Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks

Mito‐nuclear phylogenetic discordance in Bivalvia is well known. In particular, the monophyly of Amarsipobranchia (Heterodonta + Pteriomorphia), retrieved from mitochondrial markers, contrasts with the monophyly of Heteroconchia (Heterodonta + Palaeoheterodonta), retrieved from nuclear markers. However, since oxidative phosphorylation nuclear markers support the Amarsipobranchia hypothesis instead of the Heteroconchia one, interacting subunits of the mitochondrial complexes ought to share the same phylogenetic signal notwithstanding the genomic source, which is different from the signal obtained from other nuclear markers. This may be a clue of coevolution between nuclear and mitochondrial genes. In this work we inferred the phylogenetic signal from mitochondrial and nuclear oxidative phosphorylation markers exploiting different phylogenetic approaches and added two more datasets for comparison: genes of the glycolytic pathway and genes related to the biogenesis of regulative small noncoding RNAs. All trees inferred from mitochondrial and nuclear subunits of the mitochondrial complexes support the monophyly of Amarsipobranchia, regardless of the phylogenetic pipeline. However, not every single marker agrees with this topology: this is clearly visible in nuclear subunits that do not directly interact with the mitochondrial counterparts. Overall, our data support the hypothesis of a coevolution between nuclear and mitochondrial genes for the oxidative phosphorylation. Moreover, we suggest a relationship between mitochondrial topology and different nucleotide composition between clades, which could be associated to the highly variable gene arrangement in Bivalvia

Mitochondrial selfish elements and the evolution of biological novelties.

We report the present knowledge about RPHM21, a novel male-specific mitochondrial protein with a putative role in the paternal inheritance of sperm mitochondria in the Manila clam Ruditapes philippinarum, a species with doubly uniparental inheritance of mitochondria (DUI). We review all the available data on rphm21 transcription and translation, analyze in detail its female counterpart, RPHF22, discuss the homology with RPHM21, the putative function and origin, and analyze their polymorphism. The available evidence is compatible with a viral origin of RPHM21 and supports its activity during spermatogenesis. RPHM21 is progressively accumulated in mitochondria and nu- clei of spermatogenic cells, and we hypothesize it can influence mitochondrial inheritance and sex- ual differentiation. We propose a testable model that describes how the acquisition of selfish fea- tures by a mitochondrial lineage might have been responsible for the emergence of DUI, and for the evolution of separate sexes (gonochorism) from hermaphroditism. The appearance of DUI most likely entailed the invasion of at least 1 selfish element, and the extant DUI systems can be seen as resolved conflicts. It was proposed that hermaphroditism was the ancestral condition of bi- valves, and a correlation between DUI and gonochorism was documented. We hypothesize that DUI might have driven the shift from hermaphroditism to gonochorism, with androdioecy as transi- tion state. The invasion of sex-ratio distorters and the evolution of suppressors can prompt rapid changes among sex-determination mechanisms, and DUI might have been responsible for one of such changes in some bivalve species. If true, DUI would represent the first animal sex-determination system involving mtDNA-encoded proteins

Identification and localization of the bilitranslocase homologue in white grape berries (Vitis vinifera L.) during ripening

A homologue of the mammalian bilirubin transporter bilitranslocase (BTL) (TCDB 2.A.65.1.1), able to perform an apparent secondary active transport of flavonoids, has previously been found in carnation petals and red grape berries. In the present work, a BTL homologue was also shown in white berries from Vitis vinifera L. cv. Tocai/Friulano, using anti-sequence antibodies specific for rat liver BTL. This transporter, similarly to what found in red grape, was localized in the first layers of the epidermal tissue and in the vascular bundle cells of the mesocarp. In addition, a strong immunochemical reaction was detected in the placental tissue and particularly in peripheral integuments of the seed. The protein was expressed during the last maturation stages in both skin and pulp tissues and exhibited an apparent molecular mass of c. 31 kDa. Furthermore, the transport activity of such a carrier, measured as bromosulphophthalein (BSP) uptake, was detected in berry pulp microsomes, where it was inhibited by specific anti-BTL antibodies. The BTL homologue activity exhibited higher values, for both Km and Vmax, than those found in the red cultivar. Moreover, two non-pigmented flavonoids, such as quercetin (a flavonol) and eriodictyol (a flavanone), inhibited the uptake of BSP in an uncompetitive manner. Such results strengthen the hypothesis that this BTL homologue acts as a carrier involved also in the membrane transport of colourless flavonoids and demonstrate the presence of such a carrier in different organs and tissues

