Mitochondrial DNA Mutations and Ageing.

Mitochondria are subcellular organelles present in most eukaryotic cells which play a significant role in numerous aspects of cell biology. These include carbohydrate and fatty acid metabolism to generate cellular energy through oxidative phosphorylation, apoptosis, cell signalling, haem biosynthesis and reactive oxygen species production. Mitochondrial dysfunction is a feature of many human ageing tissues, and since the discovery that mitochondrial DNA mutations were a major underlying cause of changes in oxidative phosphorylation capacity, it has been proposed that they have a role in human ageing. However, there is still much debate on whether mitochondrial DNA mutations play a causal role in ageing or are simply a consequence of the ageing process. This chapter describes the structure of mammalian mitochondria, and the unique features of mitochondrial genetics, and reviews the current evidence surrounding the role of mitochondrial DNA mutations in the ageing process. It then focusses on more recent discoveries regarding the role of mitochondrial dysfunction in stem cell ageing and age-related inflammation.

Structural Studies and Thermal Analysis in the Cs2MoO4-PbMoO4 System with Elucidation of ß-Cs2Pb(MoO4)2.

The quaternary compound Cs2Pb(MoO4)2 was synthesized and its structure was characterized using X-ray and neutron diffraction from 298 to 773 K, while thermal expansion was studied from 298 to 723 K. The crystal structure of the high-temperature phase ß-Cs2Pb(MoO4)2 was elucidated, and it was found to crystallize in the space group R3̅m (No. 166), i.e., with a palmierite structure. In addition, the oxidation state of Mo in the low-temperature phase α-Cs2Pb(MoO4)2 was studied using X-ray absorption near-edge structure spectroscopy. Phase diagram equilibrium measurements in the Cs2MoO4-PbMoO4 system were performed, revisiting a previously reported phase diagram. The equilibrium phase diagram proposed here includes a different composition of the intermediate compound in this system. The obtained data can serve as relevant information for thermodynamic modeling in view of the safety assessment of next-generation lead-cooled fast reactors.

Investigation of mitochondrial biogenesis defects in single substantia nigra neurons using post-mortem human tissues.

Mitochondrial respiratory chain deficiency and mitochondrial DNA deletions are reported in substantia nigra neurons from healthy aged and Parkinson's disease cases, with extensive neuronal loss only seen in the latter. This study aimed to understand the pathological relevance of mitochondrial defects for neuronal survival. Using post-mortem human midbrain, substantia nigra neurons exposed to different types of mitochondrial defects (including mitochondrial DNA point mutations, single and multiple deletions) were compared to neurons from healthy aged and Parkinson's disease cases (either sex) at a single neuronal level. We identified mitochondrial deficiencies in all cases, though these deficiencies were more severe in the mitochondrial disease patients with multiple deletions. A significant reduction in TFAM expression was detected in Parkinson's disease compared to cases with other mitochondrial defects. Higher mitochondrial DNA copy number was detected in healthy aged neurons, despite a deletion level equivalent to Parkinson's disease. Our data support that in individuals with pathogenic mitochondrial defects, neurons respond to mitochondrial defect to survive and such an adaptation may involve TFAM.

Report of the Double-Molybdate Phase Cs2Ba(MoO4)2 with a Palmierite Structure and Its Thermodynamic Characterization.

The existence of a novel double-molybdate phase with a palmierite-type structure, Cs2Ba(MoO4)2, is revealed in this work, and its structural properties at room temperature have been characterized in detail using X-ray and neutron diffraction measurements. In addition, its thermal stability and thermal expansion are investigated in the temperature range 298-673 K using high-temperature X-ray diffraction, leading to the volumetric thermal expansion coefficient αV ≈ 43.0 × 10-6 K-1. The compound's standard enthalpy of formation at 298.15 K has been obtained using solution calorimetry, which yielded ΔfHm°(Cs2Ba(MoO4)2, cr, 298.15 K) = -3066.6 ± 3.1 kJ· mol-1, and its standard entropy at 298.15 K has been derived from low-temperature (2.1-294.3 K) thermal-relaxation calorimetry as Sm°(Cs2Ba(MoO4)2, cr, 298.15 K) = 381.2 ± 11.8 J K-1 mol-1.

