Ancestral allele of DNA polymerase gamma modifies antiviral tolerance

Mitochondria are critical modulators of antiviral tolerance through the release of mitochondrial RNA and DNA (mtDNA and mtRNA) fragments into the cytoplasm after infection, activating virus sensors and type-I interferon (IFN-I) response1-4. The relevance of these mechanisms for mitochondrial diseases remains understudied. Here we investigated mitochondrial recessive ataxia syndrome (MIRAS), which is caused by a common European founder mutation in DNA polymerase gamma (POLG1)5. Patients homozygous for the MIRAS variant p.W748S show exceptionally variable ages of onset and symptoms5, indicating that unknown modifying factors contribute to disease manifestation. We report that the mtDNA replicase POLG1 has a role in antiviral defence mechanisms to double-stranded DNA and positive-strand RNA virus infections (HSV-1, TBEV and SARS-CoV-2), and its p.W748S variant dampens innate immune responses. Our patient and knock-in mouse data show that p.W748S compromises mtDNA replisome stability, causing mtDNA depletion, aggravated by virus infection. Low mtDNA and mtRNA release into the cytoplasm and a slow IFN response in MIRAS offer viruses an early replicative advantage, leading to an augmented pro-inflammatory response, a subacute loss of GABAergic neurons and liver inflammation and necrosis. A population databank of around 300,000 Finnish individuals6 demonstrates enrichment of immunodeficient traits in carriers of the POLG1 p.W748S mutation. Our evidence suggests that POLG1 defects compromise antiviral tolerance, triggering epilepsy and liver disease. The finding has important implications for the mitochondrial disease spectrum, including epilepsy, ataxia and parkinsonism.

Efficient NMR measurement and data analysis supported by the Bayesian inference: The case of the heavy fermion compound YbCo2Zn20

We propose a data-driven technique to infer microscopic physical quantities from nuclear magnetic resonance (NMR) spectra, in which the data size and quality required for the Bayesian inference are investigated. The 59Co-NMR measurement of YbCo2Zn20 single crystal generates complex spectra with 28 peaks. By exploiting the site symmetry in the crystal structure, the isotropic Knight shift Kiso and nuclear quadrupole resonance (NQR) frequency νQ were respectively estimated to be Kiso=0.7822±0.0090% and νQ=2.008±0.016 MHz (T=20 K and H≃10.2 T) by analyzing only 30 data points from one spectrum. The estimated νQ is consistent with the precise value obtained in the NQR experiment. Our method can significantly reduce the measurement time and the computational cost of data analysis in NMR experiments.

Mosaic dysfunction of mitophagy in mitochondrial muscle disease

Mitophagy is a quality control mechanism that eliminates damaged mitochondria, yet its significance in mammalian pathophysiology and aging has remained unclear. Here, we report that mitophagy contributes to mitochondrial dysfunction in skeletal muscle of aged mice and human patients. The early disease stage is characterized by muscle fibers with central nuclei, with enhanced mitophagy around these nuclei. However, progressive mitochondrial dysfunction halts mitophagy and disrupts lysosomal homeostasis. Interestingly, activated or halted mitophagy occur in a mosaic manner even in adjacent muscle fibers, indicating cell-autonomous regulation. Rapamycin restores mitochondrial turnover, indicating mTOR-dependence of mitochondrial recycling in advanced disease stage. Our evidence suggests that (1) mitophagy is a hallmark of age-related mitochondrial pathology in mammalian muscle, (2) mosaic halting of mitophagy is a mechanism explaining mosaic respiratory chain deficiency and accumulation of pathogenic mtDNA variants in adult-onset mitochondrial diseases and normal aging, and (3) augmenting mitophagy is a promising therapeutic approach for muscle mitochondrial dysfunction.