Eco-friendly gas mixtures for Resistive Plate Chambers based on Tetrafluoropropene and Helium

Due to the recent restrictions deriving from the application of the Kyoto protocol, the main components of the gas mixtures presently used in the Resistive Plate Chambers systems of the LHC experiments will be most probably phased out of production in the coming years. Identifying possible replacements with the adequate characteristics requires an intense R&D, which was recently started, also in collaborations across the various experiments. Possible candidates have been proposed and are thoroughly investigated. Some tests on one of the most promising candidate - HFO-1234ze, an allotropic form of tetrafluoropropane- have already been reported. Here an innovative approach, based on the use of Helium, to solve the problems related to the too elevate operating voltage of HFO-1234ze based gas mixtures, is discussed and the relative first results are shown.Comment: 9 pages, 6 figures, 1 tabl

Cms gem detector material study for the hl-lhc

A study on the Gaseous Electron Multiplier (GEM) foil material is performed to determine the moisture diffusion rate, moisture saturation level and the effects on its mechanical properties. The study is focused on the foil contact with ambient air and moisture to determine the value of the diffusion coefficient of water in the foil material. The presence of water inside the detector foil can determine the changes in its mechanical and electrical properties. A simulated model is developed with COMSOL Multiphysics v. 4.3 [1] by taking into account the real GEM foil (hole dimensions, shapes and material), which describes the adsorption of water. This work describes the model, its experimental verification, the water diffusion within the entire sheet geometry of the GEM foil, thus gaining concentration profiles and the time required to saturate the system and the effects on the mechanical properties

A Novel Approach for an Integrated Straw tube-Microstrip Detector

We report on a novel concept of silicon microstrips and straw tubes detector, where integration is accomplished by a straw module with straws not subjected to mechanical tension in a Rohacell $^{\circledR}$ lattice and carbon fiber reinforced plastic shell. Results on mechanical and test beam performances are reported on as well.Comment: Accepted by Transactions on Nuclear Science (2005). 11 pages, 9 figures, uses lnfprep.st

Management of patients with lymphoma and COVID-19: Narrative review and evidence-based practical recommendations

Patients with hematologic malignancies can be immunocompromized because of their disease, anti-cancer therapy, and concomitant immunosuppressive treatment. Furthermore, these patients are usually older than 60 years and have comorbidities. For all these reasons they are highly vulnerable to infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and have an increased risk of developing severe/critical Coronavirus disease 2019 (COVID-19) compared to the general population. Although COVID-19 vaccination has proven effective in reducing the incidence of severe/critical disease, vaccinated patients with lymphoma may not be protected as they often fail to develop a sufficient antiviral immune response. There is therefore an urgent need to address the management of patients with lymphoma and COVID-19 in the setting of the ongoing pandemic. Passive immunization with monoclonal antibodies against SARS-CoV-2 is a currently available complementary drug strategy to active vaccination for lymphoma patients, while monoclonal antibodies and antiviral drugs (remdesivir, ritonavir-boosted nirmatrelvir, and molnupiravir) have proven effective in preventing the progression to severe/critical COVID-19. In this narrative review we present the most recent data documenting the characteristics and outcomes of patients with concomitant lymphoma and COVID-19. Our ultimate goal is to provide practice-oriented guidance in the management of these vulnerable patients from diagnosis to treatment and follow-up of lymphoma. To this purpose, we will first provide an overview of the main data concerning prognostic factors and fatality rate of lymphoma patients who develop COVID-19; the outcomes of COVID-19 vaccination will also be addressed. We will then discuss current COVID-19 prophylaxis and treatment options for lymphoma patients. Finally, based on the literature and our multidisciplinary experience, we will summarize a set of indications on how to manage patients with lymphoma according to COVID-19 exposure, level of disease severity and former history of infection, as typically encountered in clinical practice

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