Structural and Thermodynamic Investigation of the Perovskite Ba2NaMoO5.5.

Neutron diffraction, X-ray absorption spectroscopy (XAS), and Raman spectroscopy measurements of the quaternary perovskite phase Ba2NaMoO5.5 have been performed in this work. The cubic crystal structure in space group Fm3̅m has been refined using the Rietveld method. X-ray absorption near-edge structure spectroscopy (XANES) measurements at the Mo K-edge have confirmed the hexavalent state of molybdenum. The local structure of the molybdenum octahedra has been studied in detail using extended X-ray absorption fine structure (EXAFS) spectroscopy. The Mo-O and Mo-Ba distances have been compared to the neutron diffraction data with good agreement. The coefficient of thermal expansion measured in the temperature range of 303-923 K, using high temperature X-ray diffraction (HT-XRD) (αV = 55.8 × 10-6 K), has been determined to be ∼2 times higher than that of the barium molybdates BaMoO3 and BaMoO4. Moreover, no phase transition nor melting have been observed, neither by HT-XRD nor Raman spectroscopy nor differential scanning calorimetry, up to 1473 K. Furthermore, the standard enthalpy of formation (ΔfHm°) for Ba2NaMoO5.5(cr) has been determined to be -(2524.75 ± 4.15) kJ mol-1 at 298.15 K, using solution calorimetry. Finally, the margin for safe operation of sodium-cooled fast reactors (SFRs) has been assessed by calculating the threshold oxygen potential needed, in liquid sodium, to form the quaternary compound, following an interaction between irradiated mixed oxide (U,Pu)O2 fuel and sodium coolant.

Investigation of the Cs2(Mo,Te)O4 Solid Solution and Implications on the Joint Oxyde-Gaine System in Fast Neutron Reactors.

The formation of a thin layer, the so-called Joint Oxyde-Gaine (JOG), between the (U,Pu)O2 fuel pellets and the cladding has been observed in fast neutron reactors, due to the accumulation of volatile fission products. Cs2MoO4 is known to be one of the major components of the JOG, but other elements are also present, in particular tellurium and palladium. In this work, an investigation of the structural and thermodynamic properties of Cs2TeO4 and Cs2Mo1-xTexO4 solid solution is reported. The existence of a complete solubility between Cs2MoO4 and Cs2TeO4 is demonstrated, combining X-ray diffraction (XRD), neutron diffraction (ND), and X-ray absorption spectroscopy (XAS) results. High-temperature XRD measurements were moreover performed on Cs2TeO4, which revealed the existence of a α-ß phase transition around 712 K. Thermal expansion coefficients were also obtained from these data. Finally, phase equilibra points in the Cs2MoO4-Cs2TeO4 pseudobinary phase diagram were collected using differential scanning calorimetry and used to develop a thermodynamic model for this system using a regular solution formalism.

In situ high-temperature EXAFS measurements on radioactive and air-sensitive molten salt materials.

The development at the Delft University of Technology (TU Delft, The Netherlands) of an experimental set-up dedicated to high-temperature in situ EXAFS measurements of radioactive, air-sensitive and corrosive fluoride salts is reported. A detailed description of the sample containment cell, of the furnace design, and of the measurement geometry allowing simultaneous transmission and fluorescence measurements is given herein. The performance of the equipment is tested with the room-temperature measurement of thorium tetrafluoride, and the Th-F and Th-Th bond distances obtained by fitting of the EXAFS data are compared with the ones extracted from a refinement of neutron diffraction data collected at the PEARL beamline at TU Delft. The adequacy of the sample confinement is checked with a mapping of the thorium concentration profile of molten salt material. Finally, a few selected salt mixtures (LiF:ThF4) = (0.9:0.1), (0.75:0.25), (0.5:0.5) and (NaF:ThF4) = (0.67:0.33), (0.5:0.5) are measured in the molten state. Qualitative trends along the series are discussed, and the experimental data for the (LiF:ThF4) = (0.5:0.5) composition are compared with the EXAFS spectrum generated from molecular dynamics simulations.

The Geometry of Continuous Latent Space Models for Network Data.

