results were compared to the gene expression profile of the clearance of A\u3b2. The minor curcumin constituent, bisdemethoxycurcumin (BDC) showed the most potent protective action to decrease levels of NF-\u3baB and BACE1, decrease the inflammatory cascade and diminish A\u3b2 aggregates in cells from AD patients. Moreover, mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase (MGAT3) and vitamin D receptor (VDR) gene mRNAs were up-regulated in peripheral blood mononuclear cells from AD patients treated with BDC. BDC treatment impacts both gene expression including Mannosyl (Beta-1,4-)-Glycoprotein Beta-1,4-N-Acetylglucosaminyltransferase, Vitamin D and Toll like receptor mRNA and A\u3b2 phagocytosis. The observation of down-regulation of BACE1 and NF-\u3baB following administration of BDC to cells from AD patients as a model system may have utility in the treatment of asymptomatic AD patients

Epigenetic remodelling in human hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the most frequent primary liver cancer, being the sixth most commonly diagnosed cancer and the fourth leading cause of cancer-related death. As other heterogeneous solid tumours, HCC results from a unique synergistic combination of genetic alterations mixed with epigenetic modifications. In HCC the patterns and frequencies of somatic variations change depending on the nearby chromatin. On the other hand, epigenetic alterations often induce genomic instability prone to mutations. Epigenetics refers to heritable states of gene expression without alteration to the DNA sequence itself and, unlike genetic changes, the epigenetic modifications are reversible and affect gene expression more extensively than genetic changes. Thus, studies of epigenetic regulation and the involved molecular machinery are greatly contributing to the understanding of the mechanisms that underline HCC onset and heterogeneity. Moreover, this knowledge may help to identify biomarkers for HCC diagnosis and prognosis, as well as future new targets for more efficacious therapeutic approaches. In this comprehensive review we will discuss the state-of-the-art knowledge about the epigenetic landscape in hepatocarcinogenesis, including evidence on the diagnostic and prognostic role of non-coding RNAs, modifications occurring at the chromatin level, and their role in the era of precision medicine. Apart from other better-known risk factors that predispose to the development of HCC, characterization of the epigenetic remodelling that occurs during hepatocarcinogenesis could open the way to the identification of personalized biomarkers. It may also enable a more accurate diagnosis and stratification of patients, and the discovery of new targets for more efficient therapeutic approaches