Mito-mice∆ and mitochondrial DNA mutator mice as models of human osteoporosis caused not by aging but by hyperparathyroidism

Mitochondrial DNA (mtDNA) mutator mice showing accelerated accumulation of mtDNA with somatic mutations are potentially useful models of human aging, whereas mito-miceΔ showing accelerated accumulation of mtDNA with a deletion mutation (ΔmtDNA) are potentially useful models of mitochondrial diseases but not human aging, even though both models express an age-associated decrease in mitochondrial respiration. Because osteoporosis is the only premature aging phenotype observed in mtDNA mutator mice with the C57BL/6J nuclear genetic background, our previous study precisely examined its expression spectra and reported that both mtDNA mutator mice and mito-miceΔ, but not aged mice, developed decreased cortical bone thickness. Moreover, decreased cortical bone thickness is usually not seen in aged humans but is commonly seen in the patients with hyperparathyroidism caused by oversecretion of parathyroid hormone (PTH). In the present study, we showed higher concentrations of blood PTH in mtDNA mutator mice and mito-miceΔ than in aged mice. We also found that both models developed decreased mitochondrial respiration in the duodenum or renal tubules, which would lead to hypocalcemia, oversecretion of PTH, and ultimately osteoporosis. Thus, mtDNA mutator mice and mito-miceΔ may be useful models of human osteoporosis caused not by aging but by hyperparathyroidism.

Mice deficient in the Shmt2 gene have mitochondrial respiration defects and are embryonic lethal

Accumulation of somatic mutations in mitochondrial DNA (mtDNA) has been proposed to be responsible for human aging and age-associated mitochondrial respiration defects. However, our previous findings suggested an alternative hypothesis of human aging—that epigenetic changes but not mutations regulate age-associated mitochondrial respiration defects, and that epigenetic downregulation of nuclear-coded genes responsible for mitochondrial translation [e.g., glycine C-acetyltransferase (GCAT), serine hydroxymethyltransferase 2 (SHMT2)] is related to age-associated respiration defects. To examine our hypothesis, here we generated mice deficient in Gcat or Shmt2 and investigated whether they have respiration defects and premature aging phenotypes. Gcat-deficient mice showed no macroscopic abnormalities including premature aging phenotypes for up to 9 months after birth. In contrast, Shmt2-deficient mice showed embryonic lethality after 13.5 days post coitum (dpc), and fibroblasts obtained from 12.5-dpc Shmt2-deficient embryos had respiration defects and retardation of cell growth. Because Shmt2 substantially controls production of N-formylmethionine-tRNA (fMet-tRNA) in mitochondria, its suppression would reduce mitochondrial translation, resulting in expression of the respiration defects in fibroblasts from Shmt2-deficient embryos. These findings support our hypothesis that age-associated respiration defects in fibroblasts of elderly humans are caused not by mtDNA mutations but by epigenetic regulation of nuclear genes including SHMT2.

A somatic T15091C mutation in the Cytb gene of mouse mitochondrial DNA dominantly induces respiration defects

Our previous studies provided evidence that mammalian mitochondrial DNA (mtDNA) mutations that cause mitochondrial respiration defects behave in a recessive manner, because the induction of respiration defects could be prevented with the help of a small proportion (10%-20%) of mtDNA without the mutations. However, subsequent studies found the induction of respiration defects by the accelerated accumulation of a small proportion of mtDNA with various somatic mutations, indicating the presence of mtDNA mutations that behave in a dominant manner. Here, to provide the evidence for the presence of dominant mutations in mtDNA, we used mouse lung carcinoma P29 cells and examined whether some mtDNA molecules possess somatic mutations that dominantly induce respiration defects. Cloning and sequence analysis of 40-48 mtDNA molecules from P29 cells was carried out to screen for somatic mutations in protein-coding genes, because mutations in these genes could dominantly regulate respiration defects by formation of abnormal polypeptides. We found 108 missense mutations existing in one or more of 40-48 mtDNA molecules. Of these missense mutations, a T15091C mutation in the Cytb gene was expected to be pathogenic due to the presence of its orthologous mutation in mtDNA from a patient with cardiomyopathy. After isolation of many subclones from parental P29 cells, we obtained subclones with various proportions of T15091C mtDNA, and showed that the respiration defects were induced in a subclone with only 49% T15091C mtDNA. Because the induction of respiration defects could not be prevented with the help of the remaining 51% mtDNA without the T15091C mutation, the results indicate that the T15091C mutation in mtDNA dominantly induced the respiration defects.