We review the class of continuous latent space (statistical) models for network data, paying particular attention to the role of the geometry of the latent space. In these models, the presence/absence of network dyadic ties are assumed to be conditionally independent given the dyads' unobserved positions in a latent space. In this way, these models provide a probabilistic framework for embedding network nodes in a continuous space equipped with a geometry that facilitates the description of dependence between random dyadic ties. Specifically, these models naturally capture homophilous tendencies and triadic clustering, among other common properties of observed networks. In addition to reviewing the literature on continuous latent space models from a geometric perspective, we highlight the important role the geometry of the latent space plays on properties of networks arising from these models via intuition and simulation. Finally, we discuss results from spectral graph theory that allow us to explore the role of the geometry of the latent space, independent of network size. We conclude with conjectures about how these results might be used to infer the appropriate latent space geometry from observed networks.

A New Look at the Structural and Magnetic Properties of Potassium Neptunate K2NpO4 Combining XRD, XANES Spectroscopy, and Low-Temperature Heat Capacity.

The physicochemical properties of the potassium neptunate K2NpO4 have been investigated in this work using X-ray diffraction, X-ray absorption near edge structure (XANES) spectroscopy at the Np-L3 edge, and low-temperature heat capacity measurements. A Rietveld refinement of the crystal structure is reported for the first time. The Np(VI) valence state has been confirmed by the XANES data, and the absorption edge threshold of the XANES spectrum has been correlated to the Mössbauer isomer shift value reported in the literature. The standard entropy and heat capacity of K2NpO4 have been derived at 298.15 K from the low-temperature heat capacity data. The latter suggest the existence of a magnetic ordering transition around 25.9 K, most probably of the ferromagnetic type.

Understanding Racial Differences in Exposure to Violent Areas: Integrating Survey, Smartphone, and Administrative Data Resources.

Emerging evidence indicates that exposure to violent areas may influence youth wellbeing. We employ smartphone GPS data on youth activity spaces to examine the extent of, and potential explanations for, racial disparities in these exposures. Multilevel models of data from the Adolescent Health and Development in Context study indicate that exposures to violent areas vary significantly across days of the week and between youth who reside in the same neighborhood. African American youth are exposed to areas with substantially higher levels of violence. Residing in a disadvantaged neighborhood is significantly associated with exposure to violent areas and explains a non-trivial proportion of the racial difference in this outcome. However, neighborhood factors are incomplete explanations of the racial disparity. Characteristics of the activity locations at which youth spend time explain the residual racial disparity in exposure to violent areas. These findings highlight the importance of youth activity spaces, above and beyond their neighborhood environments.

Crystal-Field and Covalency Effects in Uranates: An X-ray Spectroscopic Study.

The electronic structure of U(V) - and U(VI) -containing uranates NaUO3 and Pb3 UO6 was studied by using an advanced technique, namely X-ray absorption spectroscopy (XAS) in high-energy-resolution fluorescence-detection (HERFD) mode. Due to a significant reduction in core-hole lifetime broadening, the crystal-field splittings of the 5f shell were probed directly in HERFD-XAS spectra collected at the U 3d edge, which is not possible by using conventional XAS. In addition, the charge-transfer satellites that result from U 5f-O 2p hybridization were clearly resolved. The crystal-field parameters, 5f occupancy, and degree of covalency of the chemical bonding in these uranates were estimated by using the Anderson impurity model by calculating the U 3d HERFD-XAS, conventional XAS, core-to-core (U 4f-3d transitions) resonant inelastic X-ray scattering (RIXS), and U 4f X-ray photoelectron spectra. The crystal field was found to be strong in these systems and the 5f occupancy was determined to be 1.32 and 0.84 electrons in the ground state for NaUO3 and Pb3 UO6 , respectively, which indicates a significant covalent character for these compounds.

Structural Properties and Charge Distribution of the Sodium Uranium, Neptunium, and Plutonium Ternary Oxides: A Combined X-ray Diffraction and XANES Study.