Epigenetic regulation of the nuclear-coded GCAT and SHMT2 genes confers human age-associated mitochondrial respiration defects

Age-associated accumulation of somatic mutations in mitochondrial DNA (mtDNA) has been proposed to be responsible for the age-associated mitochondrial respiration defects found in elderly human subjects. We carried out reprogramming of human fibroblast lines derived from elderly subjects by generating their induced pluripotent stem cells (iPSCs), and examined another possibility, namely that these aging phenotypes are controlled not by mutations but by epigenetic regulation. Here, we show that reprogramming of elderly fibroblasts restores age-associated mitochondrial respiration defects, indicating that these aging phenotypes are reversible and are similar to differentiation phenotypes in that both are controlled by epigenetic regulation, not by mutations in either the nuclear or the mitochondrial genome. Microarray screening revealed that epigenetic downregulation of the nuclear-coded GCAT gene, which is involved in glycine production in mitochondria, is partly responsible for these aging phenotypes. Treatment of elderly fibroblasts with glycine effectively prevented the expression of these aging phenotypes.

NMR study of the superconducting gap variation near the Mott transition in Cs₃C₆₀

Former extensive studies of superconductivity in the A3C60 compounds, where A is an alkali metal, have led one to consider that Bardeen-Cooper-Schrieffer electron-phonon pairing prevails in those compounds, though the incidence of electronic Coulomb repulsion has been highly debated. The discovery of two isomeric fulleride compounds Cs3C60 which exhibit a transition with pressure from a Mott insulator (MI) to a superconducting (SC) state clearly reopens that question. Using pressure (p) as a single control parameter of the C60 balls lattice spacing, one can now study the progressive evolution of the SC properties when the electronic correlations are increased towards the critical pressure p(c) of the Mott transition. We have used 13C and 133Cs NMR measurements on the cubic phase A15-Cs3C60 just above p(c)=5.0(3) kbar, where the SC transition temperature Tc displays a dome shape with decreasing cell volume. From the T dependence below T(c) of the nuclear spin lattice relaxation rate (T1)(-1) we determine the electronic excitations in the SC state, that is 2Δ, the gap value. The latter is found to be largely enhanced with respect to the Bardeen-Cooper-Schrieffer value established in the case of dense A3C60 compounds. It even increases slightly with decreasing p towards p(c), where T(c) decreases on the SC dome, so that 2Δ/k(B)T(c) increases regularly upon approaching the Mott transition. These results bring clear evidence that the increasing correlations near the Mott transition are not significantly detrimental to superconductivity. They rather suggest that repulsive electron interactions might even reinforce elecron-phonon superconductivity, being then partly responsible for the large T(c) values, as proposed by theoretical models taking the electronic correlations as a key ingredient.

Mitochondrial DNA mutations in mutator mice confer respiration defects and B-cell lymphoma development

Mitochondrial DNA (mtDNA) mutator mice are proposed to express premature aging phenotypes including kyphosis and hair loss (alopecia) due to their carrying a nuclear-encoded mtDNA polymerase with a defective proofreading function, which causes accelerated accumulation of random mutations in mtDNA, resulting in expression of respiration defects. On the contrary, transmitochondrial mito-miceΔ carrying mtDNA with a large-scale deletion mutation (ΔmtDNA) also express respiration defects, but not express premature aging phenotypes. Here, we resolved this discrepancy by generating mtDNA mutator mice sharing the same C57BL/6J (B6J) nuclear background with that of mito-miceΔ. Expression patterns of premature aging phenotypes are very close, when we compared between homozygous mtDNA mutator mice carrying a B6J nuclear background and selected mito-miceΔ only carrying predominant amounts of ΔmtDNA, in their expression of significant respiration defects, kyphosis, and a short lifespan, but not the alopecia. Therefore, the apparent discrepancy in the presence and absence of premature aging phenotypes in mtDNA mutator mice and mito-miceΔ, respectively, is partly the result of differences in the nuclear background of mtDNA mutator mice and of the broad range of ΔmtDNA proportions of mito-miceΔ used in previous studies. We also provided direct evidence that mtDNA abnormalities in homozygous mtDNA mutator mice are responsible for respiration defects by demonstrating the co-transfer of mtDNA and respiration defects from mtDNA mutator mice into mtDNA-less (ρ⁰) mouse cells. Moreover, heterozygous mtDNA mutator mice had a normal lifespan, but frequently developed B-cell lymphoma, suggesting that the mtDNA abnormalities in heterozygous mutator mice are not sufficient to induce a short lifespan and aging phenotypes, but are able to contribute to the B-cell lymphoma development during their prolonged lifespan.

PCR-RFLP genotypes associated with quinolone resistance in isolates of Flavobacterium psychrophilum

A novel genotyping method for epizootiological studies of bacterial cold-water disease caused by Flavobacterium psychrophilum and associated with quinolone resistance was developed. Polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) was performed on 244 F. psychrophilum isolates from various fish species. PCR was performed with primer pair GYRA-FP1F and GYRA-FP1R amplifying the A subunit of the DNA gyrase (GyrA) gene, which contained the quinolone resistance determining region. Digestion of PCR products with the restriction enzyme Mph1103I showed two genotypes, QR and QS. The difference between these genotypes was amino acid substitutions at position 83 of GyrA (Escherichia coli numbering). The genotype QR indicated an alanine residue at this position associated with quinolone resistance in F. psychrophilum isolates. Of the 244 isolates tested in this study, the number of QR genotype isolates was 153 (62.7%). In isolates from ayu (n=177), 146 (82.5%) were genotype QR. With combination of this technique and previously reported PCR-RFLP genotyping, eight genotypes were observed in F. psychrophilum isolates. Using this genotyping system, the relationships between genotype and host fish species, or locality of isolation, were analysed and are discussed.

The characteristics of karyotype and telomeric satellite DNA sequences in the cricket, Gryllus bimaculatus (Orthoptera, Gryllidae)

The chromosomes derived from the Japanese population of Gryllus bimaculatus were characterized by C-banding and Ag-NOR staining. The chromosome number, 2n = 28 + XX (female)/XO (male), corresponded with that of other populations of G. bimaculatus, but the chromosome configuration in idiograms varied between the populations. NORs were carried on one pair of autosomes and appeared polymorphous. The positive C-bands located at the centromere of all chromosomes and the distal regions of many chromosome pairs, and the size and the distribution pattern of the distal C-heterochromatin showed differences among the chromosomes. In addition, this paper reports on the characteristics of HindIII satellite DNA isolated from the genome of G. bimaculatus. The HindIII repetitive fragments were about 0.54 kb long, and localized at the distal C-bands of the autosomes and the interstitial C-bands of the X chromosome. Molecular analysis showed two distinct satellite DNA sequences, named the GBH535 and GBH542 families, with high AT contents of about 67 and 66%, respectively. The two repetitive families seem to be derived from a common ancestral sequence, and both families possessed the same 13-bp palindrome sequence. The results of Southern blot hybridization suggest that the sequence of the GBH535 family is conserved in the genomic DNAs of Gryllus species, whereas the GBH542 family is a species-specific sequence.

Gapless magnetic and quasiparticle excitations due to the coexistence of antiferromagnetism and superconductivity in CeRhIn5: a study of 115In NQR under pressure

We report systematic measurements of ac susceptibility, nuclear-quadrupole-resonance spectrum, and nuclear-spin-lattice-relaxation time (T1) on the pressure (P)-induced heavy-fermion superconductor CeRhIn5. The temperature (T) dependence of 1/T(1) at P=1.6 GPa has revealed that antiferromagnetism (AFM) and superconductivity (SC) coexist microscopically, exhibiting the respective transition at T(N)=2.8 K and T(MF)(c)=0.9 K. It is demonstrated that SC does not yield any trace of gap opening in low-lying excitations below T(onset)(c)=2 K, but T(MF)(c)=0.9 K, followed by a T(1)T=const law. These results point to the unconventional characteristics of SC coexisting with AFM. We highlight that both of the results deserve theoretical work on the gapless nature in the low-lying excitation spectrum due to the coexistence of AFM and SC and the lack of the mean-field regime below T(onset)(c)=2 K.