The charge distributions in α-Na2UO4, Na3NpO4, α-Na2NpO4, Na4NpO5, Na5NpO6, Na2PuO3, Na4PuO5, and Na5PuO6 are investigated in this work using X-ray absorption near-edge structure (XANES) spectroscopy at the U-L3, Np-L3, and Pu-L3 edges. In addition, a Rietveld refinement of monoclinic Na2PuO3, in space group C2/c, is reported for the first time, and the existence of the isostructural Na2NpO3 phase is revealed. In contrast to measurements in solution, the number of published XANES data for neptunium and plutonium solid phases with a valence state higher than IV is very limited. The present results cover a wide range of oxidation states, namely, IV to VII, and can serve as reference for future investigations. The sodium actinide series show a variety of local coordination geometries, and correlations between the shape of the XANES spectra and the local structural environments are discussed herein.

A new look at the structural properties of trisodium uranate Na3UO4.

The crystal structure of trisodium uranate, which forms following the interaction between sodium and hyperstoichiometric urania, has been solved for the first time using powder X-ray and neutron diffraction, X-ray absorption near-edge structure spectroscopy, and solid-state (23)Na multiquantum magic angle spinning nuclear magnetic resonance. The compound, isostructural with Na3BiO4, has monoclinic symmetry, in space group P2/c. Moreover, it has been shown that this structure can accommodate some cationic disorder, with up to 16(2)% sodium on the uranium site, corresponding to the composition α-Na3(U1-x,Nax)O4 (0 < x < 0.18). The α phase adopts a mixed valence state with the presence of U(V) and U(VI). The two polymorphs of this compound described in the literature, m- and ß-Na3(U1-x,Nax)O4, have also been investigated, and their relationship to the α phase has been established. The completely disordered low-temperature cubic phase corresponds to a metastable phase. The semiordered high-temperature ß phase is cubic, in space group Fd3̅m.

X-ray Diffraction, Mössbauer Spectroscopy, Magnetic Susceptibility, and Specific Heat Investigations of Na4NpO5 and Na5NpO6.

The hexavalent and heptavalent sodium neptunate compounds Na4NpO5 and Na5NpO6 have been investigated using X-ray powder diffraction, Mössbauer spectroscopy, magnetic susceptibility, and specific heat measurements. Na4NpO5 has tetragonal symmetry in the space group I4/m, while Na5NpO6 adopts a monoclinic unit cell in the space group C2/m. Both structures have been refined for the first time using the Rietveld method. The valence states of neptunium in these two compounds, i.e., Np(VI) and Np(VII), respectively, have been confirmed by the isomer shift values of their Mössbauer spectra. The local structural properties obtained from the X-ray refinements have also been related to the quadrupole coupling constants and asymmetry parameters determined from the Mössbauer studies. The absence of magnetic ordering has been confirmed for Na4NpO5. However, specific heat measurements at low temperatures have suggested the existence of a Schottky-type anomaly at around 7 K in this Np(VI) phase.

Toward a taxonomy of trust for probabilistic machine learning.

Probabilistic machine learning increasingly informs critical decisions in medicine, economics, politics, and beyond. To aid the development of trust in these decisions, we develop a taxonomy delineating where trust in an analysis can break down: (i) in the translation of real-world goals to goals on a particular set of training data, (ii) in the translation of abstract goals on the training data to a concrete mathematical problem, (iii) in the use of an algorithm to solve the stated mathematical problem, and (iv) in the use of a particular code implementation of the chosen algorithm. We detail how trust can fail at each step and illustrate our taxonomy with two case studies. Finally, we describe a wide variety of methods that can be used to increase trust at each step of our taxonomy. The use of our taxonomy highlights not only steps where existing research work on trust tends to concentrate and but also steps where building trust is particularly challenging.

Low-Temperature Heat Capacity of CsPbI3, Cs4PbI6, and Cs3Bi2I9.

The heat capacities of CsPbI3, Cs4PbI6, and Cs3Bi2I9 were studied using low-temperature thermal relaxation calorimetry in the temperature range of 1.9-300 K. The three compounds are insulators, with no electronic contribution to the heat capacity. None of them show detectable anomalies in the studied temperature window. Thermodynamic properties at standard conditions are derived. Previously reported results on Cs3Bi2I9 are not fully consistent with the present findings. Moreover, the magnetic susceptibilities of the three title compounds were measured.

Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters.