Sawtooth oscillation in current-carrying plasma in the large helical device

Sawtooth oscillations have been observed in current-carrying helical plasmas by using electron-cyclotron-emission diagnostics in the Large Helical Device. The plasma current, which is driven by neutral beam injection, reduces the beta threshold of the sawtooth oscillation. When the central q value is increased due to the plasma current, the core region crashes, and, when it is decreased, the edge region crashes annularly. Observed rapid mixture of the plasma in the limited region suggests that these sawtooth crashes are reconnection phenomena. Unlike previous experiments, no precursor oscillation has been observed.

Coexistence of antiferromagnetism and superconductivity near the quantum criticality of the heavy-fermion compound CeRhIn5

We report a study on the interplay between antiferromagnetism (AFM) and superconductivity (SC) in a heavy-fermion compound CeRhIn5 under pressure P=1.75 GPa. The onset of the magnetic order is evidenced from a clear split of 115In nuclear quadrupole resonance spectrum due to the spontaneous internal field below the Néel temperature T(N)=2.5 K. Simultaneously, bulk SC below T(c)=2.0 K is demonstrated by the observation of the Meissner diamagnetism signal whose size is the same as in the exclusively superconducting phase. These results indicate that the AFM coexists homogeneously with the SC at a microscopic level.

Realistic Virtual Endoscopy of the ventricle system and haptic-based surgical simulator of hydrocefalus treatment

New methods and software tools for automatic extraction of the ventricle system from magnetic resonance imagery (MRI) data, ventricle part classification, and realistic texturing are proposed to support Virtual Endoscopy (VE). Volume- and surface-based medical atlases are intensively used as templates in the methods. The processed ventricle-related surfaces are then utilized in a haptic-based system, which provides a surgeon with several basic functions simulating "virtual treatment" of hydrocephalus.

An accurate method of predicting mandibular growth potential based on bone maturity

Mandibular growth prediction provides important information for planning treatment and for evaluating occlusal stability after treatment. At present, several methods can predict mandibular growth, but it is not clear which method is the most accurate. This study compared the predictive error of several methods by using skeletal maturity indicators. Twenty-two longitudinal cephalograms and hand-wrist radiographs of female subjects (average initial age, 8.3 years; final age, 18.4 years) were collected to construct the prediction formula. Another 22 female subjects (initial age, 10.8 years; final age, 18.6 years) were examined to compare differences between the predicted values and the actual values. Mandibular total length (condylion-gnathion) at the final stage can be accurately predicted by (1) the ossification events of the third middle phalanx and the radius, (2) the growth potential method, (3) the growth percentage method, (4) the multiple regression method, and (5) the growth chart method. Bone age as a parameter was calculated by both the Tanner-Whitehouse 2 (TW2) method and the computer-aided skeletal maturity assessment system (CASMAS) that we developed. The average error between the predicted length of condylion to gnathion and the actual length at the final stage for each method was (1) 3.0 mm; (2) 2.1 mm (TW2), 2.4 mm (CASMAS); (3) 2.3 mm (TW2), 2.6 mm (CASMAS); (4) 4.3 mm (TW2), 4.9 mm (CASMAS); and (5) 3.6 mm (TW2), 3.7 mm (CASMAS). The growth potential method and the growth percentage method were the most accurate predictors of mandibular growth potential.

Unique spin dynamics and unconventional superconductivity in the layered heavy fermion compound CeIrIn5: NQR evidence

We report measurements of the 115In nuclear spin-lattice relaxation rate ( 1/T1) between T = 0.09 and 100 K in the new heavy fermion (HF) compound CeIrIn5. At 0.4 < or = T< or = 100 K, 1/T1 is strongly T-dependent, which indicates that CeIrIn5 is much more itinerant than known Ce-based HFs. We find that 1/T1T, subtracting that for LaIrIn5, follows a (1 / T+straight theta)3/4 variation with straight theta = 8 K. We argue that this novel feature points to anisotropic, due to a layered crystal structure, spin fluctuations near a magnetic ordering. The bulk superconductivity sets in at 0.40 K below which the coherence peak is absent and 1/T1 follows a T3 variation, which suggests unconventional superconductivity with line-node gap.