Murid herpesvirus 4 (MuHV-4) microRNAs were previously cloned from latently infected tumor cells and predicted to be processed from a series of RNA polymerase III primary transcripts. We detected maturely processed MuHV-4 miRNAs within total RNA from lytically infected cells in vitro and infected tissues ex vivo, using a highly sensitive reverse ligation meditated RT-PCR strategy. We determined that the MuHV-4 microRNAs are biologically active during infection by a luciferase reporter system. We experimentally demonstrated that transcription of the MuHV-4 microRNAs is by RNA polymerase III by alpha-amanitin insensitivity and by specific deletion of the RNA polymerase III type 2-like promoter elements of MuHV-4, resulting in the complete loss of miRNA detection and function. Finally, we demonstrate that these 10 viral miRNAs, each transcribed from highly conserved and novel polymerase III promoter elements, vary markedly in their relative abundance and activity.

Mitochondrial DNA mutations in ageing and cancer.

Advancing age is a major risk factor for malignant transformation and the development of cancer. As such, over 50% of neoplasms occur in individuals over the age of 70. The pathologies of both ageing and cancer have been characterized by respective groups of molecular hallmarks, and while some features are divergent between the two pathologies, several are shared. Perturbed mitochondrial function is one such common hallmark, and this observation therefore suggests that mitochondrial alterations may be of significance in age-related cancer development. There is now considerable evidence documenting the accumulation of somatic mitochondrial DNA (mtDNA) mutations in ageing human postmitotic and replicative tissues. Similarly, mutations of the mitochondrial genome have been reported in human cancers for decades. The plethora of functions in which mitochondria partake, such as oxidative phosphorylation, redox balance, apoptosis and numerous biosynthetic pathways, manifests a variety of ways in which alterations in mtDNA may contribute to tumour growth. However, the specific mechanisms by which mtDNA mutations contribute to tumour progression remain elusive and often contradictory. This review aims to consolidate current knowledge and describe future direction within the field.

Imaging mass cytometry reveals generalised deficiency in OXPHOS complexes in Parkinson's disease.

Here we report the application of a mass spectrometry-based technology, imaging mass cytometry, to perform in-depth proteomic profiling of mitochondrial complexes in single neurons, using metal-conjugated antibodies to label post-mortem human midbrain sections. Mitochondrial dysfunction, particularly deficiency in complex I has previously been associated with the degeneration of dopaminergic neurons in Parkinson's disease. To further our understanding of the nature of this dysfunction, and to identify Parkinson's disease specific changes, we validated a panel of antibodies targeting subunits of all five mitochondrial oxidative phosphorylation complexes in dopaminergic neurons from Parkinson's disease, mitochondrial disease, and control cases. Detailed analysis of the expression profile of these proteins, highlighted heterogeneity between individuals. There is a widespread decrease in expression of all complexes in Parkinson's neurons, although more severe in mitochondrial disease neurons, however, the combination of affected complexes varies between the two groups. We also provide evidence of a potential neuronal response to mitochondrial dysfunction through a compensatory increase in mitochondrial mass. This study highlights the use of imaging mass cytometry in the assessment and analysis of expression of oxidative phosphorylation proteins, revealing the complexity of deficiencies of these proteins within individual neurons which may contribute to and drive neurodegeneration in Parkinson's disease.

Age-associated mitochondrial complex I deficiency is linked to increased stem cell proliferation rates in the mouse colon.

One of the hallmarks of aging is an accumulation of cells with defects in oxidative phosphorylation (OXPHOS) due to mutations of mitochondrial DNA (mtDNA). Rapidly dividing tissues maintained by stem cells, such as the colonic epithelium, are particularly susceptible to accumulation of OXPHOS defects over time; however, the effects on the stem cells are unknown. We have crossed a mouse model in which intestinal stem cells are labelled with EGFP (Lgr5-EGFP-IRES-creERT2) with a model of accelerated mtDNA mutagenesis (PolgAmut/mut ) to investigate the effect of OXPHOS dysfunction on colonic stem cell proliferation. We show that a reduction in complex I protein levels is associated with an increased rate of stem cell cycle re-entry. These changes in stem cell homeostasis could have significant implications for age-associated intestinal pathogenesis.